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General General

Modeling structure-activity relationships with machine learning to identify GSK3-targeted small molecules as potential COVID-19 therapeutics.

In Frontiers in endocrinology ; h5-index 55.0

Coronaviruses induce severe upper respiratory tract infections, which can spread to the lungs. The nucleocapsid protein (N protein) plays an important role in genome replication, transcription, and virion assembly in SARS-CoV-2, the virus causing COVID-19, and in other coronaviruses. Glycogen synthase kinase 3 (GSK3) activation phosphorylates the viral N protein. To combat COVID-19 and future coronavirus outbreaks, interference with the dependence of N protein on GSK3 may be a viable strategy. Toward this end, this study aimed to construct robust machine learning models to identify GSK3 inhibitors from Food and Drug Administration-approved and investigational drug libraries using the quantitative structure-activity relationship approach. A non-redundant dataset consisting of 495 and 3070 compounds for GSK3α and GSK3β, respectively, was acquired from the ChEMBL database. Twelve sets of molecular descriptors were used to define these inhibitors, and machine learning algorithms were selected using the LazyPredict package. Histogram-based gradient boosting and light gradient boosting machine algorithms were used to develop predictive models that were evaluated based on the root mean square error and R-squared value. Finally, the top two drugs (selinexor and ruboxistaurin) were selected for molecular dynamics simulation based on the highest predicted activity (negative log of the half-maximal inhibitory concentration, pIC50 value) to further investigate the structural stability of the protein-ligand complexes. This artificial intelligence-based virtual high-throughput screening approach is an effective strategy for accelerating drug discovery and finding novel pharmacological targets while reducing the cost and time.

Pirzada Rameez Hassan, Ahmad Bilal, Qayyum Naila, Choi Sangdun

2023

GSK3, QSAR, coronaviruses, machine learning, molecular descriptors

General General

Deep Survival Analysis With Clinical Variables for COVID-19.

In IEEE journal of translational engineering in health and medicine

OBJECTIVE : Millions of people have been affected by coronavirus disease 2019 (COVID-19), which has caused millions of deaths around the world. Artificial intelligence (AI) plays an increasing role in all areas of patient care, including prognostics. This paper proposes a novel predictive model based on one dimensional convolutional neural networks (1D CNN) to use clinical variables in predicting the survival outcome of COVID-19 patients.

METHODS AND PROCEDURES : We have considered two scenarios for survival analysis, 1) uni-variate analysis using the Log-rank test and Kaplan-Meier estimator and 2) combining all clinical variables ([Formula: see text]=44) for predicting the short-term from long-term survival. We considered the random forest (RF) model as a baseline model, comparing to our proposed 1D CNN in predicting survival groups.

RESULTS : Our experiments using the univariate analysis show that nine clinical variables are significantly associated with the survival outcome with corrected p < 0.05. Our approach of 1D CNN shows a significant improvement in performance metrics compared to the RF and the state-of-the-art techniques (i.e., 1D CNN) in predicting the survival group of patients with COVID-19.

CONCLUSION : Our model has been tested using clinical variables, where the performance is found promising. The 1D CNN model could be a useful tool for detecting the risk of mortality and developing treatment plans in a timely manner.

CLINICAL IMPACT : The findings indicate that using both Heparin and Exnox for treatment is typically the most useful factor in predicting a patient's chances of survival from COVID-19. Moreover, our predictive model shows that the combination of AI and clinical data can be applied to point-of-care services through fast-learning healthcare systems.

Chaddad Ahmad, Hassan Lama, Katib Yousef, Bouridane Ahmed

2023

CNN, COVID-19, clinical variables

Public Health Public Health

COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19.

In Frontiers in public health

COVID-19 has taken a huge toll on our lives over the last 3 years. Global initiatives put forward by all stakeholders are still in place to combat this pandemic and help us learn lessons for future ones. While the vaccine rollout was not able to curb the spread of the disease for all strains, the research community is still trying to develop effective therapeutics for COVID-19. Although Paxlovid and remdesivir have been approved by the FDA against COVID-19, they are not free of side effects. Therefore, the search for a therapeutic solution with high efficacy continues in the research community. To support this effort, in this latest version (v3) of COVID-19Base, we have summarized the biomedical entities linked to COVID-19 that have been highlighted in the scientific literature after the vaccine rollout. Eight different topic-specific dictionaries, i.e., gene, miRNA, lncRNA, PDB entries, disease, alternative medicines registered under clinical trials, drugs, and the side effects of drugs, were used to build this knowledgebase. We have introduced a BLSTM-based deep-learning model to predict the drug-disease associations that outperforms the existing model for the same purpose proposed in the earlier version of COVID-19Base. For the very first time, we have incorporated disease-gene, disease-miRNA, disease-lncRNA, and drug-PDB associations covering the largest number of biomedical entities related to COVID-19. We have provided examples of and insights into different biomedical entities covered in COVID-19Base to support the research community by incorporating all of these entities under a single platform to provide evidence-based support from the literature. COVID-19Base v3 can be accessed from: https://covidbase-v3.vercel.app/. The GitHub repository for the source code and data dictionaries is available to the community from: https://github.com/91Abdullah/covidbasev3.0.

Basit Syed Abdullah, Qureshi Rizwan, Musleh Saleh, Guler Reto, Rahman M Sohel, Biswas Kabir H, Alam Tanvir

2023

CORD-19, COVID-19, SARS-CoV-2, deep learning, machine learning

Public Health Public Health

Blood Inflammatory Biomarkers Differentiate Inpatient and Outpatient Coronavirus Disease 2019 From Influenza.

In Open forum infectious diseases

BACKGROUND : The ongoing circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a diagnostic challenge because symptoms of coronavirus disease 2019 (COVID-19) are difficult to distinguish from other respiratory diseases. Our goal was to use statistical analyses and machine learning to identify biomarkers that distinguish patients with COVID-19 from patients with influenza.

METHODS : Cytokine levels were analyzed in plasma and serum samples from patients with influenza and COVID-19, which were collected as part of the Centers for Disease Control and Prevention's Hospitalized Adult Influenza Vaccine Effectiveness Network (inpatient network) and the US Flu Vaccine Effectiveness (outpatient network).

RESULTS : We determined that interleukin (IL)-10 family cytokines are significantly different between COVID-19 and influenza patients. The results suggest that the IL-10 family cytokines are a potential diagnostic biomarker to distinguish COVID-19 and influenza infection, especially for inpatients. We also demonstrate that cytokine combinations, consisting of up to 3 cytokines, can distinguish SARS-CoV-2 and influenza infection with high accuracy in both inpatient (area under the receiver operating characteristics curve [AUC] = 0.84) and outpatient (AUC = 0.81) groups, revealing another potential screening tool for SARS-CoV-2 infection.

CONCLUSIONS : This study not only reveals prospective screening tools for COVID-19 infections that are independent of polymerase chain reaction testing or clinical condition, but it also emphasizes potential pathways involved in disease pathogenesis that act as potential targets for future mechanistic studies.

Luciani Lauren L, Miller Leigh M, Zhai Bo, Clarke Karen, Hughes Kramer Kailey, Schratz Lucas J, Balasubramani G K, Dauer Klancie, Nowalk M Patricia, Zimmerman Richard K, Shoemaker Jason E, Alcorn John F

2023-Mar

SARS-CoV-2, cytokine, human, machine learning, pneumonia

General General

SARS-CoV-2 related adaptation mechanisms of rehabilitation clinics affecting patient-centred care: Qualitative study of online patient reports.

In JMIR rehabilitation and assistive technologies

BACKGROUND : The SARS-CoV-2 pandemic impacted the access to inpatient rehabilitation services. At the current state of research, it is unclear to what extent the adaptation of rehabilitation services to infection-protective standards affected patient-centred care in Germany.

OBJECTIVE : This study aimed to explore which aspects of patient-centred care were relevant for patients in inpatient rehabilitation clinics under early-phase pandemic conditions.

METHODS : A deductive-inductive framework analysis of online patient reports posted on a leading German hospital rating website was conducted (www.klinikbewertungen.de). The selected hospital rating website is a third party, patient-centred commercial platform which operates independently of governmental entities. Following a theoretical sampling approach, online reports of rehabilitation stays in two federal states of Germany (Brandenburg, Saarland) uploaded between March 2020 and September 2021 were included. Independently of medical specialty groups, all reports were included. Keywords addressing framework domains were analysed descriptively.

RESULTS : In total, 649 online reports reflecting inpatient rehabilitation services of 31 clinics (Brandenburg N = 23; Saarland N = 8) were analysed. Keywords addressing the care environment were most frequently reported (59.9%) followed by staff prerequisites (33.0%), patient-centred processes (4.5%) and expected outcomes (2.6%). Qualitative in depth-analysis revealed SARS-CoV-2 related reports to be associated with domains of patient-centred processes and staff prerequisites. Discontinuous communication of infection protection standards was perceived to threaten patient autonomy. This was amplified by a tangible gratification crisis of medical staff. Established and emotional supportive relationships to clinicians and peer-groups offered the potential to mitigate adverse effects of infection protection standards.

CONCLUSIONS : Patients predominantly reported feedback associated with the care environment. SARS-CoV-2 related reports were strongly affected by increased staff workloads as well as patient-centred processes addressing discontinuous communication and organizationally demanding implementation of infection protection standards which were perceived to threaten patient autonomy. Peer-relationships formed during inpatient rehabilitation had the potential to mitigate these mechanisms.

CLINICALTRIAL : Not applicable.

Kühn Lukas, Lindert Lara, Kuper Paulina, Choi Kyung-Eun Anna

2023-Mar-05

Public Health Public Health

Predictors of Cyberchondria during the COVID-19 pandemic: A cross-sectional study using supervised machine learning.

In JMIR formative research

BACKGROUND : Cyberchondria is characterized by repeated and compulsive online searches for health information, resulting in increased health anxiety and distress. It has been conceptualized as a multi-dimensional construct fueled by both anxiety and compulsivity-related factors and described as a "transdiagnostic compulsive behavioral syndrome" which is associated with health anxiety, problematic internet use and obsessive-compulsive symptoms. Cyberchondria is not included in the ICD-11 or the DSM-5, and its defining features, etiological mechanisms and assessment continue to be debated.

OBJECTIVE : This study aimed to investigate changes in the severity of cyberchondria during the pandemic and identify predictors of cyberchondria at this time.

METHODS : Data collection started on May 4, 2020 and ended on June 10, 2020, which corresponds to the first wave of the COVID-19 pandemic in Europe. At the time the present study took place, French-speaking countries in Europe (France, Switzerland, Belgium and Luxembourg) all implemented lockdown or semi-lockdown measures. The survey consisted of a questionnaire collecting demographic information (sex, age, education level and country of residence) and information on socioeconomic circumstances during the first lockdown (e.g., economic situation, housing and employment status), and was followed by several instruments assessing various psychological and health-related constructs. Inclusion criteria for the study were being at least 18 years of age and having a good understanding of French. Self-report data were collected from 725 participants aged 18 to 77 years (mean 33.29, SD 12.88 years), with females constituting the majority (416/725, 57.4%).

RESULTS : The results show that the COVID-19 pandemic affected various facets of cyberchondria: cyberchondria-related distress and interference with functioning increased (distress z=-3.651, P<.001; compulsion z=-5.697, P<.001), whereas the reassurance facet of cyberchondria decreased (z=-6.680, P<.001). Also, COVID-19-related fears and health anxiety emerged as the strongest predictors of cyberchondria-related distress and interference with functioning during the pandemic.

CONCLUSIONS : These findings provide evidence about the impact of the COVID-19 pandemic on cyberchondria and identify factors that should be considered in efforts to prevent and manage cyberchondria at times of public health crises. Also, they are consistent with the theoretical model of cyberchondria during the COVID-19 pandemic proposed by Starcevic and his colleagues in 2020. In addition, the findings have implications for the conceptualization and future assessment of cyberchondria.

Infanti Alexandre, Starcevic Vladan, Schimmenti Adriano, Khazaal Yasser, Karila Laurent, Giardina Alessandro, Flayelle Maèva, Hedayatzadeh Razavi Seyedeh Boshra, Baggio Stéphanie, Vögele Claus, Billieux Joël

2023-Mar-09

General General

Understanding Prospective Physicians' Intention to Use Artificial Intelligence in Their Future Medical Practice: Configurational Analysis.

In JMIR medical education

BACKGROUND : Prospective physicians are expected to find artificial intelligence (AI) to be a key technology in their future practice. This transformative change has caught the attention of scientists, educators, and policy makers alike, with substantive efforts dedicated to the selection and delivery of AI topics and competencies in the medical curriculum. Less is known about the behavioral perspective or the necessary and sufficient preconditions for medical students' intention to use AI in the first place.

OBJECTIVE : Our study focused on medical students' knowledge, experience, attitude, and beliefs related to AI and aimed to understand whether they are necessary conditions and form sufficient configurations of conditions associated with behavioral intentions to use AI in their future medical practice.

METHODS : We administered a 2-staged questionnaire operationalizing the variables of interest (ie, knowledge, experience, attitude, and beliefs related to AI, as well as intention to use AI) and recorded 184 responses at t0 (February 2020, before the COVID-19 pandemic) and 138 responses at t1 (January 2021, during the COVID-19 pandemic). Following established guidelines, we applied necessary condition analysis and fuzzy-set qualitative comparative analysis to analyze the data.

RESULTS : Findings from the fuzzy-set qualitative comparative analysis show that the intention to use AI is only observed when students have a strong belief in the role of AI (individually necessary condition); certain AI profiles, that is, combinations of knowledge and experience, attitudes and beliefs, and academic level and gender, are always associated with high intentions to use AI (equifinal and sufficient configurations); and profiles associated with nonhigh intentions cannot be inferred from profiles associated with high intentions (causal asymmetry).

CONCLUSIONS : Our work contributes to prior knowledge by showing that a strong belief in the role of AI in the future of medical professions is a necessary condition for behavioral intentions to use AI. Moreover, we suggest that the preparation of medical students should go beyond teaching AI competencies and that educators need to account for the different AI profiles associated with high or nonhigh intentions to adopt AI.

Wagner Gerit, Raymond Louis, Paré Guy

2023-Mar-22

artificial intelligence, attitudes and beliefs, behavioral intentions, fsQCA, fuzzy-set qualitative comparative analysis, knowledge and experience, medical education

General General

Risk Factors and Predictive Modeling for Post-Acute Sequelae of SARS-CoV-2 Infection: Findings from EHR Cohorts of the RECOVER Initiative.

In Research square

Background Patients who were SARS-CoV-2 infected could suffer from newly incidental conditions in their post-acute infection period. These conditions, denoted as the post-acute sequelae of SARS-CoV-2 infection (PASC), are highly heterogeneous and involve a diverse set of organ systems. Limited studies have investigated the predictability of these conditions and their associated risk factors. Method In this retrospective cohort study, we investigated two large-scale PCORnet clinical research networks, INSIGHT and OneFlorida+, including 11 million patients in the New York City area and 16.8 million patients from Florida, to develop machine learning prediction models for those who are at risk for newly incident PASC and to identify factors associated with newly incident PASC conditions. Adult patients aged 20 with SARS-CoV-2 infection and without recorded infection between March 1 st , 2020, and November 30 th , 2021, were used for identifying associated factors with incident PASC after removing background associations. The predictive models were developed on infected adults. Results We find several incident PASC, e.g., malnutrition, COPD, dementia, and acute kidney failure, were associated with severe acute SARS-CoV-2 infection, defined by hospitalization and ICU stay. Older age and extremes of weight were also associated with these incident conditions. These conditions were better predicted (C-index >0.8). Moderately predictable conditions included diabetes and thromboembolic disease (C-index 0.7-0.8). These were associated with a wider variety of baseline conditions. Less predictable conditions included fatigue, anxiety, sleep disorders, and depression (C-index around 0.6). Conclusions This observational study suggests that a set of likely risk factors for different PASC conditions were identifiable from EHRs, predictability of different PASC conditions was heterogeneous, and using machine learning-based predictive models might help in identifying patients who were at risk of developing incident PASC.

Zang Chengxi, Hou Yu, Schenck Edward, Xu Zhenxing, Zhang Yongkang, Xu Jie, Bian Jiang, Morozyuk Dmitry, Khullar Dhruv, Nordvig Anna, Shenkman Elizabeth, Rothman Russel, Block Jason, Lyman Kristin, Zhang Yiye, Varma Jay, Weiner Mark, Carton Thomas, Wang Fei, Kaushal Rainu, Consortium The Recover

2023-Mar-08

General General

A ventilation early warning system (VEWS) for diaphanous workspaces considering COVID-19 and future pandemics scenarios.

In Heliyon

The COVID-19 pandemic has generated new needs due to the associated health risks and, more specifically, its rapid infection rate. Prevention measures to avoid contagions in indoor spaces, especially in office and public buildings (e.g., hospitals, public administration, educational centres, etc.), have led to the need for adequate ventilation to dilute the possible concentration of the virus. This article presents our contribution to this new challenge, namely the Ventilation Early Warning System (VEWS) which has aims to adapt the operation of the current Heating, Ventilating and Air Conditioning (HVAC) systems to the ventilation needs of diaphanous workspaces, based on a Smart Campus Digital Twin (SCDT) framework approach, while maintaining sustainability. Different technologies such as the Internet of Things (IoT), Building Information Modelling (BIM) and Artificial Intelligence (AI) algorithms are combined to collect and integrate monitoring data (historical records, real-time information, and location-related patterns) to carry out forecasting simulations in this digital twin. The generated outputs serve to assist facility managers in their building governance, considering the appropriate application of health measures to reduce the risk of coronavirus contagion in combination with sustainability criteria. The article also provides the results of the implementation of the VEWS in a university workspace as a case study. Its application has made it possible to detect and warn of inadequate ventilation situations for the daily flow of people in the different controlled zones.

Costa Gonçal, Arroyo Oriol, Rueda Pablo, Briones Alan

2023-Mar

BIM, Building digital twin, COVID-19, Facilities management, IoT, Simulation, Smart building

General General

COVID-19 diagnosis: A comprehensive review of pre-trained deep learning models based on feature extraction algorithm.

In Results in engineering

Due to the augmented rise of COVID-19, clinical specialists are looking for fast faultless diagnosis strategies to restrict Covid spread while attempting to lessen the computational complexity. In this way, swift diagnosis techniques for COVID-19 with high precision can offer valuable aid to clinical specialists. RT- PCR test is an expensive and tedious COVID diagnosis technique in practice. Medical imaging is feasible to diagnose COVID-19 by X-ray chest radiography to get around the shortcomings of RT-PCR. Through a variety of Deep Transfer-learning models, this research investigates the potential of Artificial Intelligence -based early diagnosis of COVID-19 via X-ray chest radiographs. With 10,192 normal and 3616 Covid X-ray chest radiographs, the deep transfer-learning models are optimized to further the accurate diagnosis. The x-ray chest radiographs undergo a data augmentation phase before developing a modified dataset to train the Deep Transfer-learning models. The Deep Transfer-learning architectures are trained using the extracted features from the Feature Extraction stage. During training, the classification of X-ray Chest radiographs based on feature extraction algorithm values is converted into a feature label set containing the classified image data with a feature string value representing the number of edges detected after edge detection. The feature label set is further tested with the SVM, KNN, NN, Naive Bayes and Logistic Regression classifiers to audit the quality metrics of the proposed model. The quality metrics include accuracy, precision, F1 score, recall and AUC. The Inception-V3 dominates the six Deep Transfer-learning models, according to the assessment results, with a training accuracy of 84.79% and a loss function of 2.4%. The performance of Cubic SVM was superior to that of the other SVM classifiers, with an AUC score of 0.99, precision of 0.983, recall of 0.8977, accuracy of 95.8%, and F1 score of 0.9384. Cosine KNN fared better than the other KNN classifiers with an AUC score of 0.95, precision of 0.974, recall of 0.777, accuracy of 90.8%, and F1 score of 0.864. Wide NN fared better than the other NN classifiers with an AUC score of 0.98, precision of 0.975, recall of 0.907, accuracy of 95.5%, and F1 score of 0.939. According to the findings, SVM classifiers topped other classifiers in terms of performance indicators like accuracy, precision, recall, F1-score, and AUC. The SVM classifiers reported better mean optimal scores compared to other classifiers. The performance assessment metrics uncover that the proposed methodology can aid in preliminary COVID diagnosis.

Poola Rahul Gowtham, Pl Lahari, Y Siva Sankar

2023-Jun

Boundary tracing, Covid diagnosis, Deep transfer-learning, Medical imaging, Neural network models and classifiers

General General

Human Behavior in the Time of COVID-19: Learning from Big Data

ArXiv Preprint

Since the World Health Organization (WHO) characterized COVID-19 as a pandemic in March 2020, there have been over 600 million confirmed cases of COVID-19 and more than six million deaths as of October 2022. The relationship between the COVID-19 pandemic and human behavior is complicated. On one hand, human behavior is found to shape the spread of the disease. On the other hand, the pandemic has impacted and even changed human behavior in almost every aspect. To provide a holistic understanding of the complex interplay between human behavior and the COVID-19 pandemic, researchers have been employing big data techniques such as natural language processing, computer vision, audio signal processing, frequent pattern mining, and machine learning. In this study, we present an overview of the existing studies on using big data techniques to study human behavior in the time of the COVID-19 pandemic. In particular, we categorize these studies into three groups - using big data to measure, model, and leverage human behavior, respectively. The related tasks, data, and methods are summarized accordingly. To provide more insights into how to fight the COVID-19 pandemic and future global catastrophes, we further discuss challenges and potential opportunities.

Hanjia Lyu, Arsal Imtiaz, Yufei Zhao, Jiebo Luo

2023-03-23

Radiology Radiology

Impact of inactivated COVID-19 vaccines on lung injury in B.1.617.2 (Delta) variant-infected patients.

In Annals of clinical microbiology and antimicrobials

BACKGROUND : Chest computerized tomography (CT) scan is an important strategy that quantifies the severity of COVID-19 pneumonia. To what extent inactivated COVID-19 vaccines could impact the COVID-19 pneumonia on chest CT is not clear.

METHODS : This study recruited 357 SARS-COV-2 B.1.617.2 (Delta) variant-infected patients admitted to the Second Hospital of Nanjing from July to August 2021. An artificial intelligence-assisted CT imaging system was used to quantify the severity of COVID-19 pneumonia. We compared the volume of infection (VOI), percentage of infection (POI) and chest CT scores among patients with different vaccination statuses.

RESULTS : Of the 357 Delta variant-infected patients included for analysis, 105 were unvaccinated, 72 were partially vaccinated and 180 were fully vaccinated. Fully vaccination had the least lung injuries when quantified by VOI (median VOI of 222.4 cm3, 126.6 cm3 and 39.9 cm3 in unvaccinated, partially vaccinated and fully vaccinated, respectively; p < 0.001), POI (median POI of 7.60%, 3.55% and 1.20% in unvaccinated, partially vaccinated and fully vaccinated, respectively; p < 0.001) and chest CT scores (median CT score of 8.00, 6.00 and 4.00 in unvaccinated, partially vaccinated and fully vaccinated, respectively; p < 0.001). After adjustment for age, sex, comorbidity, time from illness onset to hospitalization and viral load, fully vaccination but not partial vaccination was significantly associated with less lung injuries quantified by VOI {adjust coefficient[95%CI] for "full vaccination": - 106.10(- 167.30,44.89); p < 0.001}, POI {adjust coefficient[95%CI] for "full vaccination": - 3.88(- 5.96, - 1.79); p = 0.001} and chest CT scores {adjust coefficient[95%CI] for "full vaccination": - 1.81(- 2.72, - 0.91); p < 0.001}. The extent of reduction of pulmonary injuries was more profound in fully vaccinated patients with older age, having underlying diseases, and being female sex, as demonstrated by relatively larger absolute values of adjusted coefficients. Finally, even within the non-severe COVID-19 population, fully vaccinated patients were found to have less lung injuries.

CONCLUSION : Fully vaccination but not partially vaccination could significantly protect lung injury manifested on chest CT. Our study provides additional evidence to encourage a full course of vaccination.

Lai Miao, Wang Kai, Ding Chengyuan, Yin Yi, Lin Xiaoling, Xu Chuanjun, Hu Zhiliang, Peng Zhihang

2023-Mar-21

Artificial intelligence (AI), COVID-19, COVID-19 vaccines, Chest CT, Lung injury

General General

Fault Prognosis of Turbofan Engines: Eventual Failure Prediction and Remaining Useful Life Estimation

ArXiv Preprint

In the era of industrial big data, prognostics and health management is essential to improve the prediction of future failures to minimize inventory, maintenance, and human costs. Used for the 2021 PHM Data Challenge, the new Commercial Modular Aero-Propulsion System Simulation dataset from NASA is an open-source benchmark containing simulated turbofan engine units flown under realistic flight conditions. Deep learning approaches implemented previously for this application attempt to predict the remaining useful life of the engine units, but have not utilized labeled failure mode information, impeding practical usage and explainability. To address these limitations, a new prognostics approach is formulated with a customized loss function to simultaneously predict the current health state, the eventual failing component(s), and the remaining useful life. The proposed method incorporates principal component analysis to orthogonalize statistical time-domain features, which are inputs into supervised regressors such as random forests, extreme random forests, XGBoost, and artificial neural networks. The highest performing algorithm, ANN-Flux, achieves AUROC and AUPR scores exceeding 0.95 for each classification. In addition, ANN-Flux reduces the remaining useful life RMSE by 38% for the same test split of the dataset compared to past work, with significantly less computational cost.

Joseph Cohen, Xun Huan, Jun Ni

2023-03-23

General General

Using artificial intelligence to support rapid, mixed-methods analysis: Developing an automated qualitative assistant (AQUA).

In Annals of family medicine

Context: Qualitative research - crucial for understanding human behavior - remains underutilized, in part due to the time and cost of annotating qualitative data (coding). Artificial intelligence (AI) has been suggested as a means to reduce those burdens. Older AI techniques (Latent Semantic Indexing / Latent Dirichlet Allocation (LSI/LDA)) have fallen short, in part because qualitative data is rife with idiom, non-standard expressions, and jargon. Objective: To develop an AI platform using updated techniques to augment qualitative data coding. Study Design and Analysis: We previously completed traditional qualitative analysis of a large dataset, with 11 qualitative categories and 72 subcategories (categories), and a final Cohen's kappa ≥ 0.65 as a measure of human inter-coder reliability (ICR) after coding. We built our Automated Qualitative Assistant (AQUA) using a semi-classical approach, replacing LSI/LDA with a graph-theoretic topic extraction and clustering method. AQUA was given the previously-identified qualitative categories and tasked with coding free-text data into those categories. Item coding was scored using cosine-similarity. Population Studied: Pennsylvanian adults. Instrument: Free-text responses to five open ended questions related to the COVID-19 pandemic (e.g. "What worries you most about the COVID-19 pandemic?"). Outcome Measures: AQUA's coding was compared to human coding using Cohen's kappa. This was done on all categories in aggregate, and also on category clusters to identify category groups amenable to AQUA support. AQUA's time to complete coding was compared to the time taken by the human coding team. Dataset: Five unlimited free-text survey answers from 538 responders. Results: AQUA's kappa for all categories was low (kappa~0.45), reflecting the challenge of automated analysis of diverse language. However, for several 3-category combinations (with less linguistic diversity), AQUA performed comparably to human coders, with an ICR kappa range of 0.62 to 0.72 based on test-train split. AQUA's analysis (including human interpretation) took approximately 5 hours, compared to approximately 30 person hours for traditional coding. Conclusions: AQUA enables qualitative researchers to identify categories amenable to automated coding, and to rapidly conduct that coding on the entirety of very large datasets. This saves time and money, and avoids limitations inherent in limiting qualitative analysis to limited samples of a given dataset.

Lennon Robert, Calo William, Miller Erin, Zgierska Aleksandra, Van Scoy Lauren, Fraleigh Robert

2022-Apr-01

General General

Artificial intelligence based virtual screening study for competitive and allosteric inhibitors of the SARS-CoV-2 main protease.

In Journal of biomolecular structure & dynamics

SARS-CoV-2 is a highly contagious and dangerous coronavirus that first appeared in late 2019 causing COVID-19, a pandemic of acute respiratory illnesses that is still a threat to health and the general public safety. We performed deep docking studies of 800 M unique compounds in both the active and allosteric sites of the SARS-COV-2 Main Protease (Mpro) and the 15 M and 13 M virtual hits obtained were further taken for conventional docking and molecular dynamic (MD) studies. The best XP Glide docking scores obtained were -14.242 and -12.059 kcal/mol by CHEMBL591669 and the highest binding affinities were -10.5 kcal/mol (from 444215) and -11.2 kcal/mol (from NPC95421) for active and allosteric sites, respectively. Some hits can bind both sites making them a great area of concern. Re-docking of 8 random allosteric complexes in the active site shows a significant reduction in docking scores with a t-test P value of 2.532 × 10-11 at 95% confidence. Some specific interactions have higher elevations in docking scores. MD studies on 15 complexes show that single-ligand systems are stable as compared to double-ligand systems, and the allosteric binders identified are shown to modulate the active site binding as evidenced by the changes in the interaction patterns and stability of ligands and active site residues. When an allosteric complex was docked to the second monomer to check for homodimer formation, the validated homodimer could not be re-established, further supporting the potential of the identified allosteric binders. These findings could be important in developing novel therapeutics against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Charles Ssemuyiga, Edgar Mulumba Pius, Mahapatra Rajani Kanta

2023-Mar-21

Artificial intelligence, COVID-19, SARS-CoV-2 main protease, deep docking, molecular docking, molecular dynamics simulation, neural networks

General General

Gender Differences in the Nonspecific and Health-Specific Use of Social Media Before and During the COVID-19 Pandemic: Trend Analysis Using HINTS 2017-2020 Data.

In Journal of health communication ; h5-index 36.0

The use of social media has changed since the outbreak of coronavirus disease 2019 (COVID-19). However, little is known about the gender disparity in social media use for nonspecific and health-specific issues before and during the COVID-19 pandemic. Based on a gender difference perspective, this study aimed to examine how the nonspecific and health-specific uses of social media changed in 2017-2020. The data came from the Health Information National Trends Survey Wave 5 Cycle 1-4. This study included 10,426 participants with complete data. Compared to 2017, there were higher levels of general use in 2019 and 2020, and an increased likelihood of health-related use in 2020 was reported among the general population. Female participants were more likely to be nonspecific and health-specific users than males. Moreover, the relationship of gender with general use increased in 2019 and 2020; however, concerning health-related use, it expanded in 2019 but narrowed in 2020. The COVID-19 global pandemic led to increased use of social media, especially for health-related issues among males. These findings further our understanding of the gender gap in health communication through social media, and contribute to targeted messaging to promote health and reduce disparities between different groups during the pandemic.

Ye Linglong, Chen Yang, Cai Yongming, Kao Yi-Wei, Wang Yuanxin, Chen Mingchih, Shia Ben-Chang, Qin Lei

2023-Mar-21

General General

Relationship Between Coronavirus Disease 2019 Vaccination Rates and Rare But Potentially Fatal Adverse Events: A Regression Discontinuity Analysis of Western Countries.

In Journal of Korean medical science

BACKGROUND : Owing to limited experience with the new vaccine platforms, discussion of vaccine safety is inevitable. However, media coverage of adverse events of special interest could influence the vaccination rate; thus, evaluating the outcomes of adverse events of special interest influencing vaccine administration is crucial.

METHODS : We conducted regression discontinuity in time analysis to calculate the local average treatment effect (LATE) using datasets from Our World in Data and Johns Hopkins University Center for Systems Science and Engineering. For the United States, the United Kingdom, and Europe, the cutoff points were April 23rd and June 23rd, April 7th, and the 14th week of 2021, respectively.

RESULTS : The LATE of the Advisory Committee on Immunization Practices (ACIP) meeting held on April 23rd was -0.249 for all vaccines, -0.133 (-0.189 to -0.076) for Pfizer, -0.064 (-0.115 to -0.012) for Moderna, and -0.038 (-0.047 to -0.030) for Johnson &amp; Johnson. Discontinuities were observed for all three types of vaccines in the United States. The June 23rd meeting of the ACIP (mRNA vaccines and myocarditis) did not convene any discontinuities. Furthermore, there was no significant drop in the weekly average vaccination rates in Europe following the European Medicines Agency (EMA) statement on April 7th. Conversely, there was a significant drop in the first-dose vaccination rates in the United Kingdom related to the EMA report. The first-dose vaccination rate for all vaccines changed by -0.104 (-0.176 to -0.032).

CONCLUSION : Although monitoring and reporting of adverse events of special interest are important, a careful approach towards public announcements is warranted.

Chae Seung Hoon, Park Hyung Jun, Radnaabaatar Munkhzul, Park Hojun, Jung Jaehun

2023-Mar-20

COVID-19, Regression Discontinuity Analysis, SARS-CoV-2

Public Health Public Health

Acceptability and Effectiveness of COVID-19 Contact Tracing Applications: A Case Study in Saudi Arabia of the Tawakkalna Application.

In Cureus

Background Contact tracing applications were introduced during the COVID-19 pandemic to mitigate the spread of the infection in several countries. In Saudi Arabia, the Tawakkalna application was developed. The Tawakkalna application is a mobile health solution aimed to track infection cases, save lives, and reduce the burden on health facilities. This study aims to explore the public's attitude to and acceptance levels of the Tawakkalna application and to evaluate its effectiveness regarding privacy and security. The main objective of this study is to investigate the user acceptability of contact tracing applications and explore the safety and privacy effectiveness of the COVID-19 contact tracing application, the Tawakkalna application. In addition, the study analyzes factors associated with acceptance levels and compares the results obtained to similar studies in other countries using similar applications. Methodology This study used a valid and reliable online survey that was used in similar studies conducted in other countries to assess the acceptability of the application. The survey was conducted from September to November 2021, and the final dataset included 205 participants. To investigate the privacy and security performance of the Tawakkalna application, we followed the investigation method used by similar research that investigated 28 contact tracing applications across Europe. Results Out of the 205 participants, 84.87% were in favor of the opt-in voluntary installation of the Tawakkalna application, and 49.75% of the participants were in favor of the opt-out automatic installation. Individuals' trust in the government had a huge impact on acceptance, with 60.98% of the participants supporting the application because they believed that the Tawakkalna application would help them stay healthy during the COVID-19 pandemic. Overall, 49% of the participants supporting the application also agreed to the de-identification of their collected data and providing it for research. The Tawakkalna application ranked at the top compared to other contact tracing applications regarding privacy and security. Conclusions The Tawakkalna application developed by the Saudi Data and Artificial Intelligence Authority was a response to the COVID-19 pandemic, which is considered the biggest public health crisis in recent times. The Saudi Arabian government gained the population's acceptance through effective endorsement and the spread of educational content through media channels. By complying with privacy policies, the Tawakkalna application is an effective tool to combat public health infectious diseases.

Dawood Safia, AlKadi Khulud

2023-Feb

acceptability, contact tracing, covid-19, mhealth, permission, privacy, privilege, security, tawakkalna

Public Health Public Health

Examining thematic and emotional differences across Twitter, Reddit, and YouTube: The case of COVID-19 vaccine side effects.

In Computers in human behavior ; h5-index 125.0

Social media discourse has become a key data source for understanding the public's perception of, and sentiments during a public health crisis. However, given the different niches which platforms occupy in terms of information exchange, reliance on a single platform would provide an incomplete picture of public opinions. Based on the schema theory, this study suggests a 'social media platform schema' to indicate users' different expectations based on previous usages of platform and argues that a platform's distinct characteristics foster distinct platform schema and, in turn, distinct nature of information. We analyzed COVID-19 vaccine side effect-related discussions from Twitter, Reddit, and YouTube, each of which represents a different type of the platform, and found thematic and emotional differences across platforms. Thematic analysis using k-means clustering algorithm identified seven clusters in each platform. To computationally group and contrast thematic clusters across platforms, we employed modularity analysis using the Louvain algorithm to determine a semantic network structure based on themes. We also observed differences in emotional contexts across platforms. Theoretical and public health implications are then discussed.

Kwon Soyeon, Park Albert

2023-Jul

Consumer health information, Schema theory, Social media, Social network analysis, Unsupervised machine learning

General General

CBCovid19EC: A dataset complete blood count and PCR test for COVID-19 detection in Ecuadorian population.

In Data in brief

In this work, we present the complete blood count data and PCR test results of a population of Ecuadorians from different provinces, primarily residing in the Andean region, especially in Quito. PCR was the standard test to detect Covid-19 during the pandemic since 2020. The data were obtained between March 1st and August 12th, 2021. Segurilab and Previne Salud laboratories performed the tests. The dataset contains about 400 clinical cases. Each patient agreed to participate in the study by sharing the results of their PCR (reverse transcription polymerase chain reaction) tests and CBC (complete blood count). CBC test measured several components and features of the blood, including red blood cells, white blood cells, hemoglobin, hematocrit, and platelets. The shared data are intended to provide researchers with input to analyze various events associated with the diagnosis of Covid-19 linked to potential diseases identified in the components measured in the CBC test. These data are helpful for pattern analysis of blood components in modeling prediction and clustering problems. The components measured in the complete blood count and CRP together can be helpful for the analysis of different medical conditions using machine learning algorithms.

Ordoñez-Avila R, Parraga-Alava J, Hormaza J Meza, Vaca-Cárdenas L, Portmann E, Terán L, Dorn M

2023-Apr

Ecuador, Hematological data, Machine learning, SARS-Cov-2

Public Health Public Health

Computerization of the Work of General Practitioners: Mixed Methods Survey of Final-Year Medical Students in Ireland.

In JMIR medical education

BACKGROUND : The potential for digital health technologies, including machine learning (ML)-enabled tools, to disrupt the medical profession is the subject of ongoing debate within biomedical informatics.

OBJECTIVE : We aimed to describe the opinions of final-year medical students in Ireland regarding the potential of future technology to replace or work alongside general practitioners (GPs) in performing key tasks.

METHODS : Between March 2019 and April 2020, using a convenience sample, we conducted a mixed methods paper-based survey of final-year medical students. The survey was administered at 4 out of 7 medical schools in Ireland across each of the 4 provinces in the country. Quantitative data were analyzed using descriptive statistics and nonparametric tests. We used thematic content analysis to investigate free-text responses.

RESULTS : In total, 43.1% (252/585) of the final-year students at 3 medical schools responded, and data collection at 1 medical school was terminated due to disruptions associated with the COVID-19 pandemic. With regard to forecasting the potential impact of artificial intelligence (AI)/ML on primary care 25 years from now, around half (127/246, 51.6%) of all surveyed students believed the work of GPs will change minimally or not at all. Notably, students who did not intend to enter primary care predicted that AI/ML will have a great impact on the work of GPs.

CONCLUSIONS : We caution that without a firm curricular foundation on advances in AI/ML, students may rely on extreme perspectives involving self-preserving optimism biases that demote the impact of advances in technology on primary care on the one hand and technohype on the other. Ultimately, these biases may lead to negative consequences in health care. Improvements in medical education could help prepare tomorrow's doctors to optimize and lead the ethical and evidence-based implementation of AI/ML-enabled tools in medicine for enhancing the care of tomorrow's patients.

Blease Charlotte, Kharko Anna, Bernstein Michael, Bradley Colin, Houston Muiris, Walsh Ian, D Mandl Kenneth

2023-Mar-20

COVID-19, artificial intelligence, biomedical, design, digital health, general practitioners, machine learning, medical education, medical professional, medical students, survey, technology, tool

General General

COVID-19 and pneumonia diagnosis from chest X-ray images using convolutional neural networks.

In Network modeling and analysis in health informatics and bioinformatics

X-ray is a useful imaging modality widely utilized for diagnosing COVID-19 virus that infected a high number of people all around the world. The manual examination of these X-ray images may cause problems especially when there is lack of medical staff. Usage of deep learning models is known to be helpful for automated diagnosis of COVID-19 from the X-ray images. However, the widely used convolutional neural network architectures typically have many layers causing them to be computationally expensive. To address these problems, this study aims to design a lightweight differential diagnosis model based on convolutional neural networks. The proposed model is designed to classify the X-ray images belonging to one of the four classes that are Healthy, COVID-19, viral pneumonia, and bacterial pneumonia. To evaluate the model performance, accuracy, precision, recall, and F1-Score were calculated. The performance of the proposed model was compared with those obtained by applying transfer learning to the widely used convolutional neural network models. The results showed that the proposed model with low number of computational layers outperforms the pre-trained benchmark models, achieving an accuracy value of 89.89% while the best pre-trained model (Efficient-Net B2) achieved accuracy of 85.7%. In conclusion, the proposed lightweight model achieved the best overall result in classifying lung diseases allowing it to be used on devices with limited computational power. On the other hand, all the models showed a poor precision on viral pneumonia class and confusion in distinguishing it from bacterial pneumonia class, thus a decrease in the overall accuracy.

Hariri Muhab, Avşar Ercan

2023

COVID-19, Classification, Convolutional neural networks, Deep learning, Lung diseases, Transfer learning

General General

Precision recruitment for high-risk participants in a COVID-19 cohort study.

In Contemporary clinical trials communications

BACKGROUND : Studies for developing diagnostics and treatments for infectious diseases usually require observing the onset of infection during the study period. However, when the infection base rate incidence is low, the cohort size required to measure an effect becomes large, and recruitment becomes costly and prolonged. We developed a model for reducing recruiting time and resources in a COVID-19 detection study by targeting recruitment to high-risk individuals.

METHODS : We conducted an observational longitudinal cohort study at individual sites throughout the U.S., enrolling adults who were members of an online health and research platform. Through direct and longitudinal connection with research participants, we applied machine learning techniques to compute individual risk scores from individually permissioned data about socioeconomic and behavioral data, in combination with predicted local prevalence data. The modeled risk scores were then used to target candidates for enrollment in a hypothetical COVID-19 detection study. The main outcome measure was the incidence rate of COVID-19 according to the risk model compared with incidence rates in actual vaccine trials.

RESULTS : When we used risk scores from 66,040 participants to recruit a balanced cohort of participants for a COVID-19 detection study, we obtained a 4- to 7-fold greater COVID-19 infection incidence rate compared with similar real-world study cohorts.

CONCLUSION : This risk model offers the possibility of reducing costs, increasing the power of analyses, and shortening study periods by targeting for recruitment participants at higher risk.

Mezlini Aziz M, Caddigan Eamon, Shapiro Allison, Ramirez Ernesto, Kondow-McConaghy Helena M, Yang Justin, DeMarco Kerry, Naraghi-Arani Pejman, Foschini Luca

2023-Jun

CDC, Centers for Disease Control and Prevention, COVID-19, Clinical trials, GAMs, generalized additive models, Risk modeling

Radiology Radiology

Computed tomography-based COVID-19 triage through a deep neural network using mask-weighted global average pooling.

In Frontiers in cellular and infection microbiology ; h5-index 53.0

BACKGROUND : There is an urgent need to find an effective and accurate method for triaging coronavirus disease 2019 (COVID-19) patients from millions or billions of people. Therefore, this study aimed to develop a novel deep-learning approach for COVID-19 triage based on chest computed tomography (CT) images, including normal, pneumonia, and COVID-19 cases.

METHODS : A total of 2,809 chest CT scans (1,105 COVID-19, 854 normal, and 850 non-3COVID-19 pneumonia cases) were acquired for this study and classified into the training set (n = 2,329) and test set (n = 480). A U-net-based convolutional neural network was used for lung segmentation, and a mask-weighted global average pooling (GAP) method was proposed for the deep neural network to improve the performance of COVID-19 classification between COVID-19 and normal or common pneumonia cases.

RESULTS : The results for lung segmentation reached a dice value of 96.5% on 30 independent CT scans. The performance of the mask-weighted GAP method achieved the COVID-19 triage with a sensitivity of 96.5% and specificity of 87.8% using the testing dataset. The mask-weighted GAP method demonstrated 0.9% and 2% improvements in sensitivity and specificity, respectively, compared with the normal GAP. In addition, fusion images between the CT images and the highlighted area from the deep learning model using the Grad-CAM method, indicating the lesion region detected using the deep learning method, were drawn and could also be confirmed by radiologists.

CONCLUSIONS : This study proposed a mask-weighted GAP-based deep learning method and obtained promising results for COVID-19 triage based on chest CT images. Furthermore, it can be considered a convenient tool to assist doctors in diagnosing COVID-19.

Zhang Hong-Tao, Sun Ze-Yu, Zhou Juan, Gao Shen, Dong Jing-Hui, Liu Yuan, Bai Xu, Ma Jin-Lin, Li Ming, Li Guang, Cai Jian-Ming, Sheng Fu-Geng

2023

artificial intelligence, computed tomography (CT), coronavirus disease 2019 (COVID-19), deep learning, global average pooling (GAP)

General General

Applying Blockchain Technology in Network Public Opinion Risk Management System in Big Data Environment.

In Computational intelligence and neuroscience

Network public opinion represents public social opinion to a certain extent and has an important impact on formulating national policies and judgment. Therefore, China and other countries attach great importance to the study of online public opinion. However, the current researches lack the combination of theory and practical cases and lack the intersection of social and natural sciences. This work aims to overcome the technical defects of traditional management systems, break through the difficulties and pain points of existing network public opinion risk management, and improve the efficiency of network public opinion risk management. Firstly, a network public opinion isolation strategy based on the infectious disease propagation model is proposed, and the optimal control theory is used to realize a functional control model to maximize social utility. Secondly, blockchain technology is used to build a network public opinion risk management system. The system is used to conduct a detailed study on identifying and perceiving online public opinion risk. Finally, a Chinese word segmentation scheme based on Long Short-Term Memory (LSTM) network model and a text emotion recognition scheme based on a convolutional neural network are proposed. Both schemes are validated on a typical corpus. The results show that when the system has a control strategy, the number of susceptible drops significantly. Two days after the public opinion is generated, the number of susceptible people decreased from 1,000 to 250; 3 days after the public opinion is generated, the number of susceptible people stabilized. 2 days after the public opinion is generated, the number of lurkers increased from 100 to 620; 3 days after the public opinion is generated, the number of lurkers stabilized. The data demonstrate that the designed isolation control strategy is effective. Changes in public opinion among infected people show that quarantine control strategies played a significant role in the early days of Corona Virus Disease 2019. The rate of change in the number of infections is more affected when quarantine controls are increased, especially in the days leading up to the outbreak. When the system adopts the optimal control strategy, the influence scope of public opinion becomes smaller, and the control becomes easier. When the dimension of the word vector of emergent events is 200, its accuracy may be higher. This method provides certain ideas for blockchain and deep learning technology in network public opinion control.

Luo Zhenqing, Zhang Cheng

2023

General General

Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease.

In Cell reports methods

Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection.

Zhang Zijun, Sauerwald Natalie, Cappuccio Antonio, Ramos Irene, Nair Venugopalan D, Nudelman German, Zaslavsky Elena, Ge Yongchao, Gaitas Angelo, Ren Hui, Brockman Joel, Geis Jennifer, Ramalingam Naveen, King David, McClain Micah T, Woods Christopher W, Henao Ricardo, Burke Thomas W, Tsalik Ephraim L, Goforth Carl W, Lizewski Rhonda A, Lizewski Stephen E, Weir Dawn L, Letizia Andrew G, Sealfon Stuart C, Troyanskaya Olga G

2023-Feb-27

RNA splicing, SARS-CoV-2, diagnostic biomarker, host response assays, infectious disease, viral infection

Public Health Public Health

An AI-enabled research support tool for the classification system of COVID-19.

In Frontiers in public health

The outbreak of COVID-19, a little more than 2 years ago, drastically affected all segments of society throughout the world. While at one end, the microbiologists, virologists, and medical practitioners were trying to find the cure for the infection; the Governments were laying emphasis on precautionary measures like lockdowns to lower the spread of the virus. This pandemic is perhaps also the first one of its kind in history that has research articles in all possible areas as like: medicine, sociology, psychology, supply chain management, mathematical modeling, etc. A lot of work is still continuing in this area, which is very important also for better preparedness if such a situation arises in future. The objective of the present study is to build a research support tool that will help the researchers swiftly identify the relevant literature on a specific field or topic regarding COVID-19 through a hierarchical classification system. The three main tasks done during this study are data preparation, data annotation and text data classification through bi-directional long short-term memory (bi-LSTM).

Tiwari Arti, Bhattacharjee Kamanasish, Pant Millie, Srivastava Shilpa, Snasel Vaclav

2023

Artificial Intelligence, COVID-19, bi-directional LSTM, classification, long short-term memory

Public Health Public Health

Mechanisms influencing the factors of urban built environments and coronavirus disease 2019 at macroscopic and microscopic scales: The role of cities.

In Frontiers in public health

In late 2019, the coronavirus disease 2019 (COVID-19) pandemic soundlessly slinked in and swept the world, exerting a tremendous impact on lifestyles. This study investigated changes in the infection rates of COVID-19 and the urban built environment in 45 areas in Manhattan, New York, and the relationship between the factors of the urban built environment and COVID-19. COVID-19 was used as the outcome variable, which represents the situation under normal conditions vs. non-pharmacological intervention (NPI), to analyze the macroscopic (macro) and microscopic (micro) factors of the urban built environment. Computer vision was introduced to quantify the material space of urban places from street-level panoramic images of the urban streetscape. The study then extracted the microscopic factors of the urban built environment. The micro factors were composed of two parts. The first was the urban level, which was composed of urban buildings, Panoramic View Green View Index, roads, the sky, and buildings (walls). The second was the streets' green structure, which consisted of macrophanerophyte, bush, and grass. The macro factors comprised population density, traffic, and points of interest. This study analyzed correlations from multiple levels using linear regression models. It also effectively explored the relationship between the urban built environment and COVID-19 transmission and the mechanism of its influence from multiple perspectives.

Zhang Longhao, Han Xin, Wu Jun, Wang Lei

2023

COVID-19, computer vision, deep learning, relevance, street view images, urban built environment

Public Health Public Health

PCR-like performance of rapid test with permselective tunable nanotrap.

In Nature communications ; h5-index 260.0

Highly sensitive rapid testing for COVID-19 is essential for minimizing virus transmission, especially before the onset of symptoms and in asymptomatic cases. Here, we report bioengineered enrichment tools for lateral flow assays (LFAs) with enhanced sensitivity and specificity (BEETLES2), achieving enrichment of SARS-CoV-2 viruses, nucleocapsid (N) proteins and immunoglobulin G (IgG) with 3-minute operation. The limit of detection is improved up to 20-fold. We apply this method to clinical samples, including 83% with either intermediate (35%) or low viral loads (48%), collected from 62 individuals (n = 42 for positive and n = 20 for healthy controls). We observe diagnostic sensitivity, specificity, and accuracy of 88.1%, 100%, and 91.9%, respectively, compared with commercial LFAs alone achieving 14.29%, 100%, and 41.94%, respectively. BEETLES2, with permselectivity and tunability, can enrich the SARS-CoV-2 virus, N proteins, and IgG in the nasopharyngeal/oropharyngeal swab, saliva, and blood serum, enabling reliable and sensitive point-of-care testing, facilitating fast early diagnosis.

Park Seong Jun, Lee Seungmin, Lee Dongtak, Lee Na Eun, Park Jeong Soo, Hong Ji Hye, Jang Jae Won, Kim Hyunji, Roh Seokbeom, Lee Gyudo, Lee Dongho, Cho Sung-Yeon, Park Chulmin, Lee Dong-Gun, Lee Raeseok, Nho Dukhee, Yoon Dae Sung, Yoo Yong Kyoung, Lee Jeong Hoon

2023-Mar-18

General General

Identification of medicinal plant-based phytochemicals as a potential inhibitor for SARS-CoV-2 main protease (Mpro) using molecular docking and deep learning methods.

In Computers in biology and medicine

Highly transmissive and rapidly evolving Coronavirus disease-2019 (COVID-19), a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), triggered a global pandemic, which is one of the most researched viruses in the academia. Effective drugs to treat people with COVID-19 have yet to be developed to reduce mortality and transmission. Studies on the SARS-CoV-2 virus identified that its main protease (Mpro) might be a potential therapeutic target for drug development, as this enzyme plays a key role in viral replication. In search of potential inhibitors of Mpro, we developed a phytochemical library consisting of 2431 phytochemicals from 104 Korean medicinal plants that exhibited medicinal and antioxidant properties. The library was screened by molecular docking, followed by revalidation by re-screening with a deep learning method. Recurrent Neural Networks (RNN) computing system was used to develop an inhibitory predictive model using SARS coronavirus Mpro dataset. It was deployed to screen the top 12 compounds based on their docked binding affinity that ranged from -8.0 to -8.9 kcal/mol. The top two lead compounds, Catechin gallate and Quercetin 3-O-malonylglucoside, were selected depending on inhibitory potency against Mpro. Interactions with the target protein active sites, including His41, Met49, Cys145, Met165, and Thr190 were also examined. Molecular dynamics simulation was performed to analyze root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (RG), solvent accessible surface area (SASA), and number of hydrogen bonds. Results confirmed the inflexible nature of the docked complexes. Absorption, distribution, metabolism, excretion, and toxicity (ADMET), as well as bioactivity prediction confirmed the pharmaceutical activities of the lead compound. Findings of this research might help scientists to optimize compatible drugs for the treatment of COVID-19 patients.

Hossain Alomgir, Rahman Md Ekhtiar, Rahman Md Siddiqur, Nasirujjaman Khondokar, Matin Mohammad Nurul, Faruqe Md Omar, Rabbee Muhammad Fazle

2023-Mar-11

Catechin gallate, Deep learning, Main protease, Molecular docking, SARS-CoV-2

General General

Longitudinal proteomic investigation of COVID-19 vaccination.

In Protein & cell

Although the development of COVID-19 vaccines has been a remarkable success, the heterogeneous individual antibody generation and decline over time are unknown and still hard to predict. In this study, blood samples were collected from 163 participants who next received two doses of an inactivated COVID-19 vaccine (CoronaVac®) at a 28-day interval. Using TMT-based proteomics, we identified 1,715 serum and 7,342 peripheral blood mononuclear cells (PBMCs) proteins. We proposed two sets of potential biomarkers (seven from serum, five from PBMCs) at baseline using machine learning, and predicted the individual seropositivity 57 days after vaccination (AUC = 0.87). Based on the four PBMC's potential biomarkers, we predicted the antibody persistence until 180 days after vaccination (AUC = 0.79). Our data highlighted characteristic hematological host responses, including altered lymphocyte migration regulation, neutrophil degranulation, and humoral immune response. This study proposed potential blood-derived protein biomarkers before vaccination for predicting heterogeneous antibody generation and decline after COVID-19 vaccination, shedding light on immunization mechanisms and individual booster shot planning.

Wang Yingrui, Zhu Qianru, Sun Rui, Yi Xiao, Huang Lingling, Hu Yifan, Ge Weigang, Gao Huanhuan, Ye Xinfu, Song Yu, Shao Li, Li Yantao, Li Jie, Guo Tiannan, Shi Junping

2023-Feb-06

COVID-19, machine learning, neutralizing antibodies (NAbs), proteomics, vaccination

Internal Medicine Internal Medicine

Artificial intelligence-based point-of-care lung ultrasound for screening COVID-19 pneumoniae: Comparison with CT scans.

In PloS one ; h5-index 176.0

BACKGROUND : Although lung ultrasound has been reported to be a portable, cost-effective, and accurate method to detect pneumonia, it has not been widely used because of the difficulty in its interpretation. Here, we aimed to investigate the effectiveness of a novel artificial intelligence-based automated pneumonia detection method using point-of-care lung ultrasound (AI-POCUS) for the coronavirus disease 2019 (COVID-19).

METHODS : We enrolled consecutive patients admitted with COVID-19 who underwent computed tomography (CT) in August and September 2021. A 12-zone AI-POCUS was performed by a novice observer using a pocket-size device within 24 h of the CT scan. Fifteen control subjects were also scanned. Additionally, the accuracy of the simplified 8-zone scan excluding the dorsal chest, was assessed. More than three B-lines detected in one lung zone were considered zone-level positive, and the presence of positive AI-POCUS in any lung zone was considered patient-level positive. The sample size calculation was not performed given the retrospective all-comer nature of the study.

RESULTS : A total of 577 lung zones from 56 subjects (59.4 ± 14.8 years, 23% female) were evaluated using AI-POCUS. The mean number of days from disease onset was 9, and 14% of patients were under mechanical ventilation. The CT-validated pneumonia was seen in 71.4% of patients at total 577 lung zones (53.3%). The 12-zone AI-POCUS for detecting CT-validated pneumonia in the patient-level showed the accuracy of 94.5% (85.1%- 98.1%), sensitivity of 92.3% (79.7%- 97.3%), specificity of 100% (80.6%- 100%), positive predictive value of 95.0% (89.6% - 97.7%), and Kappa of 0.33 (0.27-0.40). When simplified with 8-zone scan, the accuracy, sensitivity, and sensitivity were 83.9% (72.2%- 91.3%), 77.5% (62.5%- 87.7%), and 100% (80.6%- 100%), respectively. The zone-level accuracy, sensitivity, and specificity of AI-POCUS were 65.3% (61.4%- 69.1%), 37.2% (32.0%- 42.7%), and 97.8% (95.2%- 99.0%), respectively.

INTERPRETATION : AI-POCUS using the novel pocket-size ultrasound system showed excellent agreement with CT-validated COVID-19 pneumonia, even when used by a novice observer.

Kuroda Yumi, Kaneko Tomohiro, Yoshikawa Hitomi, Uchiyama Saori, Nagata Yuichi, Matsushita Yasushi, Hiki Makoto, Minamino Tohru, Takahashi Kazuhisa, Daida Hiroyuki, Kagiyama Nobuyuki

2023

General General

Artificial intelligence-based optimization for chitosan nanoparticles biosynthesis, characterization and in‑vitro assessment of its anti-biofilm potentiality.

In Scientific reports ; h5-index 158.0

Chitosan nanoparticles (CNPs) are promising biopolymeric nanoparticles with excellent physicochemical, antimicrobial, and biological properties. CNPs have a wide range of applications due to their unique characteristics, including plant growth promotion and protection, drug delivery, antimicrobials, and encapsulation. The current study describes an alternative, biologically-based strategy for CNPs biosynthesis using Olea europaea leaves extract. Face centered central composite design (FCCCD), with 50 experiments was used for optimization of CNPs biosynthesis. The artificial neural network (ANN) was employed for analyzing, validating, and predicting CNPs biosynthesis using Olea europaea leaves extract. Using the desirability function, the optimum conditions for maximum CNPs biosynthesis were determined theoretically and verified experimentally. The highest experimental yield of CNPs (21.15 mg CNPs/mL) was obtained using chitosan solution of 1%, leaves extract solution of 100%, initial pH 4.47, and incubation time of 60 min at 53.83°C. The SEM and TEM images revealed that CNPs had a spherical form and varied in size between 6.91 and 11.14 nm. X-ray diffraction demonstrates the crystalline nature of CNPs. The surface of the CNPs is positively charged, having a Zeta potential of 33.1 mV. FTIR analysis revealed various functional groups including C-H, C-O, CONH2, NH2, C-OH and C-O-C. The thermogravimetric investigation indicated that CNPs are thermally stable. The CNPs were able to suppress biofilm formation by P. aeruginosa, S. aureus and C. albicans at concentrations ranging from 10 to 1500 µg/mL in a dose-dependent manner. Inhibition of biofilm formation was associated with suppression of metabolic activity, protein/exopolysaccharide moieties, and hydrophobicity of biofilm encased cells (r ˃ 0.9, P = 0.00). Due to their small size, in the range of 6.91 to 11.14 nm, CNPs produced using Olea europaea leaves extract are promising for applications in the medical and pharmaceutical industries, in addition to their potential application in controlling multidrug-resistant microorganisms, especially those associated with post COVID-19 pneumonia in immunosuppressed patients.

El-Naggar Noura El-Ahmady, Dalal Shimaa R, Zweil Amal M, Eltarahony Marwa

2023-Mar-16

General General

OzNet: A New Deep Learning Approach for Automated Classification of COVID-19 Computed Tomography Scans.

In Big data

Coronavirus disease 2019 (COVID-19) is spreading rapidly around the world. Therefore, the classification of computed tomography (CT) scans alleviates the workload of experts, whose workload increased considerably during the pandemic. Convolutional neural network (CNN) architectures are successful for the classification of medical images. In this study, we have developed a new deep CNN architecture called OzNet. Moreover, we have compared it with pretrained architectures namely AlexNet, DenseNet201, GoogleNet, NASNetMobile, ResNet-50, SqueezeNet, and VGG-16. In addition, we have compared the classification success of three preprocessing methods with raw CT scans. We have not only classified the raw CT scans, but also have performed the classification with three different preprocessing methods, which are discrete wavelet transform (DWT), intensity adjustment, and gray to color red, green, blue image conversion on the data sets. Furthermore, it is known that the architecture's performance increases with the use of DWT preprocessing method rather than using the raw data set. The results are extremely promising with the CNN algorithms using the COVID-19 CT scans processed with the DWT. The proposed DWT-OzNet has achieved a high classification performance of more than 98.8% for each calculated metric.

Ozaltin Oznur, Yeniay Ozgur, Subasi Abdulhamit

2023-Mar-16

2D-DWT, CNN, COVID-19 CT scans, classification, intensity adjustment

General General

Pharmacists and pharmacy services in COVID-19 literature: A bibliometirc analysis.

In Exploratory research in clinical and social pharmacy

BACKGROUND : The COVID-19 pandemic had an enormous impact on the global economy and healthcare. Pharmacists were vital members of the healthcare system, and they participated in various strategies to reduce the effect of the pandemic. Numerous papers were published discussing their roles during the pandemic. Bibliometric analysis was used to measure the impact of publications on this topic and assessed them qualitatively and quantitatively over a specific time.

OBJECTIVE : Evaluate published literature pertaining to the roles of pharmacists and pharmacy services during the pandemic and identify gaps.

METHODS : An electronic search was conducted on PubMed database using a specific query. Eligible publications were published in English between January 2020 and January 2022 and discussed the role of pharmacists, pharmacies, and pharmacy departments during the pandemic. Clinical trials, studies on pharmacy education/training, and conference abstracts were excluded.

RESULTS : Of 954 records retrieved, 338 (35.4%) from 67 countries were included. Most papers (n = 113; 33.4%) were from the community pharmacy sector, followed by the clinical pharmacy sector (n = 89; 26.3%). Sixty-one (18%) papers were multinational, mostly involving two countries. The average number of citations of the included papers was 6 times (range 0-89). The most common MeSH terms were 'humans', 'hospitals', and 'telemedicine', where the former frequently co-appeared with the terms 'COVID-19' and 'pharmacists.'

CONCLUSIONS : Results from this study illustrate the innovative and proactive strategies developed by pharmacists during the pandemic. Pharmacists from around the world are encouraged to share their experiences for stronger healthcare systems to counter future pandemics and environmental disasters.

Thabit Abrar K, Alsulmi Wajd S, Aljereb Nourah M, Khojah Omnia M, Almehdar Khadeja O, Cobo Manuel Jesús, Jose Jimmy, Vélez-Estévez Antonio

2023-Mar

Bibliometric analysis, COVID-19, COVID-19, Coronavirus disease of 2019, DOI, Digital object identifier, MeSH, Medical subject heading, Pharmacists, Pharmacy, SciMAT, Science Mapping Analysis Software Tool, WHO, World Health Organization

General General

The softening of Chinese digital propaganda: Evidence from the People's Daily Weibo account during the pandemic.

In Frontiers in psychology ; h5-index 92.0

INTRODUCTION : Social media infuses modern relationships with vitality and brings a series of information dissemination with subjective consciousness. Studies have indicated that official Chinese media channels are transforming their communication style from didactic hard persuasion to softened emotional management in the digital era. However, previous studies have rarely provided valid empirical evidence for the communicational transformation. The study fills the gap by providing a longitudinal time-series analysis to reveal the pattern of communication of Chinese digital Chinese official media from 2019 to 2022.

METHOD : The study crawler collected 43,259 posts from the People's Daily's Weibo account from 2019 to 2021. The study analyzed the textual data with using trained artificial intelligence models.

RESULTS : This study explored the practices of the People's Daily's Weibo account from 2019 to 2021, COVID-19 is hardly normalized as it is still used as the justification for extraordinary measures in China. This study confirmed that People's Daily's Weibo account posts are undergoing softenization transformation, with the use of soft news, positive energy promotion, and the embedding of sentiment. Although the outburst of COVID-19 temporarily increased the media's use of hard news, it only occur at the initial stage of the pandemic. Emotional posts occupy a nonnegligible amount of the People's Daily Weibo content. However, the majority of posts are emotionally neutral and contribute to shaping the authoritative image of the party press.

DISCUSSION : Overall, the People's Daily has softened their communication style on digital platforms and used emotional mobilization, distraction, and timely information provision to balance the political logic of building an authoritative media agency and the media logic of constructing audience relevance.

Zhang Chang, Zhang Dechun, Shao Hsuan Lei

2023

COVID-19, China, Weibo, propoganda, state-run media

Internal Medicine Internal Medicine

The use of Smart Environments and Robots for Infection Prevention Control: a systematic literature review.

In American journal of infection control ; h5-index 43.0

Infection prevention and control (IPC) is essential to prevent nosocomial infections. The implementation of automation technologies can aid outbreak response. This manuscript aims at investigating the current use and role of robots and smart environments on IPC systems in nosocomial settings. The systematic literature review was performed following the PRISMA statement. Literature was searched for articles published in the period January 2016 to October 2022. Two authors determined the eligibility of the papers, with conflicting decisions being mitigated by a third. Relevant data was then extracted using an ad-hoc extraction table to facilitate the analysis and narrative synthesis. The quality of the included studies was appraised by two authors. The search strategy returned 1520 citations and 17 papers were included in this review. This review identified three main areas of interest: hand hygiene and personal protective equipment compliance, automatic infection cluster detection and environments cleaning (i.e., air quality control, sterilization). This review demonstrates that IPC practices within hospitals mostly do not rely on automation and robotic technology, and few advancements have been made in this field. Increasing the awareness of health care workers on these technologies, through training and involving them in the design process, is essential to accomplish the Health 4.0 transformation. Research priorities should also be considering how to implement similar or more contextualized alternatives for low-income countries.

Piaggio Davide, Zarro Marianna, Pagliara Silvio, Andellini Martina, Almuhini Abdulaziz, Maccaro Alessia, Pecchia Leandro

2023-Mar-14

Infection prevention and control, artificial intelligence, hand hygiene, health 4.0, internet of things, robot

General General

Research on Supply Chain Financial Risk Prevention Based on Machine Learning.

In Computational intelligence and neuroscience

Artificial intelligence (AI) proves decisive in today's rapidly developing society and is a motive force for the evolution of financial technology. As a subdivision of artificial intelligence research, machine learning (ML) algorithm is extensively used in all aspects of the daily operation and development of the supply chain. Using data mining, deductive reasoning, and other characteristics of machine learning algorithms can effectively help decision-makers of enterprises to make more scientific and reasonable decisions by using the existing financial index data. At present, globalization uncertainties such as COVID-19 are intensifying, and supply chain enterprises are facing bankruptcy risk. In the operation process, practical tools are needed to identify and opportunely respond to the threat in the supply chain operation promptly, predict the probability of business failure of enterprises, and take scientific and feasible measures to prevent a financial crisis in good season. Artificial intelligence decision-making technology can help traditional supply chains to transform into intelligent supply chains, realize smart management, and promote supply chain transformation and upgrading. By applying machine learning algorithms, the supply chain can not only identify potential risks in time and adopt scientific and feasible measures to deal with the crisis but also strengthen the connection and cooperation between different enterprises with the advantage of advanced technology to provide overall operation efficiency. On account of this, the paper puts forward an artificial intelligence-based corporate financial-risk-prevention (FRP) model, which includes four stages: data preprocessing, feature selection, feature classification, and parameter adjustment. Firstly, relevant financial index data are collected, and the quality of the selected data is raised through preprocessing; secondly, the chaotic grasshopper optimization algorithm (CGOA) is used to simulate the behavior of grasshoppers in nature to build a mathematical model, and the selected data sets are selected and optimized for features. Then, the support vector machine (SVM) performs classification processing on the quantitative data with reduced features. Empirical risk is calculated using the hinge loss function, and a regular operation is added to optimize the risk structure. Finally, slime mould algorithm (SMA) can optimize the process to improve the efficiency of SVM, making the algorithm more accurate and effective. In this study, Python is used to simulate the function of the corporate business finance risk prevention model. The experimental results show that the CGOA-SVM-SMA algorithm proposed in this paper achieves good results. After calculation, it is found that the prediction and decision-making capabilities are good and better than other comparative models, which can effectively help supply chain enterprises to prevent financial risks.

Lei Yang, Qiaoming Hou, Tong Zhao

2023

General General

Weibo users and Academia's foci on tourism safety: Implications from institutional differences and digital divide.

In Heliyon

Tourism safety is essential for tourists and tourism practitioners. This study conducted a bibliometric analysis using VOSviewer and CiteSpace for 2018 articles indexed on the Web of Science (WoS). It also analysed 7293 Weibo posts between 1977 and 2022 using Python, MYSQL, AI sentiment, and Tableau. The first tourism safety publication on WoS appeared in 1977, while the first Weibo microblog dated was dated back to 2011. Compared to the information posted on Weibo, the annual publications about tourism safety on WoS recorded a stable increment. On Web of Science (WoS), the academic staff and universities produced the largest number of tourism safety posts. On the flip side, the most productive organisations on Weibo are government agencies in popular tourism destinations. "Accident", "medical tourism", "environment", "mediating role", and "hospitality" were important burst nodes in tourism safety on WoS. "Quality", "accident", and health-related words were the foci on both Weibo and WoS. On Web of Science, the top 10 most popular keywords of tourism safety-related articles could be classified into two groups: health ("Covid-19", "restoration", "pandemics", "Sars-Cov-2", "Sars", "mental health") and IT terminologies ("big data", "artificial intelligence"). It has been concluded that "artificial intelligence (AI)" is more likely to be included in the keywords on tourism researched by academia. In contrast, the public may not know about or use AI in the tourism industry. Besides, the top 10 most popular keywords on Weibo related to tourism risks and hazards were drowning and traffic risks and hazards, such as drowning and traffic risks. The digital divide may explain such a difference: the academic circle benefits more from the digital age than laypersons. It may also be the result of institutional differences and information asymmetry.

Zeng Liyun, Li Rita Yi Man, Zeng Huiling

2023-Mar

Artificial intelligence, Bibliometrics, Comparative analysis, Digital divide, Information asymmetry, Tourism safety, Web of science, Weibo

General General

Multi-weight susceptible-infected model for predicting COVID-19 in China.

In Neurocomputing

The mutant strains of COVID-19 caused a global explosion of infections, including many cities of China. In 2020, a hybrid AI model was proposed by Zheng et al., which accurately predicted the epidemic in Wuhan. As the main part of the hybrid AI model, ISI method makes two important assumptions to avoid over-fitting. However, the assumptions cannot be effectively applied to new mutant strains. In this paper, a more general method, named the multi-weight susceptible-infected model (MSI) is proposed to predict COVID-19 in Chinese Mainland. First, a Gaussian pre-processing method is proposed to solve the problem of data fluctuation based on the quantity consistency of cumulative infection number and the trend consistency of daily infection number. Then, we improve the model from two aspects: changing the grouped multi-parameter strategy to the multi-weight strategy, and removing the restriction of weight distribution of viral infectivity. Experiments on the outbreaks in many places in China from the end of 2021 to May 2022 show that, in China, an individual infected by Delta or Omicron strains of SARS-CoV-2 can infect others within 3-4 days after he/she got infected. Especially, the proposed method effectively predicts the trend of the epidemics in Xi'an, Tianjin, Henan, and Shanghai from December 2021 to May 2022.

Zhang Jun, Zheng Nanning, Liu Mingyu, Yao Dingyi, Wang Yusong, Wang Jianji, Xin Jingmin

2023-May-14

COVID-19 prediction, Data processing, Epidemic model, Multi-weight susceptible-infected model

Public Health Public Health

CCTCOVID: COVID-19 detection from chest X-ray images using Compact Convolutional Transformers.

In Frontiers in public health

COVID-19 is a novel virus that attacks the upper respiratory tract and the lungs. Its person-to-person transmissibility is considerably rapid and this has caused serious problems in approximately every facet of individuals' lives. While some infected individuals may remain completely asymptomatic, others have been frequently witnessed to have mild to severe symptoms. In addition to this, thousands of death cases around the globe indicated that detecting COVID-19 is an urgent demand in the communities. Practically, this is prominently done with the help of screening medical images such as Computed Tomography (CT) and X-ray images. However, the cumbersome clinical procedures and a large number of daily cases have imposed great challenges on medical practitioners. Deep Learning-based approaches have demonstrated a profound potential in a wide range of medical tasks. As a result, we introduce a transformer-based method for automatically detecting COVID-19 from X-ray images using Compact Convolutional Transformers (CCT). Our extensive experiments prove the efficacy of the proposed method with an accuracy of 99.22% which outperforms the previous works.

Marefat Abdolreza, Marefat Mahdieh, Hassannataj Joloudari Javad, Nematollahi Mohammad Ali, Lashgari Reza

2023

COVID-19, Compact Convolutional Transformers, Convolutional Neural Networks, deep learning, vision transformers

General General

Artificial intelligence evaluation of COVID-19 restrictions and speech therapy effects on the autistic children's behavior.

In Scientific reports ; h5-index 158.0

In the present study, we aimed to quantify the effects of COVID-19 restrictions and speech treatment approaches during lockdowns on autistic children using CBCL and neuro-fuzzy artificial intelligence method. In this regard, a survey including CBCL questionnaire is prepared using online forms. In total, 87 children with diagnosed Autism spectrum disorders (ASD) participated in the survey. The influences of three treatment approaches of in-person, telehealth and public services along with no-treatment condition during lockdown were the main factors of the investigation. The main output factors were internalized and externalized problems in general and their eight subcategory syndromes. We examined the reports by parents/caregivers to find correlation between treatments and CBCL listed problems. Moreover, comparison of the eight syndromes rating scores from pre-lockdown to post-lockdown periods were performed. In addition, artificial intelligence method were engaged to find the influence of speech treatment during restrictions on the level of internalizing and externalizing problems. In this regard, a fully connected adaptive neuro fuzzy inference system is employed with type and duration of treatments as input and T-scores of the syndromes are the output of the network. The results indicate that restrictions alleviate externalizing problems while intensifying internalizing problems. In addition, it is concluded that in-person speech therapy is the most effective and satisfactory approach to deal with ASD children during stay-at-home periods.

Sabzevari Fereshteh, Amelirad Omid, Moradi Zohre, Habibi Mostafa

2023-Mar-15

General General

IRCM-Caps: An X-ray image detection method for COVID-19.

In The clinical respiratory journal

OBJECTIVE : COVID-19 is ravaging the world, but traditional reverse transcription-polymerase reaction (RT-PCR) tests are time-consuming and have a high false-negative rate and lack of medical equipment. Therefore, lung imaging screening methods are proposed to diagnose COVID-19 due to its fast test speed. Currently, the commonly used convolutional neural network (CNN) model requires a large number of datasets, and the accuracy of the basic capsule network for multiple classification is limital. For this reason, this paper proposes a novel model based on CNN and CapsNet.

METHODS : The proposed model integrates CNN and CapsNet. And attention mechanism module and multi-branch lightweight module are applied to enhance performance. Use the contrast adaptive histogram equalization (CLAHE) algorithm to preprocess the image to enhance image contrast. The preprocessed images are input into the network for training, and ReLU was used as the activation function to adjust the parameters to achieve the optimal.

RESULT : The test dataset includes 1200 X-ray images (400 COVID-19, 400 viral pneumonia, and 400 normal), and we replace CNN of VGG16, InceptionV3, Xception, Inception-Resnet-v2, ResNet50, DenseNet121, and MoblieNetV2 and integrate with CapsNet. Compared with CapsNet, this network improves 6.96%, 7.83%, 9.37%, 10.47%, and 10.38% in accuracy, area under the curve (AUC), recall, and F1 scores, respectively. In the binary classification experiment, compared with CapsNet, the accuracy, AUC, accuracy, recall rate, and F1 score were increased by 5.33%, 5.34%, 2.88%, 8.00%, and 5.56%, respectively.

CONCLUSION : The proposed embedded the advantages of traditional convolutional neural network and capsule network and has a good classification effect on small COVID-19 X-ray image dataset.

Qiu Shuo, Ma Jinlin, Ma Ziping

2023-Mar-15

CNN, COVID-19, CapseNet, X-ray, cascade network, deep learning

oncology Oncology

Investigation of liquid biopsy analytes in peripheral blood of individuals after SARS-CoV-2 infection.

In EBioMedicine

BACKGROUND : Post-acute COVID-19 syndrome (PACS) is linked to severe organ damage. The identification and stratification of at-risk SARS-CoV-2 infected individuals is vital to providing appropriate care. This exploratory study looks for a potential liquid biopsy signal for PACS using both manual and machine learning approaches.

METHODS : Using a high definition single cell assay (HDSCA) workflow for liquid biopsy, we analysed 100 Post-COVID patients and 19 pre-pandemic normal donor (ND) controls. Within our patient cohort, 73 had received at least 1 dose of vaccination prior to SARS-CoV-2 infection. We stratified the COVID patients into 25 asymptomatic, 22 symptomatic COVID-19 but not suspected for PACS and 53 PACS suspected. All COVID-19 patients investigated in this study were diagnosed between April 2020 and January 2022 with a median 243 days (range 16-669) from diagnosis to their blood draw. We did a histopathological examination of rare events in the peripheral blood and used a machine learning model to evaluate predictors of PACS.

FINDINGS : The manual classification found rare cellular and acellular events consistent with features of endothelial cells and platelet structures in the PACS-suspected cohort. The three categories encompassing the hypothesised events were observed at a significantly higher incidence in the PACS-suspected cohort compared to the ND (p-value < 0.05). The machine learning classifier performed well when separating the NDs from Post-COVID with an accuracy of 90.1%, but poorly when separating the patients suspected and not suspected of PACS with an accuracy of 58.7%.

INTERPRETATION : Both the manual and the machine learning model found differences in the Post-COVID cohort and the NDs, suggesting the existence of a liquid biopsy signal after active SARS-CoV-2 infection. More research is needed to stratify PACS and its subsyndromes.

FUNDING : This work was funded in whole or in part by Fulgent Genetics, Kathy and Richard Leventhal and Vassiliadis Research Fund. This work was also supported by the National Cancer InstituteU54CA260591.

Qi Elizabeth, Courcoubetis George, Liljegren Emmett, Herrera Ergueen, Nguyen Nathalie, Nadri Maimoona, Ghandehari Sara, Kazemian Elham, Reckamp Karen L, Merin Noah M, Merchant Akil, Mason Jeremy, Figueiredo Jane C, Shishido Stephanie N, Kuhn Peter

2023-Mar-13

COVID-19, Liquid biopsy, Long COVID, Post-COVID sequelae, Post-acute COVID-19 syndrome (PACS), SARS-CoV-2

Dermatology Dermatology

Development and Clinical Evaluation of an Artificial Intelligence Support Tool for Improving Telemedicine Photo Quality.

In JAMA dermatology ; h5-index 54.0

IMPORTANCE : Telemedicine use accelerated during the COVID-19 pandemic, and skin conditions were a common use case. However, many images submitted may be of insufficient quality for making a clinical determination.

OBJECTIVE : To determine whether an artificial intelligence (AI) decision support tool, a machine learning algorithm, could improve the quality of images submitted for telemedicine by providing real-time feedback and explanations to patients.

DESIGN, SETTING, AND PARTICIPANTS : This quality improvement study with an AI performance component and single-arm clinical pilot study component was conducted from March 2020 to October 2021. After training, the AI decision support tool was tested on 357 retrospectively collected telemedicine images from Stanford telemedicine from March 2020 to June 2021. Subsequently, a single-arm clinical pilot study was conducted to assess feasibility with 98 patients in the Stanford Department of Dermatology across 2 clinical sites from July 2021 to October 2021. For the clinical pilot study, inclusion criteria for patients included being adults (aged ≥18 years), presenting to clinic for a skin condition, and being able to photograph their own skin with a smartphone.

INTERVENTIONS : During the clinical pilot study, patients were given a handheld smartphone device with a machine learning algorithm interface loaded and were asked to take images of any lesions of concern. Patients were able to review and retake photos prior to submitting, so each submitted photo met the patient's assumed standard of clinical acceptability. A machine learning algorithm then gave the patient feedback on whether the image was acceptable. If the image was rejected, the patient was provided a reason by the AI decision support tool and allowed to retake the photos.

MAIN OUTCOMES AND MEASURES : The main outcome of the retrospective image analysis was the receiver operator curve area under the curve (ROC-AUC). The main outcome of the clinical pilot study was the image quality difference between the baseline images and the images approved by AI decision support.

RESULTS : Of the 98 patients included, the mean (SD) age was 49.8 (17.6) years, and 50 (51%) of the patients were male. On retrospective telemedicine images, the machine learning algorithm effectively identified poor-quality images (ROC-AUC of 0.78) and the reason for poor quality (blurry ROC-AUC of 0.84; lighting issues ROC-AUC of 0.70). The performance was consistent across age and sex. In the clinical pilot study, patient use of the machine learning algorithm was associated with improved image quality. An AI algorithm was associated with reduction in the number of patients with a poor-quality image by 68.0%.

CONCLUSIONS AND RELEVANCE : In this quality improvement study, patients use of the AI decision support with a machine learning algorithm was associated with improved quality of skin disease photographs submitted for telemedicine use.

Vodrahalli Kailas, Ko Justin, Chiou Albert S, Novoa Roberto, Abid Abubakar, Phung Michelle, Yekrang Kiana, Petrone Paige, Zou James, Daneshjou Roxana

2023-Mar-15

General General

A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation.

In Molecular systems biology

DNA methylation comprises a cumulative record of lifetime exposures superimposed on genetically determined markers. Little is known about methylation dynamics in humans following an acute perturbation, such as infection. We characterized the temporal trajectory of blood epigenetic remodeling in 133 participants in a prospective study of young adults before, during, and after asymptomatic and mildly symptomatic SARS-CoV-2 infection. The differential methylation caused by asymptomatic or mildly symptomatic infections was indistinguishable. While differential gene expression largely returned to baseline levels after the virus became undetectable, some differentially methylated sites persisted for months of follow-up, with a pattern resembling autoimmune or inflammatory disease. We leveraged these responses to construct methylation-based machine learning models that distinguished samples from pre-, during-, and postinfection time periods, and quantitatively predicted the time since infection. The clinical trajectory in the young adults and in a diverse cohort with more severe outcomes was predicted by the similarity of methylation before or early after SARS-CoV-2 infection to the model-defined postinfection state. Unlike the phenomenon of trained immunity, the postacute SARS-CoV-2 epigenetic landscape we identify is antiprotective.

Mao Weiguang, Miller Clare M, Nair Venugopalan D, Ge Yongchao, Amper Mary Anne S, Cappuccio Antonio, George Mary-Catherine, Goforth Carl W, Guevara Kristy, Marjanovic Nada, Nudelman German, Pincas Hanna, Ramos Irene, Sealfon Rachel S G, Soares-Schanoski Alessandra, Vangeti Sindhu, Vasoya Mital, Weir Dawn L, Zaslavsky Elena, Kim-Schulze Seunghee, Gnjatic Sacha, Merad Miriam, Letizia Andrew G, Troyanskaya Olga G, Sealfon Stuart C, Chikina Maria

2023-Mar-15

DNA methylation, SARS-CoV-2, machine learning model, temporal dynamics, trained immunity

General General

Effect of ferritin, INR, and D-dimer immunological parameters levels as predictors of COVID-19 mortality: A strong prediction with the decision trees.

In Heliyon

BACKGROUND AND OBJECTIVE : A hyperinflammatory environment is thought to be the distinctive characteristic of COVID-19 infection and an important mediator of morbidity. This study aimed to determine the effect of other immunological parameter levels, especially ferritin, as a predictor of COVID-19 mortality via decision-trees analysis.

MATERIAL AND METHOD : This is a retrospective study evaluating a total of 2568 patients who died (n = 232) and recovered (n = 2336) from COVID-19 in August and December 2021. Immunological laboratory data were compared between two groups that died and recovered from patients with COVID-19. In addition, decision trees from machine learning models were used to evaluate the performance of immunological parameters in the mortality of the COVID-19 disease.

RESULTS : Non-surviving from COVID-19 had 1.75 times higher ferritin, 10.7 times higher CRP, 2.4 times higher D-dimer, 1.14 times higher international-normalized-ratio (INR), 1.1 times higher Fibrinogen, 22.9 times higher procalcitonin, 3.35 times higher troponin, 2.77 mm/h times higher erythrocyte-sedimentation-rate (ESR), 1.13sec times longer prothrombin time (PT) when compared surviving patients. In addition, our interpretable decision tree, which was constructed with only the cut-off values of ferritin, INR, and D-dimer, correctly predicted 99.7% of surviving patients and 92.7% of non-surviving patients.

CONCLUSIONS : This study perfectly predicted the mortality of COVID-19 with our interpretable decision tree constructed with INR and D-dimer, especially ferritin. For this reason, we think that it may be important to include ferritin, INR, and D-dimer parameters and their cut-off values in the scoring systems to be planned for COVID-19 mortality.

Huyut Mehmet Tahir, Huyut Zübeyir

2023-Mar

Artificial intelligence, CHAID decision Trees, COVID-19, Coagulation tests, Ferritin, Immunological tests, Machine learning, Mortality risk biomarkers

General General

Comprehensive analysis of clinical data for COVID-19 outcome estimation with machine learning models.

In Biomedical signal processing and control

COVID-19 is a global threat for the healthcare systems due to the rapid spread of the pathogen that causes it. In such situation, the clinicians must take important decisions, in an environment where medical resources can be insufficient. In this task, the computer-aided diagnosis systems can be very useful not only in the task of supporting the clinical decisions but also to perform relevant analyses, allowing them to understand better the disease and the factors that can identify the high risk patients. For those purposes, in this work, we use several machine learning algorithms to estimate the outcome of COVID-19 patients given their clinical information. Particularly, we perform 2 different studies: the first one estimates whether the patient is at low or at high risk of death whereas the second estimates if the patient needs hospitalization or not. The results of the analyses of this work show the most relevant features for each studied scenario, as well as the classification performance of the considered machine learning models. In particular, the XGBoost algorithm is able to estimate the need for hospitalization of a patient with an AUC-ROC of 0 . 8415 ± 0 . 0217 while it can also estimate the risk of death with an AUC-ROC of 0 . 7992 ± 0 . 0104 . Results have demonstrated the great potential of the proposal to determine those patients that need a greater amount of medical resources for being at a higher risk. This provides the healthcare services with a tool to better manage their resources.

Morís Daniel I, de Moura Joaquim, Marcos Pedro J, Rey Enrique Míguez, Novo Jorge, Ortega Marcos

2023-Jul

COVID-19, Classification, Clinical data, Feature selection, Machine learning

Pathology Pathology

Paving New Roads Using Allium sativum as a Repurposed Drug and Analyzing its Antiviral Action Using Artificial Intelligence Technology.

In Iranian journal of pharmaceutical research : IJPR

CONTEXT : The whole universe is facing a coronavirus catastrophe, and prompt treatment for the health crisis is primarily significant. The primary way to improve health conditions in this battle is to boost our immunity and alter our diet patterns. A common bulb veggie used to flavor cuisine is garlic. Compounds in the plant that are physiologically active are present, contributing to its pharmacological characteristics. Among several food items with nutritional value and immunity improvement, garlic stood predominant and more resourceful natural antibiotic with a broad spectrum of antiviral potency against diverse viruses. However, earlier reports have depicted its efficacy in the treatment of a variety of viral illnesses. Nonetheless, there is no information on its antiviral activities and underlying molecular mechanisms.

OBJECTIVES : The bioactive compounds in garlic include organosulfur (allicin and alliin) and flavonoid (quercetin) compounds. These compounds have shown immunomodulatory effects and inhibited attachment of coronavirus to the angiotensin-converting enzyme 2 (ACE2) receptor and the Mpro of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Further, we have discussed the contradictory impacts of garlic used as a preventive measure against the novel coronavirus.

METHOD : The GC/MS analysis revealed 18 active chemicals, including 17 organosulfur compounds in garlic. Using the molecular docking technique, we report for the first time the inhibitory effect of the under-consideration compounds on the host receptor ACE2 protein in the human body, providing a crucial foundation for understanding individual compound coronavirus resistance on the main protease protein of SARS-CoV-2. Allyl disulfide and allyl trisulfide, which make up the majority of the compounds in garlic, exhibit the most potent activity.

RESULTS : Conventional medicine has proven its efficiency from ancient times. Currently, our article's prime spotlight was on the activity of Allium sativum on the relegation of viral load and further highlighted artificial intelligence technology to study the attachment of the allicin compound to the SARS-CoV-2 receptor to reveal its efficacy.

CONCLUSIONS : The COVID-19 pandemic has triggered interest among researchers to conduct future research on molecular docking with clinical trials before releasing salutary remedies against the deadly malady.

Atoum Manar Fayiz, Padma Kanchi Ravi, Don Kanchi Ravi

2022-Dec

Allium sativum, Flavonoid, Immunomodulatory, SARS-CoV-2

Surgery Surgery

An artificial intelligence approach for predicting death or organ failure after hospitalization for COVID-19: development of a novel risk prediction tool and comparisons with ISARIC-4C, CURB-65, qSOFA, and MEWS scoring systems.

In Respiratory research ; h5-index 45.0

BACKGROUND : We applied machine learning (ML) algorithms to generate a risk prediction tool [Collaboration for Risk Evaluation in COVID-19 (CORE-COVID-19)] for predicting the composite of 30-day endotracheal intubation, intravenous administration of vasopressors, or death after COVID-19 hospitalization and compared it with the existing risk scores.

METHODS : This is a retrospective study of adults hospitalized with COVID-19 from March 2020 to February 2021. Patients, each with 92 variables, and one composite outcome underwent feature selection process to identify the most predictive variables. Selected variables were modeled to build four ML algorithms (artificial neural network, support vector machine, gradient boosting machine, and Logistic regression) and an ensemble model to generate a CORE-COVID-19 model to predict the composite outcome and compared with existing risk prediction scores. The net benefit for clinical use of each model was assessed by decision curve analysis.

RESULTS : Of 1796 patients, 278 (15%) patients reached primary outcome. Six most predictive features were identified. Four ML algorithms achieved comparable discrimination (P > 0.827) with c-statistics ranged 0.849-0.856, calibration slopes 0.911-1.173, and Hosmer-Lemeshow P > 0.141 in validation dataset. These 6-variable fitted CORE-COVID-19 model revealed a c-statistic of 0.880, which was significantly (P < 0.04) higher than ISARIC-4C (0.751), CURB-65 (0.735), qSOFA (0.676), and MEWS (0.674) for outcome prediction. The net benefit of the CORE-COVID-19 model was greater than that of the existing risk scores.

CONCLUSION : The CORE-COVID-19 model accurately assigned 88% of patients who potentially progressed to 30-day composite events and revealed improved performance over existing risk scores, indicating its potential utility in clinical practice.

Kwok Stephen Wai Hang, Wang Guanjin, Sohel Ferdous, Kashani Kianoush B, Zhu Ye, Wang Zhen, Antpack Eduardo, Khandelwal Kanika, Pagali Sandeep R, Nanda Sanjeev, Abdalrhim Ahmed D, Sharma Umesh M, Bhagra Sumit, Dugani Sagar, Takahashi Paul Y, Murad Mohammad H, Yousufuddin Mohammed

2023-Mar-13

COVID-19, Machine learning algorithms, Mortality, Organ failure, Prediction models

General General

Benchmarking machine learning robustness in Covid-19 genome sequence classification.

In Scientific reports ; h5-index 158.0

The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome-millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses, is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches with different perturbation budgets are more robust (and accurate) than others for specific embedding methods to certain noise simulations on the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics.

Ali Sarwan, Sahoo Bikram, Zelikovsky Alexander, Chen Pin-Yu, Patterson Murray

2023-Mar-13

General General

The predictive model for COVID-19 pandemic plastic pollution by using deep learning method.

In Scientific reports ; h5-index 158.0

Pandemic plastics (e.g., masks, gloves, aprons, and sanitizer bottles) are global consequences of COVID-19 pandemic-infected waste, which has increased significantly throughout the world. These hazardous wastes play an important role in environmental pollution and indirectly spread COVID-19. Predicting the environmental impacts of these wastes can be used to provide situational management, conduct control procedures, and reduce the COVID-19 effects. In this regard, the presented study attempted to provide a deep learning-based predictive model for forecasting the expansion of the pandemic plastic in the megacities of Iran. As a methodology, a database was gathered from February 27, 2020, to October 10, 2021, for COVID-19 spread and personal protective equipment usage in this period. The dataset was trained and validated using training (80%) and testing (20%) datasets by a deep neural network (DNN) procedure to forecast pandemic plastic pollution. Performance of the DNN-based model is controlled by the confusion matrix, receiver operating characteristic (ROC) curve, and justified by the k-nearest neighbours, decision tree, random forests, support vector machines, Gaussian naïve Bayes, logistic regression, and multilayer perceptron methods. According to the comparative modelling results, the DNN-based model was found to predict more accurately than other methods and have a significant predominance over others with a lower errors rate (MSE = 0.024, RMSE = 0.027, MAPE = 0.025). The ROC curve analysis results (overall accuracy) indicate the DNN model (AUC = 0.929) had the highest score among others.

Nanehkaran Yaser A, Licai Zhu, Azarafza Mohammad, Talaei Sona, Jinxia Xu, Chen Junde, Derakhshani Reza

2023-Mar-13

General General

Analysis on factors affecting tourist involvement in coffee tourism after the COVID-19 pandemic in Thailand.

In F1000Research

Background: The world economy is affected by the coronavirus disease (COVID-19) pandemic, which affects the coffee industry. Coffee tourism is an emerging new type of tourism in Thailand that is formed in response to the growing demand from visitors with a particular affinity for coffee. Coffee tourism may contribute considerably to the expansion of Thai tourism given proper guidance and assistance. Methods: This study used a stochastic neuro-fuzzy decision tree (SNF-DT) to analyze coffee tourism in Thailand. This research surveyed 400 international and Thai coffee tourists. According to this study, Thai visitors mostly visit coffee tourism locations in Thailand for enjoyment. They also wanted to visit coffee fields to obtain personal knowledge about coffee production and marketing. Responses from foreign coffee tourists indicated that many of their journeys to coffee tourism destinations were entirely for enjoyment rather than business. They also wanted to meet local tour guides and acquire handmade and locally produced things to better understand coffee tourism. Results: According to the study results, coffee tourism management in northern Thailand appears to be well received by international tourists. We also compared the suggested model with the traditional model to demonstrate its efficacy. The performance metrics are the prediction rate, prediction error, and accuracy. The estimated results for our proposed technique are prediction rate (95%), prediction error (97%), and accuracy (94%). Recommendations: Major global businesses such as tourism have been harmed by COVID-19's unprecedented effects. This study attempts to determine the role of coffee tourism in livelihoods based on real-time data using a machine-learning approach. More research is needed to analyse the factors of the coffee tourism experience using different machine learning approaches.

Madhyamapurush Warach

2022

COVID-19 pandemic, Coffee Tourism, Foreign Tourists, Stochastic Neuro-Fuzzy Decision Tree (SNF-DT)., Tourist Behaviors

General General

Situation-Aware BDI Reasoning to Detect Early Symptoms of Covid 19 Using Smartwatch.

In IEEE sensors journal

Ambient intelligence plays a crucial role in healthcare situations. It provides a certain way to deal with emergencies to provide the essential resources such as nearest hospitals and emergency stations promptly to avoid deaths. Since the outbreak of Covid-19, several artificial intelligence techniques have been used. However, situation awareness is a key aspect to handling any pandemic situation. The situation-awareness approach gives patients a routine life where they are continuously monitored by caregivers through wearable sensors and alert the practitioners in case of any patient emergency. Therefore, in this paper, we propose a situation-aware mechanism to detect Covid-19 systems early and alert the user to be self-aware regarding the situation to take precautions if the situation seems unlikely to be normal. We provide Belief-Desire-Intention intelligent reasoning mechanism for the system to analyze the situation after acquiring the data from the wearable sensors and alert the user according to their environment. We use the case study for further demonstration of our proposed framework. We model the proposed system by temporal logic and map the system illustration into a simulation tool called NetLogo to determine the results of the proposed system.

Saleem Kiran, Saleem Misbah, Ahmad Rana Zeeshan, Javed Abdul Rehman, Alazab Mamoun, Gadekallu Thippa Reddy, Suleman Ahmad

2023-Jan

Covid-19, NetLogo, Situation-awareness, ambient intelligence, belief-desire-intention (BDI), healthcare

General General

i-Sheet: A Low-Cost Bedsheet Sensor for Remote Diagnosis of Isolated Individuals.

In IEEE sensors journal

In this article, we propose a smart bedsheet-i-Sheet-for remotely monitoring the health of COVID-19 patients. Typically, real-time health monitoring is very crucial for COVID-19 patients to prevent their health from deteriorating. Conventional healthcare monitoring systems are manual and require patient input to start monitoring health. However, it is difficult for the patients to give input in critical conditions as well as at night. For instance, if the oxygen saturation level decreases during sleep, then it is difficult to monitor. Furthermore, there is a need for a system that monitors post-COVID effects as various vitals get affected, and there are chances of their failure even after the recovery. i-Sheet exploits these features and provides the health monitoring of COVID-19 patients based on their pressure on the bedsheet. It works in three phases: 1) sensing the pressure exerted by the patient on the bedsheet; 2) categorizing the data into groups (comfortable and uncomfortable) based on the fluctuations in the data; and 3) alerting the caregiver about the condition of the patient. Experimental results demonstrate the effectiveness of i-Sheet in monitoring the health of the patient. i-Sheet effectively categorizes the condition of the patient with an accuracy of 99.3% and utilizes 17.5 W of the power. Furthermore, the delay involved in monitoring the health of patients using i-Sheet is 2 s which is very diminutive and is acceptable.

Tapwal Riya, Misra Sudip, Deb Pallav Kumar

2023-Jan

Artificial intelligence, COVID-19, remote monitoring, sensors, smart bedsheet

General General

The role of the mass vaccination programme in combating the COVID-19 pandemic: An LSTM-based analysis of COVID-19 confirmed cases.

In Heliyon

The COVID-19 virus has impacted all facets of our lives. As a global response to this threat, vaccination programmes have been initiated and administered in numerous nations. The question remains, however, as to whether mass vaccination programmes result in a decrease in the number of confirmed COVID-19 cases. In this study, we aim to predict the future number of COVID-19 confirmed cases for the top ten countries with the highest number of vaccinations in the world. A well-known Deep Learning method for time series analysis, namely, the Long Short-Term Memory (LSTM) networks, is applied as the prediction method. Using three evaluation metrics, i.e., Mean Absolute Error (MAE), Root Mean Square Error (RMSE), and Mean Absolute Percentage Error (MAPE), we found that the model built by using LSTM networks could give a good prediction of the future number and trend of COVID-19 confirmed cases in the considered countries. Two different scenarios are employed, namely: 'All Time', which includes all historical data; and 'Before Vaccination', which excludes data collected after the mass vaccination programme began. The average MAPE scores for the 'All Time' and 'Before Vaccination' scenarios are 5.977% and 10.388%, respectively. Overall, the results show that the mass vaccination programme has a positive impact on decreasing and controlling the spread of the COVID-19 disease in those countries, as evidenced by decreasing future trends after the programme was implemented.

Hansun Seng, Charles Vincent, Gherman Tatiana

2023-Mar

COVID-19, Confirmed cases, Deep learning, LSTM, Mass vaccination

Public Health Public Health

Exploring the impact of sentiment on multi-dimensional information dissemination using COVID-19 data in China.

In Computers in human behavior ; h5-index 125.0

The outbreak of information epidemic in crisis events, with the channel effect of social media, has brought severe challenges to global public health. Combining information, users and environment, understanding how emotional information spreads on social media plays a vital role in public opinion governance and affective comfort, preventing mass incidents and stabilizing the network order. Therefore, from the perspective of the information ecology and elaboration likelihood model (ELM), this study conducted a comparative analysis based on two large-scale datasets related to COVID-19 to explore the influence mechanism of sentiment on the forwarding volume, spreading depth and network influence of information dissemination. Based on machine learning and social network methods, topics, sentiments, and network variables are extracted from large-scale text data, and the dissemination characteristics and evolution rules of online public opinions in crisis events are further analyzed. The results show that negative sentiment positively affects the volume, depth, and influence compared with positive sentiment. In addition, information characteristics such as richness, authority, and topic influence moderate the relationship between sentiment and information dissemination. Therefore, the research can build a more comprehensive connection between the emotional reaction of network users and information dissemination and analyze the internal characteristics and evolution trend of online public opinion. Then it can help sentiment management and information release strategy when emergencies occur.

Luo Han, Meng Xiao, Zhao Yifei, Cai Meng

2023-Jul

COVID-19, Emotional response, Information authority, Information dissemination, Information richness, Topic influence

General General

Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions.

In Frontiers in oncology

Host-pathogen interactions (HPIs) affect and involve multiple mechanisms in both the pathogen and the host. Pathogen interactions disrupt homeostasis in host cells, with their toxins interfering with host mechanisms, resulting in infections, diseases, and disorders, extending from AIDS and COVID-19, to cancer. Studies of the three-dimensional (3D) structures of host-pathogen complexes aim to understand how pathogens interact with their hosts. They also aim to contribute to the development of rational therapeutics, as well as preventive measures. However, structural studies are fraught with challenges toward these aims. This review describes the state-of-the-art in protein-protein interactions (PPIs) between the host and pathogens from the structural standpoint. It discusses computational aspects of predicting these PPIs, including machine learning (ML) and artificial intelligence (AI)-driven, and overviews available computational methods and their challenges. It concludes with examples of how theoretical computational approaches can result in a therapeutic agent with a potential of being used in the clinics, as well as future directions.

Ozdemir Emine Sila, Nussinov Ruth

2023

artificial intelligence, cancer therapeutics, drug discovery, host-pathogen interactions, machine learning, protein-protein interactions

Pathology Pathology

Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape.

In iScience

Three-dimensional structure and dynamics are essential for protein function. Advancements in hydrogen-deuterium exchange (HDX) techniques enable probing protein dynamic information in physiologically relevant conditions. HDX-coupled mass spectrometry (HDX-MS) has been broadly applied in pharmaceutical industries. However, it is challenging to obtain dynamics information at the single amino acid resolution and time consuming to perform the experiments and process the data. Here, we demonstrate the first deep learning model, artificial intelligence-based HDX (AI-HDX), that predicts intrinsic protein dynamics based on the protein sequence. It uncovers the protein structural dynamics by combining deep learning, experimental HDX, sequence alignment, and protein structure prediction. AI-HDX can be broadly applied to drug discovery, protein engineering, and biomedical studies. As a demonstration, we elucidated receptor-binding domain structural dynamics as a potential mechanism of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody efficacy and immune escape. AI-HDX fundamentally differs from the current AI tools for protein analysis and may transform protein design for various applications.

Yu Jiali, Uzuner Ugur, Long Bin, Wang Zachary, Yuan Joshua S, Dai Susie Y

2023-Apr-21

Immunology, Virology

Public Health Public Health

An anti-infodemic virtual center for the Americas.

In Revista panamericana de salud publica = Pan American journal of public health

The Pan American Health Organization/World Health Organization (PAHO/WHO) Anti-Infodemic Virtual Center for the Americas (AIVCA) is a project led by the Department of Evidence and Intelligence for Action in Health, PAHO and the Center for Health Informatics, PAHO/WHO Collaborating Center on Information Systems for Health, at the University of Illinois, with the participation of PAHO staff and consultants across the region. Its goal is to develop a set of tools-pairing AI with human judgment-to help ministries of health and related health institutions respond to infodemics. Public health officials will learn about emerging threats detected by the center and get recommendations on how to respond. The virtual center is structured with three parallel teams: detection, evidence, and response. The detection team will employ a mixture of advanced search queries, machine learning, and other AI techniques to sift through more than 800 million new public social media posts per day to identify emerging infodemic threats in both English and Spanish. The evidence team will use the EasySearch federated search engine backed by AI, PAHO's knowledge management team, and the Librarian Reserve Corps to identify the most relevant authoritative sources. The response team will use a design approach to communicate recommended response strategies based on behavioural science, storytelling, and information design approaches.

Brooks Ian, D’Agostino Marcelo, Marti Myrna, McDowell Kate, Mejia Felipe, Betancourt-Cravioto Miguel, Gatzke Lisa, Hicks Elaine, Kyser Rebecca, Leicht Kevin, Pereira Dos Santos Eliane, Saw Jessica Jia-Wen, Tomio Ailin, Garcia Saiso Sebastian

2023

Americas, COVID-19, Public Health Informatics, artificial intelligence, communication, social media

Public Health Public Health

IPs-GRUAtt: An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection.

In Molecular therapy. Nucleic acids

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has generated tremendous concern and poses a serious threat to international public health. Phosphorylation is a common post-translational modification affecting many essential cellular processes and is inextricably linked to SARS-CoV-2 infection. Hence, accurate identification of phosphorylation sites will be helpful to understand the mechanisms of SARS-CoV-2 infection and mitigate the ongoing COVID-19 pandemic. In the present study, an attention-based bidirectional gated recurrent unit network, called IPs-GRUAtt, was proposed to identify phosphorylation sites in SARS-CoV-2-infected host cells. Comparative results demonstrated that IPs-GRUAtt surpassed both state-of-the-art machine-learning methods and existing models for identifying phosphorylation sites. Moreover, the attention mechanism made IPs-GRUAtt able to extract the key features from protein sequences. These results demonstrated that the IPs-GRUAtt is a powerful tool for identifying phosphorylation sites. For facilitating its academic use, a freely available online web server for IPs-GRUAtt is provided at http://cbcb.cdutcm.edu.cn/phosphory/.

Zhang Guiyang, Tang Qiang, Feng Pengmian, Chen Wei

2023-Jun-13

MT: Bioinformatics, SARS-CoV-2, attention mechanism, bidirectional gated recurrent unit, deep learning, interpretation, phosphorylation

Ophthalmology Ophthalmology

Implementation of deep learning artificial intelligence in vision-threatening disease screenings for an underserved community during COVID-19.

In Journal of telemedicine and telecare ; h5-index 28.0

INTRODUCTION : Age-related macular degeneration, diabetic retinopathy, and glaucoma are vision-threatening diseases that are leading causes of vision loss. Many studies have validated deep learning artificial intelligence for image-based diagnosis of vision-threatening diseases. Our study prospectively investigated deep learning artificial intelligence applications in student-run non-mydriatic screenings for an underserved, primarily Hispanic community during COVID-19.

METHODS : Five supervised student-run community screenings were held in West New York, New Jersey. Participants underwent non-mydriatic 45-degree retinal imaging by medical students. Images were uploaded to a cloud-based deep learning artificial intelligence for vision-threatening disease referral. An on-site tele-ophthalmology grader and remote clinical ophthalmologist graded images, with adjudication by a senior ophthalmologist to establish the gold standard diagnosis, which was used to assess the performance of deep learning artificial intelligence.

RESULTS : A total of 385 eyes from 195 screening participants were included (mean age 52.43  ±  14.5 years, 40.0% female). A total of 48 participants were referred for at least one vision-threatening disease. Deep learning artificial intelligence marked 150/385 (38.9%) eyes as ungradable, compared to 10/385 (2.6%) ungradable as per the human gold standard (p < 0.001). Deep learning artificial intelligence had 63.2% sensitivity, 94.5% specificity, 32.0% positive predictive value, and 98.4% negative predictive value in vision-threatening disease referrals. Deep learning artificial intelligence successfully referred all 4 eyes with multiple vision-threatening diseases. Deep learning artificial intelligence graded images (35.6  ±  13.3 s) faster than the tele-ophthalmology grader (129  ±  41.0) and clinical ophthalmologist (68  ±  21.9, p < 0.001).

DISCUSSION : Deep learning artificial intelligence can increase the efficiency and accessibility of vision-threatening disease screenings, particularly in underserved communities. Deep learning artificial intelligence should be adaptable to different environments. Consideration should be given to how deep learning artificial intelligence can best be utilized in a real-world application, whether in computer-aided or autonomous diagnosis.

Zhu Aretha, Tailor Priya, Verma Rashika, Zhang Isis, Schott Brian, Ye Catherine, Szirth Bernard, Habiel Miriam, Khouri Albert S

2023-Mar-13

COVID-19, Tele-ophthalmology, deep learning artificial intelligence, vision screenings

General General

Computational prediction of interactions between Paxlovid and prescription drugs.

In Proceedings of the National Academy of Sciences of the United States of America

Pfizer's Paxlovid has recently been approved for the emergency use authorization (EUA) from the US Food and Drug Administration (FDA) for the treatment of mild-to-moderate COVID-19. Drug interactions can be a serious medical problem for COVID-19 patients with underlying medical conditions, such as hypertension and diabetes, who have likely been taking other drugs. Here, we use deep learning to predict potential drug-drug interactions between Paxlovid components (nirmatrelvir and ritonavir) and 2,248 prescription drugs for treating various diseases.

Kim Yeji, Ryu Jae Yong, Kim Hyun Uk, Lee Sang Yup

2023-Mar-21

COVID-19, DeepDDI2, Paxlovid, drug interactions

General General

Big data and infectious disease epidemiology: A bibliometric analysis and research agenda.

In Interactive journal of medical research

BACKGROUND : Infectious diseases represent a major challenge for health systems worldwide. With the recent global pandemic of COVID-19, the need to research strategies to treat these health problems has become even more pressing. Although the literature on big data and data science in health has grown rapidly, few studies have synthesized these individual studies, and none has identified the utility of big data in infectious disease surveillance and modeling.

OBJECTIVE : This paper aims to synthesize research and identify hotspots of big data in infectious disease epidemiology.

METHODS : Bibliometric data from 3054 documents that satisfied the inclusion criteria were retrieved from the Web of Science database over 22 years (2000-2022) were analyzed and reviewed. The search retrieval occurred on October 17, 2022. Bibliometric analysis was performed to illustrate the relationships between research constituents, topics, and key terms in the retrieved documents.

RESULTS : The bibliometric analysis revealed internet searches and social media as the most utilized big data sources for infectious disease surveillance or modeling. It also placed the US and Chinese institutions as leaders in this research area. Disease monitoring and surveillance, utility of electronic health (or medical) records, methodology framework for infodemiology tools, and machine/deep learning were identified as the core research themes.

CONCLUSIONS : Proposals for future studies are made based on these findings. This study will provide healthcare informatics scholars with a comprehensive understanding of big data research in infectious disease epidemiology.

Amusa Lateef Babatunde, Twinomurinzi Hossana, Phalane Edith, Phaswana-Mafuya Refilwe Nancy

2022-Nov-29

General General

Minimizing Viral Transmission in COVID-19 Like Pandemics: Technologies, Challenges, and Opportunities.

In IEEE sensors journal

Coronavirus (COVID-19) pandemic has incurred huge loss to human lives throughout the world. Scientists, researchers, and doctors are trying their best to develop and distribute the COVID-19 vaccine throughout the world at the earliest. In current circumstances, different tracking systems are utilized to control or stop the spread of the virus till the whole population of the world gets vaccinated. To track and trace patients in COVID-19 like pandemics, various tracking systems based on different technologies are discussed and compared in this paper. These technologies include, cellular, cyber, satellite-based radio navigation and low range wireless technologies. The main aim of this paper is to conduct a comprehensive survey that can overview all such tracking systems, which are used in minimizing the spread of COVID-19 like pandemics. This paper also highlights the shortcoming of each tracking systems and suggests new mechanisms to overcome such limitations. In addition, the authors propose some futuristic approaches to track patients in prospective pandemics, based on artificial intelligence and big data analysis. Potential research directions, challenges, and the introduction of next-generation tracking systems for minimizing the spread of prospective pandemics, are also discussed at the end.

Nisar Shibli, Wakeel Abdul, Tahir Wania, Tariq Muhammad

2023-Jan

COVID-19, artificial intelligence, cellular forensics, hidden patterns, pandemic, tracking systems

Public Health Public Health

A machine learning analysis of correlates of mortality among patients hospitalized with COVID-19.

In Scientific reports ; h5-index 158.0

It is vital to determine how patient characteristics that precede COVID-19 illness relate to COVID-19 mortality. This is a retrospective cohort study of patients hospitalized with COVID-19 across 21 healthcare systems in the US. All patients (N = 145,944) had COVID-19 diagnoses and/or positive PCR tests and completed their hospital stays from February 1, 2020 through January 31, 2022. Machine learning analyses revealed that age, hypertension, insurance status, and healthcare system (hospital site) were especially predictive of mortality across the full sample. However, multiple variables were especially predictive in subgroups of patients. The nested effects of risk factors such as age, hypertension, vaccination, site, and race accounted for large differences in mortality likelihood with rates ranging from about 2-30%. Subgroups of patients are at heightened risk of COVID-19 mortality due to combinations of preadmission risk factors; a finding of potential relevance to outreach and preventive actions.

Baker Timothy B, Loh Wei-Yin, Piasecki Thomas M, Bolt Daniel M, Smith Stevens S, Slutske Wendy S, Conner Karen L, Bernstein Steven L, Fiore Michael C

2023-Mar-11

General General

A novel use of an artificially intelligent Chatbot and a live, synchronous virtual question-and answer session for fellowship recruitment.

In BMC medical education

INTRODUCTION : Academic departments universally communicate information about their programs using static websites. In addition to websites, some programs have even ventured out into social media (SM). These bidirectional forms of SM interaction show great promise; even hosting a live Question and Answer (Q&A) session has the potential for program branding. Artificial Intelligence (AI) usage in the form of a chatbot has expanded on websites and in SM. The potential use of chatbots, for the purposes of trainee recruitment, is novel and underutilized. With this pilot study, we aimed to answer the question; can the use of an Artificially Intelligent Chatbot and a Virtual Question-and-Answer Session aid in recruitment in a Post-COVID-19 era?

METHODS : We held three structured Question-and-Answer Sessions over a period of 2 weeks. This preliminary study was performed after completion of the three Q&A sessions, in March-May, 2021. All 258 applicants to the pain fellowship program were invited via email to participate in the survey after attending one of the Q&A sessions. A 16-item survey assessing participants' perception of the chatbot was administered.

RESULTS : Forty-eight pain fellowship applicants completed the survey, for an average response rate of 18.6%. In all, 35 (73%) of survey respondents had used the website chatbot, and 84% indicated that it had found them the information they were seeking.

CONCLUSION : We employed an artificially intelligent chatbot on the department website to engage in a bidirectional exchange with users to adapt to changes brought on by the pandemic. SM engagement via chatbot and Q&A sessions can leave a favorable impression and improve the perception of a program.

Yi Peter K, Ray Neil D, Segall Noa

2023-Mar-11

Artificial intelligence, Graduate medical education, Innovation and technology, Recruitment, Social media

General General

New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.

In BMC bioinformatics

BACKGROUND : In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2.

RESULTS : In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256.

CONCLUSIONS : The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs.

de Souza Luísa C, Azevedo Karolayne S, de Souza Jackson G, Barbosa Raquel de M, Fernandes Marcelo A C

2023-Mar-11

CGR DFT, COVID-19, Deep learning, GSP, SARS-CoV-2

Public Health Public Health

A hybrid deep learning approach for COVID-19 detection based on genomic image processing techniques.

In Scientific reports ; h5-index 158.0

The coronavirus disease 2019 (COVID-19) pandemic has been spreading quickly, threatening the public health system. Consequently, positive COVID-19 cases must be rapidly detected and treated. Automatic detection systems are essential for controlling the COVID-19 pandemic. Molecular techniques and medical imaging scans are among the most effective approaches for detecting COVID-19. Although these approaches are crucial for controlling the COVID-19 pandemic, they have certain limitations. This study proposes an effective hybrid approach based on genomic image processing (GIP) techniques to rapidly detect COVID-19 while avoiding the limitations of traditional detection techniques, using whole and partial genome sequences of human coronavirus (HCoV) diseases. In this work, the GIP techniques convert the genome sequences of HCoVs into genomic grayscale images using a genomic image mapping technique known as the frequency chaos game representation. Then, the pre-trained convolution neural network, AlexNet, is used to extract deep features from these images using the last convolution (conv5) and second fully-connected (fc7) layers. The most significant features were obtained by removing the redundant ones using the ReliefF and least absolute shrinkage and selection operator (LASSO) algorithms. These features are then passed to two classifiers: decision trees and k-nearest neighbors (KNN). Results showed that extracting deep features from the fc7 layer, selecting the most significant features using the LASSO algorithm, and executing the classification process using the KNN classifier is the best hybrid approach. The proposed hybrid deep learning approach detected COVID-19, among other HCoV diseases, with 99.71% accuracy, 99.78% specificity, and 99.62% sensitivity.

Hammad Muhammed S, Ghoneim Vidan F, Mabrouk Mai S, Al-Atabany Walid I

2023-Mar-10

General General

A generalized distributed delay model of COVID-19: An endemic model with immunity waning.

In Mathematical biosciences and engineering : MBE

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading worldwide for over two years, with millions of reported cases and deaths. The deployment of mathematical modeling in the fight against COVID-19 has recorded tremendous success. However, most of these models target the epidemic phase of the disease. The development of safe and effective vaccines against SARS-CoV-2 brought hope of safe reopening of schools and businesses and return to pre-COVID normalcy, until mutant strains like the Delta and Omicron variants, which are more infectious, emerged. A few months into the pandemic, reports of the possibility of both vaccine- and infection-induced immunity waning emerged, thereby indicating that COVID-19 may be with us for longer than earlier thought. As a result, to better understand the dynamics of COVID-19, it is essential to study the disease with an endemic model. In this regard, we developed and analyzed an endemic model of COVID-19 that incorporates the waning of both vaccine- and infection-induced immunities using distributed delay equations. Our modeling framework assumes that the waning of both immunities occurs gradually over time at the population level. We derived a nonlinear ODE system from the distributed delay model and showed that the model could exhibit either a forward or backward bifurcation depending on the immunity waning rates. Having a backward bifurcation implies that $ R_c < 1 $ is not sufficient to guarantee disease eradication, and that the immunity waning rates are critical factors in eradicating COVID-19. Our numerical simulations show that vaccinating a high percentage of the population with a safe and moderately effective vaccine could help in eradicating COVID-19.

Iyaniwura Sarafa A, Musa Rabiu, Kong Jude D

2023-Jan-12

** COVID-19 , SARS-CoV-2 , distributed delay equations , endemic model , global stability , immunity waning , linear chain trick , vaccination **

General General

Research of mortality risk prediction based on hospital admission data for COVID-19 patients.

In Mathematical biosciences and engineering : MBE

As COVID-19 continues to spread across the world and causes hundreds of millions of infections and millions of deaths, medical institutions around the world keep facing a crisis of medical runs and shortages of medical resources. In order to study how to effectively predict whether there are risks of death in patients, a variety of machine learning models have been used to learn and predict the clinical demographics and physiological indicators of COVID-19 patients in the United States of America. The results show that the random forest model has the best performance in predicting the risk of death in hospitalized patients with COVID-19, as the COVID-19 patients' mean arterial pressures, ages, C-reactive protein tests' values, values of blood urea nitrogen and their clinical troponin values are the most important implications for their risk of death. Healthcare organizations can use the random forest model to predict the risks of death based on data from patients admitted to a hospital due to COVID-19, or to stratify patients admitted to a hospital due to COVID-19 based on the five key factors this can optimize the diagnosis and treatment process by appropriately arranging ventilators, the intensive care unit and doctors, thus promoting the efficient use of limited medical resources during the COVID-19 pandemic. Healthcare organizations can also establish databases of patient physiological indicators and use similar strategies to deal with other pandemics that may occur in the future, as well as save more lives threatened by infectious diseases. Governments and people also need to take action to prevent possible future pandemics.

Shen Qian

2023-Jan-11

** COVID-19 , death risk feature , emergency triage strategy , ensemble learning , machine learning , tree model **

General General

An application of artificial intelligence for investigating the effect of COVID-19 lockdown on three-dimensional temperature variation in equatorial Africa.

In Geoscience frontiers

We present interesting application of artificial intelligence for investigating effect of the COVID-19 lockdown on 3-dimensional temperature variation across Nigeria (2°-15° E, 4°-14° N), in equatorial Africa. Artificial neural networks were trained to learn time-series temperature variation patterns using radio occultation measurements of atmospheric temperature from the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC). Data used for training, validation and testing of the neural networks covered period prior to the lockdown. There was also an investigation into the viability of solar activity indicator (represented by the sunspot number) as an input for the process. The results indicated that including the sunspot number as an input for the training did not improve the network prediction accuracy. The trained network was then used to predict values for the lockdown period. Since the network was trained using pre-lockdown dataset, predictions from the network are regarded as expected temperatures, should there have been no lockdown. By comparing with the actual COSMIC measurements during the lockdown period, effects of the lockdown on atmospheric temperatures were deduced. In overall, the mean altitudinal temperatures rose by about 1.1 °C above expected values during the lockdown. An altitudinal breakdown, at 1 km resolution, reveals that the values were typically below 0.5 °C at most of the altitudes, but exceeded 1 °C at 28 and 29 km altitudes. The temperatures were also observed to drop below expected values at altitudes of 0-2 km, and 17-20 km.

Okoh Daniel, Onuorah Loretta, Rabiu Babatunde, Obafaye Aderonke, Audu Dauda, Yusuf Najib, Owolabi Oluwafisayo

2022-Mar

COVID-19 lockdown, Equatorial Africa, Neural network, Sunspot number, Temperature, Time-series

Radiology Radiology

CoviExpert: COVID-19 detection from chest X-ray using CNN.

In Measurement. Sensors

COVID-19 continues to threaten the world with its impact and severity. This pandemic has created a sense of havoc and shook the world stretching the medical fraternity to an unimaginable extent, who are now facing fatigue and exhaustion. Due to the rapid increase in cases all across the globe demanding extensive medical care, people are hunting for resources like testing facilities, medical drugs and even hospital beds. Even people with mild to moderate infection are panicking and mentally giving up due to anxiety and desperation. To combat these issues, it is necessary to find an inexpensive and faster way to save lives and bring about a much-needed change. The most fundamental way through which this can be achieved is with the help of radiology which involves examination of Chest X rays. They are primarily used for the diagnosis of this disease. But due to panic and severity of this disease a recent trend of performing CT scans has been observed. This has been under scrutiny since it exposes patients to a very high level of radiation known to increase the probability of cancer. As quoted by the AIIMS Director, one CT scan is equivalent to around 300-400 Chest X-rays. Also, it is relatively a much costlier testing method. Hence, in this report, we have presented a Deep learning approach which can detect covid 19 positive cases from Chest X ray images. It involves creation of a Deep learning based Convolutional Neural Network (CNN) using Keras (python library) and integrating the model with a front-end user interface for ease of use. This leads up to the creation of a software which we have named as CoviExpert. It uses the sequential Keras model which is built layer by layer. All the layers are trained independently to make independent predictions which are then combined to give the final output. 1584 images of Chest X-rays of both COVID-19 positive and negative patients have been used as training data. 177 images have been used as testing data. The proposed approach gives a classification accuracy of 99%. CoviExpert can be used on any device by any medical professional to detect Covid positive patients within a few seconds.

Arivoli A, Golwala Devdatt, Reddy Rayirth

2022-Oct

CNN, COVID-19, CT scan, CoviExpert, Deep learning, X-ray

General General

Artificial intelligence and discrete-event simulation for capacity management of intensive care units during the Covid-19 pandemic: A case study.

In Journal of business research

The Covid-19 pandemic has pushed the Intensive Care Units (ICUs) into significant operational disruptions. The rapid evolution of this disease, the bed capacity constraints, the wide variety of patient profiles, and the imbalances within health supply chains still represent a challenge for policymakers. This paper aims to use Artificial Intelligence (AI) and Discrete-Event Simulation (DES) to support ICU bed capacity management during Covid-19. The proposed approach was validated in a Spanish hospital chain where we initially identified the predictors of ICU admission in Covid-19 patients. Second, we applied Random Forest (RF) to predict ICU admission likelihood using patient data collected in the Emergency Department (ED). Finally, we included the RF outcomes in a DES model to assist decision-makers in evaluating new ICU bed configurations responding to the patient transfer expected from downstream services. The results evidenced that the median bed waiting time declined between 32.42 and 48.03 min after intervention.

Ortiz-Barrios Miguel, Arias-Fonseca Sebastián, Ishizaka Alessio, Barbati Maria, Avendaño-Collante Betty, Navarro-Jiménez Eduardo

2023-May

Artificial Intelligence (AI), Covid-19, Discrete-Event Simulation (DES), Healthcare, Intensive Care Unit (ICU), Random Forest (RF)

General General

Assessing the effects of data drift on the performance of machine learning models used in clinical sepsis prediction.

In International journal of medical informatics ; h5-index 49.0

BACKGROUND : Data drift can negatively impact the performance of machine learning algorithms (MLAs) that were trained on historical data. As such, MLAs should be continuously monitored and tuned to overcome the systematic changes that occur in the distribution of data. In this paper, we study the extent of data drift and provide insights about its characteristics for sepsis onset prediction. This study will help elucidate the nature of data drift for prediction of sepsis and similar diseases. This may aid with the development of more effective patient monitoring systems that can stratify risk for dynamic disease states in hospitals.

METHODS : We devise a series of simulations that measure the effects of data drift in patients with sepsis, using electronic health records (EHR). We simulate multiple scenarios in which data drift may occur, namely the change in the distribution of the predictor variables (covariate shift), the change in the statistical relationship between the predictors and the target (concept shift), and the occurrence of a major healthcare event (major event) such as the COVID-19 pandemic. We measure the impact of data drift on model performances, identify the circumstances that necessitate model retraining, and compare the effects of different retraining methodologies and model architecture on the outcomes. We present the results for two different MLAs, eXtreme Gradient Boosting (XGB) and Recurrent Neural Network (RNN).

RESULTS : Our results show that the properly retrained XGB models outperform the baseline models in all simulation scenarios, hence signifying the existence of data drift. In the major event scenario, the area under the receiver operating characteristic curve (AUROC) at the end of the simulation period is 0.811 for the baseline XGB model and 0.868 for the retrained XGB model. In the covariate shift scenario, the AUROC at the end of the simulation period for the baseline and retrained XGB models is 0.853 and 0.874 respectively. In the concept shift scenario and under the mixed labeling method, the retrained XGB models perform worse than the baseline model for most simulation steps. However, under the full relabeling method, the AUROC at the end of the simulation period for the baseline and retrained XGB models is 0.852 and 0.877 respectively. The results for the RNN models were mixed, suggesting that retraining based on a fixed network architecture may be inadequate for an RNN. We also present the results in the form of other performance metrics such as the ratio of observed to expected probabilities (calibration) and the normalized rate of positive predictive values (PPV) by prevalence, referred to as lift, at a sensitivity of 0.8.

CONCLUSION : Our simulations reveal that retraining periods of a couple of months or using several thousand patients are likely to be adequate to monitor machine learning models that predict sepsis. This indicates that a machine learning system for sepsis prediction will probably need less infrastructure for performance monitoring and retraining compared to other applications in which data drift is more frequent and continuous. Our results also show that in the event of a concept shift, a full overhaul of the sepsis prediction model may be necessary because it indicates a discrete change in the definition of sepsis labels, and mixing the labels for the sake of incremental training may not produce the desired results.

Rahmani Keyvan, Thapa Rahul, Tsou Peiling, Casie Chetty Satish, Barnes Gina, Lam Carson, Foon Tso Chak

2022-Nov-19

Clinical decision support, Data drift, Machine learning, Sepsis

Public Health Public Health

Does social distancing impact pediatric upper airway infections? An observational controlled study and a brief literature review.

In American journal of otolaryngology ; h5-index 23.0

PURPOSE : SARS-CoV-2 pandemic has reduced social interaction even among children. The objective of the study was to assess the role of social distancing in the course of common pediatric upper airway recurrent diseases.

MATERIALS AND METHODS : Patients aged ≤14 years with at least one ENT-related clinical condition were retrospectively recruited. All patients had two outpatient evaluations in the same period (April - September): the control group had the first evaluation in 2018 and second in 2019, whereas the case group had the first evaluation in 2019 and second in 2020. Patients of each group were individually compared between their two visits and deemed improved/unchanged/worsened for each specific ENT condition. The percentage of children improved/unchanged/worsened were then collectively compared between the two groups for each condition.

RESULTS : Patients who experienced social distancing presented a significantly higher improvement rate than controls for recurrent acute otitis media episodes (35.1 % vs. 10.8 %; Fisher's exact test p = 0.033) and for tympanogram type (54.5 % vs. 11.1 %, Fisher's exact test p = 0.009).

CONCLUSIONS : The anti-contagion social restrictions decreased the prevalence of middle ear infections and effusion in children. Further studies on larger cohorts are required to better elucidate these findings.

Franchella Sebastiano, Favaretto Niccolò, Frigo Annachiara, Franz Leonardo, Pilo Simona, Mularoni Francesca, Marciani Silvia, Nicolai Piero, Marioni Gino, Cazzador Diego

2023-Mar-01

COVID-19, Pediatric, SARS-CoV-2, Social distancing, Upper airways infection

Public Health Public Health

Determinants of COVID-19 vaccine hesitancy among students and parents in Sentinel Schools Network of Catalonia, Spain.

In PloS one ; h5-index 176.0

Vaccine hesitancy is defined as a delay in acceptance of vaccines despite its availability, caused by many determinants. Our study presents the key reasons, determinants and characteristics associated with COVID-19 vaccine acceptability among students over 16 years and parents of students under 16 years and describe the COVID-19 vaccination among students in the settings of sentinel schools of Catalonia, Spain. This is a cross-sectional study that includes 3,383 students and the parents between October 2021 and January 2022. We describe the student's vaccination status and proceed a univariate and multivariate analysis using a Deletion Substitution Addition (DSA) machine learning algorithm. Vaccination against COVID-19 reached 70.8% in students under 16 years and 95.8% in students over 16 years at the end of the study project. The acceptability among unvaccinated students was 40.9% and 20.8% in October and January, respectively, and among parents was proportionally higher among students aged 5-11 (70.2%) in October and aged 3-4 (47.8%) in January. The key reason to not vaccinate themselves, or their children, were concern about side effects, insufficient research about the effect of the vaccine in children, rapid development of vaccines, necessity for more information and previous infection by SARS-CoV-2. Several variables were associated with refusal end hesitancy. For students, the main ones were risk perception and use of alternative therapies. For parents, the age of students, sociodemographic variables, socioeconomic impact related to the pandemic, and use of alternative therapies were more evident. Monitoring vaccine acceptance and refusal among children and their parents has been important to understand the interaction between different multilevel determinants and we hope it will be useful to improve public health strategies for future interventions in this population.

Ganem Fabiana, Folch Cinta, Colom-Cadena Andreu, Bordas Anna, Alonso Lucia, Soriano-Arandes Antoni, Casabona Jordi

2023

General General

Assessing the effects of therapeutic combinations on SARS-CoV-2 infected patient outcomes: A big data approach.

In PloS one ; h5-index 176.0

BACKGROUND : The COVID-19 pandemic has demonstrated the need for efficient and comprehensive, simultaneous assessment of multiple combined novel therapies for viral infection across the range of illness severity. Randomized Controlled Trials (RCT) are the gold standard by which efficacy of therapeutic agents is demonstrated. However, they rarely are designed to assess treatment combinations across all relevant subgroups. A big data approach to analyzing real-world impacts of therapies may confirm or supplement RCT evidence to further assess effectiveness of therapeutic options for rapidly evolving diseases such as COVID-19.

METHODS : Gradient Boosted Decision Tree, Deep and Convolutional Neural Network classifiers were implemented and trained on the National COVID Cohort Collaborative (N3C) data repository to predict the patients' outcome of death or discharge. Models leveraged the patients' characteristics, the severity of COVID-19 at diagnosis, and the calculated proportion of days on different treatment combinations after diagnosis as features to predict the outcome. Then, the most accurate model is utilized by eXplainable Artificial Intelligence (XAI) algorithms to provide insights about the learned treatment combination impacts on the model's final outcome prediction.

RESULTS : Gradient Boosted Decision Tree classifiers present the highest prediction accuracy in identifying patient outcomes with area under the receiver operator characteristic curve of 0.90 and accuracy of 0.81 for the outcomes of death or sufficient improvement to be discharged. The resulting model predicts the treatment combinations of anticoagulants and steroids are associated with the highest probability of improvement, followed by combined anticoagulants and targeted antivirals. In contrast, monotherapies of single drugs, including use of anticoagulants without steroid or antivirals are associated with poorer outcomes.

CONCLUSIONS : This machine learning model by accurately predicting the mortality provides insights about the treatment combinations associated with clinical improvement in COVID-19 patients. Analysis of the model's components suggests benefit to treatment with combination of steroids, antivirals, and anticoagulant medication. The approach also provides a framework for simultaneously evaluating multiple real-world therapeutic combinations in future research studies.

Moradi Hamidreza, Bunnell H Timothy, Price Bradley S, Khodaverdi Maryam, Vest Michael T, Porterfield James Z, Anzalone Alfred J, Santangelo Susan L, Kimble Wesley, Harper Jeremy, Hillegass William B, Hodder Sally L

2023

General General

A hybrid CNN and ensemble model for COVID-19 lung infection detection on chest CT scans.

In PloS one ; h5-index 176.0

COVID-19 is highly infectious and causes acute respiratory disease. Machine learning (ML) and deep learning (DL) models are vital in detecting disease from computerized chest tomography (CT) scans. The DL models outperformed the ML models. For COVID-19 detection from CT scan images, DL models are used as end-to-end models. Thus, the performance of the model is evaluated for the quality of the extracted feature and classification accuracy. There are four contributions included in this work. First, this research is motivated by studying the quality of the extracted feature from the DL by feeding these extracted to an ML model. In other words, we proposed comparing the end-to-end DL model performance against the approach of using DL for feature extraction and ML for the classification of COVID-19 CT scan images. Second, we proposed studying the effect of fusing extracted features from image descriptors, e.g., Scale-Invariant Feature Transform (SIFT), with extracted features from DL models. Third, we proposed a new Convolutional Neural Network (CNN) to be trained from scratch and then compared to the deep transfer learning on the same classification problem. Finally, we studied the performance gap between classic ML models against ensemble learning models. The proposed framework is evaluated using a CT dataset, where the obtained results are evaluated using five different metrics The obtained results revealed that using the proposed CNN model is better than using the well-known DL model for the purpose of feature extraction. Moreover, using a DL model for feature extraction and an ML model for the classification task achieved better results in comparison to using an end-to-end DL model for detecting COVID-19 CT scan images. Of note, the accuracy rate of the former method improved by using ensemble learning models instead of the classic ML models. The proposed method achieved the best accuracy rate of 99.39%.

Akl Ahmed A, Hosny Khalid M, Fouda Mostafa M, Salah Ahmad

2023

Radiology Radiology

COVID-19 imaging, where do we go from here? Bibliometric analysis of medical imaging in COVID-19.

In European radiology ; h5-index 62.0

OBJECTIVES : We conducted a systematic and comprehensive bibliometric analysis of COVID-19-related medical imaging to determine the current status and indicate possible future directions.

METHODS : This research provides an analysis of Web of Science Core Collection (WoSCC) indexed articles on COVID-19 and medical imaging published between 1 January 2020 and 30 June 2022, using the search terms "COVID-19" and medical imaging terms (such as "X-ray" or "CT"). Publications based solely on COVID-19 themes or medical image themes were excluded. CiteSpace was used to identify the predominant topics and generate a visual map of countries, institutions, authors, and keyword networks.

RESULTS : The search included 4444 publications. The journal with the most publications was European Radiology, and the most co-cited journal was Radiology. China was the most frequently cited country in terms of co-authorship, with the Huazhong University of Science and Technology being the institution contributing with the highest number of relevant co-authorships. Research trends and leading topics included: assessment of initial COVID-19-related clinical imaging features, differential diagnosis using artificial intelligence (AI) technology and model interpretability, diagnosis systems construction, COVID-19 vaccination, complications, and predicting prognosis.

CONCLUSIONS : This bibliometric analysis of COVID-19-related medical imaging helps clarify the current research situation and developmental trends. Subsequent trends in COVID-19 imaging are likely to shift from lung structure to function, from lung tissue to other related organs, and from COVID-19 to the impact of COVID-19 on the diagnosis and treatment of other diseases. Key Points • We conducted a systematic and comprehensive bibliometric analysis of COVID-19-related medical imaging from 1 January 2020 to 30 June 2022. • Research trends and leading topics included assessment of initial COVID-19-related clinical imaging features, differential diagnosis using AI technology and model interpretability, diagnosis systems construction, COVID-19 vaccination, complications, and predicting prognosis. • Future trends in COVID-19-related imaging are likely to involve a shift from lung structure to function, from lung tissue to other related organs, and from COVID-19 to the impact of COVID-19 on the diagnosis and treatment of other diseases.

Wen Ru, Zhang Mudan, Xu Rui, Gao Yingming, Liu Lin, Chen Hui, Wang Xingang, Zhu Wenyan, Lin Huafang, Liu Chen, Zeng Xianchun

2023-Mar-09

Bibliometrics, COVID-19, CiteSpace, Medical imaging, Treads

Radiology Radiology

Artificial intelligence for assistance of radiology residents in chest CT evaluation for COVID-19 pneumonia: a comparative diagnostic accuracy study.

In Acta radiologica (Stockholm, Sweden : 1987)

BACKGROUND : In hospitals, it is crucial to rule out coronavirus disease 2019 (COVID-19) timely and reliably. Artificial intelligence (AI) provides sufficient accuracy to identify chest computed tomography (CT) scans with signs of COVID-19.

PURPOSE : To compare the diagnostic accuracy of radiologists with different levels of experience with and without assistance of AI in CT evaluation for COVID-19 pneumonia and to develop an optimized diagnostic pathway.

MATERIAL AND METHODS : The retrospective, single-center, comparative case-control study included 160 consecutive participants who had undergone chest CT scan between March 2020 and May 2021 without or with confirmed diagnosis of COVID-19 pneumonia in a ratio of 1:3. Index tests were chest CT evaluation by five radiological senior residents, five junior residents, and an AI software. Based on the diagnostic accuracy in every group and on comparison of groups, a sequential CT assessment pathway was developed.

RESULTS : Areas under receiver operating curves were 0.95 (95% confidence interval [CI]=0.88-0.99), 0.96 (95% CI=0.92-1.0), 0.77 (95% CI=0.68-0.86), and 0.95 (95% CI=0.9-1.0) for junior residents, senior residents, AI, and sequential CT assessment, respectively. Proportions of false negatives were 9%, 3%, 17%, and 2%, respectively. With the developed diagnostic pathway, junior residents evaluated all CT scans with the support of AI. Senior residents were only required as second readers in 26% (41/160) of the CT scans.

CONCLUSION : AI can support junior residents with chest CT evaluation for COVID-19 and reduce the workload of senior residents. A review of selected CT scans by senior residents is mandatory.

Mlynska Lucja, Malouhi Amer, Ingwersen Maja, Güttler Felix, Gräger Stephanie, Teichgräber Ulf

2023-Mar-08

Artificial intelligence, COVID-19, SARS-CoV-2, computed tomography, deep learning, neural networks

Radiology Radiology

Machine learning prediction for COVID-19 disease severity at hospital admission.

In BMC medical informatics and decision making ; h5-index 38.0

IMPORTANCE : Early prognostication of patients hospitalized with COVID-19 who may require mechanical ventilation and have worse outcomes within 30 days of admission is useful for delivering appropriate clinical care and optimizing resource allocation.

OBJECTIVE : To develop machine learning models to predict COVID-19 severity at the time of the hospital admission based on a single institution data.

DESIGN, SETTING, AND PARTICIPANTS : We established a retrospective cohort of patients with COVID-19 from University of Texas Southwestern Medical Center from May 2020 to March 2022. Easily accessible objective markers including basic laboratory variables and initial respiratory status were assessed using Random Forest's feature importance score to create a predictive risk score. Twenty-five significant variables were identified to be used in classification models. The best predictive models were selected with repeated tenfold cross-validation methods.

MAIN OUTCOMES AND MEASURES : Among patients with COVID-19 admitted to the hospital, severity was defined by 30-day mortality (30DM) rates and need for mechanical ventilation.

RESULTS : This was a large, single institution COVID-19 cohort including total of 1795 patients. The average age was 59.7 years old with diverse heterogeneity. 236 (13%) required mechanical ventilation and 156 patients (8.6%) died within 30 days of hospitalization. Predictive accuracy of each predictive model was validated with the 10-CV method. Random Forest classifier for 30DM model had 192 sub-trees, and obtained 0.72 sensitivity and 0.78 specificity, and 0.82 AUC. The model used to predict MV has 64 sub-trees and returned obtained 0.75 sensitivity and 0.75 specificity, and 0.81 AUC. Our scoring tool can be accessed at https://faculty.tamuc.edu/mmete/covid-risk.html .

CONCLUSIONS AND RELEVANCE : In this study, we developed a risk score based on objective variables of COVID-19 patients within six hours of admission to the hospital, therefore helping predict a patient's risk of developing critical illness secondary to COVID-19.

Raman Ganesh, Ashraf Bilal, Demir Yusuf Kemal, Kershaw Corey D, Cheruku Sreekanth, Atis Murat, Atis Ahsen, Atar Mustafa, Chen Weina, Ibrahim Ibrahim, Bat Taha, Mete Mutlu

2023-Mar-07

COVID-19, Classification, Laboratory markers, Machine learning, Prediction, SARS-CoV-2, Scoring

General General

Effects of Antidepressants on COVID Outcome: A Retrospective Study on Large Scale Electronic Health Record Data.

In Interactive journal of medical research

BACKGROUND : Antidepressants are a type of medication used to treat clinical depression or prevent it recurring. Antidepressants exert an anticholinergic effect in varying degrees and various classes of antidepressants also can produce a different effect on immune function. While early usage of antidepressants has notional role on COVID-19 outcomes, the relationship between the risk of COVID-19 severity and the use of all kinds of antidepressants is not properly investigated before due to the exceeding cost involved with clinical trials. Large-scale observational data such as electronic health records and recent advancement of statistical analysis provide ample opportunity to virtualize clinical trial to discover detrimental effects of early usage of these drugs.

OBJECTIVE : By mining a large-scale electronic health record data set of COVID-19 positive patients, we aim to identify common drugs that are associated with COVID-19 outcome. However, whereas the statisticians have made great progress toward using such rich association estimation methods for risk estimation, precise effects of the medicines as treatments require causal models. Thus, our central aim of this paper lies on investigating electronic health record analytic for causal effect estimation and utilize that in discovering causal effects of early antidepressants use on COVID-19 outcomes. As a secondary aim, we develop methods for validating our causal effect estimation pipeline.

METHODS : We focus on antidepressants, a commonly used category of drugs that have been linked to unexpected effects on diverse inflammatory and cardiovascular outcomes and infer early use of such drug use effects on COVID-19 outcomes. However, whereas the machine learning and statistics community have made great progress toward using rich inference models, precise effects of the medicines as treatments require causal models, for which there is significantly less theoretical and practical guidance available. We used National COVID Cohort Collaborative (N3C), a database aggregating health history for over 12+ million people in the USA, including 5+ million with a positive COVID-19 test. We selected 241,952 COVID-19 positive patients with at least one year of medical history and age>13 that included 18,584-dimensional covariate vector for each person and 16 different antidepressants usage histories. We used propensity score weighting based on logistic regression method to estimate causal effect on whole data. Then we used Node2Vec embedding method to encode SNOMED medical code and apply random forest regression to estimate causal effect. We use both methods to estimate causal effects of antidepressants on COVID-19 outcome. We also selected few negatively effective conditions on COVID-19 outcomes and estimated their effects using our proposed methods to validate their efficacy.

RESULTS : Average Treatment Effect (ATE) of using any one of the antidepressants is -0.076 with 95% CI from -0.082 to - 0.069 with propensity score weighting method. The result is statistically significant at p<0.0001. In case of the method using SNOMED medical embedding, the ATE of using any one of the antidepressants is -0.423 with 95% CI from -0.382 to -0.463. This result is also statistically significant at p<0.0001.

CONCLUSIONS : In this study, we apply multiple causal inference methods incorporating with a novel application of health embeddings to investigate the effects of antidepressants on COVID-19 outcome. Additionally, we propose a novel non-affecting drug effect analysis-based evaluation technique to justify the efficacy of proposed method. This study offers causal inference methods on large-scale EHR data to discover common antidepressants' effects on COVID-19 hospitalization, or a worse outcome. The study finds that common antidepressants may increase risk of COVID-19 complications and uncovers a pattern where certain antidepressants are associated with lower risk of hospitalization. While discovering detrimental effects of these drugs on outcome could guide preventive care, identification of beneficial effects would allow us to propose drug repurposing for COVID-19 treatment.

Rahman Md Mahmudur, Mahi Atqiya Munawara, Melamed Rachel D, Alam Mohammad Arif Ul

2023-Mar-05

General General

Development and validation of a respiratory-responsive vocal biomarker-based tool for generalizable detection of respiratory impairment: independent case-control studies in multiple respiratory conditions including asthma, chronic obstructive pulmonary disease, and COVID-19.

In Journal of medical Internet research ; h5-index 88.0

BACKGROUND : Vocal biomarker-based machine learning approaches have shown promising results in detecting various health conditions, including respiratory diseases such as asthma. In this study, we aim to validate a respiratory-responsive vocal-biomarker (RRVB) platform initially trained on an asthma and healthy volunteer dataset for its ability to differentiate, without modification, active COVID-19 infection vs. healthy volunteers in patients presenting to hospitals in the US and India.

OBJECTIVE : The objective of this study was to determine whether the RRVB model can differentiate patients with active COVID-19 infection vs. asymptomatic healthy volunteers by assessing its sensitivity, specificity, and odds ratio. Another objective was to evaluate whether the RRVB model outputs correlate with symptom severity in COVID-19.

METHODS : A logistic regression model using a weighted sum of voice acoustic features was previously trained and validated on a dataset of about 1,700 patients with a confirmed asthma diagnosis vs. a similar number of healthy controls. The same model has shown generalizability to patients with chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), and cough. In the present study, a total of 497 participants (46% male, 54% female; 94% < 65 years, 6% >= 65 years; 51% Marathi, 45% English, 5% Spanish speakers) were enrolled across four clinical sites in US and India and provided voice samples and symptom reports on their personal smartphones. The participants included symptomatic COVID-19 positive and negative patients as well as asymptomatic healthy volunteers. The RRVB model performance was assessed by comparison with clinical diagnosis of COVID-19 confirmed by RT-PCR.

RESULTS : The RRVB model's ability to differentiate patients with respiratory conditions vs. healthy controls was previously demonstrated on validation data in asthma, COPD, ILD and cough with odds ratios of 4.3, 9.1, 3.1, and 3.9 respectively. The same RRVB model in the present study in COVID-19 performed with a sensitivity of 73.2%, specificity of 62.9%, and odds ratio of 4.64 (p<0.0001). Patients experiencing respiratory symptoms were detected more frequently than those not experiencing respiratory symptoms and completely asymptomatic patients (78.4% vs. 67.4% vs. 68.0%).

CONCLUSIONS : The RRVB model has shown good generalizability across respiratory conditions, geographies, and language. Results in COVID-19 demonstrate its meaningful potential to serve as a pre-screening tool for identifying subjects at risk for COVID-19 infection in combination with temperature and symptom reports. Although not a COVID-19 test, these results suggest that the RRVB model could encourage targeted testing. Moreover, the generalizability of this model for detecting respiratory symptoms across different linguistic and geographic contexts suggests a potential path to development and validation of voice-based tools for broader disease surveillance and monitoring applications in the future.

CLINICALTRIAL : ClinicalTrials.gov (NCT04582331.

Kaur Savneet, Larsen Erik, Harper James, Purandare Bharat, Uluer Ahmet, Hasdianda Mohammad Adrian, Umale Nikita, Killeen James, Castillo Edward, Jariwala Sunit

2023-Feb-28

General General

Interpretation of lung disease classification with light attention connected module.

In Biomedical signal processing and control

Lung diseases lead to complications from obstructive diseases, and the COVID-19 pandemic has increased lung disease-related deaths. Medical practitioners use stethoscopes to diagnose lung disease. However, an artificial intelligence model capable of objective judgment is required since the experience and diagnosis of respiratory sounds differ. Therefore, in this study, we propose a lung disease classification model that uses an attention module and deep learning. Respiratory sounds were extracted using log-Mel spectrogram MFCC. Normal and five types of adventitious sounds were effectively classified by improving VGGish and adding a light attention connected module to which the efficient channel attention module (ECA-Net) was applied. The performance of the model was evaluated for accuracy, precision, sensitivity, specificity, f1-score, and balanced accuracy, which were 92.56%, 92.81%, 92.22%, 98.50%, 92.29%, and 95.4%, respectively. We confirmed high performance according to the attention effect. The classification causes of lung diseases were analyzed using gradient-weighted class activation mapping (Grad-CAM), and the performances of their models were compared using open lung sounds measured using a Littmann 3200 stethoscope. The experts' opinions were also included. Our results will contribute to the early diagnosis and interpretation of diseases in patients with lung disease by utilizing algorithms in smart medical stethoscopes.

Choi Youngjin, Lee Hongchul

2023-Jul

Attention, ECA-Net, Grad-CAM, Lung disease, Respiratory sound, eXplainable AI

General General

Remote scoring models of rigidity and postural stability of Parkinson's disease based on indirect motions and a low-cost RGB algorithm.

In Frontiers in aging neuroscience ; h5-index 64.0

BACKGROUND AND OBJECTIVES : The Movement Disorder Society's Unified Parkinson's Disease Rating Scale Part III (MDS-UPDRS III) is mostly common used for assessing the motor symptoms of Parkinson's disease (PD). In remote circumstances, vision-based techniques have many strengths over wearable sensors. However, rigidity (item 3.3) and postural stability (item 3.12) in the MDS-UPDRS III cannot be assessed remotely since participants need to be touched by a trained examiner during testing. We developed the four scoring models of rigidity of the neck, rigidity of the lower extremities, rigidity of the upper extremities, and postural stability based on features extracted from other available and touchless motions.

METHODS : The red, green, and blue (RGB) computer vision algorithm and machine learning were combined with other available motions from the MDS-UPDRS III evaluation. A total of 104 patients with PD were split into a train set (89 individuals) and a test set (15 individuals). The light gradient boosting machine (LightGBM) multiclassification model was trained. Weighted kappa (k), absolute accuracy (ACC ± 0), and Spearman's correlation coefficient (rho) were used to evaluate the performance of model.

RESULTS : For model of rigidity of the upper extremities, k = 0.58 (moderate), ACC ± 0 = 0.73, and rho = 0.64 (moderate). For model of rigidity of the lower extremities, k = 0.66 (substantial), ACC ± 0 = 0.70, and rho = 0.76 (strong). For model of rigidity of the neck, k = 0.60 (moderate), ACC ± 0 = 0.73, and rho = 0.60 (moderate). For model of postural stability, k = 0.66 (substantial), ACC ± 0 = 0.73, and rho = 0.68 (moderate).

CONCLUSION : Our study can be meaningful for remote assessments, especially when people have to maintain social distance, e.g., in situations such as the coronavirus disease-2019 (COVID-19) pandemic.

Ma Ling-Yan, Shi Wei-Kun, Chen Cheng, Wang Zhan, Wang Xue-Mei, Jin Jia-Ning, Chen Lu, Ren Kang, Chen Zhong-Lue, Ling Yun, Feng Tao

2023

Parkinson’s disease, computer vision, machine learning, postural stability, remote, rigidity

General General

STG-Net: A COVID-19 prediction network based on multivariate spatio-temporal information.

In Biomedical signal processing and control

The modern urban population features a high population density and a fast population flow, and COVID-19 has strong transmission ability, long incubation period, and other characteristics. Considering only the time sequence of COVID-19 transmission cannot effectively respond to the current epidemic transmission situation. The distance between cities and population density information also have a significant impact on the transmission of the virus. Currently, cross-domain transmission prediction models do not fully exploit the time-space information and fluctuation trend of data, and cannot reasonably predict the trend of infectious diseases by integrating time-space multi-source information. To solve this problem, this paper proposes the COVID-19 prediction network (STG-Net) based on multivariate spatio-temporal information, which introduces the Spatial Information Mining module (SIM) and the Temporal Information Mining module (TIM) to mine the spatio-temporal information of the data in a deeper level, and uses the slope feature method to further mine the fluctuation trend of the data. Also, we introduce the Gramian Angular Field module (GAF), which converts one-dimensional data into two-dimensional images, further enhancing the network's feature mining capability in the time and feature dimension, ultimately combining spatiotemporal information to predict daily newly confirmed cases. We tested the network on datasets from China, Australia, the United Kingdom, France, and Netherlands. The experimental results show that STG-Net has better prediction performance than existing prediction models, with an average decision coefficient R2 of 98.23% on the datasets from five countries, as well as good long- and short-term prediction ability and overall good robustness.

Song Yucheng, Chen Huaiyi, Song Xiaomeng, Liao Zhifang, Zhang Yan

2023-Jul

COVID-19, Confirmed cases forecasting, Deep learning, STG-Net, Spatial information, Time series

General General

Continuous diagnosis and prognosis by controlling the update process of deep neural networks.

In Patterns (New York, N.Y.)

Continuous diagnosis and prognosis are essential for critical patients. They can provide more opportunities for timely treatment and rational allocation. Although deep-learning techniques have demonstrated superiority in many medical tasks, they frequently forget, overfit, and produce results too late when performing continuous diagnosis and prognosis. In this work, we summarize the four requirements; propose a concept, continuous classification of time series (CCTS); and design a training method for deep learning, restricted update strategy (RU). The RU outperforms all baselines and achieves average accuracies of 90%, 97%, and 85% on continuous sepsis prognosis, COVID-19 mortality prediction, and eight disease classifications, respectively. The RU can also endow deep learning with interpretability, exploring disease mechanisms through staging and biomarker discovery. We find four sepsis stages, three COVID-19 stages, and their respective biomarkers. Further, our approach is data and model agnostic. It can be applied to other diseases and even in other fields.

Sun Chenxi, Li Hongyan, Song Moxian, Cai Derun, Zhang Baofeng, Hong Shenda

2023-Feb-10

COVID-19, biomarker, continuous classification, deep learning, diagnosis, disease staging, prognosis, sepsis, time series

General General

Present and future perspectives in early diagnosis and monitoring for progressive fibrosing interstitial lung diseases.

In Frontiers in medicine

Progressive fibrosing interstitial lung diseases (PF-ILDs) represent a group of conditions of both known and unknown origin which continue to worsen despite standard treatments, leading to respiratory failure and early mortality. Given the potential to slow down progression by initiating antifibrotic therapies where appropriate, there is ample opportunity to implement innovative strategies for early diagnosis and monitoring with the goal of improving clinical outcomes. Early diagnosis can be facilitated by standardizing ILD multidisciplinary team (MDT) discussions, implementing machine learning algorithms for chest computed-tomography quantitative analysis and novel magnetic-resonance imaging techniques, as well as measuring blood biomarker signatures and genetic testing for telomere length and identification of deleterious mutations in telomere-related genes and other single-nucleotide polymorphisms (SNPs) linked to pulmonary fibrosis such as rs35705950 in the MUC5B promoter region. Assessing disease progression in the post COVID-19 era also led to a number of advances in home monitoring using digitally-enabled home spirometers, pulse oximeters and other wearable devices. While validation for many of these innovations is still in progress, significant changes to current clinical practice for PF-ILDs can be expected in the near future.

Stanel Stefan Cristian, Rivera-Ortega Pilar

2023

PF-ILD, PPF, idiopathic pulmonary fibrosis, interstitial lung disease, progressive fibrosing interstitial lung disease, progressive pulmonary fibrosis

Cardiology Cardiology

A multi-use deep learning method for CITE-seq and single-cell RNA-seq data integration with cell surface protein prediction and imputation.

In Nature machine intelligence

CITE-seq, a single-cell multi-omics technology that measures RNA and protein expression simultaneously in single cells, has been widely applied in biomedical research, especially in immune related disorders and other diseases such as influenza and COVID-19. Despite the proliferation of CITE-seq, it is still costly to generate such data. Although data integration can increase information content, this raises computational challenges. First, combining multiple datasets is prone to batch effects that need to be addressed. Secondly, it is difficult to combine multiple CITE-seq datasets because the protein panels in different datasets may only partially overlap. Integrating multiple CITE-seq and single-cell RNA-seq (scRNA-seq) datasets is important because this allows the utilization of as many data as possible to uncover cell population heterogeneity. To overcome these challenges, we present sciPENN, a multi-use deep learning approach that supports CITE-seq and scRNA-seq data integration, protein expression prediction for scRNA-seq, protein expression imputation for CITE-seq, quantification of prediction and imputation uncertainty, and cell type label transfer from CITE-seq to scRNA-seq. Comprehensive evaluations spanning multiple datasets demonstrate that sciPENN outperforms other current state-of-the-art methods.

Lakkis Justin, Schroeder Amelia, Su Kenong, Lee Michelle Y Y, Bashore Alexander C, Reilly Muredach P, Li Mingyao

2022-Nov

CITE-seq, deep learning, protein prediction, single-cell RNA-seq, single-cell multi-omics

General General

Identifying resilience strategies for disruption management in the healthcare supply chain during COVID-19 by digital innovations: A systematic literature review.

In Informatics in medicine unlocked

The worldwide spread of the COVID-19 disease has had a catastrophic effect on healthcare supply chains. The current manuscript systematically analyzes existing studies mitigating strategies for disruption management in the healthcare supply chain during COVID-19. Using a systematic approach, we recognized 35 related papers. Artificial intelligence (AI), block chain, big data analytics, and simulation are the most important technologies employed in supply chain management in healthcare. The findings reveal that the published research has concentrated mainly on generating resilience plans for the management of COVID-19 impacts. Furthermore, the vulnerability of healthcare supply chains and the necessity of establishing better resilience methods are emphasized in most of the research. However, the practical application of these emerging tools for managing disturbance and warranting resilience in the supply chain has been examined only rarely. This article provides directions for additional research, which can guide researchers to develop and conduct impressive studies related to the healthcare supply chain for different disasters.

Arji Goli, Ahmadi Hossein, Avazpoor Pejman, Hemmat Morteza

2023

COVID-19, Healthcare supply chain, Literature review, Pandemics, Supply chain management

General General

Rough-set based learning: Assessing patterns and predictability of anxiety, depression, and sleep scores associated with the use of cannabinoid-based medicine during COVID-19.

In Frontiers in artificial intelligence

Recently, research is emerging highlighting the potential of cannabinoids' beneficial effects related to anxiety, mood, and sleep disorders as well as pointing to an increased use of cannabinoid-based medicines since COVID-19 was declared a pandemic. The objective of this research is 3 fold: i) to evaluate the relationship of the clinical delivery of cannabinoid-based medicine for anxiety, depression and sleep scores by utilizing machine learning specifically rough set methods; ii) to discover patterns based on patient features such as specific cannabinoid recommendations, diagnosis information, decreasing/increasing levels of clinical assessment tools (CAT) scores over a period of time; and iii) to predict whether new patients could potentially experience either an increase or decrease in CAT scores. The dataset for this study was derived from patient visits to Ekosi Health Centres, Canada over a 2 year period including the COVID timeline. Extensive pre-processing and feature engineering was performed. A class feature indicative of their progress or lack thereof due to the treatment received was introduced. Six Rough/Fuzzy-Rough classifiers as well as Random Forest and RIPPER classifiers were trained on the patient dataset using a 10-fold stratified CV method. The highest overall accuracy, sensitivity and specificity measures of over 99% was obtained using the rule-based rough-set learning model. In this study, we have identified rough-set based machine learning model with high accuracy that could be utilized for future studies regarding cannabinoids and precision medicine.

Ramanna Sheela, Ashrafi Negin, Loster Evan, Debroni Karen, Turner Shelley

2023

cannabinoid medicine, electronic health records, machine learning, mental health, rough sets, rough-fuzzy sets

General General

Coronavirus diagnosis using cough sounds: Artificial intelligence approaches.

In Frontiers in artificial intelligence

INTRODUCTION : The Coronavirus disease 2019 (COVID-19) pandemic has caused irreparable damage to the world. In order to prevent the spread of pathogenicity, it is necessary to identify infected people for quarantine and treatment. The use of artificial intelligence and data mining approaches can lead to prevention and reduction of treatment costs. The purpose of this study is to create data mining models in order to diagnose people with the disease of COVID-19 through the sound of coughing.

METHOD : In this research, Supervised Learning classification algorithms have been used, which include Support Vector Machine (SVM), random forest, and Artificial Neural Networks, that based on the standard "Fully Connected" neural network, Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM) recurrent neural networks have been established. The data used in this research was from the online site sorfeh.com/sendcough/en, which has data collected during the spread of COVID-19.

RESULT : With the data we have collected (about 40,000 people) in different networks, we have reached acceptable accuracies.

CONCLUSION : These findings show the reliability of this method for using and developing a tool as a screening and early diagnosis of people with COVID-19. This method can also be used with simple artificial intelligence networks so that acceptable results can be expected. Based on the findings, the average accuracy was 83% and the best model was 95%.

Askari Nasab Kazem, Mirzaei Jamal, Zali Alireza, Gholizadeh Sarfenaz, Akhlaghdoust Meisam

2023

artificial intelligence, coronavirus, cough, deep learning, machine learning, respiratory sounds

General General

MCSC-Net: COVID-19 detection using deep-Q-neural network classification with RFNN-based hybrid whale optimization.

In Journal of X-ray science and technology

BACKGROUND : COVID-19 is the most dangerous virus, and its accurate diagnosis saves lives and slows its spread. However, COVID-19 diagnosis takes time and requires trained professionals. Therefore, developing a deep learning (DL) model on low-radiated imaging modalities like chest X-rays (CXRs) is needed.

OBJECTIVE : The existing DL models failed to diagnose COVID-19 and other lung diseases accurately. This study implements a multi-class CXR segmentation and classification network (MCSC-Net) to detect COVID-19 using CXR images.

METHODS : Initially, a hybrid median bilateral filter (HMBF) is applied to CXR images to reduce image noise and enhance the COVID-19 infected regions. Then, a skip connection-based residual network-50 (SC-ResNet50) is used to segment (localize) COVID-19 regions. The features from CXRs are further extracted using a robust feature neural network (RFNN). Since the initial features contain joint COVID-19, normal, pneumonia bacterial, and viral properties, the conventional methods fail to separate the class of each disease-based feature. To extract the distinct features of each class, RFNN includes a disease-specific feature separate attention mechanism (DSFSAM). Furthermore, the hunting nature of the Hybrid whale optimization algorithm (HWOA) is used to select the best features in each class. Finally, the deep-Q-neural network (DQNN) classifies CXRs into multiple disease classes.

RESULTS : The proposed MCSC-Net shows the enhanced accuracy of 99.09% for 2-class, 99.16% for 3-class, and 99.25% for 4-class classification of CXR images compared to other state-of-art approaches.

CONCLUSION : The proposed MCSC-Net enables to conduct multi-class segmentation and classification tasks applying to CXR images with high accuracy. Thus, together with gold-standard clinical and laboratory tests, this new method is promising to be used in future clinical practice to evaluate patients.

Deepak Gerard, Madiajagan M, Kulkarni Sanjeev, Ahmed Ahmed Najat, Gopatoti Anandbabu, Ammisetty Veeraswamy

2023-Feb-28

COVID-19, chest X-Ray, deep-Q-neural networks, hybrid median bilateral filter, robust feature neural network

General General

Data driven contagion risk management in low-income countries using machine learning applications with COVID-19 in South Asia.

In Scientific reports ; h5-index 158.0

In the absence of real-time surveillance data, it is difficult to derive an early warning system and potential outbreak locations with the existing epidemiological models, especially in resource-constrained countries. We proposed a contagion risk index (CR-Index)-based on publicly available national statistics-founded on communicable disease spreadability vectors. Utilizing the daily COVID-19 data (positive cases and deaths) from 2020 to 2022, we developed country-specific and sub-national CR-Index for South Asia (India, Pakistan, and Bangladesh) and identified potential infection hotspots-aiding policymakers with efficient mitigation planning. Across the study period, the week-by-week and fixed-effects regression estimates demonstrate a strong correlation between the proposed CR-Index and sub-national (district-level) COVID-19 statistics. We validated the CR-Index using machine learning methods by evaluating the out-of-sample predictive performance. Machine learning driven validation showed that the CR-Index can correctly predict districts with high incidents of COVID-19 cases and deaths more than 85% of the time. This proposed CR-Index is a simple, replicable, and easily interpretable tool that can help low-income countries prioritize resource mobilization to contain the disease spread and associated crisis management with global relevance and applicability. This index can also help to contain future pandemics (and epidemics) and manage their far-reaching adverse consequences.

Shonchoy Abu S, Mahzab Moogdho M, Mahmood Towhid I, Ali Manhal

2023-Mar-06

Public Health Public Health

Application of machine learning approach in emergency department to support clinical decision making for SARS-CoV-2 infected patients.

In Journal of integrative bioinformatics

To support physicians in clinical decision process on patients affected by Coronavirus Disease 2019 (COVID-19) in areas with a low vaccination rate, we devised and evaluated the performances of several machine learning (ML) classifiers fed with readily available clinical and laboratory data. Our observational retrospective study collected data from a cohort of 779 COVID-19 patients presenting to three hospitals of the Lazio-Abruzzo area (Italy). Based on a different selection of clinical and respiratory (ROX index and PaO2/FiO2 ratio) variables, we devised an AI-driven tool to predict safe discharge from ED, disease severity and mortality during hospitalization. To predict safe discharge our best classifier is an RF integrated with ROX index that reached AUC of 0.96. To predict disease severity the best classifier was an RF integrated with ROX index that reached an AUC of 0.91. For mortality prediction the best classifier was an RF integrated with ROX index, that reached an AUC of 0.91. The results obtained thanks to our algorithms are consistent with the scientific literature an accomplish significant performances to forecast safe discharge from ED and severe clinical course of COVID-19.

Casano Nicolò, Santini Silvano Junior, Vittorini Pierpaolo, Sinatti Gaia, Carducci Paolo, Mastroianni Claudio Maria, Ciardi Maria Rosa, Pasculli Patrizia, Petrucci Emiliano, Marinangeli Franco, Balsano Clara

2023-Mar-07

COVID-19, ROX index, SARS-CoV-2, emergency medicine, machine learning

General General

Unveiling mutation effects on the structural dynamics of the main protease from SARS-CoV-2 with hybrid simulation methods.

In Journal of molecular graphics & modelling

The main protease of SARS-CoV-2 (called Mpro or 3CLpro) is essential for processing polyproteins encoded by viral RNA. Several Mpro mutations were found in SARS-CoV-2 variants, which are related to higher transmissibility, pathogenicity, and resistance to neutralization antibodies. Macromolecules adopt several favored conformations in solution depending on their structure and shape, determining their dynamics and function. In this study, we used a hybrid simulation method to generate intermediate structures along the six lowest frequency normal modes and sample the conformational space and characterize the structural dynamics and global motions of WT SARS-CoV-2 Mpro and 48 mutations, including mutations found in P.1, B.1.1.7, B.1.351, B.1.525 and B.1.429+B.1.427 variants. We tried to contribute to the elucidation of the effects of mutation in the structural dynamics of SARS-CoV-2 Mpro. A machine learning analysis was performed following the investigation regarding the influence of the K90R, P99L, P108S, and N151D mutations on the dimeric interface assembling of the SARS-CoV-2 Mpro. The parameters allowed the selection of potential structurally stable dimers, which demonstrated that some single surface aa substitutions not located at the dimeric interface (K90R, P99L, P108S, and N151D) are able to induce significant quaternary changes. Furthermore, our results demonstrated, by a Quantum Mechanics method, the influence of SARS-CoV-2 Mpro mutations on the catalytic mechanism, confirming that only one of the chains of the WT and mutant SARS-CoV-2 Mpros are prone to cleave substrates. Finally, it was also possible to identify the aa residue F140 as an important factor related to the increasing enzymatic reactivity of a significant number of SARS-CoV-2 Mpro conformations generated by the normal modes-based simulations.

Gasparini P, Philot E A, Pantaleão S Q, Torres-Bonfim N E S M, Kliousoff A, Quiroz R C N, Perahia D, Simões R P, Magro A J, Scott A L

2023-Feb-22

Main protease, Molecular dynamics, Mutation, Normal modes, Quantum mechanics, Residue F140, SARS-CoV-2, Structural dynamics

oncology Oncology

ATR-FTIR spectrum analysis of plasma samples for rapid identification of recovered COVID-19 individuals.

In Journal of biophotonics

The development of fast, cheap and reliable methods to determine seroconversion against infectious agents is of great practical importance. In the context of the COVID-19 pandemic, an important issue is to study the rate of formation of the immune layer in the population of different regions, as well as the study of the formation of post-vaccination immunity in individuals after vaccination. Currently, the main method for this kind of research is enzyme immunoassay (ELISA, enzyme-linked immunosorbent assay). This technique is sufficiently sensitive and specific, but it requires significant time and material costs. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in blood plasma to detecting seroconversion against SARS-CoV-2. The study included samples of 60 patients. Clear spectral differences in plasma samples from recovered COVID-19 patients and conditionally healthy donors were identified using multivariate and statistical analysis. The results showed that ATR-FTIR spectroscopy, combined with principal components analysis (PCA) and linear discriminant analysis (LDA) or artificial neural network (ANN), made it possible to efficiently identify specimens from recovered COVID-19 patients. We built a classification models based on principal component analysis (PCA) associated with linear discriminant analysis (LDA) and artificial neural network (ANN). Our analysis led to 87% accuracy for PCA-LDA model and 91% accuracy for ANN, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective tool for detecting seroconversion against SARS-CoV-2. This approach could be used as an alternative to ELISA. This article is protected by copyright. All rights reserved.

Karas Boris Yu, Sitnikova Vera E, Nosenko Tatiana, Dedkov Vladimir G, Arsentieva Natalia A, Gavrilenko Natalia V, Moiseev Ivan S, Totolian Areg A, Kajava Andrey V, Uspenskaya Mayya V

2023-Mar-03

ANN, ATR-FTIR spectroscopy, COVID-19, PCA-LDA, chemometric, plasma, sepsis

General General

Structural causal model with expert augmented knowledge to estimate the effect of oxygen therapy on mortality in the ICU.

In Artificial intelligence in medicine ; h5-index 34.0

Recent advances in causal inference techniques, more specifically, in the theory of structural causal models, provide the framework for identifying causal effects from observational data in cases where the causal graph is identifiable, i.e., the data generation mechanism can be recovered from the joint distribution. However, no such studies have been performed to demonstrate this concept with a clinical example. We present a complete framework to estimate the causal effects from observational data by augmenting expert knowledge in the model development phase and with a practical clinical application. Our clinical application entails a timely and essential research question, the effect of oxygen therapy intervention in the intensive care unit (ICU). The result of this project is helpful in a variety of disease conditions, including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) patients in the ICU. We used data from the MIMIC-III database, a widely used health care database in the machine learning community with 58,976 admissions from an ICU in Boston, MA, to estimate the oxygen therapy effect on morality. We also identified the model's covariate-specific effect on oxygen therapy for more personalized intervention.

Gani Md Osman, Kethireddy Shravan, Adib Riddhiman, Hasan Uzma, Griffin Paul, Adibuzzaman Mohammad

2023-Mar

Causal inference, Critical care, Expert augmented knowledge, Oxygen therapy, Structural causal model

General General

Benchmarking of Machine Learning classifiers on plasma proteomic for COVID-19 severity prediction through interpretable artificial intelligence.

In Artificial intelligence in medicine ; h5-index 34.0

The SARS-CoV-2 pandemic highlighted the need for software tools that could facilitate patient triage regarding potential disease severity or even death. In this article, an ensemble of Machine Learning (ML) algorithms is evaluated in terms of predicting the severity of their condition using plasma proteomics and clinical data as input. An overview of AI-based technical developments to support COVID-19 patient management is presented outlining the landscape of relevant technical developments. Based on this review, the use of an ensemble of ML algorithms that analyze clinical and biological data (i.e., plasma proteomics) of COVID-19 patients is designed and deployed to evaluate the potential use of AI for early COVID-19 patient triage. The proposed pipeline is evaluated using three publicly available datasets for training and testing. Three ML "tasks" are defined, and several algorithms are tested through a hyperparameter tuning method to identify the highest-performance models. As overfitting is one of the typical pitfalls for such approaches (mainly due to the size of the training/validation datasets), a variety of evaluation metrics are used to mitigate this risk. In the evaluation procedure, recall scores ranged from 0.6 to 0.74 and F1-score from 0.62 to 0.75. The best performance is observed via Multi-Layer Perceptron (MLP) and Support Vector Machines (SVM) algorithms. Additionally, input data (proteomics and clinical data) were ranked based on corresponding Shapley additive explanation (SHAP) values and evaluated for their prognosticated capacity and immuno-biological credence. This "interpretable" approach revealed that our ML models could discern critical COVID-19 cases predominantly based on patient's age and plasma proteins on B cell dysfunction, hyper-activation of inflammatory pathways like Toll-like receptors, and hypo-activation of developmental and immune pathways like SCF/c-Kit signaling. Finally, the herein computational workflow is corroborated in an independent dataset and MLP superiority along with the implication of the abovementioned predictive biological pathways are corroborated. Regarding limitations of the presented ML pipeline, the datasets used in this study contain less than 1000 observations and a significant number of input features hence constituting a high-dimensional low-sample (HDLS) dataset which could be sensitive to overfitting. An advantage of the proposed pipeline is that it combines biological data (plasma proteomics) with clinical-phenotypic data. Thus, in principle, the presented approach could enable patient triage in a timely fashion if used on already trained models. However, larger datasets and further systematic validation are needed to confirm the potential clinical value of this approach. The code is available on Github: https://github.com/inab-certh/Predicting-COVID-19-severity-through-interpretable-AI-analysis-of-plasma-proteomics.

Dimitsaki Stella, Gavriilidis George I, Dimitriadis Vlasios K, Natsiavas Pantelis

2023-Mar

Artificial intelligence, COVID-19, Forecasting, Machine Learning, Severity prediction

General General

The voice of COVID-19: Breath and cough recording classification with temporal decision trees and random forests.

In Artificial intelligence in medicine ; h5-index 34.0

Symbolic learning is the logic-based approach to machine learning, and its mission is to provide algorithms and methodologies to extract logical information from data and express it in an interpretable way. Interval temporal logic has been recently proposed as a suitable tool for symbolic learning, specifically via the design of an interval temporal logic decision tree extraction algorithm. In order to improve their performances, interval temporal decision trees can be embedded into interval temporal random forests, mimicking the corresponding schema at the propositional level. In this article we consider a dataset of cough and breath sample recordings of volunteer subjects, labeled with their COVID-19 status, originally collected by the University of Cambridge. By interpreting such recordings as multivariate time series, we study the problem of their automated classification using interval temporal decision trees and forests. While this problem has been approached with the same dataset as well as with other datasets, in all cases, non-symbolic learning methods (usually, deep learning-based) have been applied to solve it; in this article we apply a symbolic approach, and show that it does not only outperform the state-of-the-art obtained with the same dataset, but its results are also superior to those of most non-symbolic techniques applied on other datasets. As an added bonus, thanks to the symbolic nature of our approach, we are also able to extract explicit knowledge to help physicians characterize typical COVID-positive cough and breath.

Manzella F, Pagliarini G, Sciavicco G, Stan I E

2023-Mar

COVID-19, Interval temporal decision trees and forests, Symbolic models

General General

The effect of COVID-19 on self-reported safety incidents in aviation: An examination of the heterogeneous effects using causal machine learning.

In Journal of safety research

INTRODUCTION : Disruptions to aviation operations occur daily on a micro-level with negligible impacts beyond the inconvenience of rebooking and changing aircrew schedules. The unprecedented disruption in global aviation due to COVID-19 highlighted a need to evaluate emergent safety issues rapidly.

METHOD : This paper uses causal machine learning to examine the heterogeneous effects of COVID-19 on reported aircraft incursions/excursions. The analysis utilized self report data from NASA Aviation Safety Reporting System collected from 2018 to 2020. The report attributes include self identified group characteristics and expert categorization of factors and outcomes. The analysis identified attributes and subgroup characteristics that were most sensitive to COVID-19 in inducing incursions/excursions. The method included the generalized random forest and difference-in-difference techniques to explore causal effects.

RESULTS : The analysis indicates first officers are more prone to experiencing incursion/excursion events during the pandemic. In addition, events categorized with the human factors confusion, distraction, and the causal factor fatigue increased incursion/excursion events.

PRACTICAL APPLICATIONS : Understanding the attributes associated with the likelihood of incursion/excursion events provides policymakers and aviation organizations insights to improve prevention mechanisms for future pandemics or extended periods of reduced aviation operations.

Choi Youngran, Gibson James R

2023-Feb

Aviation incursions/excursions, COVID-19, Heterogeneous treatment effects, Machine learning

Internal Medicine Internal Medicine

A Computational Approach in the Diagnostic Process of COVID-19: The Missing Link between the Laboratory and Emergency Department.

In Frontiers in bioscience (Landmark edition)

BACKGROUND : The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic and so it is crucial the right evaluation of viral infection. According to the Centers for Disease Control and Prevention (CDC), the Real-Time Reverse Transcription PCR (RT-PCR) in respiratory samples is the gold standard for confirming the disease. However, it has practical limitations as time-consuming procedures and a high rate of false-negative results. We aim to assess the accuracy of COVID-19 classifiers based on Arificial Intelligence (AI) and statistical classification methods adapted on blood tests and other information routinely collected at the Emergency Departments (EDs).

METHODS : Patients admitted to the ED of Careggi Hospital from April 7th-30th 2020 with pre-specified features of suspected COVID-19 were enrolled. Physicians prospectively dichotomized them as COVID-19 likely/unlikely case, based on clinical features and bedside imaging support. Considering the limits of each method to identify a case of COVID-19, further evaluation was performed after an independent clinical review of 30-day follow-up data. Using this as a gold standard, several classifiers were implemented: Logistic Regression (LR), Quadratic Discriminant Analysis (QDA), Random Forest (RF), Support Vector Machine (SVM), Neural Networks (NN), K-nearest neighbor (K-NN), Naive Bayes (NB).

RESULTS : Most of the classifiers show a ROC >0.80 on both internal and external validation samples but the best results are obtained applying RF, LR and NN. The performance from the external validation sustains the proof of concept to use such mathematical models fast, robust and efficient for a first identification of COVID-19 positive patients. These tools may constitute both a bedside support while waiting for RT-PCR results, and a tool to point to a deeper investigation, by identifying which patients are more likely to develop into positive cases within 7 days.

CONCLUSIONS : Considering the obtained results and with a rapidly changing virus, we believe that data processing automated procedures may provide a valid support to the physicians facing the decision to classify a patient as a COVID-19 case or not.

Lanzilao Luisa, Mariniello Antonella, Polenzani Bianca, Aldinucci Alessandra, Nazerian Peiman, Prota Alessio, Grifoni Stefano, Tonietti Barbara, Neri Chiara, Turco Livia, Fanelli Alessandra, Amedei Amedeo, Stanghellini Elena

2023-Feb-22

COVID-19, automated classifiers, diagnosis, laboratory medicine, machine learning, “physicians gestalt”

General General

The future of automated infection detection: Innovation to transform practice (Part III/III).

In Antimicrobial stewardship & healthcare epidemiology : ASHE

Current methods of emergency-room-based syndromic surveillance were insufficient to detect early community spread of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in the United States, which slowed the infection prevention and control response to the novel pathogen. Emerging technologies and automated infection surveillance have the potential to improve upon current practice standards and to revolutionize the practice of infection detection, prevention and control both inside and outside of healthcare settings. Genomics, natural language processing, and machine learning can be leveraged to improve identification of transmission events and aid and evaluate outbreak response. In the near future, automated infection detection strategies can be used to advance a true "Learning Healthcare System" that will support near-real-time quality improvement efforts and advance the scientific basis for the practice of infection control.

Branch-Elliman Westyn, Sundermann Alexander J, Wiens Jenna, Shenoy Erica S

2023

Radiology Radiology

Robust framework for COVID-19 identication from a multicenter dataset of chest CT scans.

In PloS one ; h5-index 176.0

The main objective of this study is to develop a robust deep learning-based framework to distinguish COVID-19, Community-Acquired Pneumonia (CAP), and Normal cases based on volumetric chest CT scans, which are acquired in different imaging centers using different scanners and technical settings. We demonstrated that while our proposed model is trained on a relatively small dataset acquired from only one imaging center using a specific scanning protocol, it performs well on heterogeneous test sets obtained by multiple scanners using different technical parameters. We also showed that the model can be updated via an unsupervised approach to cope with the data shift between the train and test sets and enhance the robustness of the model upon receiving a new external dataset from a different center. More specifically, we extracted the subset of the test images for which the model generated a confident prediction and used the extracted subset along with the training set to retrain and update the benchmark model (the model trained on the initial train set). Finally, we adopted an ensemble architecture to aggregate the predictions from multiple versions of the model. For initial training and development purposes, an in-house dataset of 171 COVID-19, 60 CAP, and 76 Normal cases was used, which contained volumetric CT scans acquired from one imaging center using a single scanning protocol and standard radiation dose. To evaluate the model, we collected four different test sets retrospectively to investigate the effects of the shifts in the data characteristics on the model's performance. Among the test cases, there were CT scans with similar characteristics as the train set as well as noisy low-dose and ultra-low-dose CT scans. In addition, some test CT scans were obtained from patients with a history of cardiovascular diseases or surgeries. This dataset is referred to as the "SPGC-COVID" dataset. The entire test dataset used in this study contains 51 COVID-19, 28 CAP, and 51 Normal cases. Experimental results indicate that our proposed framework performs well on all test sets achieving total accuracy of 96.15% (95%CI: [91.25-98.74]), COVID-19 sensitivity of 96.08% (95%CI: [86.54-99.5]), CAP sensitivity of 92.86% (95%CI: [76.50-99.19]), Normal sensitivity of 98.04% (95%CI: [89.55-99.95]) while the confidence intervals are obtained using the significance level of 0.05. The obtained AUC values (One class vs Others) are 0.993 (95%CI: [0.977-1]), 0.989 (95%CI: [0.962-1]), and 0.990 (95%CI: [0.971-1]) for COVID-19, CAP, and Normal classes, respectively. The experimental results also demonstrate the capability of the proposed unsupervised enhancement approach in improving the performance and robustness of the model when being evaluated on varied external test sets.

Khademi Sadaf, Heidarian Shahin, Afshar Parnian, Enshaei Nastaran, Naderkhani Farnoosh, Rafiee Moezedin Javad, Oikonomou Anastasia, Shafiee Akbar, Babaki Fard Faranak, Plataniotis Konstantinos N, Mohammadi Arash

2023

Public Health Public Health

Optimizing non-pharmaceutical intervention strategies against COVID-19 using artificial intelligence.

In Frontiers in public health

One key task in the early fight against the COVID-19 pandemic was to plan non-pharmaceutical interventions to reduce the spread of the infection while limiting the burden on the society and economy. With more data on the pandemic being generated, it became possible to model both the infection trends and intervention costs, transforming the creation of an intervention plan into a computational optimization problem. This paper proposes a framework developed to help policy-makers plan the best combination of non-pharmaceutical interventions and to change them over time. We developed a hybrid machine-learning epidemiological model to forecast the infection trends, aggregated the socio-economic costs from the literature and expert knowledge, and used a multi-objective optimization algorithm to find and evaluate various intervention plans. The framework is modular and easily adjustable to a real-world situation, it is trained and tested on data collected from almost all countries in the world, and its proposed intervention plans generally outperform those used in real life in terms of both the number of infections and intervention costs.

Janko Vito, Reščič Nina, Vodopija Aljoša, Susič David, De Masi Carlo, Tušar Tea, Gradišek Anton, Vandepitte Sophie, De Smedt Delphine, Javornik Jana, Gams Matjaž, Luštrek Mitja

2023

COVID-19, epidemiological modeling, intervention plans, machine learning, multi-objective optimization

Public Health Public Health

Development and testing of a multi-lingual Natural Language Processing-based deep learning system in 10 languages for COVID-19 pandemic crisis: A multi-center study.

In Frontiers in public health

PURPOSE : The COVID-19 pandemic has drastically disrupted global healthcare systems. With the higher demand for healthcare and misinformation related to COVID-19, there is a need to explore alternative models to improve communication. Artificial Intelligence (AI) and Natural Language Processing (NLP) have emerged as promising solutions to improve healthcare delivery. Chatbots could fill a pivotal role in the dissemination and easy accessibility of accurate information in a pandemic. In this study, we developed a multi-lingual NLP-based AI chatbot, DR-COVID, which responds accurately to open-ended, COVID-19 related questions. This was used to facilitate pandemic education and healthcare delivery.

METHODS : First, we developed DR-COVID with an ensemble NLP model on the Telegram platform (https://t.me/drcovid_nlp_chatbot). Second, we evaluated various performance metrics. Third, we evaluated multi-lingual text-to-text translation to Chinese, Malay, Tamil, Filipino, Thai, Japanese, French, Spanish, and Portuguese. We utilized 2,728 training questions and 821 test questions in English. Primary outcome measurements were (A) overall and top 3 accuracies; (B) Area Under the Curve (AUC), precision, recall, and F1 score. Overall accuracy referred to a correct response for the top answer, whereas top 3 accuracy referred to an appropriate response for any one answer amongst the top 3 answers. AUC and its relevant matrices were obtained from the Receiver Operation Characteristics (ROC) curve. Secondary outcomes were (A) multi-lingual accuracy; (B) comparison to enterprise-grade chatbot systems. The sharing of training and testing datasets on an open-source platform will also contribute to existing data.

RESULTS : Our NLP model, utilizing the ensemble architecture, achieved overall and top 3 accuracies of 0.838 [95% confidence interval (CI): 0.826-0.851] and 0.922 [95% CI: 0.913-0.932] respectively. For overall and top 3 results, AUC scores of 0.917 [95% CI: 0.911-0.925] and 0.960 [95% CI: 0.955-0.964] were achieved respectively. We achieved multi-linguicism with nine non-English languages, with Portuguese performing the best overall at 0.900. Lastly, DR-COVID generated answers more accurately and quickly than other chatbots, within 1.12-2.15 s across three devices tested.

CONCLUSION : DR-COVID is a clinically effective NLP-based conversational AI chatbot, and a promising solution for healthcare delivery in the pandemic era.

Yang Lily Wei Yun, Ng Wei Yan, Lei Xiaofeng, Tan Shaun Chern Yuan, Wang Zhaoran, Yan Ming, Pargi Mohan Kashyap, Zhang Xiaoman, Lim Jane Sujuan, Gunasekeran Dinesh Visva, Tan Franklin Chee Ping, Lee Chen Ee, Yeo Khung Keong, Tan Hiang Khoon, Ho Henry Sun Sien, Tan Benedict Wee Bor, Wong Tien Yin, Kwek Kenneth Yung Chiang, Goh Rick Siow Mong, Liu Yong, Ting Daniel Shu Wei

2023

Artificial Intelligence, COVID-19, Natural Language Processing, conversational chatbot, health education, pandemic education

General General

Potential and limitations of machine meta-learning (ensemble) methods for predicting COVID-19 mortality in a large inhospital Brazilian dataset.

In Scientific reports ; h5-index 158.0

The majority of early prediction scores and methods to predict COVID-19 mortality are bound by methodological flaws and technological limitations (e.g., the use of a single prediction model). Our aim is to provide a thorough comparative study that tackles those methodological issues, considering multiple techniques to build mortality prediction models, including modern machine learning (neural) algorithms and traditional statistical techniques, as well as meta-learning (ensemble) approaches. This study used a dataset from a multicenter cohort of 10,897 adult Brazilian COVID-19 patients, admitted from March/2020 to November/2021, including patients [median age 60 (interquartile range 48-71), 46% women]. We also proposed new original population-based meta-features that have not been devised in the literature. Stacking has shown to achieve the best results reported in the literature for the death prediction task, improving over previous state-of-the-art by more than 46% in Recall for predicting death, with AUROC 0.826 and MacroF1 of 65.4%. The newly proposed meta-features were highly discriminative of death, but fell short in producing large improvements in final prediction performance, demonstrating that we are possibly on the limits of the prediction capabilities that can be achieved with the current set of ML techniques and (meta-)features. Finally, we investigated how the trained models perform on different hospitals, showing that there are indeed large differences in classifier performance between different hospitals, further making the case that errors are produced by factors that cannot be modeled with the current predictors.

de Paiva Bruno Barbosa Miranda, Pereira Polianna Delfino, de Andrade Claudio Moisés Valiense, Gomes Virginia Mara Reis, Souza-Silva Maira Viana Rego, Martins Karina Paula Medeiros Prado, Sales Thaís Lorenna Souza, de Carvalho Rafael Lima Rodrigues, Pires Magda Carvalho, Ramos Lucas Emanuel Ferreira, Silva Rafael Tavares, de Freitas Martins Vieira Alessandra, Nunes Aline Gabrielle Sousa, de Oliveira Jorge Alzira, de Oliveira Maurílio Amanda, Scotton Ana Luiza Bahia Alves, da Silva Carla Thais Candida Alves, Cimini Christiane Corrêa Rodrigues, Ponce Daniela, Pereira Elayne Crestani, Manenti Euler Roberto Fernandes, Rodrigues Fernanda d’Athayde, Anschau Fernando, Botoni Fernando Antônio, Bartolazzi Frederico, Grizende Genna Maira Santos, Noal Helena Carolina, Duani Helena, Gomes Isabela Moraes, Costa Jamille Hemétrio Salles Martins, di Sabatino Santos Guimarães Júlia, Tupinambás Julia Teixeira, Rugolo Juliana Machado, Batista Joanna d’Arc Lyra, de Alvarenga Joice Coutinho, Chatkin José Miguel, Ruschel Karen Brasil, Zandoná Liege Barella, Pinheiro Lílian Santos, Menezes Luanna Silva Monteiro, de Oliveira Lucas Moyses Carvalho, Kopittke Luciane, Assis Luisa Argolo, Marques Luiza Margoto, Raposo Magda Cesar, Floriani Maiara Anschau, Bicalho Maria Aparecida Camargos, Nogueira Matheus Carvalho Alves, de Oliveira Neimy Ramos, Ziegelmann Patricia Klarmann, Paraiso Pedro Gibson, de Lima Martelli Petrônio José, Senger Roberta, Menezes Rochele Mosmann, Francisco Saionara Cristina, Araújo Silvia Ferreira, Kurtz Tatiana, Fereguetti Tatiani Oliveira, de Oliveira Thainara Conceição, Ribeiro Yara Cristina Neves Marques Barbosa, Ramires Yuri Carlotto, Lima Maria Clara Pontello Barbosa, Carneiro Marcelo, Bezerra Adriana Falangola Benjamin, Schwarzbold Alexandre Vargas, de Moura Costa André Soares, Farace Barbara Lopes, Silveira Daniel Vitorio, de Almeida Cenci Evelin Paola, Lucas Fernanda Barbosa, Aranha Fernando Graça, Bastos Gisele Alsina Nader, Vietta Giovanna Grunewald, Nascimento Guilherme Fagundes, Vianna Heloisa Reniers, Guimarães Henrique Cerqueira, de Morais Julia Drumond Parreiras, Moreira Leila Beltrami, de Oliveira Leonardo Seixas, de Deus Sousa Lucas, de Souza Viana Luciano, de Souza Cabral Máderson Alvares, Ferreira Maria Angélica Pires, de Godoy Mariana Frizzo, de Figueiredo Meire Pereira, Guimarães-Junior Milton Henriques, de Paula de Sordi Mônica Aparecida, da Cunha Severino Sampaio Natália, Assaf Pedro Ledic, Lutkmeier Raquel, Valacio Reginaldo Aparecido, Finger Renan Goulart, de Freitas Rufino, Guimarães Silvana Mangeon Meirelles, Oliveira Talita Fischer, Diniz Thulio Henrique Oliveira, Gonçalves Marcos André, Marcolino Milena Soriano

2023-Mar-01

General General

Biases associated with database structure for COVID-19 detection in X-ray images.

In Scientific reports ; h5-index 158.0

Several artificial intelligence algorithms have been developed for COVID-19-related topics. One that has been common is the COVID-19 diagnosis using chest X-rays, where the eagerness to obtain early results has triggered the construction of a series of datasets where bias management has not been thorough from the point of view of patient information, capture conditions, class imbalance, and careless mixtures of multiple datasets. This paper analyses 19 datasets of COVID-19 chest X-ray images, identifying potential biases. Moreover, computational experiments were conducted using one of the most popular datasets in this domain, which obtains a 96.19% of classification accuracy on the complete dataset. Nevertheless, when evaluated with the ethical tool Aequitas, it fails on all the metrics. Ethical tools enhanced with some distribution and image quality considerations are the keys to developing or choosing a dataset with fewer bias issues. We aim to provide broad research on dataset problems, tools, and suggestions for future dataset developments and COVID-19 applications using chest X-ray images.

Arias-Garzón Daniel, Tabares-Soto Reinel, Bernal-Salcedo Joshua, Ruz Gonzalo A

2023-Mar-01

General General

Speaking with mask in the COVID-19 era: Multiclass machine learning classification of acoustic and perceptual parameters.

In The Journal of the Acoustical Society of America

The intensive use of personal protective equipment often requires increasing voice intensity, with possible development of voice disorders. This paper exploits machine learning approaches to investigate the impact of different types of masks on sustained vowels /a/, /i/, and /u/ and the sequence /a'jw/ inside a standardized sentence. Both objective acoustical parameters and subjective ratings were used for statistical analysis, multiple comparisons, and in multivariate machine learning classification experiments. Significant differences were found between mask+shield configuration and no-mask and between mask and mask+shield conditions. Power spectral density decreases with statistical significance above 1.5 kHz when wearing masks. Subjective ratings confirmed increasing discomfort from no-mask condition to protective masks and shield. Machine learning techniques proved that masks alter voice production: in a multiclass experiment, random forest (RF) models were able to distinguish amongst seven masks conditions with up to 94% validation accuracy, separating masked from unmasked conditions with up to 100% validation accuracy and detecting the shield presence with up to 86% validation accuracy. Moreover, an RF classifier allowed distinguishing male from female subject in masked conditions with 100% validation accuracy. Combining acoustic and perceptual analysis represents a robust approach to characterize masks configurations and quantify the corresponding level of discomfort.

Calà F, Manfredi C, Battilocchi L, Frassineti L, Cantarella G

2023-Feb

General General

Using machine learning models to predict the willingness to carry lightweight goods by bike and kick-scooter.

In Transportation research interdisciplinary perspectives

The social transformation caused by the COVID-19 pandemic can help cities become healthier and more sustainable, with more space for active modes of transportation. This research addresses people's willingness to go shopping by bike or kick-scooter and to transport lightweight goods in cities with low maturity for cycling and scooting. Data collection was based on a survey, applied in the two largest cities of Brazil (São Paulo and Rio de Janeiro) and Portugal (Lisbon and Porto). The dataset was processed considering only two categories of respondents (i.e., potential users and regular users) and then four machine learning models (K-Nearest Neighbor, Support Vector Machine, Decision Tree, and Random Forest) were applied to predict shopping by bike or kick-scooter. In terms of all performance measures, the Support Vector Machine model was the optimum. The results indicate that people are willing to transport lightweight goods by bike or kick-scooter, as long as the infrastructure is safe and comfortable. This research contributes to understanding mobility behavior changes and identifying barriers to going shopping by bike or kick-scooter. It also presents some policy recommendations for improving cycling and scooting use for shopping, which public authorities can carry out.

Silveira-Santos Tulio, Manuel Vassallo Jose, Torres Ewerton

2022-Mar

Behavioral change, COVID-19, Classifier model, Machine learning, Shopping trips, Urban cycling and scooting

General General

The role of digital social innovations to address SDGs: A systematic review.

In Environment, development and sustainability

The impact of the COVID-19 pandemic has increased the search for solutions to social problems associated with the Sustainable Development Goals (SDGs). Main actors are turning to Digital Social Innovations (DSIs), defined as collaborative innovations where enterprises, users and communities collaborate using digital technologies to promote solutions at scale and speed, connecting innovation, the social world and digital ecosystems to reach the 2030 Agenda. This study aims to identify how digital transformations and social innovations solve social problems and address SDGs. We conducted a systematic review based on a sample of 45 peer-reviewed articles published from 2010 to 2022, combining a bibliometric study and a content analysis focusing on opportunities and threats impacting these fields. We observed the spread and increasing use of technologies associated with all 17 SDGs, specially blockchain, IoT, artificial intelligence, and autonomous robots that are increasing their role and presence exponentially, completely changing the current way of doing things, offering a dramatic evolution in many different segments, such as health care, smart cities, agriculture, and the combat against poverty and inequalities. We identified many threats concerning ethics, especially with the increased use of public data, and concerns about the impacts on the labor force and the possible instability and impact it may cause in low skill/low pay jobs. We expect that our findings advance the concept of digital social innovations and the benefits of its adoption to promote social advancements.

Dionisio Marcelo, de Souza Junior Sylvio Jorge, Paula Fábio, Pellanda Paulo César

2023-Feb-23

Digital transformation, Industry 4.0, Social innovation, Systematic literature review, UN sustainable goals

General General

TransCode: Uncovering COVID-19 transmission patterns via deep learning.

In Infectious diseases of poverty ; h5-index 31.0

BACKGROUND : The heterogeneity of COVID-19 spread dynamics is determined by complex spatiotemporal transmission patterns at a fine scale, especially in densely populated regions. In this study, we aim to discover such fine-scale transmission patterns via deep learning.

METHODS : We introduce the notion of TransCode to characterize fine-scale spatiotemporal transmission patterns of COVID-19 caused by metapopulation mobility and contact behaviors. First, in Hong Kong, China, we construct the mobility trajectories of confirmed cases using their visiting records. Then we estimate the transmissibility of individual cases in different locations based on their temporal infectiousness distribution. Integrating the spatial and temporal information, we represent the TransCode via spatiotemporal transmission networks. Further, we propose a deep transfer learning model to adapt the TransCode of Hong Kong, China to achieve fine-scale transmission characterization and risk prediction in six densely populated metropolises: New York City, San Francisco, Toronto, London, Berlin, and Tokyo, where fine-scale data are limited. All the data used in this study are publicly available.

RESULTS : The TransCode of Hong Kong, China derived from the spatial transmission information and temporal infectiousness distribution of individual cases reveals the transmission patterns (e.g., the imported and exported transmission intensities) at the district and constituency levels during different COVID-19 outbreaks waves. By adapting the TransCode of Hong Kong, China to other data-limited densely populated metropolises, the proposed method outperforms other representative methods by more than 10% in terms of the prediction accuracy of the disease dynamics (i.e., the trend of case numbers), and the fine-scale spatiotemporal transmission patterns in these metropolises could also be well captured due to some shared intrinsically common patterns of human mobility and contact behaviors at the metapopulation level.

CONCLUSIONS : The fine-scale transmission patterns due to the metapopulation level mobility (e.g., travel across different districts) and contact behaviors (e.g., gathering in social-economic centers) are one of the main contributors to the rapid spread of the virus. Characterization of the fine-scale transmission patterns using the TransCode will facilitate the development of tailor-made intervention strategies to effectively contain disease transmission in the targeted regions.

Ren Jinfu, Liu Mutong, Liu Yang, Liu Jiming

2023-Feb-28

COVID-19, Deep transfer learning, Densely populated regions, Human mobility and contact behaviors, Meta-population, Spatiotemporal transmission dynamics and heterogeneity, TransCode

General General

New, fast, and precise method of COVID-19 detection in nasopharyngeal and tracheal aspirate samples combining optical spectroscopy and machine learning.

In Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]

Fast, precise, and low-cost diagnostic testing to identify persons infected with SARS-CoV-2 virus is pivotal to control the global pandemic of COVID-19 that began in late 2019. The gold standard method of diagnostic recommended is the RT-qPCR test. However, this method is not universally available, and is time-consuming and requires specialized personnel, as well as sophisticated laboratories. Currently, machine learning is a useful predictive tool for biomedical applications, being able to classify data from diverse nature. Relying on the artificial intelligence learning process, spectroscopic data from nasopharyngeal swab and tracheal aspirate samples can be used to leverage characteristic patterns and nuances in healthy and infected body fluids, which allows to identify infection regardless of symptoms or any other clinical or laboratorial tests. Hence, when new measurements are performed on samples of unknown status and the corresponding data is submitted to such an algorithm, it will be possible to predict whether the source individual is infected or not. This work presents a new methodology for rapid and precise label-free diagnosing of SARS-CoV-2 infection in clinical samples, which combines spectroscopic data acquisition and analysis via artificial intelligence algorithms. Our results show an accuracy of 85% for detection of SARS-CoV-2 in nasopharyngeal swab samples collected from asymptomatic patients or with mild symptoms, as well as an accuracy of 97% in tracheal aspirate samples collected from critically ill COVID-19 patients under mechanical ventilation. Moreover, the acquisition and processing of the information is fast, simple, and cheaper than traditional approaches, suggesting this methodology as a promising tool for biomedical diagnosis vis-à-vis the emerging and re-emerging viral SARS-CoV-2 variant threats in the future.

Ceccon Denny M, Amaral Paulo Henrique R, Andrade Lídia M, da Silva Maria I N, Andrade Luis A F, Moraes Thais F S, Bagno Flavia F, Rocha Raissa P, de Almeida Marques Daisymara Priscila, Ferreira Geovane Marques, Lourenço Alice Aparecida, Ribeiro Ágata Lopes, Coelho-Dos-Reis Jordana G A, da Fonseca Flavio G, Gonzalez J C

2023-Feb-28

Artificial intelligence, COVID-19, Label-free diagnosis, Machine learning, Optical spectroscopy

General General

Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors

bioRxiv Preprint

The COVID-19 pandemic was a stark reminder that a barren global antiviral pipeline has grave humanitarian consequences. Pandemics could be prevented in principle by accessible, easily deployable broad-spectrum oral antivirals. Here we report the results of the COVID Moonshot, a fully open-science, crowd sourced, structure-enabled drug discovery campaign targeting the SARS-CoV-2 main protease. We discovered a novel chemical series that is differentiated from current Mpro inhibitors in that it maintains a new non-covalent, non-peptidic scaffold with nanomolar potency. Our approach leveraged crowdsourcing, high-throughput structural biology, machine learning, and exascale molecular simulations and high-throughput chemistry. In the process, we generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. In a first for a structure-based drug discovery campaign, all compound designs (>18,000 designs), crystallographic data (>840 ligand-bound X-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2,400 compounds) for this campaign were shared rapidly and openly, creating a rich open and IP-free knowledgebase for future anti-coronavirus drug discovery.

The COVID Moonshot Consortium, ; Achdout, H.; Aimon, A.; Alonzi, D. S.; Arbon, R.; Bar-David, E.; Barr, H.; Ben-Shmuel, A.; Bennett, J.; Bilenko, V. A.; Bilenko, V. A.; Boby, M. L.; Borden, B.; Boulet, P.; Bowman, G. R.; Brun, J.; Brwewitz, L.; BVNBS, S.; Calmiano, M.; Carbery, A.; Carney, D.; Cattermole, E.; Chang, E.; Chernyshenko, E.; Chodera, J. D.; Clyde, A.; Coffland, J. E.; Cohen, G.; Cole, J.; Contini, A.; Cox, L.; Croll, T. I.; Cvitkovic, M.; Dias, A.; Donckers, K.; Dotson, D. L.; Douangamath, A.; Duberstein, S.; Dudgeon, T.; Dunnett, L.; Eastman, P. K.; Erez, N.; Eyermann, C. J.; Fa

2023-03-02

Surgery Surgery

Multi-omics and immune cells' profiling of COVID-19 patients for ICU admission prediction: in silico analysis and an integrated machine learning-based approach in the framework of Predictive, Preventive, and Personalized Medicine.

In The EPMA journal

BACKGROUND : Intensive care unit admission (ICUA) triage has been urgent need for solving the shortage of ICU beds, during the coronavirus disease 2019 (COVID-19) surge. In silico analysis and integrated machine learning (ML) approach, based on multi-omics and immune cells (ICs) profiling, might provide solutions for this issue in the framework of predictive, preventive, and personalized medicine (PPPM).

METHODS : Multi-omics was used to screen the synchronous differentially expressed protein-coding genes (SDEpcGs), and an integrated ML approach to develop and validate a nomogram for prediction of ICUA. Finally, the independent risk factor (IRF) with ICs profiling of the ICUA was identified.

RESULTS : Colony-stimulating factor 1 receptor (CSF1R) and peptidase inhibitor 16 (PI16) were identified as SDEpcGs, and each fold change (FCij) of CSF1R and PI16 was selected to develop and validate a nomogram to predict ICUA. The area under curve (AUC) of the nomogram was 0.872 (95% confidence interval (CI): 0.707 to 0.950) on the training set, and 0.822 (95% CI: 0.659 to 0.917) on the testing set. CSF1R was identified as an IRF of ICUA, expressed in and positively correlated with monocytes which had a lower fraction in COVID-19 ICU patients.

CONCLUSION : The nomogram and monocytes could provide added value to ICUA prediction and targeted prevention, which are cost-effective platform for personalized medicine of COVID-19 patients. The log2fold change (log2FC) of the fraction of monocytes could be monitored simply and economically in primary care, and the nomogram offered an accurate prediction for secondary care in the framework of PPPM.

SUPPLEMENTARY INFORMATION : The online version contains supplementary material available at 10.1007/s13167-023-00317-5.

Zhu Kun, Chen Zhonghua, Xiao Yi, Lai Dengming, Wang Xiaofeng, Fang Xiangming, Shu Qiang

2023-Feb-21

COVID-19, CSF1R, Immune cells, Machine learning, Monocytes, Nomogram, PI16, Predictive Preventive Personalized medicine (PPPM / 3PM), Predictive model, Triage

Public Health Public Health

Understanding Covid-19 Mobility Through Human Capital: A Unified Causal Framework.

In Computational economics

This paper seeks to identify the causal impact of educational human capital on social distancing behavior at workplace in Turkey using district-level data for the period of April 2020 - February 2021. We adopt a unified causal framework, predicated on domain knowledge, theory-justified constraints anda data-driven causal structure discovery using causal graphs. We answer our causal query by employing machine learning prediction algorithms; instrumental variables in the presence of latent confounding and Heckman's model in the presence of selection bias. Results show that educated regions are able to distance-work and educational human capital is a key factor in reducing workplace mobility, possibly through its impact on employment. This pattern leads to higher workplace mobility for less educated regions and translates into higher Covid-19 infection rates. The future of the pandemic lies in less educated segments of developing countries and calls for public health action to decrease its unequal and pervasive impact.

Bilgel Fırat, Karahasan Burhan Can

2023-Feb-21

Causal structure discovery, Do-calculus, Instrumental variables, Machine learning, Sample selection, Workplace mobility

General General

Detection of COVID-19 Case from Chest CT Images Using Deformable Deep Convolutional Neural Network.

In Journal of healthcare engineering

The infectious coronavirus disease (COVID-19) has become a great threat to global human health. Timely and rapid detection of COVID-19 cases is very crucial to control its spreading through isolation measures as well as for proper treatment. Though the real-time reverse transcription-polymerase chain reaction (RT-PCR) test is a widely used technique for COVID-19 infection, recent researches suggest chest computed tomography (CT)-based screening as an effective substitute in cases of time and availability limitations of RT-PCR. In consequence, deep learning-based COVID-19 detection from chest CT images is gaining momentum. Furthermore, visual analysis of data has enhanced the opportunities of maximizing the prediction performance in this big data and deep learning realm. In this article, we have proposed two separate deformable deep networks converting from the conventional convolutional neural network (CNN) and the state-of-the-art ResNet-50, to detect COVID-19 cases from chest CT images. The impact of the deformable concept has been observed through performance comparative analysis among the designed deformable and normal models, and it is found that the deformable models show better prediction results than their normal form. Furthermore, the proposed deformable ResNet-50 model shows better performance than the proposed deformable CNN model. The gradient class activation mapping (Grad-CAM) technique has been used to visualize and check the targeted regions' localization effort at the final convolutional layer and has been found excellent. Total 2481 chest CT images have been used to evaluate the performance of the proposed models with a train-valid-test data splitting ratio of 80 : 10 : 10 in random fashion. The proposed deformable ResNet-50 model achieved training accuracy of 99.5% and test accuracy of 97.6% with specificity of 98.5% and sensitivity of 96.5% which are satisfactory compared with related works. The comprehensive discussion demonstrates that the proposed deformable ResNet-50 model-based COVID-19 detection technique can be useful for clinical applications.

Foysal Md, Hossain A B M Aowlad, Yassine Abdulsalam, Hossain M Shamim

2023

General General

Classification modeling of intention to donate for victims of Typhoon Odette using deep learning neural network.

In Environmental development

The need for stability in the economy for world development has been a challenge due to the COVID-19 pandemic. In addition, the increase of natural disasters and their aftermath have been increasing causing damages to infrastructure, the economy, livelihood, and lives in general. This study aimed to determine factors affecting the intention to donate for victims of Typhoon Odette, a recent super typhoon that hit the Philippines leading to affect 38 out of 81 provinces of the most natural disaster-prone countries. Determining the most significant factor affecting the intention to donate may help in increasing the engagement of donations among other people to help establish a more stable economy to heighten world development. With the use of deep learning neural network, a 97.12% accuracy was obtained for the classification model. It could be deduced that when donors understand and perceive both severity and vulnerability to be massive and highly damaging, then a more positive intention to donate to victims of typhoons will be observed. In addition, the influence of other people, the holiday season when the typhoon happened, and the media as a platform have greatly contributed to heightening the intention to donate and control over the donor's behavior. The findings of this study could be applied and utilized by government agencies and donation platforms to help engage and promote communication among donors. Moreover, the framework and methodology considered in this study may be extended to evaluate intention, natural disasters, and behavioral studies worldwide.

German Josephine D, Ong Ardvin Kester S, Redi Anak Agung Ngurah Perwira, Prasetyo Yogi Tri, Robas Kirstien Paola E, Nadlifatin Reny, Chuenyindee Thanatorn

2023-Mar

Deep learning neural network, Donation, Natural disaster, Typhoon odette, Typhoon victims

General General

Emerging trends in point-of-care biosensing strategies for molecular architectures and antibodies of SARS-CoV-2.

In Biosensors & bioelectronics: X

COVID-19, a highly contagious viral infection caused by the occurrence of severe acute respiratory syndrome coronavirus (SARS-CoV-2), has turned out to be a viral pandemic then ravaged many countries worldwide. In the recent years, point-of-care (POC) biosensors combined with state-of-the-art bioreceptors, and transducing systems enabled the development of novel diagnostic tools for rapid and reliable detection of biomarkers associated with SARS-CoV-2. The present review thoroughly summarises and discusses various biosensing strategies developed for probing SARS-CoV-2 molecular architectures (viral genome, S Protein, M protein, E protein, N protein and non-structural proteins) and antibodies as a potential diagnostic tool for COVID-19. This review discusses the various structural components of SARS-CoV-2, their binding regions and the bioreceptors used for recognizing the structural components. The various types of clinical specimens investigated for rapid and POC detection of SARS-CoV-2 is also highlighted. The importance of nanotechnology and artificial intelligence (AI) approaches in improving the biosensor performance for real-time and reagent-free monitoring the biomarkers of SARS-CoV-2 is also summarized. This review also encompasses existing practical challenges and prospects for developing new POC biosensors for clinical monitoring of COVID-19.

Karuppaiah Gopi, Vashist Arti, Nair Madhavan, Veerapandian Murugan, Manickam Pandiaraj

2023-May

Biomarkers, COVID-19, Electrochemical and optical biosensors, Infectious diseases, Nanobiosensors

General General

Exploration of SARS-CoV-2 Mpro Noncovalent Natural Inhibitors Using Structure-Based Approaches.

In ACS omega

With the emergence of antibody-evasive omicron subvariants (BA.2.12.1, BA.4, and BA.5), which can compromise the efficacy of vaccination, it is of utmost importance to widen the finite therapeutic options for COVID-19. Although more than 600 co-crystal complexes of Mpro with inhibitors have been revealed, utilizing them to search for novel Mpro inhibitors remains limited. Although there were two major groups of Mpro inhibitors, covalent and noncovalent inhibitors, noncovalent inhibitors were our main focus due to the safety concerns with their covalent counterparts. Hence, this study aimed to explore Mpro noncovalent inhibition ability of phytochemicals extracted from Vietnamese herbals by combining multiple structure-based approaches. By closely inspecting 223 complexes of Mpro with noncovalent inhibitors, a 3D-pharmacophore model representing typical chemical features of Mpro noncovalent inhibitors was generated with good validation scores (sensitivity = 92.11%, specificity = 90.42%, accuracy = 90.65%, and goodness-of-hit score = 0.61). Afterward, the pharmacophore model was applied to explore the potential Mpro inhibitors from our in-house Vietnamese phytochemical database, revealing 18 substances, 5 of which were in vitro assayed. The remaining 13 substances were then examined by induced-fit molecular docking, revealing 12 suitable compounds. A machine-learning activity prediction model was developed to rank the hit, suggesting nigracin and calycosin-7-O-β-glucopyranoside as promising Mpro natural noncovalent inhibitors.

Duong Cuong Quoc, Nguyen Phuong Thuy Viet

2023-Feb-21

General General

SARS-CoV-2 Diagnosis Using Transcriptome Data: A Machine Learning Approach.

In SN computer science

UNLABELLED : SARS-CoV-2 pandemic is the big issue of the whole world right now. The health community is struggling to rescue the public and countries from this spread, which revives time to time with different waves. Even the vaccination seems to be not prevents this spread. Accurate identification of infected people on time is essential these days to control the spread. So far, Polymerase chain reaction (PCR) and rapid antigen tests are widely used in this identification, accepting their own drawbacks. False negative cases are the menaces in this scenario. To avoid these problems, this study uses machine learning techniques to build a classification model with higher accuracy to filter the COVID-19 cases from the non-COVID individuals. Transcriptome data of the SARS-CoV-2 patients along with the control are used in this stratification using three different feature selection algorithms and seven classification models. Differently expressed genes also studied between these two groups of people and used in this classification. Results shows that mutual information (or DEGs) along with naïve Bayes (or SVM) gives the best accuracy (0.98 ± 0.04) among these methods.

SUPPLEMENTARY INFORMATION : The online version contains supplementary material available at 10.1007/s42979-023-01703-6.

Jeyananthan Pratheeba

2023

COVID-19 diagnosis, Differently expressed genes, Feature selection, GO analysis, Machine learning models, Transcriptome data

Public Health Public Health

Detecting Tweets Containing Cannabidiol-Related COVID-19 Misinformation Using Transformer Language Models and Warning Letters From Food and Drug Administration: Content Analysis and Identification.

In JMIR infodemiology

BACKGROUND : COVID-19 has introduced yet another opportunity to web-based sellers of loosely regulated substances, such as cannabidiol (CBD), to promote sales under false pretenses of curing the disease. Therefore, it has become necessary to innovate ways to identify such instances of misinformation.

OBJECTIVE : We sought to identify COVID-19 misinformation as it relates to the sales or promotion of CBD and used transformer-based language models to identify tweets semantically similar to quotes taken from known instances of misinformation. In this case, the known misinformation was the publicly available Warning Letters from Food and Drug Administration (FDA).

METHODS : We collected tweets using CBD- and COVID-19-related terms. Using a previously trained model, we extracted the tweets indicating commercialization and sales of CBD and annotated those containing COVID-19 misinformation according to the FDA definitions. We encoded the collection of tweets and misinformation quotes into sentence vectors and then calculated the cosine similarity between each quote and each tweet. This allowed us to establish a threshold to identify tweets that were making false claims regarding CBD and COVID-19 while minimizing the instances of false positives.

RESULTS : We demonstrated that by using quotes taken from Warning Letters issued by FDA to perpetrators of similar misinformation, we can identify semantically similar tweets that also contain misinformation. This was accomplished by identifying a cosine distance threshold between the sentence vectors of the Warning Letters and tweets.

CONCLUSIONS : This research shows that commercial CBD or COVID-19 misinformation can potentially be identified and curbed using transformer-based language models and known prior instances of misinformation. Our approach functions without the need for labeled data, potentially reducing the time at which misinformation can be identified. Our approach shows promise in that it is easily adapted to identify other forms of misinformation related to loosely regulated substances.

Turner Jason, Kantardzic Mehmed, Vickers-Smith Rachel, Brown Andrew G

2023

COVID-19, Twitter, cannabidiol, content analysis, deep learning, health information, infodemic, infodemiology, language model, misinformation, pandemic, sentence vector, social media, transformer

General General

MonkeyNet: A robust deep convolutional neural network for monkeypox disease detection and classification.

In Neural networks : the official journal of the International Neural Network Society

The monkeypox virus poses a new pandemic threat while we are still recovering from COVID-19. Despite the fact that monkeypox is not as lethal and contagious as COVID-19, new patient cases are recorded every day. If preparations are not made, a global pandemic is likely. Deep learning (DL) techniques are now showing promise in medical imaging for figuring out what diseases a person has. The monkeypox virus-infected human skin and the region of the skin can be used to diagnose the monkeypox early because an image has been used to learn more about the disease. But there is still no reliable Monkeypox database that is available to the public that can be used to train and test DL models. As a result, it is essential to collect images of monkeypox patients. The "MSID" dataset, short form of "Monkeypox Skin Images Dataset", which was developed for this research, is free to use and can be downloaded from the Mendeley Data database by anyone who wants to use it. DL models can be built and used with more confidence using the images in this dataset. These images come from a variety of open-source and online sources and can be used for research purposes without any restrictions. Furthermore, we proposed and evaluated a modified DenseNet-201 deep learning-based CNN model named MonkeyNet. Using the original and augmented datasets, this study suggested a deep convolutional neural network that was able to correctly identify monkeypox disease with an accuracy of 93.19% and 98.91% respectively. This implementation also shows the Grad-CAM which indicates the level of the model's effectiveness and identifies the infected regions in each class image, which will help the clinicians. The proposed model will also help doctors make accurate early diagnoses of monkeypox disease and protect against the spread of the disease.

Bala Diponkor, Hossain Md Shamim, Hossain Mohammad Alamgir, Abdullah Md Ibrahim, Rahman Md Mizanur, Manavalan Balachandran, Gu Naijie, Islam Mohammad S, Huang Zhangjin

2023-Feb-22

Classification, Convolutional neural network, Dataset, Deep learning, Machine learning, Monkeypox disease

General General

How to avoid a local epidemic becoming a global pandemic.

In Proceedings of the National Academy of Sciences of the United States of America

Here, we combine international air travel passenger data with a standard epidemiological model of the initial 3 mo of the COVID-19 pandemic (January through March 2020; toward the end of which the entire world locked down). Using the information available during this initial phase of the pandemic, our model accurately describes the main features of the actual global development of the pandemic demonstrated by the high degree of coherence between the model and global data. The validated model allows for an exploration of alternative policy efficacies (reducing air travel and/or introducing different degrees of compulsory immigration quarantine upon arrival to a country) in delaying the global spread of SARS-CoV-2 and thus is suggestive of similar efficacy in anticipating the spread of future global disease outbreaks. We show that a lesson from the recent pandemic is that reducing air travel globally is more effective in reducing the global spread than adopting immigration quarantine. Reducing air travel out of a source country has the most important effect regarding the spreading of the disease to the rest of the world. Based upon our results, we propose a digital twin as a further developed tool to inform future pandemic decision-making to inform measures intended to control the spread of disease agents of potential future pandemics. We discuss the design criteria for such a digital twin model as well as the feasibility of obtaining access to the necessary online data on international air travel.

Stenseth Nils Chr, Schlatte Rudolf, Liu Xiaoli, Pielke Roger, Li Ruiyun, Chen Bin, Bjørnstad Ottar N, Kusnezov Dimitri, Gao George F, Fraser Christophe, Whittington Jason D, Bai Yuqi, Deng Ke, Gong Peng, Guan Dabo, Xiao Yixiong, Xu Bing, Johnsen Einar Broch

2023-Mar-07

Disease X, coupled simulation model, data science, digital twin model, epidemiology

General General

Temporal analysis of academic performance in higher education before, during and after COVID-19 confinement using artificial intelligence.

In PloS one ; h5-index 176.0

This study provides the profiles and success predictions of students considering data before, during, and after the COVID-19 pandemic. Using a field experiment of 396 students and more than 7400 instances, we have analyzed students' performance considering the temporal distribution of autonomous learning during courses from 2016/2017 to 2020/2021. After applying unsupervised learning, results show 3 main profiles from the clusters obtained in the simulations: students who work continuously, those who do it in the last-minute, and those with a low performance in the whole autonomous learning. We have found that the highest success ratio is related to students that work in a continuous basis. However, last-minute working is not necessarily linked to failure. We have also found that students' marks can be predicted successfully taking into account the whole data sets. However, predictions are worse when removing data from the month before the final exam. These predictions are useful to prevent students' wrong learning strategies, and to detect malpractices such as copying. We have done all these analyses taking into account the effect of the COVID-19 pandemic, founding that students worked in a more continuous basis in the confinement. This effect was still present one year after. Finally, We have also included an analysis of the techniques that could be more effective to keep in a future non-pandemic scenario the good habits that were detected in the confinement.

Subirats Laia, Palacios Corral Aina, Pérez-Ruiz Sof Ia, Fort Santi, Sacha Go Mez-Mon Ivas

2023

Internal Medicine Internal Medicine

Evaluation of EfficientNet models for COVID-19 detection using lung parenchyma.

In Neural computing & applications

When the COVID-19 pandemic broke out in the beginning of 2020, it became crucial to enhance early diagnosis with efficient means to reduce dangers and future spread of the viruses as soon as possible. Finding effective treatments and lowering mortality rates is now more important than ever. Scanning with a computer tomography (CT) scanner is a helpful method for detecting COVID-19 in this regard. The present paper, as such, is an attempt to contribute to this process by generating an open-source, CT-based image dataset. This dataset contains the CT scans of lung parenchyma regions of 180 COVID-19-positive and 86 COVID-19-negative patients taken at the Bursa Yuksek Ihtisas Training and Research Hospital. The experimental studies show that the modified EfficientNet-ap-nish method uses this dataset effectively for diagnostic purposes. Firstly, a smart segmentation mechanism based on the k-means algorithm is applied to this dataset as a preprocessing stage. Then, performance pretrained models are analyzed using different CNN architectures and with our Nish activation function. The statistical rates are obtained by the various EfficientNet models and the highest detection score is obtained with the EfficientNet-B4-ap-nish version, which provides a 97.93% accuracy rate and a 97.33% F1-score. The implications of the proposed method are immense both for present-day applications and future developments.

Kurt Zuhal, Işık Şahin, Kaya Zeynep, Anagün Yıldıray, Koca Nizameddin, Çiçek Sümeyye

2023-Feb-20

COVID-19 detection, CT scan, Deep learning, EfficientNet, K-means, Lung parenchyma

Public Health Public Health

Impact of human mobility on COVID-19 transmission according to mobility distance, locations and demographic factors in the Greater Bay area of China：a population-based study.

In JMIR public health and surveillance

BACKGROUND : Mobility restriction is one of the primary measures used to restrain the spread of COVID-19 in the pandemic all over the world. Governments implemented and relaxed various mobility restriction measures in the absence of evidence for almost three years, which caused severe adverse outcomes in health, society and economy.

OBJECTIVE : This study aims to quantify the impact of mobility reduction on COVID-19 transmission according to mobility distance, locations and demographic factors to identify hotspots of transmission and guide public health policies.

METHODS : Millions of the anonymized, aggregated mobile phone position data between Jan 1 and Feb 24, 2020 was collected for the nine mega cities Greater Bay Area (GBA), China. A generalized linear model (GLM) was established to test the association between mobility volume (number of trips) and COVID-19 transmission. Subgroups analysis was also performed for sex, age, travel locations and travel distance. The statistical interaction terms were included in a variety of models that express different relations between the involved variables.

RESULTS : The GLM analysis demonstrated a significant association between the COVID-19 growth rate ratio (GR) and mobility volume. A stratification analysis revealed a higher effect of mobility volume on the COVID-19 growth rate ratio (GR) among people aged 50-59 years (a decrease of 13.17% for GR per 10% reduction of mobility volume for persons 50-59 years, P <.001) than for other age groups (a decrease of 7.80%, 10.43%, 7.48%, 8.01%, 10.43% for age groups of ≤18, 19-29, 30-39, 40-49, ≥ 60 years, respectively, Pinteraction=.024). The impact of mobility reduction on COVID-19 transmission was higher in transit stations and shopping areas: a decrease of 0.67, 0.53, 0.30, 0.37, 0.44, 0.32 for instantaneous reproduction number R(t) per 10% reduction in mobility volume to transit stations, shopping, work, school, recreation, and other locations, separately (Pinteraction=.016). The association between reduction in mobility volume and COVID-19 transmission was lower with decreasing mobility distance as there was significant interaction between mobility volume and mobility distance on R(t) (Pinteraction<.001). Specifically, the R(t) reduced by 11.97% per 10% reduction of mobility volume when the mobility distance increased to 110% (Spring Festival), by 6.74% when distance remained unchanged and by 1.52% when the distance decreased to 90%.

CONCLUSIONS : The association between mobility reduction and COVID-19 transmission significantly varied by mobility distance, locations and age. The substantially higher impact of mobility volume on COVID-19 transmission in longer travel distance, certain age groups, and for specific travel destinations highlights the potential to optimize the effectiveness of mobility restriction strategies. The results from our study demonstrate the power of having a mobility network using mobile phone data for surveillance that monitor movement at a detailed level to measure the potential impacts of future pandemics.

Xia Jizhe, Yin Kun, Yue Yang, Li Qingquan, Wang Xiling, Hu Dongsheng, Wang Xiong, Du Zhanwei, Cowling Ben J, Chen Erzhen, Zhou Ying

2023-Feb-23

Ophthalmology Ophthalmology

Glaucoma and Telemedicine.

In Journal of glaucoma

The coronavirus disease 2019 (COVID-19) pandemic drastically impacted global health, forcing institutions to provide alternative models of safe and reliable health care. In this context, telemedicine has been successfully used to overcome distance barriers and improve access to medical services. Teleglaucoma is the application of telemedicine to screen and monitor glaucoma, a chronic and progressive optic neuropathy. Teleglaucoma screening aims to detect the disease at an earlier stage, especially in high-risk populations and underserved areas, also identifying patients who require more urgent treatment. Teleglaucoma monitoring seeks to provide remote management through virtual clinics, where classical in-person visits are replaced by synchronous data collection (clinical measurements) performed by non-ophthalmologists and asynchronous review (decision-making) by ophthalmologists. This may be employed for low-risk patients with early disease, improving health care logistics, reducing number of face-to-face consultations, and saving time and costs. New technologies may also allow home monitoring of patients in teleglaucoma programs, with addition of artificial intelligence methods, which are expected to increase accuracy of remote glaucoma screening/ monitoring, and to support clinical decision-making. However, for incorporation of teleglaucoma into clinical practice, a complex system for collection, transfer, flow, and interpretation of data is still necessary, in addition to clearer regulatory markers by government agencies and medical entities.

Brandão-de-Resende Camilo, de Alcântara Liliane de Abreu Rosa, Vasconcelos-Santos Daniel Vítor, Diniz-Filho Alberto

2023-Feb-28

Public Health Public Health

Artificial Intelligence Functionalities During the COVID-19 Pandemic.

In Disaster medicine and public health preparedness

BACKGROUND : The coronavirus disease 2019 (COVID-19) pandemic has led us to use virtual solutions and emerging technologies such as artificial intelligence (AI). Recent studies have clearly demonstrated the role of AI in health care and medical practice; however, a comprehensive review can identify potential yet not fulfilled functionalities of such technologies in pandemics. Therefore, this scoping review study aims at assessing AI functionalities in the COVID-19 pandemic in 2022.

METHODS : A systematic search was carried out in PubMed, Cochran Library, Scopus, Science Direct, ProQuest, and Web of Science from 2019 to May 9, 2022. Researchers selected the articles according to the search keywords. Finally, the articles mentioning the functionalities of AI in the COVID-19 pandemic were evaluated. Two investigators performed this process.

RESULTS : Initial search resulted in 9123 articles. After reviewing the title, abstract, and full text of these articles, and applying the inclusion and exclusion criteria, 4 articles were selectd for the final analysis. All 4 were cross-sectional studies. Two studies (50%) were performed in the United States, 1 (25%) in Israel, and 1 (25%) in Saudi Arabia. They covered the functionalities of AI in the prediction, detection, and diagnosis of COVID-19.

CONCLUSIONS : To the extent of the researchers' knowledge, this study is the first scoping review that assesses the AI functionalities in the COVID-19 pandemic. Health-care organizations need decision support technologies and evidence-based apparatuses that can perceive, think, and reason not dissimilar to human beings. Potential functionalities of such technologies can be used to predict mortality, detect, screen, and trace current and former patients, analyze health data, prioritize high-risk patients, and better allocate hospital resources in pandemics, and generally in health-care settings.

Ahmadi Marzaleh Milad, Peyravi Mahmoudreza, Mousavi Shahrokh, Sarpourian Fatemeh, Seyedi Milad, Shalyari Naseh

2023-Feb-27

COVID-19, artificial intelligence, deep learning, machine learning, neural networks

Public Health Public Health

Can we predict critical care mortality with non-conventional inflammatory markers in SARS-CoV-2 infected patients?

In Clinical hemorheology and microcirculation

BACKGROUND : Severe COVID-19 disease is associated with multiple organ involvement,then failure and often fatal outcomes.In addition,inflammatory mechanisms and cytokine storms,documented in many COVID-19 patients,are responsible for the progression of the disease and high mortality rates.Inflammatory parameters,such as procalcitonin(PCT) and C-reactive protein(CRP), are widely used in clinical practice.

OBJECTIVE : To evaluate the predictive power of non-conventional inflammatory markers regarding mortality risk.

METHODS : In our prospective study 52 patients were followed for 5 days after admission to an intensive care unit immediately with severe SARS-CoV-2 infection.We compared leukocyte-,platelet antisedimentation rate (LAR, PAR),neutrophil lymphocyte ratio(NLR), CRP, PCT levels.

RESULTS : In non-surviving(NSU) patients LAR remained largely constant from D1 to D4 with a statistically significant drop(p <  0.05) only seen on D5.The NSU group showed statistically significant(p <  0.05) elevated LAR medians on D4 and D5, compared to the SU group.NLR values were continually higher in the non-survivor group.The difference between the SU and NSU groups were statistically significant on every examined day.PAR, CRP and PCT levels didn't show any significant differences between the SU and NSU groups.

CONCLUSIONS : In conclusion, this study suggests that LAR and NLR are especially worthy of further investigation as prognostic markers.LAR might be of particular relevance as it is not routinely obtained in current clinical practice.It would seem beneficial to include LAR in data sets to train prognostic artificial intelligence.

Rozanovic Martin, Domokos Kamilla, Márovics Gergő, Rohonczi Mirtill, Csontos Csaba, Bogár Lajos, Rendeki Szilárd, Kiss Tamás, Rozanovic Melánia Nacira, Loibl Csaba

2023-Feb-18

C-reactive protein, COVID-19, infection, inflammatory response, leukocyte antisedimentation rate, neutrophil-lymphocyte ratio, procalcitonin

General General

A new sentiment analysis method to detect and Analyse sentiments of Covid-19 moroccan tweets using a recommender approach.

In Multimedia tools and applications

Since the beginning of the covid-19 crisis, people from all over the world have used social media platforms to publish their opinions, sentiments, and ideas about the coronavirus epidemic and their news. Due to the nature of social networks, users share an immense amount of data every day in a freeway, which gives them the possibility to express opinions and sentiments about the coronavirus pandemic regardless of the time and the place. Moreover, The rapid number of exponential cases globally has become the apprehension of panic, fear, and anxiety among people. In this paper, we propose a new sentiment analysis approach to detect sentiments in Moroccan tweets related to covid-19 from March to October 2020. The proposed model is a recommender approach using the advantages of recommendation systems for classifying each tweet into three classes: positive, negative, or neutral. Experimental results show that our method gives good accuracy(86%) and outperforms the well-known machine learning algorithms. We find also that the sentiments of users changed from period to period, and that the evolution of the epidemiological situation in morocco affects the sentiments of users.

Madani Youness, Erritali Mohammed, Bouikhalene Belaid

2023-Feb-22

Classification, Collaborative filtering, Covid-19, Recommendation system, Sentiment analysis

General General

Conv-CapsNet: capsule based network for COVID-19 detection through X-Ray scans.

In Multimedia tools and applications

Coronavirus, a virus that spread worldwide rapidly and was eventually declared a pandemic. The rapid spread made it essential to detect Coronavirus infected people to control the further spread. Recent studies show that radiological images such as X-Rays and CT scans provide essential information in detecting infection using deep learning models. This paper proposes a shallow architecture based on Capsule Networks with convolutional layers to detect COVID-19 infected persons. The proposed method combines the ability of the capsule network to understand spatial information with convolutional layers for efficient feature extraction. Due to the model's shallow architecture, it has 23M parameters to train and requires fewer training samples. The proposed system is fast and robust and correctly classifies the X-Ray images into three classes, i.e. COVID-19, No Findings, and Viral Pneumonia. Experimental results on the X-Ray dataset show that our model performs well despite having fewer samples for the training and achieved an average accuracy of 96.47% for multi-class and 97.69% for binary classification on 5-fold cross-validation. The proposed model would be useful to researchers and medical professionals for assistance and prognosis for COVID-19 infected patients.

Sharma Pulkit, Arya Rhythm, Verma Richa, Verma Bindu

2023-Feb-21

COVID-19 detection, Capsule networks, Chest X-ray classification, Medical imaging

Public Health Public Health

Visual Positioning of Nasal Swab Robot Based on Hierarchical Decision.

In Journal of Shanghai Jiaotong University (science)

This study focuses on a robot vision localization method for coping with the operational task of automatic nasal swab sampling. The application is important in the detection and epidemic prevention of Corona Virus Disease 2019 (COVID-19) to alleviate the large-scale negative impact of individuals suffering from pneumonia owing to COVID-19. In this method, the idea of a hierarchical decision network is used to consider the strong infectious characteristics of the COVID-19, which is followed by processing the robot behavior constraint condition. The visual navigation and positioning method using a single-arm robot for sampling is also planned, which considers the operation characteristics of medical staff. In the decision network, the risk factor for potential contact infection caused by swab sampling operations is established to avoid the spread among personnel. A robot visual servo control with artificial intelligence characteristics is developed to achieve a stable and safe nasal swab sampling operation. Experiments demonstrate that the proposed method can achieve good vision positioning for the robots and provide technical support for managing new major public health situations.

Li Guozhi, Zou Shuizhong, Ding Shuxue

2023-Feb-21

hierarchical decision, nasal swab sampling, surgical robot, vision servo

Internal Medicine Internal Medicine

A dataset of COVID-19 x-ray chest images.

In Data in brief

The distinction between normal chest x-ray (CXR) images and abnormal ones containing features of disease (e.g., opacities, consolidation, etc.) is important for accurate medical diagnosis. CXR images contain valuable information concerning the physiological and pathological state of the lungs and airways. In addition, they provide information about the heart, chest bones, and some arteries (e.g., Aorta and pulmonary arteries). Deep learning artificial intelligence has taken great strides in the development of sophisticated medical models in a wide range of applications. More specifically, it has been shown to provide highly accurate diagnosis and detection tools. The dataset presented in this article contains the chest x-ray images from the examination of confirmed COVID-19 subjects, who were admitted for a multiday stay at a local hospital in northern Jordan. To provide a diverse dataset, only one CXR image per subject was included in the data. The dataset can be used for the development of automated methods that detect COVID-19 from CXR images (COVID-19 vs. normal) and distinguish pneumonia caused by COVID-19 from other pulmonary diseases. ©202x The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Fraiwan Mohammad, Khasawneh Natheer, Khassawneh Basheer, Ibnian Ali

2023-Apr

Artificial intelligence, COVID-19, Chest X-ray, Deep learning, Detection, Diagnosis

General General

Investigating brain cortical activity in patients with post-COVID-19 brain fog.

In Frontiers in neuroscience ; h5-index 72.0

Brain fog is a kind of mental problem, similar to chronic fatigue syndrome, and appears about 3 months after the infection with COVID-19 and lasts up to 9 months. The maximum magnitude of the third wave of COVID-19 in Poland was in April 2021. The research referred here aimed at carrying out the investigation comprising the electrophysiological analysis of the patients who suffered from COVID-19 and had symptoms of brain fog (sub-cohort A), suffered from COVID-19 and did not have symptoms of brain fog (sub-cohort B), and the control group that had no COVID-19 and no symptoms (sub-cohort C). The aim of this article was to examine whether there are differences in the brain cortical activity of these three sub-cohorts and, if possible differentiate and classify them using the machine-learning tools. he dense array electroencephalographic amplifier with 256 electrodes was used for recordings. The event-related potentials were chosen as we expected to find the differences in the patients' responses to three different mental tasks arranged in the experiments commonly known in experimental psychology: face recognition, digit span, and task switching. These potentials were plotted for all three patients' sub-cohorts and all three experiments. The cross-correlation method was used to find differences, and, in fact, such differences manifested themselves in the shape of event-related potentials on the cognitive electrodes. The discussion of such differences will be presented; however, an explanation of such differences would require the recruitment of a much larger cohort. In the classification problem, the avalanche analysis for feature extractions from the resting state signal and linear discriminant analysis for classification were used. The differences between sub-cohorts in such signals were expected to be found. Machine-learning tools were used, as finding the differences with eyes seemed impossible. Indeed, the A&B vs. C, B&C vs. A, A vs. B, A vs. C, and B vs. C classification tasks were performed, and the efficiency of around 60-70% was achieved. In future, probably there will be pandemics again due to the imbalance in the natural environment, resulting in the decreasing number of species, temperature increase, and climate change-generated migrations. The research can help to predict brain fog after the COVID-19 recovery and prepare the patients for better convalescence. Shortening the time of brain fog recovery will be beneficial not only for the patients but also for social conditions.

Wojcik Grzegorz M, Shriki Oren, Kwasniewicz Lukasz, Kawiak Andrzej, Ben-Horin Yarden, Furman Sagi, Wróbel Krzysztof, Bartosik Bernadetta, Panas Ewelina

2023

COVID-19, EEG, ERP, LDA, brain fog, cortical activity

Public Health Public Health

Barriers to and solutions for representative inclusion across the lifespan and in life course research: The need for structural competency highlighted by the COVID-19 pandemic.

In Journal of clinical and translational science

Exclusion of special populations (older adults; pregnant women, children, and adolescents; individuals of lower socioeconomic status and/or who live in rural communities; people from racial and ethnic minority groups; individuals from sexual or gender minority groups; and individuals with disabilities) in research is a pervasive problem, despite efforts and policy changes by the National Institutes of Health and other organizations. These populations are adversely impacted by social determinants of health (SDOH) that reduce access and ability to participate in biomedical research. In March 2020, the Northwestern University Clinical and Translational Sciences Institute hosted the "Lifespan and Life Course Research: integrating strategies" "Un-Meeting" to discuss barriers and solutions to underrepresentation of special populations in biomedical research. The COVID-19 pandemic highlighted how exclusion of representative populations in research can increase health inequities. We applied findings of this meeting to perform a literature review of barriers and solutions to recruitment and retention of representative populations in research and to discuss how findings are important to research conducted during the ongoing COVID-19 pandemic. We highlight the role of SDOH, review barriers and solutions to underrepresentation, and discuss the importance of a structural competency framework to improve research participation and retention among special populations.

LeCroy Madison N, Potter Lindsey N, Bandeen-Roche Karen, Bianco Monica E, Cappola Anne R, Carter Ebony B, Dayan Peter S, Eckstrom Elizabeth, Edwards Dorothy F, Farabi Sarah S, Fisher Sheehan D, Giordano Judy, Hanson Heidi A, Jenkins Emerald, Juhn Young, Kaskel Frederick, Stake Christine E, Reeds Dominic N, Schleiss Mark R, Wafford Q Eileen, McColley Susanna A

2023

Life course research, research participation, social determinants of health, special populations, structural competency

General General

Multi-scale Triplet Hashing for Medical Image Retrieval.

In Computers in biology and medicine

For medical image retrieval task, deep hashing algorithms are widely applied in large-scale datasets for auxiliary diagnosis due to the retrieval efficiency advantage of hash codes. Most of which focus on features learning, whilst neglecting the discriminate area of medical images and hierarchical similarity for deep features and hash codes. In this paper, we tackle these dilemmas with a new Multi-scale Triplet Hashing (MTH) algorithm, which can leverage multi-scale information, convolutional self-attention and hierarchical similarity to learn effective hash codes simultaneously. The MTH algorithm first designs multi-scale DenseBlock module to learn multi-scale information of medical images. Meanwhile, a convolutional self-attention mechanism is developed to perform information interaction of the channel domain, which can capture the discriminate area of medical images effectively. On top of the two paths, a novel loss function is proposed to not only conserve the category-level information of deep features and the semantic information of hash codes in the learning process, but also capture the hierarchical similarity for deep features and hash codes. Extensive experiments on the Curated X-ray Dataset, Skin Cancer MNIST Dataset and COVID-19 Radiography Dataset illustrate that the MTH algorithm can further enhance the effect of medical retrieval compared to other state-of-the-art medical image retrieval algorithms.

Chen Yaxiong, Tang Yibo, Huang Jinghao, Xiong Shengwu

2023-Feb-08

Convolutional self-attention, Deep hashing, Hierarchical similarity, Medical image retrieval

General General

Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization.

In The journal of physical chemistry. B

A potential therapeutic strategy for neutralizing SARS-CoV-2 infection is engineering high-affinity soluble ACE2 decoy proteins to compete for binding to the viral spike (S) protein. Previously, a deep mutational scan of ACE2 was performed and has led to the identification of a triple mutant variant, named sACE22.v.2.4, that exhibits subnanomolar affinity to the receptor-binding domain (RBD) of S. Using a recently developed transfer learning algorithm, TLmutation, we sought to identify other ACE2 variants that may exhibit similar binding affinity with decreased mutational load. Upon training a TLmutation model on the effects of single mutations, we identified multiple ACE2 double mutants that bind SARS-CoV-2 S with tighter affinity as compared to the wild type, most notably L79V;N90D that binds RBD similarly to ACE22.v.2.4. The experimental validation of the double mutants successfully demonstrates the use of machine learning approaches for engineering protein-protein interactions and identifying high-affinity ACE2 peptides for targeting SARS-CoV-2.

Chan Matthew C, Chan Kui K, Procko Erik, Shukla Diwakar

2023-Feb-24

General General

Novel Light Convolutional Neural Network for COVID Detection with Watershed Based Region Growing Segmentation.

In Journal of imaging

A rapidly spreading epidemic, COVID-19 had a serious effect on millions and took many lives. Therefore, for individuals with COVID-19, early discovery is essential for halting the infection's progress. To quickly and accurately diagnose COVID-19, imaging modalities, including computed tomography (CT) scans and chest X-ray radiographs, are frequently employed. The potential of artificial intelligence (AI) approaches further explored the creation of automated and precise COVID-19 detection systems. Scientists widely use deep learning techniques to identify coronavirus infection in lung imaging. In our paper, we developed a novel light CNN model architecture with watershed-based region-growing segmentation on Chest X-rays. Both CT scans and X-ray radiographs were employed along with 5-fold cross-validation. Compared to earlier state-of-the-art models, our model is lighter and outperformed the previous methods by achieving a mean accuracy of 98.8% on X-ray images and 98.6% on CT scans, predicting the rate of 0.99% and 0.97% for PPV (Positive predicted Value) and NPV (Negative predicted Value) rate of 0.98% and 0.99%, respectively.

Khan Hassan Ali, Gong Xueqing, Bi Fenglin, Ali Rashid

2023-Feb-13

CNN, COVID-19, CT scans, X-rays, classification, convolutional neural network, segmentation, watershed segmentation

General General

Masked Face Recognition Using Histogram-Based Recurrent Neural Network.

In Journal of imaging

Masked face recognition (MFR) is an interesting topic in which researchers have tried to find a better solution to improve and enhance performance. Recently, COVID-19 caused most of the recognition system fails to recognize facial images since the current face recognition cannot accurately capture or detect masked face images. This paper introduces the proposed method known as histogram-based recurrent neural network (HRNN) MFR to solve the undetected masked face problem. The proposed method includes the feature descriptor of histograms of oriented gradients (HOG) as the feature extraction process and recurrent neural network (RNN) as the deep learning process. We have proven that the combination of both approaches works well and achieves a high true acceptance rate (TAR) of 99 percent. In addition, the proposed method is designed to overcome the underfitting problem and reduce computational burdens with large-scale dataset training. The experiments were conducted on two benchmark datasets which are RMFD (Real-World Masked Face Dataset) and Labeled Face in the Wild Simulated Masked Face Dataset (LFW-SMFD) to vindicate the viability of the proposed HRNN method.

Chong Wei-Jie Lucas, Chong Siew-Chin, Ong Thian-Song

2023-Feb-08

deep learning, histogram of gradients, masked face recognition, neural network, recurrent

General General

Impact of Wavelet Kernels on Predictive Capability of Radiomic Features: A Case Study on COVID-19 Chest X-ray Images.

In Journal of imaging

Radiomic analysis allows for the detection of imaging biomarkers supporting decision-making processes in clinical environments, from diagnosis to prognosis. Frequently, the original set of radiomic features is augmented by considering high-level features, such as wavelet transforms. However, several wavelets families (so called kernels) are able to generate different multi-resolution representations of the original image, and which of them produces more salient images is not yet clear. In this study, an in-depth analysis is performed by comparing different wavelet kernels and by evaluating their impact on predictive capabilities of radiomic models. A dataset composed of 1589 chest X-ray images was used for COVID-19 prognosis prediction as a case study. Random forest, support vector machine, and XGBoost were trained (on a subset of 1103 images) after a rigorous feature selection strategy to build-up the predictive models. Next, to evaluate the models generalization capability on unseen data, a test phase was performed (on a subset of 486 images). The experimental findings showed that Bior1.5, Coif1, Haar, and Sym2 kernels guarantee better and similar performance for all three machine learning models considered. Support vector machine and random forest showed comparable performance, and they were better than XGBoost. Additionally, random forest proved to be the most stable model, ensuring an appropriate balance between sensitivity and specificity.

Prinzi Francesco, Militello Carmelo, Conti Vincenzo, Vitabile Salvatore

2023-Jan-30

COVID-19 prognosis, chest X-ray images, machine learning models, predictive capability, radiomic features, wavelet kernels, wavelet-derived features

General General

Cardiovascular and Renal Comorbidities Included into Neural Networks Predict the Outcome in COVID-19 Patients Admitted to an Intensive Care Unit: Three-Center, Cross-Validation, Age- and Sex-Matched Study.

In Journal of cardiovascular development and disease

Here, we performed a multicenter, age- and sex-matched study to compare the efficiency of various machine learning algorithms in the prediction of COVID-19 fatal outcomes and to develop sensitive, specific, and robust artificial intelligence tools for the prompt triage of patients with severe COVID-19 in the intensive care unit setting. In a challenge against other established machine learning algorithms (decision trees, random forests, extra trees, neural networks, k-nearest neighbors, and gradient boosting: XGBoost, LightGBM, and CatBoost) and multivariate logistic regression as a reference, neural networks demonstrated the highest sensitivity, sufficient specificity, and excellent robustness. Further, neural networks based on coronary artery disease/chronic heart failure, stage 3-5 chronic kidney disease, blood urea nitrogen, and C-reactive protein as the predictors exceeded 90% sensitivity and 80% specificity, reaching AUROC of 0.866 at primary cross-validation and 0.849 at secondary cross-validation on virtual samples generated by the bootstrapping procedure. These results underscore the impact of cardiovascular and renal comorbidities in the context of thrombotic complications characteristic of severe COVID-19. As aforementioned predictors can be obtained from the case histories or are inexpensive to be measured at admission to the intensive care unit, we suggest this predictor composition is useful for the triage of critically ill COVID-19 patients.

Ovcharenko Evgeny, Kutikhin Anton, Gruzdeva Olga, Kuzmina Anastasia, Slesareva Tamara, Brusina Elena, Kudasheva Svetlana, Bondarenko Tatiana, Kuzmenko Svetlana, Osyaev Nikolay, Ivannikova Natalia, Vavin Grigory, Moses Vadim, Danilov Viacheslav, Komossky Egor, Klyshnikov Kirill

2023-Jan-23

C-reactive protein, COVID-19, blood urea nitrogen, chronic kidney disease, coronary artery disease, lymphocyte count, machine learning, neural networks, neutrophil-to-lymphocyte ratio, prognostication

Pathology Pathology

Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development.

In Frontiers in pharmacology

Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates. Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models. Result: Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact analysis protruding that Omicron is more transmissible. Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.

Islam Md Aminul, Shahi Shatila, Marzan Abdullah Al, Amin Mohammad Ruhul, Hasan Mohammad Nayeem, Hoque M Nazmul, Ghosh Ajit, Barua Abanti, Khan Abbas, Dhama Kuldeep, Chakraborty Chiranjib, Bhattacharya Prosun, Wei Dong-Qing

2023

COVID-19, SARS-CoV-2, deleterious mutation, delta variant, immune response, omicron variant, unique mutation, vaccine designing

Public Health Public Health

Anti-vaccination attitude trends during the COVID-19 pandemic: A machine learning-based analysis of tweets.

In Digital health

OBJECTIVE : Vaccine hesitancy has been ranked by the World Health Organization among the top 10 threats to global health. With a surge in misinformation and conspiracy theories against vaccination observed during the COVID-19 pandemic, attitudes toward vaccination may be worsening. This study investigates trends in anti-vaccination attitudes during the COVID-19 pandemic and within the United States, Canada, the United Kingdom, and Australia.

METHODS : Vaccine-related English tweets published between 1 January 2020 and 27 June 2021 were used. A deep learning model using a dynamic word embedding method, Bidirectional Encoder Representations from Transformers (BERTs), was developed to identify anti-vaccination tweets. The classifier achieved a micro F1 score of 0.92. Time series plots and country maps were used to examine vaccination attitudes globally and within countries.

RESULTS : Among 9,352,509 tweets, 232,975 (2.49%) were identified as anti-vaccination tweets. The overall number of vaccine-related tweets increased sharply after the implementation of the first vaccination round since November 2020 (daily average of 6967 before vs. 31,757 tweets after 9/11/2020). The number of anti-vaccination tweets increased after conspiracy theories spread on social media. Percentages of anti-vaccination tweets were 3.45%, 2.74%, 2.46%, and 1.86% for the United States, the United Kingdom, Australia, and Canada, respectively.

CONCLUSIONS : Strategies and information campaigns targeting vaccination misinformation may need to be specifically designed for regions with the highest anti-vaccination Twitter activity and when new vaccination campaigns are initiated.

To Quyen G, To Kien G, Huynh Van-Anh N, Nguyen Nhung Tq, Ngo Diep Tn, Alley Stephanie, Tran Anh Nq, Tran Anh Np, Pham Ngan Tt, Bui Thanh X, Vandelanotte Corneel

2023

deep learning, neural network, social media, stance analysis, twitter, vaccine hesitancy

General General

A wearable device for at-home obstructive sleep apnea assessment: State-of-the-art and research challenges.

In Frontiers in neurology

In the last 3 years, almost all medical resources have been reserved for the screening and treatment of patients with coronavirus disease (COVID-19). Due to a shortage of medical staff and equipment, diagnosing sleep disorders, such as obstructive sleep apnea (OSA), has become more difficult than ever. In addition to being diagnosed using polysomnography at a hospital, people seem to pay more attention to alternative at-home OSA detection solutions. This study aims to review state-of-the-art assessment techniques for out-of-center detection of the main characteristics of OSA, such as sleep, cardiovascular function, oxygen balance and consumption, sleep position, breathing effort, respiratory function, and audio, as well as recent progress in the implementation of data acquisition and processing and machine learning techniques that support early detection of severe OSA levels.

Tran Ngoc Thai, Tran Huu Nam, Mai Anh Tuan

2023

COVID-19, OSA, SCOPER, machine learning, wearable device

oncology Oncology

Targeted plasma proteomics reveals signatures discriminating COVID-19 from sepsis with pneumonia.

In Respiratory research ; h5-index 45.0

BACKGROUND : COVID-19 remains a major public health challenge, requiring the development of tools to improve diagnosis and inform therapeutic decisions. As dysregulated inflammation and coagulation responses have been implicated in the pathophysiology of COVID-19 and sepsis, we studied their plasma proteome profiles to delineate similarities from specific features.

METHODS : We measured 276 plasma proteins involved in Inflammation, organ damage, immune response and coagulation in healthy controls, COVID-19 patients during acute and convalescence phase, and sepsis patients; the latter included (i) community-acquired pneumonia (CAP) caused by Influenza, (ii) bacterial CAP, (iii) non-pneumonia sepsis, and (iv) septic shock patients.

RESULTS : We identified a core response to infection consisting of 42 proteins altered in both COVID-19 and sepsis, although higher levels of cytokine storm-associated proteins were evident in sepsis. Furthermore, microbiologic etiology and clinical endotypes were linked to unique signatures. Finally, through machine learning, we identified biomarkers, such as TRIM21, PTN and CASP8, that accurately differentiated COVID-19 from CAP-sepsis with higher accuracy than standard clinical markers.

CONCLUSIONS : This study extends the understanding of host responses underlying sepsis and COVID-19, indicating varying disease mechanisms with unique signatures. These diagnostic and severity signatures are candidates for the development of personalized management of COVID-19 and sepsis.

Palma Medina Laura M, Babačić Haris, Dzidic Majda, Parke Åsa, Garcia Marina, Maleki Kimia T, Unge Christian, Lourda Magda, Kvedaraite Egle, Chen Puran, Muvva Jagadeeswara Rao, Cornillet Martin, Emgård Johanna, Moll Kirsten, Michaëlsson Jakob, Flodström-Tullberg Malin, Brighenti Susanna, Buggert Marcus, Mjösberg Jenny, Malmberg Karl-Johan, Sandberg Johan K, Gredmark-Russ Sara, Rooyackers Olav, Svensson Mattias, Chambers Benedict J, Eriksson Lars I, Pernemalm Maria, Björkström Niklas K, Aleman Soo, Ljunggren Hans-Gustaf, Klingström Jonas, Strålin Kristoffer, Norrby-Teglund Anna

2023-Feb-24

COVID-19, Community acquired pneumonia, Olink proximity extension assays, Sepsis, Septic shock

Radiology Radiology

Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients.

In BMC medical informatics and decision making ; h5-index 38.0

BACKGROUND : Two years into the COVID-19 pandemic and with more than five million deaths worldwide, the healthcare establishment continues to struggle with every new wave of the pandemic resulting from a new coronavirus variant. Research has demonstrated that there are variations in the symptoms, and even in the order of symptom presentations, in COVID-19 patients infected by different SARS-CoV-2 variants (e.g., Alpha and Omicron). Textual data in the form of admission notes and physician notes in the Electronic Health Records (EHRs) is rich in information regarding the symptoms and their orders of presentation. Unstructured EHR data is often underutilized in research due to the lack of annotations that enable automatic extraction of useful information from the available extensive volumes of textual data.

METHODS : We present the design of a COVID Interface Terminology (CIT), not just a generic COVID-19 terminology, but one serving a specific purpose of enabling automatic annotation of EHRs of COVID-19 patients. CIT was constructed by integrating existing COVID-related ontologies and mining additional fine granularity concepts from clinical notes. The iterative mining approach utilized the techniques of 'anchoring' and 'concatenation' to identify potential fine granularity concepts to be added to the CIT. We also tested the generalizability of our approach on a hold-out dataset and compared the annotation coverage to the coverage obtained for the dataset used to build the CIT.

RESULTS : Our experiments demonstrate that this approach results in higher annotation coverage compared to existing ontologies such as SNOMED CT and Coronavirus Infectious Disease Ontology (CIDO). The final version of CIT achieved about 20% more coverage than SNOMED CT and 50% more coverage than CIDO. In the future, the concepts mined and added into CIT could be used as training data for machine learning models for mining even more concepts into CIT and further increasing the annotation coverage.

CONCLUSION : In this paper, we demonstrated the construction of a COVID interface terminology that can be utilized for automatically annotating EHRs of COVID-19 patients. The techniques presented can identify frequently documented fine granularity concepts that are missing in other ontologies thereby increasing the annotation coverage.

Keloth Vipina K, Zhou Shuxin, Lindemann Luke, Zheng Ling, Elhanan Gai, Einstein Andrew J, Geller James, Perl Yehoshua

2023-Feb-24

COVID-19 ontologies, Concept mining, EHR annotation, Interface terminology

Cardiology Cardiology

Association of statin use with outcomes of patients admitted with COVID-19: an analysis of electronic health records using superlearner.

In BMC infectious diseases ; h5-index 58.0

IMPORTANCE : Statin use prior to hospitalization for Coronavirus Disease 2019 (COVID-19) is hypothesized to improve inpatient outcomes including mortality, but prior findings from large observational studies have been inconsistent, due in part to confounding. Recent advances in statistics, including incorporation of machine learning techniques into augmented inverse probability weighting with targeted maximum likelihood estimation, address baseline covariate imbalance while maximizing statistical efficiency.

OBJECTIVE : To estimate the association of antecedent statin use with progression to severe inpatient outcomes among patients admitted for COVD-19.

DESIGN, SETTING AND PARTICIPANTS : We retrospectively analyzed electronic health records (EHR) from individuals ≥ 40-years-old who were admitted between March 2020 and September 2022 for ≥ 24 h and tested positive for SARS-CoV-2 infection in the 30 days before to 7 days after admission.

EXPOSURE : Antecedent statin use-statin prescription ≥ 30 days prior to COVID-19 admission.

MAIN OUTCOME : Composite end point of in-hospital death, intubation, and intensive care unit (ICU) admission.

RESULTS : Of 15,524 eligible COVID-19 patients, 4412 (20%) were antecedent statin users. Compared with non-users, statin users were older (72.9 (SD: 12.6) versus 65.6 (SD: 14.5) years) and more likely to be male (54% vs. 51%), White (76% vs. 71%), and have ≥ 1 medical comorbidity (99% vs. 86%). Unadjusted analysis demonstrated that a lower proportion of antecedent users experienced the composite outcome (14.8% vs 19.3%), ICU admission (13.9% vs 18.3%), intubation (5.1% vs 8.3%) and inpatient deaths (4.4% vs 5.2%) compared with non-users. Risk differences adjusted for labs and demographics were estimated using augmented inverse probability weighting with targeted maximum likelihood estimation using Super Learner. Statin users still had lower rates of the composite outcome (adjusted risk difference: - 3.4%; 95% CI: - 4.6% to - 2.1%), ICU admissions (- 3.3%; - 4.5% to - 2.1%), and intubation (- 1.9%; - 2.8% to - 1.0%) but comparable inpatient deaths (0.6%; - 1.3% to 0.1%).

CONCLUSIONS AND RELEVANCE : After controlling for confounding using doubly robust methods, antecedent statin use was associated with minimally lower risk of severe COVID-19-related outcomes, ICU admission and intubation, however, we were not able to corroborate a statin-associated mortality benefit.

Rivera Adovich S, Al-Heeti Omar, Petito Lucia C, Feinstein Mathew J, Achenbach Chad J, Williams Janna, Taiwo Babafemi

2023-Feb-24

COVID-19, Critical care, Mortality, Observational studies, Statin, Targeted maximum likelihood estimation

Public Health Public Health

MSCCov19Net: multi-branch deep learning model for COVID-19 detection from cough sounds.

In Medical & biological engineering & computing ; h5-index 32.0

Coronavirus has an impact on millions of lives and has been added to the important pandemics that continue to affect with its variants. Since it is transmitted through the respiratory tract, it has had significant effects on public health and social relations. Isolating people who are COVID positive can minimize the transmission, therefore several exams are proposed to detect the virus such as reverse transcription-polymerase chain reaction (RT-PCR), chest X-Ray, and computed tomography (CT). However, these methods suffer from either a low detection rate or high radiation dosage, along with being expensive. In this study, deep neural network-based model capable of detecting coronavirus from only coughing sound, which is fast, remotely operable and has no harmful side effects, has been proposed. The proposed multi-branch model takes M el Frequency Cepstral Coefficients (MFCC), S pectrogram, and C hromagram as inputs and is abbreviated as MSCCov19Net. The system is trained on publicly available crowdsourced datasets, and tested on two unseen (used only for testing) clinical and non-clinical datasets. Experimental outcomes represent that the proposed system outperforms the 6 popular deep learning architectures on four datasets by representing a better generalization ability. The proposed system has reached an accuracy of 61.5 % in Virufy and 90.4 % in NoCoCoDa for unseen test datasets.

Ulukaya Sezer, Sarıca Ahmet Alp, Erdem Oğuzhan, Karaali Ali

2023-Feb-24

Coronavirus, Coughing, Deep learning, Ensemble learning, Telehealth

General General

Machine learning on large scale perturbation screens for SARS-CoV-2 host factors identifies β-catenin/CBP inhibitor PRI-724 as a potent antiviral

bioRxiv Preprint

Expanding antiviral treatment options against SARS-CoV-2 remains crucial as the virus evolves rapidly and drug resistant strains have emerged. Broad spectrum host-directed antivirals (HDA) are promising therapeutic options, however the robust identification of relevant host factors by CRISPR/Cas9 or RNA interference screens remains challenging due to low consistency in the resulting hits. To address this issue, we employed machine learning based on experimental data from knockout screens and a drug screen. As gold standard, we assembled perturbed genes reducing virus replication or protecting the host cells. The machines based their predictions on features describing cellular localization, protein domains, annotated gene sets from Gene Ontology, gene and protein sequences, and experimental data from proteomics, phospho-proteomics, protein interaction and transcriptomic profiles of SARS-CoV-2 infected cells. The models reached a remarkable performance with a balanced accuracy of 0.82 (knockout based classifier) and 0.71 (drugs screen based classifier), suggesting patterns of intrinsic data consistency. The predicted host dependency factors were enriched in sets of genes particularly coding for development, morphogenesis, and neural related processes. Focusing on development and morphogenesis-associated gene sets, we found {beta}-catenin to be central and selected PRI-724, a canonical {beta}-catenin/CBP disruptor, as a potential HDA. PRI-724 limited infection with SARS-CoV-2 variants, SARS-CoV-1, MERS-CoV and IAV in different cell line models. We detected a concentration-dependent reduction in CPE development, viral RNA replication, and infectious virus production in SARS-CoV-2 and SARS-CoV-1-infected cells. Independent of virus infection, PRI-724 treatment caused cell cycle deregulation which substantiates its potential as a broad spectrum antiviral. Our proposed machine learning concept may support focusing and accelerating the discovery of host dependency factors and the design of antiviral therapies.

Kelch, M. A.; Vera-Guapi, A. L.; Beder, T.; Oswald, M.; Hiemisch, A.; Beil, N.; Wajda, P.; Ciesek, S.; Erfle, H.; Toptan, T.; König, R.

2023-02-24

General General

Make it or break it: On-time vaccination intent at the time of Covid-19.

In Vaccine ; h5-index 70.0

On-time effective vaccination is critical to curbing a pandemic, but this is often hampered by citizens' hesitancy to get quickly vaccinated. This research concentrates on the hypothesis that, besides traditional factors in the literature, vaccination success would hinge on two dimensions: a) addressing a broader set of risk perception factors than health-related issues only, and b) securing sufficient social and institutional trust at the time of vaccination campaign launch. We test this hypothesis regarding Covid-19 vaccination preferences in six European countries and at the early stage of the pandemic by April 2020. We find that addressing the two roadblock dimensions could further boost Covid-19 vaccination coverage by 22%. The study also offers three extra innovations. The first is that the traditional segmentation logic between vaccine "acceptors", "hesitants" and "refusers" is further justified by the fact that segments have different attitudes: refusers care less about health issues than they are worried about family tensions and finance (dimension 1 of our hypothesis). In contrast, hesitants are the battlefield for more transparency by media and government actions (dimension 2 of our hypothesis). The second added value is that we extend our hypothesis testing with a supervised non-parametric machine learning technique (Random Forests). Again, consistent with our hypothesis, this method picks up higher-order interaction between risk and trust variables that strongly predict on-time vaccination intent. We finally explicitly adjust survey responses to account for possible reporting bias. Among others, vaccine-reluctant citizens may under-report their limited will to get vaccinated.

Bughin Jacques, Cincera Michele, Peters Kelly, Reykowska Dorota, Żyszkiewicz Marcin, Ohme Rafal

2023-Feb-08

Covid-19, Machine Learning, Random-forest, Social trust, Vaccine strategy

Public Health Public Health

Telehealth utilization in U.S. medicare beneficiaries aged 65 years and older during the COVID-19 pandemic.

In BMC public health ; h5-index 82.0

BACKGROUND : The COVID-19 pandemic has become a serious public health concern for older adults and amplified the value of deploying telehealth solutions. The purpose of this study was to investigate telehealth offered by providers among U.S. Medicare beneficiaries aged 65 years and older during the COVID-19 pandemic.

METHODS : This cross-sectional study analyzed Medicare beneficiaries aged 65 years and older using data from the Medicare Current Beneficiary Survey, Winter 2021 COVID-19 Supplement ([Formula: see text]). We identified variables that were associated with telehealth offered by primary care physicians and beneficiaries' access to the Internet through a multivariate classification analysis utilizing Random Forest machine learning techniques.

FINDINGS : For study participants interviewed by telephone, 81.06% of primary care providers provided telehealth services, and 84.62% of the Medicare beneficiaries had access to the Internet. The survey response rates for each outcome were 74.86% and 99.55% respectively. The two outcomes were positively correlated ([Formula: see text]). The Our machine learning model predicted the outcomes accurately utilizing 44 variables. Residing area and race/ethnicity were most informative for predicting telehealth coverage, and Medicare-Medicaid dual eligibility and income were most informative for predicting Internet access. Other strong correlates included age, ability to access basic needs and certain mental and physical health conditions. Interactions were found among statuses of residing area, age, Medicare Advantage and heart conditions that intensified the disparity of outcomes.

CONCLUSIONS : We found that telehealth offered by providers likely increased during the COVID-19 pandemic for older beneficiaries, providing important access to care for certain subgroups. Policymakers must continue to identify effective means of delivering telehealth services, modernize the framework of regulatory, accreditation and reimbursement, and address disparities in access to telehealth with a particular focus on underserved communities.

Lu Min, Liao Xinyi

2023-Feb-20

COVID-19, Medicare, Older adults, Primary care, Telehealth, Telemedicine

Public Health Public Health

A digital health platform to manage COVID-19: decentralizing technology to empower rural and remote jurisdictions.

In Rural and remote health

INTRODUCTION : The variation of coronavirus disease (COVID-19) outbreaks across rural and remote jurisdictions makes it imperative to invest in scalable digital health platforms to not only minimize the impact of subsequent COVID-19 outbreaks, but also to utilize such approaches to predict and prevent future communicable and non-communicable diseases.

METHODS : The methodology of the digital health platform comprised: (1) Ethical Real-Time Surveillance to Monitor Risk: evidence-based artificial intelligence-driven individual and community risk assessment of COVID-19 by engaging citizens using their own smartphones; (2) Citizen Empowerment and Data Ownership: active engagement of citizens using smartphone application (app) features, while enabling data ownership; and (3) Privacy: development of algorithms that store sensitive data directly on mobile devices.

RESULTS : The result is a community-engaged, innovative, and scalable digital health platform, with three key features: (1) Prevention: this feature is based on risky and healthy behaviours, and has the sophistication to continuously engage citizens; (2) Public Health Communication: based on their risk profile and behaviour, citizens receive specific public health communication that helps them make informed decisions; and (3) Precision Medicine: risk assessment and behaviour modification is individualized so that the frequency, type, and intensity of engagement is based on individual risk profile.

DISCUSSION : This digital health platform enables the decentralization of digital technology to effect systems-level changes. With more than 6 billion smartphone subscriptions globally, digital health platforms enable direct engagement with large populations in near real-time to monitor, mitigate, and manage public health crises, particularly in rural communities that do not have equitable access to health services.

Katapally Tarun

2023-Jan

General General

Analysis of COVID-19 vaccine adverse event using language model and unsupervised machine learning.

In PloS one ; h5-index 176.0

BACKGROUND : After the COVID-19 pandemic, the world has made efforts to recover from the chaotic situation. Vaccination is a way to help control infectious diseases, and many people have been vaccinated against COVID-19 by this point. However, an extremely small number of those who received the vaccine have experienced diverse side effects.

METHODS AND FINDINGS : In this study, we examined people who experienced adverse events with the COVID-19 vaccine by gender, age, vaccine manufacturer, and dose of vaccinations by using the Vaccine Adverse Event Reporting System datasets. Then we used a language model to vectorize symptom words and reduced their dimensionality. We also clustered symptoms by using unsupervised machine learning and analyzed the characteristics of each symptom cluster. Lastly, to discover any association rules among adverse events, we used a data mining approach. The frequency of adverse events was higher for women than men, for Moderna than for Pfizer or Janssen, and for the first dose than for the second dose. However, we found that characteristics of vaccine adverse events, including gender, vaccine manufacturer, age, and underlying diseases were different for each symptom cluster, and that fatal cases were significantly related to a particular cluster (associated with hypoxia). Also, as a result of the association analysis, the {chills ↔ pyrexia} and {vaccination site pruritus ↔ vaccination site erythema} rules had the highest support value of 0.087 and 0.046, respectively.

CONCLUSIONS : We aim to contribute accurate information on the adverse events of the COVID-19 vaccine to relieve public anxiety due to unconfirmed statements about vaccines.

Cheon Saeyeon, Methiyothin Thanin, Ahn Insung

2023

General General

Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL.

In Biophysical chemistry

Structures can now be predicted for any protein using programs like AlphaFold and Rosetta, which rely on a foundation of experimentally determined structures of architecturally diverse proteins. The accuracy of such artificial intelligence and machine learning (AI/ML) approaches benefits from the specification of restraints which assist in navigating the universe of folds to converge on models most representative of a given protein's physiological structure. This is especially pertinent for membrane proteins, with structures and functions that depend on their presence in lipid bilayers. Structures of proteins in their membrane environments could conceivably be predicted from AI/ML approaches with user-specificized parameters that describe each element of the architecture of a membrane protein accompanied by its lipid environment. We propose the Classification Of Membrane Proteins based On Structures Engaging Lipids (COMPOSEL), which builds on existing nomenclature types for monotopic, bitopic, polytopic and peripheral membrane proteins as well as lipids. Functional and regulatory elements are also defined in the scripts, as shown with membrane fusing synaptotagmins, multidomain PDZD8 and Protrudin proteins that recognize phosphoinositide (PI) lipids, the intrinsically disordered MARCKS protein, caveolins, the β barrel assembly machine (BAM), an adhesion G-protein coupled receptor (aGPCR) and two lipid modifying enzymes - diacylglycerol kinase DGKε and fatty aldehyde dehydrogenase FALDH. This demonstrates how COMPOSEL communicates lipid interactivity as well as signaling mechanisms and binding of metabolites, drug molecules, polypeptides or nucleic acids to describe the operations of any protein. Moreover COMPOSEL can be scaled to express how genomes encode membrane structures and how our organs are infiltrated by pathogens such as SARS-CoV-2.

Overduin Michael, Kervin Troy A, Klarenbach Zachary, Adra Trixie Rae C, Bhat Rakesh K

2023-Feb-08

Bilayer insertion, Intrinsically disordered region, Ligand complex, Lipid interaction, Monotopic, Myristoylation, Palmitoylation, Peripheral membrane domain, Polytopic, Protein classification, Transmembrane

General General

Interpreting biologically informed neural networks for enhanced biomarker discovery and pathway analysis

bioRxiv Preprint

The advent of novel methods in mass spectrometry-based proteomics allows for the identification of biomarkers and biological pathways which are crucial for the understanding of complex diseases. However, contemporary analytical methods often omit essential information, such as protein abundance and protein co-regulation, and therefore miss crucial relationships in the data. Here, we introduce a generalized workflow that incorporates proteins, their abundances, and associated pathways into a deep learning-based methodology to improve biomarker identification and pathway analysis through the creation and interpretation of biologically informed neural networks (BINNs). We successfully employ BINNs to differentiate between two subphenotypes of septic acute kidney injury (AKI) and COVID-19 from the plasma proteome and utilize feature attribution-methods to introspect the networks to identify which proteins and pathways are important for distinguishing between subphenotypes. Compared to existing methods, BINNs achieved the highest predictive accuracy and revealed that metabolic processes were key to differentiating between septic AKI subphenotypes, while the immune system was more important to the classification of COVID-19 subphenotypes. The methodology behind creating, interpreting, and visualizing BINNs were implemented in a free and open source Python-package: https://github.com/InfectionMedicineProteomics/BINN.

Hartman, E.; Scott, A. M.; Malmström, L.; Malmström, J.

2023-02-21

General General

Multilingual Content Moderation: A Case Study on Reddit

ArXiv Preprint

Content moderation is the process of flagging content based on pre-defined platform rules. There has been a growing need for AI moderators to safeguard users as well as protect the mental health of human moderators from traumatic content. While prior works have focused on identifying hateful/offensive language, they are not adequate for meeting the challenges of content moderation since 1) moderation decisions are based on violation of rules, which subsumes detection of offensive speech, and 2) such rules often differ across communities which entails an adaptive solution. We propose to study the challenges of content moderation by introducing a multilingual dataset of 1.8 Million Reddit comments spanning 56 subreddits in English, German, Spanish and French. We perform extensive experimental analysis to highlight the underlying challenges and suggest related research problems such as cross-lingual transfer, learning under label noise (human biases), transfer of moderation models, and predicting the violated rule. Our dataset and analysis can help better prepare for the challenges and opportunities of auto moderation.

Meng Ye, Karan Sikka, Katherine Atwell, Sabit Hassan, Ajay Divakaran, Malihe Alikhani

2023-02-19

General General

Understanding how the use of AI decision support tools affect critical thinking and over-reliance on technology by drug dispensers in Tanzania

ArXiv Preprint

The use of AI in healthcare is designed to improve care delivery and augment the decisions of providers to enhance patient outcomes. When deployed in clinical settings, the interaction between providers and AI is a critical component for measuring and understanding the effectiveness of these digital tools on broader health outcomes. Even in cases where AI algorithms have high diagnostic accuracy, healthcare providers often still rely on their experience and sometimes gut feeling to make a final decision. Other times, providers rely unquestioningly on the outputs of the AI models, which leads to a concern about over-reliance on the technology. The purpose of this research was to understand how reliant drug shop dispensers were on AI-powered technologies when determining a differential diagnosis for a presented clinical case vignette. We explored how the drug dispensers responded to technology that is framed as always correct in an attempt to measure whether they begin to rely on it without any critical thought of their own. We found that dispensers relied on the decision made by the AI 25 percent of the time, even when the AI provided no explanation for its decision.

Ally Jr Salim, Megan Allen, Kelvin Mariki, Kevin James Masoy, Jafary Liana

2023-02-19

General General

Turning any bed into an intensive care unit with the Internet of things and artificial intelligence technology. Presenting the enhanced mechanical ventilator.

In F1000Research

The recent Coronavirus disease 2019 (COVID-19) pandemic displayed weaknesses in the healthcare infrastructures worldwide and exposed a lack of specialized personnel to cover the demands of a massive calamity. We have developed a portable ventilator that uses real-time vitals read from the patient to estimate -- through artificial intelligence -- the optimal operation point. The ventilator has redundant telecommunication capabilities; therefore, the remote assistance model can protect specialists and relatives from highly contagious agents. Additionally, we have designed a system that automatically publishes information in a proprietary cloud centralizer to keep physicians and relatives informed. The system was tested in a residential last-mile connection, and transaction times below the second were registered. The timing scheme allows us to operate up to 200 devices concurrently on these lowest-specification transmission control protocol/internet protocol (TCP/IP) services, promptly transmitting data for online processing and reporting. The ventilator is a proof of concept of automation that has behavioral and cognitive inputs to cheaply, yet reliably, extend the installed capacity of the healthcare systems and multiply the response of the skilled medical personnel to cover high-demanding scenarios and improve service quality.

Pulido Morales Leidy Lorena, Buitrago Romero Juan Sebastian, Ardila Sanchez Ismael A, Yepes-Calderon Fernando

2022

AWS implementations, Artificial Neuronal Networks in medicine, Artificial intelligence in medicine, Covid 19 mitigation, Evalu@ implementations, Intense care units everywhere, Technology in healthcare, mechanical ventilators

General General

Infrared image method for possible COVID-19 detection through febrile and subfebrile people screening.

In Journal of thermal biology

This study proposed an infrared image-based method for febrile and subfebrile people screening to comply with the society need for alternative, quick response, and effective methods for COVID-19 contagious people screening. The methodology consisted of: (i) Developing a method based on facial infrared imaging for possible COVID-19 early detection in people with and without fever (subfebrile state); (ii) Using 1206 emergency room (ER) patients to develop an algorithm for general application of the method, and (iii) Testing the method and algorithm effectiveness in 2558 cases (RT-qPCR tested for COVID-19) from 227,261 workers evaluations in five different countries. Artificial intelligence was used through a convolutional neural network (CNN) to develop the algorithm that took facial infrared images as input and classified the tested individuals in three groups: fever (high risk), subfebrile (medium risk), and no fever (low risk). The results showed that suspicious and confirmed COVID-19 (+) cases characterized by temperatures below the 37.5 °C fever threshold were identified. Also, average forehead and eye temperatures greater than 37.5 °C were not enough to detect fever similarly to the proposed CNN algorithm. Most RT-qPCR confirmed COVID-19 (+) cases found in the 2558 cases sample (17 cases/89.5%) belonged to the CNN selected subfebrile group. The COVID-19 (+) main risk factor was to be in the subfebrile group, in comparison to age, diabetes, high blood pressure, smoking and others. In sum, the proposed method was shown to be a potentially important new tool for COVID-19 (+) people screening for air travel and public places in general.

Brioschi Marcos Leal, Dalmaso Neto Carlos, Toledo Marcos de, Neves Eduardo Borba, Vargas José Viriato Coelho, Teixeira Manoel Jacobsen

2023-Feb

Artificial intelligence, Convolutional neural network, Infrared imaging

General General

An efficient method for qualitation and quantitation of multi-components of the herbal medicine Qingjin Yiqi Granules.

In Journal of pharmaceutical and biomedical analysis

Qingjin Yiqi Granules (QJYQ) is a Traditional Chinese Medicines (TCMs) prescription for the patients with post-COVID-19 condition. It is essential to carry out the quality evaluation of QJYQ. A comprehensive investigation was conducted by establishing deep-learning assisted mass defect filter (deep-learning MDF) mode for qualitative analysis, ultra-high performance liquid chromatography and scheduled multiple reaction monitoring method (UHPLC-sMRM) for precise quantitation to evaluate the quality of QJYQ. Firstly, a deep-learning MDF was used to classify and characterize the whole phytochemical components of QJYQ based on the mass spectrum (MS) data of ultra-high performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UHPLC-Q-TOF/MS). Secondly, the highly sensitive UHPLC-sMRM data-acquisition method was established to quantify the multi-ingredients of QJYQ. Totally, nine major types of phytochemical compounds in QJYQ were intelligently classified and 163 phytochemicals were initially identified. Furthermore, fifty components were rapidly quantified. The comprehensive evaluation strategy established in this study would provide an effective tool for accurately evaluating the quality of QJYQ as a whole.

Yang Xiaohua, Wang Shangqi, Qi Lina, Chen Shujing, Du Kunze, Shang Ye, Guo Jiading, Fang Shiming, Li Jin, Zhang Han, Chang Yanxu

2023-Feb-11

COVID-19, Deep-learning MDF, Qingjin Yiqi Granules, UHPLC-Q-TOF/MS, UHPLC-sMRM

Radiology Radiology

Deep Learning With Chest Radiographs for Making Prognoses in Patients With COVID-19: Retrospective Cohort Study.

In Journal of medical Internet research ; h5-index 88.0

BACKGROUND : An artificial intelligence (AI) model using chest radiography (CXR) may provide good performance in making prognoses for COVID-19.

OBJECTIVE : We aimed to develop and validate a prediction model using CXR based on an AI model and clinical variables to predict clinical outcomes in patients with COVID-19.

METHODS : This retrospective longitudinal study included patients hospitalized for COVID-19 at multiple COVID-19 medical centers between February 2020 and October 2020. Patients at Boramae Medical Center were randomly classified into training, validation, and internal testing sets (at a ratio of 8:1:1, respectively). An AI model using initial CXR images as input, a logistic regression model using clinical information, and a combined model using the output of the AI model (as CXR score) and clinical information were developed and trained to predict hospital length of stay (LOS) ≤2 weeks, need for oxygen supplementation, and acute respiratory distress syndrome (ARDS). The models were externally validated in the Korean Imaging Cohort of COVID-19 data set for discrimination and calibration.

RESULTS : The AI model using CXR and the logistic regression model using clinical variables were suboptimal to predict hospital LOS ≤2 weeks or the need for oxygen supplementation but performed acceptably in the prediction of ARDS (AI model area under the curve [AUC] 0.782, 95% CI 0.720-0.845; logistic regression model AUC 0.878, 95% CI 0.838-0.919). The combined model performed better in predicting the need for oxygen supplementation (AUC 0.704, 95% CI 0.646-0.762) and ARDS (AUC 0.890, 95% CI 0.853-0.928) compared to the CXR score alone. Both the AI and combined models showed good calibration for predicting ARDS (P=.079 and P=.859).

CONCLUSIONS : The combined prediction model, comprising the CXR score and clinical information, was externally validated as having acceptable performance in predicting severe illness and excellent performance in predicting ARDS in patients with COVID-19.

Lee Hyun Woo, Yang Hyun Jun, Kim Hyungjin, Kim Ue-Hwan, Kim Dong Hyun, Yoon Soon Ho, Ham Soo-Youn, Nam Bo Da, Chae Kum Ju, Lee Dabee, Yoo Jin Young, Bak So Hyeon, Kim Jin Young, Kim Jin Hwan, Kim Ki Beom, Jung Jung Im, Lim Jae-Kwang, Lee Jong Eun, Chung Myung Jin, Lee Young Kyung, Kim Young Seon, Lee Sang Min, Kwon Woocheol, Park Chang Min, Kim Yun-Hyeon, Jeong Yeon Joo, Jin Kwang Nam, Goo Jin Mo

2023-Feb-16

AI model, COVID-19, artificial intelligence, clinical outcome, deep learning, machine learning, medical imaging, prediction model, prognosis, radiography, thoracic

General General

Forecasting the concentration of NO2 using statistical and machine learning methods: A case study in the UAE.

In Heliyon

Nitrogen dioxide (NO2) is the most active pollutant gas emitted in the industrial era and is highly correlated with human activities. Tracking NO2 emissions and predicting their concentrations represent important steps toward controlling pollution and setting rules to protect people's health indoors, such as in factories, and in outdoor environments. The concentration of NO2 was affected by the COVID-19 lockdown period and decreased because of restrictions on outdoor activities. In this study, the concentration of NO2 was predicted at 14 ground stations in the United Arab Emirates (UAE) during December 2020 based on training over a full time period of two years (2019-2020). Statistical and machine learning models, such as autoregressive integrated moving average (ARIMA), seasonal autoregressive integrated moving average (SARIMA), long short-term memory (LSTM), and nonlinear autoregressive neural network (NAR-NN), are used with both open- and closed-loop architectures. The mean absolute percentage error (MAPE) was used to evaluate the performance of the models, and the results ranged from "very good" (MAPE of 8.64% at the Liwa station with the closed loop) to "acceptable" (MAPE of 42.45% at the Khadejah School station with the open loop). The results show that the predictions based on the open loop are generally better than those based on the closed loop because they yield statistically significantly lower MAPE values. For both loop types, we selected stations exhibiting the lowest, medium, and highest MAPE values as representative cases. In addition, we demonstrated that the MAPE value is highly correlated with the relative standard deviation of NO2 concentration values.

Al Yammahi Aishah, Aung Zeyar

2023-Feb

ARIMA, Classical statistics, LSTM, Machine learning, NAR, NO2, SARIMA

General General

DRaW: prediction of COVID-19 antivirals by deep learning-an objection on using matrix factorization.

In BMC bioinformatics

BACKGROUND : Due to the high resource consumption of introducing a new drug, drug repurposing plays an essential role in drug discovery. To do this, researchers examine the current drug-target interaction (DTI) to predict new interactions for the approved drugs. Matrix factorization methods have much attention and utilization in DTIs. However, they suffer from some drawbacks.

METHODS : We explain why matrix factorization is not the best for DTI prediction. Then, we propose a deep learning model (DRaW) to predict DTIs without having input data leakage. We compare our model with several matrix factorization methods and a deep model on three COVID-19 datasets. In addition, to ensure the validation of DRaW, we evaluate it on benchmark datasets. Furthermore, as an external validation, we conduct a docking study on the COVID-19 recommended drugs.

RESULTS : In all cases, the results confirm that DRaW outperforms matrix factorization and deep models. The docking results approve the top-ranked recommended drugs for COVID-19.

CONCLUSIONS : In this paper, we show that it may not be the best choice to use matrix factorization in the DTI prediction. Matrix factorization methods suffer from some intrinsic issues, e.g., sparsity in the domain of bioinformatics applications and fixed-unchanged size of the matrix-related paradigm. Therefore, we propose an alternative method (DRaW) that uses feature vectors rather than matrix factorization and demonstrates better performance than other famous methods on three COVID-19 and four benchmark datasets.

Hashemi S Morteza, Zabihian Arash, Hooshmand Mohsen, Gharaghani Sajjad

2023-Feb-15

COVID-19, Deep learning, Drug repurposing, Matrix factorization

General General

Efficient Classification of SARS-CoV-2 Spike Sequences Using Federated Learning

ArXiv Preprint

This paper presents a federated learning (FL) approach to train an AI model for SARS-Cov-2 coronavirus variant identification. We analyze the SARS-CoV-2 spike sequences in a distributed way, without data sharing, to detect different variants of the rapidly mutating coronavirus. A vast amount of sequencing data of SARS-CoV-2 is available due to various genomic monitoring initiatives by several nations. However, privacy concerns involving patient health information and national public health conditions could hinder openly sharing this data. In this work, we propose a lightweight FL paradigm to cooperatively analyze the spike protein sequences of SARS-CoV-2 privately, using the locally stored data to train a prediction model from remote nodes. Our method maintains the confidentiality of local data (that could be stored in different locations) yet allows us to reliably detect and identify different known and unknown variants of the novel coronavirus SARS-CoV-2. We compare the performance of our approach on spike sequence data with the recently proposed state-of-the-art methods for classification from spike sequences. Using the proposed approach, we achieve an overall accuracy of $93\%$ on the coronavirus variant identification task. To the best of our knowledge, this is the first work in the federated learning paradigm for biological sequence analysis. Since the proposed model is distributed in nature, it could scale on ``Big Data'' easily. We plan to use this proof-of-concept to implement a privacy-preserving pandemic response strategy.

Prakash Chourasia, Taslim Murad, Zahra Tayebi, Sarwan Ali, Imdad Ullah Khan, Murray Patterson

2023-02-17

General General

LDANet: Automatic lung parenchyma segmentation from CT images.

In Computers in biology and medicine

Automatic segmentation of the lung parenchyma from computed tomography (CT) images is helpful for the subsequent diagnosis and treatment of patients. In this paper, based on a deep learning algorithm, a lung dense attention network (LDANet) is proposed with two mechanisms: residual spatial attention (RSA) and gated channel attention (GCA). RSA is utilized to weight the spatial information of the lung parenchyma and suppress feature activation in irrelevant regions, while the weights of each channel are adaptively calibrated using GCA to implicitly predict potential key features. Then, a dual attention guidance module (DAGM) is designed to maximize the integration of the advantages of both mechanisms. In addition, LDANet introduces a lightweight dense block (LDB) that reuses feature information and a positioned transpose block (PTB) that realizes accurate positioning and gradually restores the image resolution until the predicted segmentation map is generated. Experiments are conducted on two public datasets, LIDC-IDRI and COVID-19 CT Segmentation, on which LDANet achieves Dice similarity coefficient values of 0.98430 and 0.98319, respectively, outperforming a state-of-the-art lung segmentation model. Additionally, the effectiveness of the main components of LDANet is demonstrated through ablation experiments.

Chen Ying, Feng Longfeng, Zheng Cheng, Zhou Taohui, Liu Lan, Liu Pengfei, Chen Yi

2023-Feb-10

CT images, DAGM, LDB, Lung parenchyma segmentation

General General

Artificial intelligence assessment of the potential of tocilizumab along with corticosteroids therapy for the management of COVID-19 evoked acute respiratory distress syndrome.

In PloS one ; h5-index 176.0

Acute respiratory distress syndrome (ARDS), associated with high mortality rate, affects up to 67% of hospitalized COVID-19 patients. Early evidence indicated that the pathogenesis of COVID-19 evoked ARDS is, at least partially, mediated by hyperinflammatory cytokine storm in which interleukin 6 (IL-6) plays an essential role. The corticosteroid dexamethasone is an effective treatment for severe COVID-19 related ARDS. However, trials of other immunomodulatory therapies, including anti-IL6 agents such as tocilizumab and sarilumab, have shown limited evidence of benefit as monotherapy. But recently published large trials have reported added benefit of tocilizumab in combination with dexamethasone in severe COVID-19 related ARDS. In silico tools can be useful to shed light on the mechanisms evoked by SARS-CoV-2 infection and of the potential therapeutic approaches. Therapeutic performance mapping system (TPMS), based on systems biology and artificial intelligence, integrate available biological, pharmacological and medical knowledge to create mathematical models of the disease. This technology was used to identify the pharmacological mechanism of dexamethasone, with or without tocilizumab, in the management of COVID-19 evoked ARDS. The results showed that while dexamethasone would be addressing a wider range of pathological processes with low intensity, tocilizumab might provide a more direct and intense effect upon the cytokine storm. Based on this in silico study, we conclude that the use of tocilizumab alongside dexamethasone is predicted to induce a synergistic effect in dampening inflammation and subsequent pathological processes, supporting the beneficial effect of the combined therapy in critically ill patients. Future research will allow identifying the ideal subpopulation of patients that would benefit better from this combined treatment.

Segú-Vergés Cristina, Artigas Laura, Coma Mireia, Peck Richard W

2023

General General

Using machine learning to improve our understanding of COVID-19 infection in children.

In PloS one ; h5-index 176.0

PURPOSE : Children are at elevated risk for COVID-19 (SARS-CoV-2) infection due to their social behaviors. The purpose of this study was to determine if usage of radiological chest X-rays impressions can help predict whether a young adult has COVID-19 infection or not.

METHODS : A total of 2572 chest impressions from 721 individuals under the age of 18 years were considered for this study. An ensemble learning method, Random Forest Classifier (RFC), was used for classification of patients suffering from infection.

RESULTS : Five RFC models were implemented with incremental features and the best model achieved an F1-score of 0.79 with Area Under the ROC curve as 0.85 using all input features. Hyper parameter tuning and cross validation was performed using grid search cross validation and SHAP model was used to determine feature importance. The radiological features such as pneumonia, small airways disease, and atelectasis (confounded with catheter) were found to be highly associated with predicting the status of COVID-19 infection.

CONCLUSIONS : In this sample, radiological X-ray films can predict the status of COVID-19 infection with good accuracy. The multivariate model including symptoms presented around the time of COVID-19 test yielded good prediction score.

Piparia Shraddha, Defante Andrew, Tantisira Kelan, Ryu Julie

2023

General General

Examining Rural and Urban Sentiment Difference in COVID-19-Related Topics on Twitter: Word Embedding-Based Retrospective Study.

In Journal of medical Internet research ; h5-index 88.0

BACKGROUND : By the end of 2022, more than 100 million people were infected with COVID-19 in the United States, and the cumulative death rate in rural areas (383.5/100,000) was much higher than in urban areas (280.1/100,000). As the pandemic spread, people used social media platforms to express their opinions and concerns about COVID-19-related topics.

OBJECTIVE : This study aimed to (1) identify the primary COVID-19-related topics in the contiguous United States communicated over Twitter and (2) compare the sentiments urban and rural users expressed about these topics.

METHODS : We collected tweets containing geolocation data from May 2020 to January 2022 in the contiguous United States. We relied on the tweets' geolocations to determine if their authors were in an urban or rural setting. We trained multiple word2vec models with several corpora of tweets based on geospatial and timing information. Using a word2vec model built on all tweets, we identified hashtags relevant to COVID-19 and performed hashtag clustering to obtain related topics. We then ran an inference analysis for urban and rural sentiments with respect to the topics based on the similarity between topic hashtags and opinion adjectives in the corresponding urban and rural word2vec models. Finally, we analyzed the temporal trend in sentiments using monthly word2vec models.

RESULTS : We created a corpus of 407 million tweets, 350 million (86%) of which were posted by users in urban areas, while 18 million (4.4%) were posted by users in rural areas. There were 2666 hashtags related to COVID-19, which clustered into 20 topics. Rural users expressed stronger negative sentiments than urban users about COVID-19 prevention strategies and vaccination (P<.001). Moreover, there was a clear political divide in the perception of politicians by urban and rural users; these users communicated stronger negative sentiments about Republican and Democratic politicians, respectively (P<.001). Regarding misinformation and conspiracy theories, urban users exhibited stronger negative sentiments about the "covidiots" and "China virus" topics, while rural users exhibited stronger negative sentiments about the "Dr. Fauci" and "plandemic" topics. Finally, we observed that urban users' sentiments about the economy appeared to transition from negative to positive in late 2021, which was in line with the US economic recovery.

CONCLUSIONS : This study demonstrates there is a statistically significant difference in the sentiments of urban and rural Twitter users regarding a wide range of COVID-19-related topics. This suggests that social media can be relied upon to monitor public sentiment during pandemics in disparate types of regions. This may assist in the geographically targeted deployment of epidemic prevention and management efforts.

Liu Yongtai, Yin Zhijun, Ni Congning, Yan Chao, Wan Zhiyu, Malin Bradley

2023-Feb-15

COVID-19, Twitter, data, epidemic, machine learning, management, model, prevention, rural, sentiment analysis, social media, topic analysis, training, urban, vaccination, word embedding

General General

Grayscale Image Statistical Attributes Effectively Distinguish the Severity of Lung Abnormalities in CT Scan Slices of COVID-19 Patients.

In SN computer science

Grayscale statistical attributes analysed for 513 extract images taken from pulmonary computed tomography (CT) scan slices of 57 individuals (49 confirmed COVID-19 positive; eight confirmed COVID-19 negative) are able to accurately predict a visual score (VS from 0 to 4) used by a clinician to assess the severity of lung abnormalities in the patients. Some of these attributes can be used graphically to distinguish useful but overlapping distributions for the VS classes. Using machine and deep learning (ML/DL) algorithms with twelve grayscale image attributes as inputs enables the VS classes to be accurately distinguished. A convolutional neural network achieves this with better than 96% accuracy (only 18 images misclassified out of 513) on a supervised learning basis. Analysis of confusion matrices enables the VS prediction performance of ML/DL algorithms to be explored in detail. Those matrices demonstrate that the best performing ML/DL algorithms successfully distinguish between VS classes 0 and 1, which clinicians cannot readily do with the naked eye. Just five image grayscale attributes can also be used to generate an algorithmically defined scoring system (AS) that can also graphically distinguish the degree of pulmonary impacts in the dataset evaluated. The AS classification illustrated involves less overlap between its classes than the VS system and could be exploited as an automated expert system. The best-performing ML/DL models are able to predict the AS classes with better than 99% accuracy using twelve grayscale attributes as inputs. The decision tree and random forest algorithms accomplish that distinction with just one classification error in the 513 images tested.

Ghashghaei Sara, Wood David A, Sadatshojaei Erfan, Jalilpoor Mansooreh

2023

COVID-19 lung abnormalities, Computed tomography (CT) scan analysis, Confusion matrices, Grayscale image attributes, Machine and deep learning predictions, Visual and algorithmic classifications

General General

A multimodal facial cues based engagement detection system in e-learning context using deep learning approach.

In Multimedia tools and applications

Due to the COVID-19 crisis, the education sector has been shifted to a virtual environment. Monitoring the engagement level and providing regular feedback during e-classes is one of the major concerns, as this facility lacks in the e-learning environment due to no physical observation of the teacher. According to present study, an engagement detection system to ensure that the students get immediate feedback during e-Learning. Our proposed engagement system analyses the student's behaviour throughout the e-Learning session. The proposed novel approach evaluates three modalities based on the student's behaviour, such as facial expression, eye blink count, and head movement, from the live video streams to predict student engagement in e-learning. The proposed system is implemented based on deep-learning approaches such as VGG-19 and ResNet-50 for facial emotion recognition and the facial landmark approach for eye-blinking and head movement detection. The results from different modalities (for which the algorithms are proposed) are combined to determine the EI (engagement index). Based on EI value, an engaged or disengaged state is predicted. The present study suggests that the proposed facial cues-based multimodal system accurately determines student engagement in real time. The experimental research achieved an accuracy of 92.58% and showed that the proposed engagement detection approach significantly outperforms the existing approaches.

Gupta Swadha, Kumar Parteek, Tekchandani Rajkumar

2023-Feb-10

Deep learning, Emotion detection, Engagement detection, Eye-blinking, Facial expressions, Head-movement, Online learning, Real-time

Public Health Public Health

A Potential Role of the Spike Protein in Neurodegenerative Diseases: A Narrative Review.

In Cureus

Human prion protein and prion-like protein misfolding are widely recognized as playing a causal role in many neurodegenerative diseases. Based on in vitro and in vivo experimental evidence relating to prion and prion-like disease, we extrapolate from the compelling evidence that the spike glycoprotein of SARS-CoV-2 contains extended amino acid sequences characteristic of a prion-like protein to infer its potential to cause neurodegenerative disease. We propose that vaccine-induced spike protein synthesis can facilitate the accumulation of toxic prion-like fibrils in neurons. We outline various pathways through which these proteins could be expected to distribute throughout the body. We review both cellular pathologies and the expression of disease that could become more frequent in those who have undergone mRNA vaccination. Specifically, we describe the spike protein's contributions, via its prion-like properties, to neuroinflammation and neurodegenerative diseases; to clotting disorders within the vasculature; to further disease risk due to suppressed prion protein regulation in the context of widely prevalent insulin resistance; and to other health complications. We explain why these prion-like characteristics are more relevant to vaccine-related mRNA-induced spike proteins than natural infection with SARS-CoV-2. We note with an optimism an apparent loss of prion-like properties among the current Omicron variants. We acknowledge that the chain of pathological events described throughout this paper is only hypothetical and not yet verified. We also acknowledge that the evidence we usher in, while grounded in the research literature, is currently largely circumstantial, not direct. Finally, we describe the implications of our findings for the general public, and we briefly discuss public health recommendations we feel need urgent consideration. An earlier version of this article was previously posted to the Authorea preprint server on August 16, 2022.

Seneff Stephanie, Kyriakopoulos Anthony M, Nigh Greg, McCullough Peter A

2023-Feb

amyloidosis, cd16+ monocytes, diabetes, exosomes, g quadruplexes, mrna vaccines, neurodegeneration, prion disease, sars-cov-2, spike protein

Public Health Public Health

Scientific novelty beyond the experiment.

In Microbial biotechnology

Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.

Hallsworth John E, Udaondo Zulema, Pedrós-Alió Carlos, Höfer Juan, Benison Kathleen C, Lloyd Karen G, Cordero Radamés J B, de Campos Claudia B L, Yakimov Michail M, Amils Ricardo

2023-Feb-14

General General

A novel firefly algorithm approach for efficient feature selection with COVID-19 dataset.

In Microprocessors and microsystems

Feature selection is one of the most important challenges in machine learning and data science. This process is usually performed in the data preprocessing phase, where the data is transformed to a proper format for further operations by machine learning algorithm. Many real-world datasets are highly dimensional with many irrelevant, even redundant features. These kinds of features do not improve classification accuracy and can even shrink down performance of a classifier. The goal of feature selection is to find optimal (or sub-optimal) subset of features that contain relevant information about the dataset from which machine learning algorithms can derive useful conclusions. In this manuscript, a novel version of firefly algorithm (FA) is proposed and adapted for feature selection challenge. Proposed method significantly improves performance of the basic FA, and also outperforms other state-of-the-art metaheuristics for both, benchmark bound-constrained and practical feature selection tasks. Method was first validated on standard unconstrained benchmarks and later it was applied for feature selection by using 21 standard University of California, Irvine (UCL) datasets. Moreover, presented approach was also tested for relatively novel COVID-19 dataset for predicting patients health, and one microcontroller microarray dataset. Results obtained in all practical simulations attest robustness and efficiency of proposed algorithm in terms of convergence, solutions' quality and classification accuracy. More precisely, the proposed approach obtained the best classification accuracy on 13 out of 21 total datasets, significantly outperforming other competitor methods.

Bacanin Nebojsa, Venkatachalam K, Bezdan Timea, Zivkovic Miodrag, Abouhawwash Mohamed

2023-Apr

COVID-19 dataset, Feature selection, Firefly algorithm, Genetic operators, Quasi-reflection-based learning, Swarm intelligence

General General

Transcriptomics secondary analysis of severe human infection with SARS-CoV-2 identifies gene expression changes and predicts three transcriptional biomarkers in leukocytes.

In Computational and structural biotechnology journal

SARS-CoV-2 is the causative agent of COVID-19, which has greatly affected human health since it first emerged. Defining the human factors and biomarkers that differentiate severe SARS-CoV-2 infection from mild infection has become of increasing interest to clinicians. To help address this need, we retrieved 269 public RNA-seq human transcriptome samples from GEO that had qualitative disease severity metadata. We then subjected these samples to a robust RNA-seq data processing workflow to calculate gene expression in PBMCs, whole blood, and leukocytes, as well as to predict transcriptional biomarkers in PBMCs and leukocytes. This process involved using Salmon for read mapping, edgeR to calculate significant differential expression levels, and gene ontology enrichment using Camera. We then performed a random forest machine learning analysis on the read counts data to identify genes that best classified samples based on the COVID-19 severity phenotype. This approach produced a ranked list of leukocyte genes based on their Gini values that includes TGFBI, TTYH2, and CD4, which are associated with both the immune response and inflammation. Our results show that these three genes can potentially classify samples with severe COVID-19 with accuracy of ∼88% and an area under the receiver operating characteristic curve of 92.6--indicating acceptable specificity and sensitivity. We expect that our findings can help contribute to the development of improved diagnostics that may aid in identifying severe COVID-19 cases, guide clinical treatment, and improve mortality rates.

Clancy Jeffrey, Hoffmann Curtis S, Pickett Brett E

2023

AUC, Area under the curve, Bioinformatics, Biomarkers, COVID-19, COVID-19, Coronavirus Disease of 2019, DEG, Differentially expressed gene, Data mining, GEO, Gene Expression Omnibus, GO, Gene Ontology, RNA, RNA-sequencing, ROC, Receiver-operator characteristic, SARS-CoV-2, SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2, Virus

General General

Systematic review of MCDM approach applied to the medical case studies of COVID-19: trends, bibliographic analysis, challenges, motivations, recommendations, and future directions.

In Complex & intelligent systems

When COVID-19 spread in China in December 2019, thousands of studies have focused on this pandemic. Each presents a unique perspective that reflects the pandemic's main scientific disciplines. For example, social scientists are concerned with reducing the psychological impact on the human mental state especially during lockdown periods. Computer scientists focus on establishing fast and accurate computerized tools to assist in diagnosing, preventing, and recovering from the disease. Medical scientists and doctors, or the frontliners, are the main heroes who received, treated, and worked with the millions of cases at the expense of their own health. Some of them have continued to work even at the expense of their lives. All these studies enforce the multidisciplinary work where scientists from different academic disciplines (social, environmental, technological, etc.) join forces to produce research for beneficial outcomes during the crisis. One of the many branches is computer science along with its various technologies, including artificial intelligence, Internet of Things, big data, decision support systems (DSS), and many more. Among the most notable DSS utilization is those related to multicriterion decision making (MCDM), which is applied in various applications and across many contexts, including business, social, technological and medical. Owing to its importance in developing proper decision regimens and prevention strategies with precise judgment, it is deemed a noteworthy topic of extensive exploration, especially in the context of COVID-19-related medical applications. The present study is a comprehensive review of COVID-19-related medical case studies with MCDM using a systematic review protocol. PRISMA methodology is utilized to obtain a final set of (n = 35) articles from four major scientific databases (ScienceDirect, IEEE Xplore, Scopus, and Web of Science). The final set of articles is categorized into taxonomy comprising five groups: (1) diagnosis (n = 6), (2) safety (n = 11), (3) hospital (n = 8), (4) treatment (n = 4), and (5) review (n = 3). A bibliographic analysis is also presented on the basis of annual scientific production, country scientific production, co-occurrence, and co-authorship. A comprehensive discussion is also presented to discuss the main challenges, motivations, and recommendations in using MCDM research in COVID-19-related medial case studies. Lastly, we identify critical research gaps with their corresponding solutions and detailed methodologies to serve as a guide for future directions. In conclusion, MCDM can be utilized in the medical field effectively to optimize the resources and make the best choices particularly during pandemics and natural disasters.

Alamoodi A H, Zaidan B B, Albahri O S, Garfan Salem, Ahmaro Ibraheem Y Y, Mohammed R T, Zaidan A A, Ismail Amelia Ritahani, Albahri A S, Momani Fayiz, Al-Samarraay Mohammed S, Jasim Ali Najm

2023-Feb-03

COVID-19, Data privacy, Federated learning, Monoclonal antibodies, Multi-criterion decision making, Treatment

General General

The Effect of Machine Learning Algorithms on the Prediction of Layer-by-Layer Coating Properties.

In ACS omega

Layer-by-layer film (LbL) coatings made of polyelectrolytes are a powerful tool for surface modification, including the applications in the biomedical field, for food packaging, and in many electrochemical systems. However, despite the number of publications related to LbL assembly, predicting LbL coating properties represents quite a challenge, can take a long time, and be very costly. Machine learning (ML) methodologies that are now emerging can accelerate and improve new coating development and potentially revolutionize the field. Recently, we have demonstrated a preliminary ML-based model for coating thickness prediction. In this paper, we compared several ML algorithms for optimizing a methodology for coating thickness prediction, namely, linear regression, Support Vector Regressor, Random Forest Regressor, and Extra Tree Regressor. The current research has shown that learning algorithms are effective in predicting the coating output value, with the Extra Tree Regressor algorithm demonstrating superior predictive performance, when used in combination with optimized hyperparameters and with missing data imputation. The best predictors of the coating thickness were determined, and they can be later used to accurately predict coating thickness, avoiding measurement of multiple parameters. The development of optimized methodologies will ensure different reliable predictive models for coating property/function relations. As a continuation, the methodology can be adapted and used for predicting the outputs connected to antimicrobial, anti-inflammatory, and antiviral properties in order to be able to respond to actual biomedical problems such as antibiotic resistance, implant rejection, or COVID-19 outbreak.

Šušteršič Tijana, Gribova Varvara, Nikolic Milica, Lavalle Philippe, Filipovic Nenad, Vrana Nihal Engin

2023-Feb-07

General General

Improved Reptile Search Algorithm by Salp Swarm Algorithm for Medical Image Segmentation.

In Journal of bionic engineering

This study proposes a novel nature-inspired meta-heuristic optimizer based on the Reptile Search Algorithm combed with Salp Swarm Algorithm for image segmentation using gray-scale multi-level thresholding, called RSA-SSA. The proposed method introduces a better search space to find the optimal solution at each iteration. However, we proposed RSA-SSA to avoid the searching problem in the same area and determine the optimal multi-level thresholds. The obtained solutions by the proposed method are represented using the image histogram. The proposed RSA-SSA employed Otsu's variance class function to get the best threshold values at each level. The performance measure for the proposed method is valid by detecting fitness function, structural similarity index, peak signal-to-noise ratio, and Friedman ranking test. Several benchmark images of COVID-19 validate the performance of the proposed RSA-SSA. The results showed that the proposed RSA-SSA outperformed other metaheuristics optimization algorithms published in the literature.

Abualigah Laith, Habash Mahmoud, Hanandeh Essam Said, Hussein Ahmad MohdAziz, Shinwan Mohammad Al, Zitar Raed Abu, Jia Heming

2023-Feb-07

Bioinspired, Image segmentation, Meta-heuristic algorithm, Multi-level thresholding, Reptile Search Algorithm, Salp Swarm Algorithm

Public Health Public Health

Governing AI during a pandemic crisis: Initiatives at the EU level.

In Technology in society

After the outbreak of Covid-19, the European Commission (EC) promptly took the initiative to lead and coordinate a common European response. The actions unfolded in several directions, paving the way to the uptake of AI-related solutions and placing hope in these tools to face crises, namely of a public health and global nature. In this article, we focus on initiatives for the uptake of AI-related solutions from the experimental level towards implementation. The Repository of AI and Robotics solutions, launched in 2020, is an example of an initiative put forth to leverage and disseminate knowledge on AI, expanding the fields of application and fostering the development and adaptation of cutting-edge technologies to explore how they can assist in tackling specific tasks during a public health crisis. Using this database, the article outlines AI as a hope for handling specific needs and tasks thus supporting humans in overcoming obstacles and improving the chances for an effective response. Other initiatives frame the uptake of AI from a regulatory and risk mitigation perspective, focusing on establishing frameworks for AI governance in an ethical and trustworthy manner by defining principles and standards that aim to protect the underlying values deemed fundamental. A third approach intends to portray how AI is more than a promise and has proved its role in global geographies through investment, successful testing and adoption.

Fontes Catarina, Corrigan Caitlin, Lütge Christoph

2023-Feb-03

AI Ethics, AI Governance, Artificial intelligence, Covid-19, Robotics

General General

An optimized EBRSA-Bi LSTM model for highly undersampled rapid CT image reconstruction.

In Biomedical signal processing and control

COVID-19 has spread all over the world, causing serious panic around the globe. Chest computed tomography (CT) images are integral in confirming COVID positive patients. Several investigations were conducted to improve or maintain the image reconstruction quality for the sample image reconstruction. Deep learning (DL) methods have recently been proposed to achieve fast reconstruction, but many have focused on a single domain, such as the image domain of k-space. In this research, the highly under-sampled enhanced battle royale self-attention based bi-directional long short-term (EBRSA-bi LSTM) CT image reconstruction model is proposed to reconstruct the image from the under-sampled data. The research is adapted with two phases, namely, pre-processing and reconstruction. The extended cascaded filter (ECF) is proposed for image pre-processing and tends to suppress the noise and enhance the reconstruction accuracy. In the reconstruction model, the battle royale optimization (BrO) is intended to diminish the loss function of the reconstruction network model and weight updation. The proposed model is tested with two datasets, COVID-CT- and SARS-CoV-2 CT. The reconstruction accuracy of the proposed model with two datasets is 93.5 % and 97.7 %, respectively. Also, the image quality assessment parameters such as Peak-Signal to Noise Ratio (PSNR), Root Mean Square Error (RMSE) and Structural Similarity Index metric (SSIM) are evaluated, and it yields an outcome of (45 and 46 dB), (0.0026 and 0.0022) and (0.992, 0.996) with two datasets.

Sarvari A V P, Sridevi K

2023-May

Computed tomography (CT), Deep learning, Image reconstruction, K-space data, Under-sampling

General General

Improved autoregressive integrated moving average model for COVID-19 prediction by using statistical significance and clustering techniques.

In Heliyon

PURPOSE : The COVID-19 pandemic has affected more than 192 countries. The condition results in a respiratory illness (e.g., influenza) with signs and symptoms such as cold, cough, fever, and breathing difficulties. Predicting new instances of COVID-19 is always a challenging task.

METHODS : This study improved the autoregressive integrated moving average (ARIMA)-based time series prediction model by incorporating statistical significance for feature selection and k-means clustering for outlier detection. The accuracy of the improved model (ARIMAI) was examined using World Health Organization's official data on the COVID-19 pandemic worldwide and compared with that of many modern, cutting-edge algorithms.

RESULTS : The ARIMAI model (RSS score = 0.279, accuracy = 97.75%) outperformed the current ARIMA model (RSS score = 0.659, accuracy = 93%).

CONCLUSIONS : The ARIMAI model is not only an efficient but also a rapid and simple technique to forecast COVID-19 trends. The usage of this model enables the prediction of any disease that will affect patients in the future pandemics.

Ilu Saratu Yusuf, Prasad Rajesh

2023-Feb

ARIMA, And clustering, Coronavirus, Feature selection, Machine learning, Prediction

Surgery Surgery

Elevated IFNA1 and suppressed IL12p40 associated with persistent hyperinflammation in COVID-19 pneumonia.

In Frontiers in immunology ; h5-index 100.0

INTRODUCTION : Despite of massive endeavors to characterize inflammation in COVID-19 patients, the core network of inflammatory mediators responsible for severe pneumonia stillremain remains elusive.

METHODS : Here, we performed quantitative and kinetic analysis of 191 inflammatory factors in 955 plasma samples from 80 normal controls (sample n = 80) and 347 confirmed COVID-19 pneumonia patients (sample n = 875), including 8 deceased patients.

RESULTS : Differential expression analysis showed that 76% of plasmaproteins (145 factors) were upregulated in severe COVID-19 patients comparedwith moderate patients, confirming overt inflammatory responses in severe COVID-19 pneumonia patients. Global correlation analysis of the plasma factorsrevealed two core inflammatory modules, core I and II, comprising mainly myeloid cell and lymphoid cell compartments, respectively, with enhanced impact in a severity-dependent manner. We observed elevated IFNA1 and suppressed IL12p40, presenting a robust inverse correlation in severe patients, which was strongly associated with persistent hyperinflammation in 8.3% of moderate pneumonia patients and 59.4% of severe patients.

DISCUSSION : Aberrant persistence of pulmonary and systemic inflammation might be associated with long COVID-19 sequelae. Our comprehensive analysis of inflammatory mediators in plasmarevealed the complexity of pneumonic inflammation in COVID-19 patients anddefined critical modules responsible for severe pneumonic progression.

Jeon Kyeongseok, Kim Yuri, Kang Shin Kwang, Park Uni, Kim Jayoun, Park Nanhee, Koh Jaemoon, Shim Man-Shik, Kim Minsoo, Rhee Youn Ju, Jeong Hyeongseok, Lee Siyoung, Park Donghyun, Lim Jinyoung, Kim Hyunsu, Ha Na-Young, Jo Hye-Yeong, Kim Sang Cheol, Lee Ju-Hee, Shon Jiwon, Kim Hoon, Jeon Yoon Kyung, Choi Youn-Soo, Kim Hye Young, Lee Won-Woo, Choi Murim, Park Hyun-Young, Park Woong-Yang, Kim Yeon-Sook, Cho Nam-Hyuk

2023

COVID-19, IFNa, IL-12p40, SARS-CoV-2, inflammation, pneumonia

Public Health Public Health

Machine-learning prediction of BMI change among doctors and nurses in North China during the COVID-19 pandemic.

In Frontiers in nutrition

OBJECTIVE : The COVID-19 pandemic has become a major public health concern over the past 3 years, leading to adverse effects on front-line healthcare workers. This study aimed to develop a Body Mass Index (BMI) change prediction model among doctors and nurses in North China during the COVID-19 pandemic, and further identified the predicting effects of lifestyles, sleep quality, work-related conditions, and personality traits on BMI change.

METHODS : The present study was a cross-sectional study conducted in North China, during May-August 2022. A total of 5,400 doctors and nurses were randomly recruited from 39 COVID-19 designated hospitals and 5,271 participants provided valid responses. Participants' data related to social-demographics, dietary behavior, lifestyle, sleep, personality, and work-related conflicts were collected with questionnaires. Deep Neural Network (DNN) was applied to develop a BMI change prediction model among doctors and nurses during the COVID-19 pandemic.

RESULTS : Of participants, only 2,216 (42.0%) individuals kept a stable BMI. Results showed that personality traits, dietary behaviors, lifestyles, sleep quality, burnout, and work-related conditions had effects on the BMI change among doctors and nurses. The prediction model for BMI change was developed with a 33-26-20-1 network framework. The DNN model achieved high prediction efficacy, and values of R 2, MAE, MSE, and RMSE for the model were 0.940, 0.027, 0.002, and 0.038, respectively. Among doctors and nurses, the top five predictors in the BMI change prediction model were unbalanced nutritional diet, poor sleep quality, work-family conflict, lack of exercise, and soft drinks consumption.

CONCLUSION : During the COVID-19 pandemic, BMI change was highly prevalent among doctors and nurses in North China. Machine learning models can provide an automated identification mechanism for the prediction of BMI change. Personality traits, dietary behaviors, lifestyles, sleep quality, burnout, and work-related conditions have contributed to the BMI change prediction. Integrated treatment measures should be taken in the management of weight and BMI by policymakers, hospital administrators, and healthcare workers.

Wang Qihe, Chu Haiyun, Qu Pengfeng, Fang Haiqin, Liang Dong, Liu Sana, Li Jinliang, Liu Aidong

2023

BMI change, COVID-19 pandemic, China, doctors and nurses, machine learning

General General

A Survey on harnessing the Applications of Mobile Computing in Healthcare during the COVID-19 Pandemic: Challenges and Solutions.

In Computer networks

The COVID-19 pandemic ravaged almost every walk of life but it triggered many challenges for the healthcare system, globally. Different cutting-edge technologies such as Internet of things (IoT), machine learning, Virtual Reality (VR), Big data, Blockchain etc. have been adopted to cope with this menace. In this regard, various surveys have been conducted to highlight the importance of these technologies. However, among these technologies, the role of mobile computing is of paramount importance which is not found in the existing literature. Hence, this survey in mainly targeted to highlight the significant role of mobile computing in alleviating the impacts of COVID-19 in healthcare sector. The major applications of mobile computing such as software-based solutions, hardware-based solutions and wireless communication-based support for diagnosis, prevention, self-symptom reporting, contact tracing, social distancing, telemedicine and treatment related to coronavirus are discussed in detailed and comprehensive fashion. A state-of-the-art work is presented to identify the challenges along with possible solutions in adoption of mobile computing with respect to COVID-19 pandemic. Hopefully, this research will help the researchers, policymakers and healthcare professionals to understand the current research gaps and future research directions in this domain. To the best level of our knowledge, this is the first survey of its type to address the COVID-19 pandemic by exploring the holistic contribution of mobile computing technologies in healthcare area.

Ali Yasir, Khan Habib Ullah

2023-Apr

COVID-19, Coronavirus, Healthcare, Mobile computing, Pervasive computing, SARS-COV-2

General General

Predicting the antigenic evolution of SARS-COV-2 with deep learning

bioRxiv Preprint

The severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) antigenic profile evolves in response to the vaccine and natural infection-derived immune pressure, resulting in immune escape and threatening public health. Exploring the possible antigenic evolutionary potentials improves public health preparedness, but it is limited by the lack of experimental assays as the sequence space is exponentially large. Here we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithm to model the viral fitness landscape and explore the antigenic evolution via in silico directed evolution. As demonstrated by existing SARS-COV-2 variants, MLAEP can infer the order of variants along antigenic evolutionary trajectories, which is also strongly correlated with their sampling time. The novel mutations predicted by MLAEP are also found in immunocompromised covid patients and newly emerging variants, like XBB1.5. The predictions of MLAEP were validated by conducting in vitro neutralizing antibody binding assay, which demonstrated that the model-generated variants displayed significantly increased immune evasion ability compared with the controls. In sum, our approach enables profiling existing variants and forecasting prospective antigenic variants, thus may help guide the development of vaccines and increase preparedness against future variants. Our model is available at https://mlaep.cbrc.kaust.edu.sa.

Han, W.; Chen, N.; Xu, X.; Sahil, A.; Zhou, J.; Li, Z.; Zhong, H.; Gao, E.; Zhang, R.; Wang, Y.; Sun, S.; Gao, X.; Cheung, P. P.-H.

2023-02-14

Public Health Public Health

Home alone: A population neuroscience investigation of brain morphology substrates.

In NeuroImage ; h5-index 117.0

As a social species, ready exchange with peers is a pivotal asset - our "social capital". Yet, single-person households have come to pervade metropolitan cities worldwide, with unknown consequences in the long run. Here, we systematically explore the morphological manifestations associated with singular living in ∼40,000 UK Biobank participants. The uncovered population-level signature spotlights the highly associative default mode network, in addition to findings such as in the amygdala central, cortical and corticoamygdaloid nuclei groups, as well as the hippocampal fimbria and dentate gyrus. Both positive effects, equating to greater gray matter volume associated with living alone, and negative effects, which can be interpreted as greater grey matter associations with not living alone, were found across the cortex and subcortical structures Sex-stratified analyses revealed male-specific neural substrates, including somatomotor, saliency and visual systems, while female-specific neural substrates centred on the dorsomedial prefrontal cortex. In line with our demographic profiling results, the discovered neural pattern of living alone is potentially linked to alcohol and tobacco consumption, anxiety, sleep quality as well as daily TV watching. The persistent trend for solitary living will require new answers from public-health decision makers. SIGNIFICANCE STATEMENT: Living alone has profound consequences for mental and physical health. Despite this, there has been a rapid increase in single-person households worldwide, with the long-term consequences yet unknown. In the largest study of its kind, we investigate how the objective lack of everyday social interaction, through living alone, manifests in the brain. Our population neuroscience approach uncovered a gray matter signature that converged on the 'default network', alongside targeted subcortical, sex and demographic profiling analyses. The human urge for social relationships is highlighted by the evolving COVID-19 pandemic. Better understanding of how social isolation relates to the brain will influence health and social policy decision-making of pandemic planning, as well as social interventions in light of global shifts in houseful structures.

Noonan MaryAnn, Zajner Chris, Bzdok Danilo

2023-Feb-11

Bayesian hierarchical modelling, Population neuroscience, amygdala nuclei groups, hippocampus subfields, social brain

General General

Classifying COVID-19 patients from Chest X-ray Images Using Hybrid Machine Learning Techniques: Development and Evaluation.

In JMIR formative research

BACKGROUND : The COVID-19 pandemic has raised global concern, with moderate to severe cases displaying lung inflammation and respiratory failure. Chest X-ray (CXR) imaging is crucial for diagnosis and is usually interpreted by experienced medical specialists. Machine learning has been applied with acceptable accuracy, but computational efficiency has received less attention.

OBJECTIVE : We introduced a novel hybrid machine learning model to accurately classify COVID-19, non-COVID-19, and Healthy patients from chest X-ray (CXR) images with reduced computational time and promising results. Our proposed model was thoroughly evaluated and compared to existing models.

METHODS : A retrospective study was conducted to analyze 5 public datasets containing 4,200 chest X-ray (CXR) images using machine learning techniques including decision trees, support vector machines, and neural networks. The images were pre-processed to undergo image segmentation, enhancement, and feature extraction. The best-performing machine learning technique was selected and combined into a Multi-Layer Hybrid Classification model for COVID-19 (MLHC-COVID-19). The model consisted of two layers. The first layer was designed to differentiate healthy subjects from infected patients, while the second layer aimed to classify COVID-19 and non-COVID-19 patients.

RESULTS : The MLHC-COVID-19 model was trained and evaluated on unseen COVID-19 CXR images, achieving reasonably high accuracy and F-measures of 0.962 and 0.962, respectively. These results show the effectiveness of the MLHC-COVID-19 in classifying COVID-19 CXR images, with improved accuracy and a reduction in interpretation time. The model was also embedded into a web-based MLHC-COVID-19 computer-aided diagnosis (CADx) system, which was made publicly available.

CONCLUSIONS : The study found that the MLHC-COVID-19 model effectively differentiated CXR images of COVID-19 patients from those of healthy and non-COVID-19 individuals. It outperformed other state-of-the-art deep learning techniques and showed promising results. These results suggest that the MLHC-COVID-19 model could have been instrumental in early detection and diagnosis of COVID-19 patients, thus playing a significant role in controlling and managing the pandemic. Although the pandemic has slowed down, this model can be adapted and utilized for future similar situations. The model was also integrated into a publicly accessible web-based computer-aided diagnosis system.

Phumkuea Thanakorn, Wongsirichot Thakerng, Damkliang Kasikrit, Navasakulpong Asma

2023-Feb-13

General General

Hybrid model for early identification post-Covid-19 sequelae.

In Journal of ambient intelligence and humanized computing

Artificial Intelligence techniques based on Machine Learning algorithms, Neural Networks and Naïve Bayes can optimise the diagnostic process of the SARS-CoV-2 or Covid-19. The most significant help of these techniques is analysing data recorded by health professionals when treating patients with this disease. Health professionals' more specific focus is due to the reduction in the number of observable signs and symptoms, ranging from an acute respiratory condition to severe pneumonia, showing an efficient form of attribute engineering. It is important to note that the clinical diagnosis can vary from asymptomatic to extremely harsh conditions. About 80% of patients with Covid-19 may be asymptomatic or have few symptoms. Approximately 20% of the detected cases require hospital care because they have difficulty breathing, of which about 5% may require ventilatory support in the Intensive Care Unit. Also, the present study proposes a hybrid approach model, structured in the composition of Artificial Intelligence techniques, using Machine Learning algorithms, associated with multicriteria methods of decision support based on the Verbal Decision Analysis methodology, aiming at the discovery of knowledge, as well as exploring the predictive power of specific data in this study, to optimise the diagnostic models of Covid-19. Thus, the model will provide greater accuracy to the diagnosis sought through clinical observation.

de Andrade Evandro Carvalho, Pinheiro Luana Ibiapina C C, Pinheiro Plácido Rogério, Nunes Luciano Comin, Pinheiro Mirian Calíope Dantas, Pereira Maria Lúcia Duarte, de Abreu Wilson Correia, Filho Raimir Holanda, Simão Filho Marum, Pinheiro Pedro Gabriel C D, Nunes Rafael Espíndola Comin

2023-Feb-06

Covid-19, Decision support systems, Hybrid model, Machine learning, Medical diagnostic optimization, Verbal decision analysis

General General

Adoption of AI in response to COVID-19-a configurational perspective.

In Personal and ubiquitous computing

Although the importance of artificial intelligence (AI) has often been highlighted in strategic agility and decision outcomes, whether it helps firms strengthen their competitiveness and the means firms use to achieve such competitiveness are still under-researched. Our research thus joins the recent discussion on digitalization trends and strategic responses to COVID-19 to better understand how firms strengthen their competitiveness during such challenging times. Namely, this study incorporates the strategic responses to COVID-19 into the technology-organization-environment (TOE) framework by investigating the impacts of different configurations of TOE contexts and strategic responses on a firm's competitive advantage. We used fuzzy-set qualitative comparative analysis to investigate how TOE contexts and strategic responses integrate into configurations and impact a firm's competiveness. By applying a configurational approach with data from 514 exporting firms in China, we find a strong indication of the equifinality of different strategies, indicating that multiple strategic paths can be used to respond to crises. The adoption of AI, while important, is not sufficient to enhance a firm's competitiveness. Our results stress the significance of data quality, organizational resources and capabilities, and digital business model innovation for AI adoption. We also identify successful strategic paths of AI adoption aversion and ambidextrous strategies. The findings have practical implications for firms seeking effective strategies to respond to future crises and sustain their competitive advantages.

Mi Lili, Liu Wei, Yuan Yu-Hsi, Shao Xuefeng, Zhong Yifan

2023-Feb-07

Artificial intelligence, Fuzzy-set qualitative comparative analysis, Strategic responses to COVID-19, Technology–organization–environment framework

General General

Single-cell multi-omic topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures.

In bioRxiv : the preprint server for biology

The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells and explore cell heterogeneity. However, the high dimensional, discrete, and sparse nature of the data make the downstream analysis particularly challenging. Most of the existing computational methods for single-cell data analysis are either limited to single modality or lack flexibility and interpretability. In this study, we propose an interpretable deep learning method called multi-omic embedded topic model (moETM) to effectively perform integrative analysis of high-dimensional single-cell multimodal data. moETM integrates multiple omics data via a product-of-experts in the encoder for efficient variational inference and then employs multiple linear decoders to learn the multi-omic signatures of the gene regulatory programs. Through comprehensive experiments on public single-cell transcriptome and chromatin accessibility data (i.e., scRNA+scATAC), as well as scRNA and proteomic data (i.e., CITE-seq), moETM demonstrates superior performance compared with six state-of-the-art single-cell data analysis methods on seven publicly available datasets. By applying moETM to the scRNA+scATAC data in human peripheral blood mononuclear cells (PBMCs), we identified sequence motifs corresponding to the transcription factors that regulate immune gene signatures. Applying moETM analysis to CITE-seq data from the COVID-19 patients revealed not only known immune cell-type-specific signatures but also composite multi-omic biomarkers of critical conditions due to COVID-19, thus providing insights from both biological and clinical perspectives.

Zhou Manqi, Zhang Hao, Bai Zilong, Mann-Krzisnik Dylan, Wang Fei, Li Yue

2023-Jan-31

General General

Evaluating deep learning predictions for COVID-19 from X-ray images using leave-one-out predictive densities.

In Neural computing & applications

Early detection of the COVID-19 virus is an important task for controlling the spread of the pandemic. Imaging techniques such as chest X-ray are relatively inexpensive and accessible, but its interpretation requires expert knowledge to evaluate the disease severity. Several approaches for automatic COVID-19 detection using deep learning techniques have been proposed. While most approaches show high accuracy on the COVID-19 detection task, there is not enough evidence on external evaluation for this technique. Furthermore, data scarcity and sampling biases make difficult to properly evaluate model predictions. In this paper, we propose stochastic gradient Langevin dynamics (SGLD) to take into account the model uncertainty. Four different deep learning architectures are trained using SGLD and compared to their baselines using stochastic gradient descent. The model uncertainties are also evaluated according to their convergence properties and the leave-one-out predictive densities. The proposed approach is able to reduce overconfidence of the baseline estimators while also retaining predictive accuracy for the best-performing cases.

Hernández Sergio, López-Córtes Xaviera

2023-Feb-06

Bayesian learning, COVID X-ray, Markov chain Monte Carlo

Public Health Public Health

Characterizing Human Collective Behaviors During COVID-19 - Hong Kong SAR, China, 2020.

In China CDC weekly

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC? : People are likely to engage in collective behaviors online during extreme events, such as the coronavirus disease 2019 (COVID-19) crisis, to express awareness, take action, and work through concerns.

WHAT IS ADDED BY THIS REPORT? : This study offers a framework for evaluating interactions among individuals' emotions, perceptions, and online behaviors in Hong Kong Special Administrative Region (SAR) during the first two waves of COVID-19 (February to June 2020). Its results indicate a strong correlation between online behaviors, such as Google searches, and the real-time reproduction numbers. To validate the model's output of risk perception, this investigation conducted 10 rounds of cross-sectional telephone surveys on 8,593 local adult residents from February 1 through June 20 in 2020 to quantify risk perception levels over time.

WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE? : Compared to the survey results, the estimates of the risk perception of individuals using our network-based mechanistic model capture 80% of the trend of people's risk perception (individuals who are worried about being infected) during the studied period. We may need to reinvigorate the public by involving people as part of the solution that reduced the risk to their lives.

Du Zhanwei, Zhang Xiao, Wang Lin, Yao Sidan, Bai Yuan, Tan Qi, Xu Xiaoke, Pei Sen, Xiao Jingyi, Tsang Tim K, Liao Qiuyan, Lau Eric H Y, Wu Peng, Gao Chao, Cowling Benjamin J

2023-Jan-27

COVID-19, Collective Behavior, Hong Kong

General General

Feature selection of pre-trained shallow CNN using the QLESCA optimizer: COVID-19 detection as a case study.

In Applied intelligence (Dordrecht, Netherlands)

According to the World Health Organization, millions of infections and a lot of deaths have been recorded worldwide since the emergence of the coronavirus disease (COVID-19). Since 2020, a lot of computer science researchers have used convolutional neural networks (CNNs) to develop interesting frameworks to detect this disease. However, poor feature extraction from the chest X-ray images and the high computational cost of the available models introduce difficulties for an accurate and fast COVID-19 detection framework. Moreover, poor feature extraction has caused the issue of 'the curse of dimensionality', which will negatively affect the performance of the model. Feature selection is typically considered as a preprocessing mechanism to find an optimal subset of features from a given set of all features in the data mining process. Thus, the major purpose of this study is to offer an accurate and efficient approach for extracting COVID-19 features from chest X-rays that is also less computationally expensive than earlier approaches. To achieve the specified goal, we design a mechanism for feature extraction based on shallow conventional neural network (SCNN) and used an effective method for selecting features by utilizing the newly developed optimization algorithm, Q-Learning Embedded Sine Cosine Algorithm (QLESCA). Support vector machines (SVMs) are used as a classifier. Five publicly available chest X-ray image datasets, consisting of 4848 COVID-19 images and 8669 non-COVID-19 images, are used to train and evaluate the proposed model. The performance of the QLESCA is evaluated against nine recent optimization algorithms. The proposed method is able to achieve the highest accuracy of 97.8086% while reducing the number of features from 100 to 38. Experiments prove that the accuracy of the model improves with the usage of the QLESCA as the dimensionality reduction technique by selecting relevant features.

Hamad Qusay Shihab, Samma Hussein, Suandi Shahrel Azmin

2023-Feb-06

Features extraction, Features selection, Q-learning embedded sine cosine algorithm (QLESCA), SVM, Shallow convolutional neural networks, Swarm intelligence

Public Health Public Health

Generalizable machine learning approach for COVID-19 mortality risk prediction using on-admission clinical and laboratory features.

In Scientific reports ; h5-index 158.0

We aimed to propose a mortality risk prediction model using on-admission clinical and laboratory predictors. We used a dataset of confirmed COVID-19 patients admitted to three general hospitals in Tehran. Clinical and laboratory values were gathered on admission. Six different machine learning models and two feature selection methods were used to assess the risk of in-hospital mortality. The proposed model was selected using the area under the receiver operator curve (AUC). Furthermore, a dataset from an additional hospital was used for external validation. 5320 hospitalized COVID-19 patients were enrolled in the study, with a mortality rate of 17.24% (N = 917). Among 82 features, ten laboratories and 27 clinical features were selected by LASSO. All methods showed acceptable performance (AUC > 80%), except for K-nearest neighbor. Our proposed deep neural network on features selected by LASSO showed AUC scores of 83.4% and 82.8% in internal and external validation, respectively. Furthermore, our imputer worked efficiently when two out of ten laboratory parameters were missing (AUC = 81.8%). We worked intimately with healthcare professionals to provide a tool that can solve real-world needs. Our model confirmed the potential of machine learning methods for use in clinical practice as a decision-support system.

Barough Siavash Shirzadeh, Safavi-Naini Seyed Amir Ahmad, Siavoshi Fatemeh, Tamimi Atena, Ilkhani Saba, Akbari Setareh, Ezzati Sadaf, Hatamabadi Hamidreza, Pourhoseingholi Mohamad Amin

2023-Feb-10

General General

A year of pandemic: Levels, changes and validity of well-being data from Twitter. Evidence from ten countries.

In PloS one ; h5-index 176.0

We use daily happiness scores (Gross National Happiness (GNH)) to illustrate how happiness changed throughout 2020 in ten countries across Europe and the Southern hemisphere. More frequently and regularly available than survey data, the GNH reveals how happiness sharply declined at the onset of the pandemic and lockdown, quickly recovered, and then trended downward throughout much of the year in Europe. GNH is derived by applying sentiment and emotion analysis-based on Natural Language Processing using machine learning algorithms-to Twitter posts (tweets). Using a similar approach, we generate another 11 variables: eight emotions and three new context-specific variables, in particular: trust in national institutions, sadness in relation to loneliness, and fear concerning the economy. Given the novelty of the dataset, we use multiple methods to assess validity. We also assess the correlates of GNH. The results indicate that GNH is negatively correlated with new COVID-19 cases, containment policies, and disgust and positively correlated with staying at home, surprise, and generalised trust. Altogether the analyses indicate tools based on Big Data, such as the GNH, offer relevant data that often fill information gaps and can valuably supplement traditional tools. In this case, the GNH results suggest that both the severity of the pandemic and containment policies negatively correlated with happiness.

Sarracino Francesco, Greyling Talita, O’Connor Kelsey, Peroni Chiara, Rossouw Stephanié

2023

General General

Trajectory tracking of changes digital divide prediction factors in the elderly through machine learning.

In PloS one ; h5-index 176.0

RESEARCH MOTIVATION : Recently, the digital divide problem among elderly individuals has been intensifying. A larger problem is that the level of use of digital technology varies from person to person. Therefore, a digital divide may even exist among elderly individuals. Considering the recent accelerating digital transformation in our society, it is highly likely that elderly individuals are experiencing many difficulties in their daily life. Therefore, it is necessary to quickly address and manage these difficulties.

RESEARCH OBJECTIVE : This study aims to predict the digital divide in the elderly population and provide essential insights into managing it. To this end, predictive analysis is performed using public data and machine learning techniques.

METHODS AND MATERIALS : This study used data from the '2020 Report on Digital Information Divide Survey' published by the Korea National Information Society Agency. In establishing the prediction model, various independent variables were used. Ten variables with high importance for predicting the digital divide were identified and used as critical, independent variables to increase the convenience of analyzing the model. The data were divided into 70% for training and 30% for testing. The model was trained on the training set, and the model's predictive accuracy was analyzed on the test set. The prediction accuracy was analyzed using logistic regression (LR), support vector machine (SVM), K-nearest neighbor (KNN), decision tree (DT), and eXtreme gradient boosting (XGBoost). A convolutional neural network (CNN) was used to further improve the accuracy. In addition, the importance of variables was analyzed using data from 2019 before the COVID-19 outbreak, and the results were compared with the results from 2020.

RESULTS : The study results showed that the variables with high importance in the 2020 data predicting the digital divide of elderly individuals were the demographic perspective, internet usage perspective, self-efficacy perspective, and social connectedness perspective. These variables, as well as the social support perspective, were highly important in 2019. The highest prediction accuracy was achieved using the CNN-based model (accuracy: 80.4%), followed by the XGBoost model (accuracy: 79%) and LR model (accuracy: 78.3%). The lowest accuracy (accuracy: 72.6%) was obtained using the DT model.

DISCUSSION : The results of this analysis suggest that support that can strengthen the practical connection of elderly individuals through digital devices is becoming more critical than ever in a situation where digital transformation is accelerating in various fields. In addition, it is necessary to comprehensively use classification algorithms from various academic fields when constructing a classification model to obtain higher prediction accuracy.

CONCLUSION : The academic significance of this study is that the CNN, which is often employed in image and video processing, was extended and applied to a social science field using structured data to improve the accuracy of the prediction model. The practical significance of this study is that the prediction models and the analytical methodologies proposed in this article can be applied to classify elderly people affected by the digital divide, and the trained models can be used to predict the people of younger generations who may be affected by the digital divide. Another practical significance of this study is that, as a method for managing individuals who are affected by a digital divide, the self-efficacy perspective about acquiring and using ICTs and the socially connected perspective are suggested in addition to the demographic perspective and the internet usage perspective.

Park Jung Ryeol, Feng Yituo

2023

General General

Blood transcriptome and machine learning identified the crosstalk between COVID-19 and fibromyalgia: a preliminary study.

In Clinical and experimental rheumatology ; h5-index 43.0

OBJECTIVES : The COVID-19 pandemic caused by SARS-CoV-2 has seriously threatened the human health. Growing evidence shows that COVID-19 patients who recovery will persist with symptoms of fibromyalgia (FM). However, the common molecular mechanism between COVID-19 and FM remains unclear.

METHODS : We obtained blood transcriptome data of COVID-19 (GSE177477) and FM (GSE67311) patients from GEO database, respectively. Subsequently, we applied Limma, GSEA, Wikipathway, KEGG, GO, and machine learning analysis to confirm the common pathogenesis between COVID-19 and FM, and screened key genes for the diagnosis of COVID-19 related FM.

RESULTS : A total of 2505 differentially expressed genes (DEGs) were identified in the FM dataset. Functional enrichment analysis revealed that the occurrence of FM was intimately associated with viral infection. Moreover, WGCNA analysis identified 243 genes firmly associated with the pathological process of COVID-19. Subsequently, 50 common genes were screened between COVID-19 and FM, and functional enrichment analysis of these common genes primarily involved in immunerelated pathways. Among these common genes, 3 key genes were recognised by machine learning for the diagnosis of COVID-19 related FM. We also developed a diagnostic nomogram to predict the risk of FM occurrence which showed excellent predictive performance. Finally, we found that these 3 key genes were closely relevant to immune cells and screened potential drugs that interacted with the key genes.

CONCLUSIONS : Our study revealed the bridge role of immune dysregulation between COVID-19 and fibromyalgia, and screened underlying biomarkers to provide new clues for further clinical research.

Zhang Zhao, Zhu Zhijie, Liu Dong, Mi Zhenz, Tao Huiren, Fan Hongbin

2023-Feb-08

Public Health Public Health

Predicting the distribution of COVID-19 through CGAN-Taking Macau as an example.

In Frontiers in big data

Machine learning (ML) is an innovative method that is widely used in data prediction. Predicting the COVID-19 distribution using ML is essential for urban security risk assessment and governance. This study uses conditional generative adversarial network (CGAN) to construct a method to predict the COVID-19 hotspot distribution through urban texture and business formats and establishes a relationship between urban elements and COVID-19 so that machines can automatically predict the epidemic hotspots in cities. Taking Macau as an example, this method is used to determine the correlation between the urban texture and business hotspots of Macau and the new epidemic hotspot clusters. Different types of samples afforded different epidemic prediction accuracies. The results show the following: (1) CGAN can accurately predict the distribution area of COVID-19, and the accuracy can exceed 70%. (2) The results of predicting the COVID-19 distribution through urban texture and POI data of hospitals and stations are the best, with an accuracy of more than 60% in experiments in different regions of Macau. (3) The proposed method can also predict other areas in the city that may be at risk of COVID-19 and help urban epidemic prevention and control.

Zheng Liang, Chen Yile, Jiang Shan, Song Junxin, Zheng Jianyi

2023

CGAN, epidemic hotspots, machine learning, risk assessment, urban public health

General General

Fireworks explosion boosted Harris Hawks optimization for numerical optimization: Case of classifying the severity of COVID-19.

In Frontiers in neuroinformatics

Harris Hawks optimization (HHO) is a swarm optimization approach capable of handling a broad range of optimization problems. HHO, on the other hand, is commonly plagued by inadequate exploitation and a sluggish rate of convergence for certain numerical optimization. This study combines the fireworks algorithm's explosion search mechanism into HHO and proposes a framework for fireworks explosion-based HHo to address this issue (FWHHO). More specifically, the proposed FWHHO structure is comprised of two search phases: harris hawk search and fireworks explosion search. A search for fireworks explosion is done to identify locations where superior hawk solutions may be developed. On the CEC2014 benchmark functions, the FWHHO approach outperforms the most advanced algorithms currently available. Moreover, the new FWHHO framework is compared to four existing HHO and fireworks algorithms, and the experimental results suggest that FWHHO significantly outperforms existing HHO and fireworks algorithms. Finally, the proposed FWHHO is employed to evolve a kernel extreme learning machine for diagnosing COVID-19 utilizing biochemical indices. The statistical results suggest that the proposed FWHHO can discriminate and classify the severity of COVID-19, implying that it may be a computer-aided approach capable of providing adequate early warning for COVID-19 therapy and diagnosis.

Wang Mingjing, Chen Long, Heidari Ali Asghar, Chen Huiling

2022

CEC2014 benchmark functions, COVID-19, Harris Hawks optimization, fireworks algorithm, numerical optimization

General General

Prediction models for the impact of the COVID-19 pandemic on research activities of Japanese nursing researchers using deep learning.

In Japan journal of nursing science : JJNS

AIM : This study aimed to construct and evaluate prediction models using deep learning to explore the impact of attributes and lifestyle factors on research activities of nursing researchers during the COVID-19 pandemic.

METHODS : A secondary data analysis was conducted from a cross-sectional online survey by the Japanese Society of Nursing Science at the inception of the COVID-19 pandemic. A total of 1089 respondents from nursing faculties were divided into a training dataset and a test dataset. We constructed two prediction models with the training dataset using artificial intelligence (AI) predictive analysis tools; motivation and time were used as predictor items for negative impact on research activities. Predictive factors were attributes, lifestyle, and predictor items for each other. The models' accuracy and internal validity were evaluated using an ordinal logistic regression analysis to assess goodness-of-fit; the test dataset was used to assess external validity. Predicted contributions by each factor were also calculated.

RESULTS : The models' accuracy and goodness-of-fit were good. The prediction contribution analysis showed that no increase in research motivation and lack of increase in research time strongly influenced each other. Other factors that negatively influenced research motivation and research time were residing outside the special alert area and lecturer position and living with partner/spouse and associate professor position, respectively.

CONCLUSIONS : Deep learning is a research method enabling early prediction of unexpected events, suggesting new applicability in nursing science. To continue research activities during the COVID-19 pandemic and future contingencies, the research environment needs to be improved, workload corrected by position, and considered in terms of work-life balance.

Lee Kumsun, Takahashi Fusako, Kawasaki Yuki, Yoshinaga Naoki, Sakai Hiroko

2023-Feb-09

COVID-19, Japan, deep learning, nursing research, university

Pathology Pathology

A machine learning approach identifies distinct early-symptom cluster phenotypes which correlate with hospitalization, failure to return to activities, and prolonged COVID-19 symptoms.

In PloS one ; h5-index 176.0

BACKGROUND : Accurate COVID-19 prognosis is a critical aspect of acute and long-term clinical management. We identified discrete clusters of early stage-symptoms which may delineate groups with distinct disease severity phenotypes, including risk of developing long-term symptoms and associated inflammatory profiles.

METHODS : 1,273 SARS-CoV-2 positive U.S. Military Health System beneficiaries with quantitative symptom scores (FLU-PRO Plus) were included in this analysis. We employed machine-learning approaches to identify symptom clusters and compared risk of hospitalization, long-term symptoms, as well as peak CRP and IL-6 concentrations.

RESULTS : We identified three distinct clusters of participants based on their FLU-PRO Plus symptoms: cluster 1 ("Nasal cluster") is highly correlated with reporting runny/stuffy nose and sneezing, cluster 2 ("Sensory cluster") is highly correlated with loss of smell or taste, and cluster 3 ("Respiratory/Systemic cluster") is highly correlated with the respiratory (cough, trouble breathing, among others) and systemic (body aches, chills, among others) domain symptoms. Participants in the Respiratory/Systemic cluster were twice as likely as those in the Nasal cluster to have been hospitalized, and 1.5 times as likely to report that they had not returned-to-activities, which remained significant after controlling for confounding covariates (P < 0.01). Respiratory/Systemic and Sensory clusters were more likely to have symptoms at six-months post-symptom-onset (P = 0.03). We observed higher peak CRP and IL-6 in the Respiratory/Systemic cluster (P < 0.01).

CONCLUSIONS : We identified early symptom profiles potentially associated with hospitalization, return-to-activities, long-term symptoms, and inflammatory profiles. These findings may assist in patient prognosis, including prediction of long COVID risk.

Epsi Nusrat J, Powers John H, Lindholm David A, Mende Katrin, Malloy Allison, Ganesan Anuradha, Huprikar Nikhil, Lalani Tahaniyat, Smith Alfred, Mody Rupal M, Jones Milissa U, Bazan Samantha E, Colombo Rhonda E, Colombo Christopher J, Ewers Evan C, Larson Derek T, Berjohn Catherine M, Maldonado Carlos J, Blair Paul W, Chenoweth Josh, Saunders David L, Livezey Jeffrey, Maves Ryan C, Sanchez Edwards Margaret, Rozman Julia S, Simons Mark P, Tribble David R, Agan Brian K, Burgess Timothy H, Pollett Simon D

2023

General General

Association of Recent SARS-CoV-2 Infection With New-Onset Alcohol Use Disorder, January 2020 Through January 2022.

In JAMA network open

IMPORTANCE : The COVID-19 pandemic affects many diseases, including alcohol use disorders (AUDs). As the pandemic evolves, understanding the association of a new diagnosis of AUD with COVID-19 over time is required to mitigate negative consequences.

OBJECTIVE : To examine the association of COVID-19 infection with new diagnosis of AUD over time from January 2020 through January 2022.

DESIGN, SETTING, AND PARTICIPANTS : In this retrospective cohort study of electronic health records of US patients 12 years of age or older, new diagnoses of AUD were compared between patients with COVID-19 and patients with other respiratory infections who had never had COVID-19 by 3-month intervals from January 20, 2020, through January 27, 2022.

EXPOSURES : SARS-CoV-2 infection or non-SARS-CoV-2 respiratory infection.

MAIN OUTCOMES AND MEASURES : New diagnoses of AUD were compared in COVID-19 and propensity score-matched control cohorts by hazard ratios (HRs) and 95% CIs from either 14 days to 3 months or 3 to 6 months after the index event.

RESULTS : This study comprised 1 201 082 patients with COVID-19 (56.9% female patients; 65.7% White; mean [SD] age at index, 46.2 [18.9] years) and 1 620 100 patients with other respiratory infections who had never had COVID-19 (60.4% female patients; 71.1% White; mean [SD] age at index, 44.5 [20.6] years). There was a significantly increased risk of a new diagnosis of AUD in the 3 months after COVID-19 was contracted during the first 3 months of the pandemic (block 1) compared with control cohorts (HR, 2.53 [95% CI, 1.82-3.51]), but the risk decreased to nonsignificance in the next 3 time blocks (April 2020 to January 2021). The risk for AUD diagnosis increased after infection in January to April 2021 (HR, 1.30 [95% CI, 1.08-1.56]) and April to July 2021 (HR, 1.80 [95% CI, 1.47-2.21]). The result became nonsignificant again in blocks 7 and 8 (COVID-19 diagnosis between July 2021 and January 2022). A similar temporal pattern was seen for new diagnosis of AUD 3 to 6 months after infection with COVID-19 vs control index events.

CONCLUSIONS AND RELEVANCE : Elevated risk for AUD after COVID-19 infection compared with non-COVID-19 respiratory infections during some time frames may suggest an association of SARS-CoV-2 infection with the pandemic-associated increase in AUD. However, the lack of excess hazard in most time blocks makes it likely that the circumstances surrounding the pandemic and the fear and anxiety they created also were important factors associated with new diagnoses of AUD.

Olaker Veronica R, Kendall Ellen K, Wang Christina X, Parran Theodore V, Terebuh Pauline, Kaelber David C, Xu Rong, Davis Pamela B

2023-Feb-01

General General

Machine learning-augmented surface-enhanced spectroscopy toward next-generation molecular diagnostics.

In Nanoscale advances

The world today is witnessing the significant role and huge demand for molecular detection and screening in healthcare and medical diagnosis, especially during the outbreak of COVID-19. Surface-enhanced spectroscopy techniques, including Surface-Enhanced Raman Scattering (SERS) and Infrared Absorption (SEIRA), provide lattice and molecular vibrational fingerprint information which is directly linked to the molecular constituents, chemical bonds, and configuration. These properties make them an unambiguous, nondestructive, and label-free toolkit for molecular diagnostics and screening. However, new issues in molecular diagnostics, such as increasing molecular species, faster spread of viruses, and higher requirements for detection accuracy and sensitivity, have brought great challenges to detection technology. Advancements in artificial intelligence and machine learning (ML) techniques show promising potential in empowering SERS and SEIRA with rapid analysis and automatic data processing to jointly tackle the challenge. This review introduces the combination of ML and SERS/SEIRA by investigating how ML algorithms can be beneficial to SERS/SEIRA, discussing the general process of combining ML and SEIRA/SERS, highlighting the molecular diagnostics and screening applications based on ML-combined SEIRA/SERS, and providing perspectives on the future development of ML-integrated SEIRA/SERS. In general, this review offers comprehensive knowledge about the recent advances and the future outlook regarding ML-integrated SEIRA/SERS for molecular diagnostics and screening.

Zhou Hong, Xu Liangge, Ren Zhihao, Zhu Jiaqi, Lee Chengkuo

2023-Jan-31

General General

Learning virus genotype-fitness landscape in embedding space

bioRxiv Preprint

Predicting the SARS-CoV-2 epidemic and "immune escape" mutations remain crucial problems. We present a theoretical framework called Phenotype-Embedding (P-E) theorem and prove that the virus fitness can calculate by selecting appropriate sequence embedding under the VAE framework. Starting from the P-E theorem and based on a modified Transformer model, we obtain a calculable quantitative relationship between "immune escape" mutations and the fitness of the virus lineage and plot a genotype-fitness landscape in the embedded space. We accurately calculated the viral fitness and basic replication number (R0) using only the sequence data of SARS-CoV-2 spike protein. In addition, our model can simulate viral neutral evolution and spatio-temporal selection, decipher the effects of epistasis and recombination, and more accurately predict viral mutations associated with immune escape. Our work provides a theoretical framework for constructing genotype-phenotype landscapes and a paradigm for the interpretability of deep learning in virus evolution research.

Liu, Y.; Luo, Y.; Lu, X.; Gao, H.; He, R.; Zhang, X.; Zhang, X.; Li, Y.

2023-02-10

Public Health Public Health

Early detection of SARS-CoV-2 variants through dynamic co-mutation network surveillance.

In Frontiers in public health

BACKGROUND : Precise public health and clinical interventions for the COVID-19 pandemic has spurred a global rush on SARS-CoV-2 variant tracking, but current approaches to variant tracking are challenged by the flood of viral genome sequences leading to a loss of timeliness, accuracy, and reliability. Here, we devised a new co-mutation network framework, aiming to tackle these difficulties in variant surveillance.

METHODS : To avoid simultaneous input and modeling of the whole large-scale data, we dynamically investigate the nucleotide covarying pattern of weekly sequences. The community detection algorithm is applied to a co-occurring genomic alteration network constructed from mutation corpora of weekly collected data. Co-mutation communities are identified, extracted, and characterized as variant markers. They contribute to the creation and weekly updates of a community-based variant dictionary tree representing SARS-CoV-2 evolution, where highly similar ones between weeks have been merged to represent the same variants. Emerging communities imply the presence of novel viral variants or new branches of existing variants. This process was benchmarked with worldwide GISAID data and validated using national level data from six COVID-19 hotspot countries.

RESULTS : A total of 235 co-mutation communities were identified after a 120 weeks' investigation of worldwide sequence data, from March 2020 to mid-June 2022. The dictionary tree progressively developed from these communities perfectly recorded the time course of SARS-CoV-2 branching, coinciding with GISAID clades. The time-varying prevalence of these communities in the viral population showed a good match with the emergence and circulation of the variants they represented. All these benchmark results not only exhibited the methodology features but also demonstrated high efficiency in detection of the pandemic variants. When it was applied to regional variant surveillance, our method displayed significantly earlier identification of feature communities of major WHO-named SARS-CoV-2 variants in contrast with Pangolin's monitoring.

CONCLUSION : An efficient genomic surveillance framework built from weekly co-mutation networks and a dynamic community-based variant dictionary tree enables early detection and continuous investigation of SARS-CoV-2 variants overcoming genomic data flood, aiding in the response to the COVID-19 pandemic.

Huang Qiang, Qiu Huining, Bible Paul W, Huang Yong, Zheng Fangfang, Gu Jing, Sun Jian, Hao Yuantao, Liu Yu

2023

SARS-CoV-2, co-mutation, community detection, network, surveillance

General General

Deep learning approaches to viral phylogeography are fast and as robust as likelihood methods to model misspecification

bioRxiv Preprint

Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among five locations and found they achieve similar levels of accuracy to Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Thompson, A.; Liebeskind, B.; Scully, E. J.; Landis, M.

2023-02-10

General General

A data-driven approach to the "Everesting" cycling challenge.

In Scientific reports ; h5-index 158.0

The "Everesting" challenge is a cycling activity in which a cyclist repeats a hill until accumulating an elevation gain equal to the elevation of Mount Everest in a single ride. The challenge experienced a surge in interest during the COVID-19 pandemic and the cancelation of cycling races around the world that prompted cyclists to pursue alternative, individual activities. The time to complete the Everesting challenge depends on the fitness and talent of the cyclist, but also on the length and gradient of the hill, among other parameters. Hence, preparing an Everesting attempt requires understanding the relationship between the Everesting parameters and the time to complete the challenge. We use web-scraping to compile a database of publicly available Everesting attempts, and we quantify and rank the parameters that determine the time to complete the challenge. We also use unsupervised machine learning algorithms to segment cyclists into distinct groups according to their characteristics and performance. We conclude that the power per unit body mass of the cyclist and the tradeoff between the gradient of the hill and the distance are the most important considerations when attempting the Everesting challenge. As such, elite cyclists best select a hill with gradient > 12%, whereas amateur and recreational cyclists best select a hill with gradient < 10% to minimize the time to complete the Everesting challenge.

Seo Junhyeon, Raeymaekers Bart

2023-Feb-08

General General

Outcome classification model for Covid-19 patients using artificial intelligence.

In Salud publica de Mexico

Not available.

Saad-Manzanera María Isabel, Hernández-Galván Jesús Alan, González-Cristóbal Sofía Carolina, Vázquez-Torres Eliden, Ramírez-Alonso Graciela María de Jesús, Valenzuela-Aldaba Yaeli Estefanía, Hinojos-Gallardo Luis Carlos, Enríquez-Sánchez Luis Bernardo

2023-Jan-02

General General

COVID-19 Predictive Models Based on Grammatical Evolution.

In SN computer science

A feature construction method that incorporates a grammatical guided procedure is presented here to predict the monthly mortality rate of the COVID-19 pandemic. Three distinct use cases were obtained from publicly available data and three corresponding datasets were created for that purpose. The proposed method is based on constructing artificial features from the original ones. After the artificial features are generated, the original data set is modified based on these features and a machine learning model, such as an artificial neural network, is applied to the modified data. From the comparative experiments done, it was clear that feature construction has an advantage over other machine learning methods for predicting pandemic elements.

Tsoulos Ioannis G, Stylios Chrysostomos, Charalampous Vlasis

2023

COVID-19, Feature construction, Grammatical evolution, Machine learning, Predictive models

General General

Recent development of machine learning models for the prediction of drug-drug interactions.

In The Korean journal of chemical engineering

Polypharmacy, the co-administration of multiple drugs, has become an area of concern as the elderly population grows and an unexpected infection, such as COVID-19 pandemic, keeps emerging. However, it is very costly and time-consuming to experimentally examine the pharmacological effects of polypharmacy. To address this challenge, machine learning models that predict drug-drug interactions (DDIs) have actively been developed in recent years. In particular, the growing volume of drug datasets and the advances in machine learning have facilitated the model development. In this regard, this review discusses the DDI-predicting machine learning models that have been developed since 2018. Our discussion focuses on dataset sources used to develop the models, featurization approaches of molecular structures and biological information, and types of DDI prediction outcomes from the models. Finally, we make suggestions for research opportunities in this field.

Hong Eujin, Jeon Junhyeok, Kim Hyun Uk

2023

Adverse Drug Reaction, Drug-Drug Interaction, Featurization, Machine Learning, Polypharmacy

General General

A smartphone-based zero-effort method for mitigating epidemic propagation.

In EURASIP journal on advances in signal processing

A large number of epidemics, including COVID-19 and SARS, quickly swept the world and claimed the precious lives of large numbers of people. Due to the concealment and rapid spread of the virus, it is difficult to track down individuals with mild or asymptomatic symptoms with limited human resources. Building a low-cost and real-time epidemic early warning system to identify individuals who have been in contact with infected individuals and determine whether they need to be quarantined is an effective means to mitigate the spread of the epidemic. In this paper, we propose a smartphone-based zero-effort epidemic warning method for mitigating epidemic propagation. Firstly, we recognize epidemic-related voice activity relevant to epidemics spread by hierarchical attention mechanism and temporal convolutional network. Subsequently, we estimate the social distance between users through sensors built-in smartphone. Furthermore, we combine Wi-Fi network logs and social distance to comprehensively judge whether there is spatiotemporal contact between users and determine the duration of contact. Finally, we estimate infection risk based on epidemic-related vocal activity, social distance, and contact time. We conduct a large number of well-designed experiments in typical scenarios to fully verify the proposed method. The proposed method does not rely on any additional infrastructure and historical training data, which is conducive to integration with epidemic prevention and control systems and large-scale applications.

Wang Qu, Fu Meixia, Wang Jianquan, Sun Lei, Huang Rong, Li Xianda, Jiang Zhuqing

2023

COVID-19, Contact tracing, Epidemic warning, Human activity recognition, Indoor positioning, Social distance

General General

Real-time face mask position recognition system based on MobileNet model.

In Smart health (Amsterdam, Netherlands)

COVID-19 is a highly contagious disease that was first identified in 2019, and has since taken more than six million lives world wide till date, while also causing considerable economic, social, cultural and political turmoil. As a way to limit its spread, the World Health Organization and medical experts have advised properly wearing face masks, social distancing and hand sanitization, besides vaccination. However, people wear masks sometimes uncovering their mouths and/or noses consciously or unconsciously, thereby lessening the effectiveness of the protection they provide. A system capable of automatic recognition of face mask position could alert and ensure that an individual is wearing a mask properly before entering a crowded public area and putting themselves and others at risk. We first develop and publicly release a dataset of face mask images, which are collected from 391 individuals of different age groups and gender. Then, we study six different architectures of pre-trained deep learning models, and finally propose a model developed by fine tuning the pre-trained state of the art MobileNet model. We evaluate the performance (accuracy, F1-score, and Cohen's Kappa) of this model on the proposed dataset and MaskedFace-Net, a publicly available synthetic dataset created by image editing. Its performance is also compared to other existing methods. The proposed MobileNet is found as the best model providing an accuracy, F1-score, and Cohen's Kappa of 99.23%, 99.22%, and 99.19%, respectively for face mask position recognition. It outperforms the accuracy of the best existing model by about 2%. Finally, an automatic face mask position recognition system has been developed, which can recognize if an individual is wearing a mask correctly or incorrectly. The proposed model performs very well with no drop in recognition accuracy from real images captured by a camera.

Rahman Md Hafizur, Jannat Mir Kanon Ara, Islam Md Shafiqul, Grossi Giuliano, Bursic Sathya, Aktaruzzaman Md

2023-Jan-31

COVID-19, Dataset, Face-mask position recognition, MobileNet, Real-time, Transfer learning

Internal Medicine Internal Medicine

Machine learning models for predicting severe COVID-19 outcomes in hospitals.

In Informatics in medicine unlocked

The aim of this observational retrospective study is to improve early risk stratification of hospitalized Covid-19 patients by predicting in-hospital mortality, transfer to intensive care unit (ICU) and mechanical ventilation from electronic health record data of the first 24 h after admission. Our machine learning model predicts in-hospital mortality (AUC = 0.918), transfer to ICU (AUC = 0.821) and the need for mechanical ventilation (AUC = 0.654) from a few laboratory data of the first 24 h after admission. Models based on dichotomous features indicating whether a laboratory value exceeds or falls below a threshold perform nearly as good as models based on numerical features. We devise completely data-driven and interpretable machine-learning models for the prediction of in-hospital mortality, transfer to ICU and mechanical ventilation for hospitalized Covid-19 patients within 24 h after admission. Numerical values of. CRP and blood sugar and dichotomous indicators for increased partial thromboplastin time (PTT) and glutamic oxaloacetic transaminase (GOT) are amongst the best predictors.

Wendland Philipp, Schmitt Vanessa, Zimmermann Jörg, Häger Lukas, Göpel Siri, Schenkel-Häger Christof, Kschischo Maik

2023

Clinical decision support, Covid-19, Machine learning, Predictive modelling

General General

Omnidirectional 2.5D representation for COVID-19 diagnosis using chest CTs.

In Journal of visual communication and image representation

The Coronavirus Disease 2019 (COVID-19) has drastically overwhelmed most countries in the last two years, and image-based approaches using computerized tomography (CT) have been used to identify pulmonary infections. Recent methods based on deep learning either require time-consuming per-slice annotations (2D) or are highly data- and hardware-demanding (3D). This work proposes a novel omnidirectional 2.5D representation of volumetric chest CTs that allows exploring efficient 2D deep learning architectures while requiring volume-level annotations only. Our learning approach uses a siamese feature extraction backbone applied to each lung. It combines these features into a classification head that explores a novel combination of Squeeze-and-Excite strategies with Class Activation Maps. We experimented with public and in-house datasets and compared our results with state-of-the-art techniques. Our analyses show that our method provides better or comparable prediction quality and accurately distinguishes COVID-19 infections from other kinds of pneumonia and healthy lungs.

da Silveira Thiago L T, Pinto Paulo G L, Lermen Thiago S, Jung Cláudio R

2023-Mar

2.5D representation, COVID-19 diagnosis, Ground-glass opacity, Omnidirectional imaging

General General

A Comparative Analysis of Multidimensional COVID-19 Poverty Determinants: An Observational Machine Learning Approach.

In New generation computing

Poverty is a glaring issue in the twenty-first century, even after concerted efforts of organizations to eliminate the same. Predicting poverty using machine learning can offer practical models for facilitating the process of elimination of poverty. This paper uses Multidimensional Poverty Index Data from the Oxford Poverty and Human Development Initiative across the years 2019 and 2021 to make predictions of multidimensional poverty before and during the pandemic. Several poverty indicators under health, education and living standards are taken into consideration. The work implements several data analysis techniques like feature correlation and selection, and graphical visualizations to answer research questions about poverty. Various machine learning, such as Multiple Linear Regression, Decision Tree Regressor, Random Forest Regressor, XGBoost, AdaBoost, Gradient Boosting, Linear Support Vector Regressor (SVR), Ridge Regression, Lasso Regression, ElasticNet Regression, and K-Nearest Neighbor Regression algorithm, have been implemented to predict poverty across four datasets on a national and a subnational level. Regularization is used to increase the performance of the models, and cross-validation is used for estimation. Through a rigorous analysis and comparison of different models, this work identifies important poverty determinants and concludes that overall, Ridge Regression model performs the best with the highest R 2 score.

Satapathy Sandeep Kumar, Saravanan Shreyaa, Mishra Shruti, Mohanty Sachi Nandan

2023-Feb-01

Feature selection, Machine learning, Multidimensional, Poverty, Prediction, Regression

General General

Transfer learning for the efficient detection of COVID-19 from smartphone audio data.

In Pervasive and mobile computing

Disease detection from smartphone data represents an open research challenge in mobile health (m-health) systems. COVID-19 and its respiratory symptoms are an important case study in this area and their early detection is a potential real instrument to counteract the pandemic situation. The efficacy of this solution mainly depends on the performances of AI algorithms applied to the collected data and their possible implementation directly on the users' mobile devices. Considering these issues, and the limited amount of available data, in this paper we present the experimental evaluation of 3 different deep learning models, compared also with hand-crafted features, and of two main approaches of transfer learning in the considered scenario: both feature extraction and fine-tuning. Specifically, we considered VGGish, YAMNET, and L3-Net (including 12 different configurations) evaluated through user-independent experiments on 4 different datasets (13,447 samples in total). Results clearly show the advantages of L3-Net in all the experimental settings as it overcomes the other solutions by 12.3% in terms of Precision-Recall AUC as features extractor, and by 10% when the model is fine-tuned. Moreover, we note that to fine-tune only the fully-connected layers of the pre-trained models generally leads to worse performances, with an average drop of 6.6% with respect to feature extraction. Finally, we evaluate the memory footprints of the different models for their possible applications on commercial mobile devices.

Campana Mattia Giovanni, Delmastro Franca, Pagani Elena

2023-Feb

COVID-19, Deep audio embeddings, Deep learning, Transfer learning, m-health

General General

A novel approach for detection of COVID-19 and Pneumonia using only binary classification from chest CT-scans.

In Neuroscience informatics

The novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread all over the world, causing a dramatic shift in circumstances that resulted in a massive pandemic, affecting the world's well-being and stability. It is an RNA virus that can infect both humans as well as animals. Diagnosis of the virus as soon as possible could contain and avoid a serious COVID-19 outbreak. Current pharmaceutical techniques and diagnostic methods tests such as Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Serology tests are time-consuming, expensive, and require a well-equipped laboratory for analysis, making them restrictive and inaccessible to everyone. Deep Learning has grown in popularity in recent years, and it now plays a crucial role in Image Classification, which also involves Medical Imaging. Using chest CT scans, this study explores the problem statement automation of differentiating COVID-19 contaminated individuals from healthy individuals. Convolutional Neural Networks (CNNs) can be trained to detect patterns in computed tomography scans (CT scans). Hence, different CNN models were used in the current study to identify variations in chest CT scans, with accuracies ranging from 91% to 98%. The Multiclass Classification method is used to build these architectures. This study also proposes a new approach for classifying CT images that use two binary classifications combined to work together, achieving 98.38% accuracy. All of these architectures' performances are compared using different classification metrics.

Hasija Sanskar, Akash Peddaputha, Bhargav Hemanth Maganti, Kumar Ankit, Sharma Sanjeev

2022-Dec

CNN, COVID-19, Chest CT scan, Classification metrics, Multiclass classification, Two binary classifications

General General

Configurational patterns for COVID-19 related social media rumor refutation effectiveness enhancement based on machine learning and fsQCA.

In Information processing & management

Infodemics are intertwined with the COVID-19 pandemic, affecting people's perception and social order. To curb the spread of COVID-19 related false rumors, fuzzy-set qualitative comparative analysis (fsQCA) is used to find configurational pathways to enhance rumor refutation effectiveness. In this paper, a total of 1,903 COVID-19 related false rumor refutation microblogs on Sina Weibo are collected by a web crawler from January 1, 2022 to April 20, 2022, and 10 main conditions affecting rumor refutation effectiveness index (REI) are identified based on "three rules of epidemics". To reduce data redundancy, five ensemble machine learning models are established and tuned, among which Light Gradient Boosting Machine (LGBM) regression model has the best performance. Then five core conditions are extracted by feature importance ranking of LGBM. Based on fsQCA with the five core conditions, REI enhancement can be achieved through three different pathway elements configurations solutions: "Highly influential microblogger * high followers' stickiness microblogger", "high followers' stickiness microblogger * highly active microblogger * concise information description" and "high followers' stickiness microblogger * the sentiment tendency of the topic * concise information description". Finally, decision-making suggestions for false rumor refutation platforms and new ideas for improving false rumor refutation effectiveness are proposed. The innovation of this paper reflects in exploring the REI enhancement strategy from the perspective of configuration for the first time.

Li Zongmin, Zhao Ye, Duan Tie, Dai Jingqi

2023-May

COVID-19, Fuzzy-set qualitative comparative analysis (FsQCA), Infodemic, LGBM regression model, Rumor refutation effectiveness

General General

Modeling the artificial intelligence-based imperatives of industry 5.0 towards resilient supply chains: A post-COVID-19 pandemic perspective.

In Computers & industrial engineering

The recent COVID-19 pandemic has significantly affected emerging economies' global supply chains (SCs) by disrupting their manufacturing activities. To ensure business survivability during the current and post-COVID-19 era, it is crucial to adopt artificial intelligence (AI) technologies to renovate traditional manufacturing activities. The fifth industrial revolution, Industry 5.0 (I5.0), and artificial intelligence (AI) offer the overwhelming potential to build an inclusive digital future by ensuring supply chain (SC) resiliency and sustainability. Accordingly, this research aims to identify, assess, and prioritize the AI-based imperatives of I5.0 to improve SC resiliency. An integrated and intelligent approach consisting of Pareto analysis, the Bayesian approach, and the Best-Worst Method (BWM) was developed to fulfill the objectives. Based on the literature review and expert opinions, nine AI-based imperatives were identified and analyzed using Bayesian-BWM to evaluate their potential applicability. The findings reveal that real-time tracking of SC activities using the Internet of Things (IoT) is the most crucial AI-based imperative to improving a manufacturing SC's survivability. The research insights can assist industry leaders, practitioners, and relevant stakeholders in dealing with the impacts of large-scale SC disruptions in the post-COVID-19 era.

Ahmed Tazim, Lekha Karmaker Chitra, Benta Nasir Sumaiya, Abdul Moktadir Md, Kumar Paul Sanjoy

2023-Jan-31

Bayesian Best-Worst Method, Industry 5.0, Post-COVID-19 pandemic, artificial intelligence, supply chain resilience

General General

AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection.

In Scientific reports ; h5-index 158.0

Protein-ligand docking is a computational method for identifying drug leads. The method is capable of narrowing a vast library of compounds down to a tractable size for downstream simulation or experimental testing and is widely used in drug discovery. While there has been progress in accelerating scoring of compounds with artificial intelligence, few works have bridged these successes back to the virtual screening community in terms of utility and forward-looking development. We demonstrate the power of high-speed ML models by scoring 1 billion molecules in under a day (50 k predictions per GPU seconds). We showcase a workflow for docking utilizing surrogate AI-based models as a pre-filter to a standard docking workflow. Our workflow is ten times faster at screening a library of compounds than the standard technique, with an error rate less than 0.01% of detecting the underlying best scoring 0.1% of compounds. Our analysis of the speedup explains that another order of magnitude speedup must come from model accuracy rather than computing speed. In order to drive another order of magnitude of acceleration, we share a benchmark dataset consisting of 200 million 3D complex structures and 2D structure scores across a consistent set of 13 million "in-stock" molecules over 15 receptors, or binding sites, across the SARS-CoV-2 proteome. We believe this is strong evidence for the community to begin focusing on improving the accuracy of surrogate models to improve the ability to screen massive compound libraries 100 × or even 1000 × faster than current techniques and reduce missing top hits. The technique outlined aims to be a fast drop-in replacement for docking for screening billion-scale molecular libraries.

Clyde Austin, Liu Xuefeng, Brettin Thomas, Yoo Hyunseung, Partin Alexander, Babuji Yadu, Blaiszik Ben, Mohd-Yusof Jamaludin, Merzky Andre, Turilli Matteo, Jha Shantenu, Ramanathan Arvind, Stevens Rick

2023-Feb-06

General General

Evolution of Clinical Phenotypes of COVID-19 Patients During Intensive Care Treatment: An Unsupervised Machine Learning Analysis.

In Journal of intensive care medicine ; h5-index 29.0

BACKGROUND : Identification of clinical phenotypes in critically ill COVID-19 patients could improve understanding of the disease heterogeneity and enable prognostic and predictive enrichment. However, previous attempts did not take into account temporal dynamics with high granularity. By including the dimension of time, we aim to gain further insights into the heterogeneity of COVID-19.

METHODS : We used granular data from 3202 adult COVID patients in the Dutch Data Warehouse that were admitted to one of 25 Dutch ICUs between February 2020 and March 2021. Parameters including demographics, clinical observations, medications, laboratory values, vital signs, and data from life support devices were selected. Twenty-one datasets were created that each covered 24 h of ICU data for each day of ICU treatment. Clinical phenotypes in each dataset were identified by performing cluster analyses. Both evolution of the clinical phenotypes over time and patient allocation to these clusters over time were tracked.

RESULTS : The final patient cohort consisted of 2438 COVID-19 patients with a ICU mortality outcome. Forty-one parameters were chosen for cluster analysis. On admission, both a mild and a severe clinical phenotype were found. After day 4, the severe phenotype split into an intermediate and a severe phenotype for 11 consecutive days. Heterogeneity between phenotypes appears to be driven by inflammation and dead space ventilation. During the 21-day period, only 8.2% and 4.6% of patients in the initial mild and severe clusters remained assigned to the same phenotype respectively. The clinical phenotype half-life was between 5 and 6 days for the mild and severe phenotypes, and about 3 days for the medium severe phenotype.

CONCLUSIONS : Patients typically do not remain in the same cluster throughout intensive care treatment. This may have important implications for prognostic or predictive enrichment. Prominent dissimilarities between clinical phenotypes are predominantly driven by inflammation and dead space ventilation.

Siepel Sander, Dam Tariq A, Fleuren Lucas M, Girbes Armand R J, Hoogendoorn Mark, Thoral Patrick J, Elbers Paul W G, Bennis Frank C

2023-Feb-06

clinical phenotype half-life, clinical phenotypes, clustering, coronavirus disease 2019, endotypes, intensive care, subphenotypes

General General

A new YOLO-based method for real-time crowd detection from video and performance analysis of YOLO models.

In Journal of real-time image processing

As seen in the COVID-19 pandemic, one of the most important measures is physical distance in viruses transmitted from person to person. According to the World Health Organization (WHO), it is mandatory to have a limited number of people in indoor spaces. Depending on the size of the indoors, the number of persons that can fit in that area varies. Then, the size of the indoor area should be measured and the maximum number of people should be calculated accordingly. Computers can be used to ensure the correct application of the capacity rule in indoors monitored by cameras. In this study, a method is proposed to measure the size of a prespecified region in the video and count the people there in real time. According to this method: (1) predetermining the borders of a region on the video, (2) identification and counting of people in this specified region, (3) it is aimed to estimate the size of the specified area and to find the maximum number of people it can take. For this purpose, the You Only Look Once (YOLO) object detection model was used. In addition, Microsoft COCO dataset pre-trained weights were used to identify and label persons. YOLO models were tested separately in the proposed method and their performances were analyzed. Mean average precision (mAP), frame per second (fps), and accuracy rate metrics were found for the detection of persons in the specified region. While the YOLO v3 model achieved the highest value in accuracy rate and mAP (both 0.50 and 0.75) metrics, the YOLO v5s model achieved the highest fps rate among non-Tiny models.

Gündüz Mehmet Şirin, Işık Gültekin

2023

Area estimation, Deep learning, People counting, Person detection, Real-time video processing, YOLO

General General

[Performance in prognostic capacity and efficiency of the Thoracic Care Suite GE AI tool applied to chest radiography of patients with COVID-19 pneumonia].

In Radiologia

OBJECTIVE : Rapid progression of COVID-19 pneumonia may put patients at risk of requiring ventilatory support, such as non-invasive mechanical ventilation or endotracheal intubation. Implementing tools that detect COVID-19 pneumonia can improve the patient's healthcare. We aim to evaluate the efficacy and efficiency of the artificial intelligence (AI) tool GE Healthcare's Thoracic Care Suite (featuring Lunit INSIGHT CXR, TCS) to predict the ventilatory support need based on pneumonic progression of COVID-19 on consecutive chest X-rays.

METHODS : Outpatients with confirmed SARS-CoV-2 infection, with chest X-ray (CXR) findings probable or indeterminate for COVID-19 pneumonia, who required a second CXR due to unfavorable clinical course, were collected. The number of affected lung fields for the two CXRs was assessed using the AI tool.

RESULTS : One hundred fourteen patients (57.4 ± 14.2 years, 65 -57%- men) were retrospectively collected. Fifteen (13.2%) required ventilatory support. Progression of pneumonic extension ≥ 0.5 lung fields per day compared to pneumonia onset, detected using the TCS tool, increased the risk of requiring ventilatory support by 4-fold. Analyzing the AI output required 26 seconds of radiological time.

CONCLUSIONS : Applying the AI tool, Thoracic Care Suite, to CXR of patients with COVID-19 pneumonia allows us to anticipate ventilatory support requirements requiring less than half a minute.

Plasencia-Martínez Juana María, Pérez-Costa Rafael, Ballesta-Ruiz Mónica, María García-Santos José

2023-Jan-31

AI (Artificial Intelligence), Biomedical Technology, COVID 19, Coronavirus, Prognoses, Radiography

Public Health Public Health

Effect of daily new cases of COVID-19 on public sentiment and concern: Deep learning-based sentiment classification and semantic network analysis.

In Zeitschrift fur Gesundheitswissenschaften = Journal of public health

AIM : This study explored the influence of daily new case videos posted by public health agencies (PHAs) on TikTok in the context of COVID-19 normalization, as well as public sentiment and concerns. Five different stages were used, based on the Crisis and Emergency Risk Communication model, amidst the 2022 Shanghai lockdown.

SUBJECT AND METHODS : After dividing the duration of the 2022 Shanghai lockdown into stages, we crawled all the user comments of videos posted by Healthy China on TikTok with the theme of daily new cases based on these five stages. Third, we constructed the pre-training model, ERNIE, to classify the sentiment of user comments. Finally, we performed semantic network analyses based on the sentiment classification results.

RESULTS : First, the high cost of fighting the epidemic during the 2022 Shanghai lockdown was why ordinary people were reluctant to cooperate with the anti-epidemic policy in the pre-crisis stage. Second, Shanghai unilaterally revised the definition of asymptomatic patients led to an escalation of risk levels and control conditions in other regions, ultimately affecting the lives and work of ordinary people in the area during the initial event stage. Third, the public reported specific details that affected their lives due to the long-term resistance to the epidemic in the maintenance stage. Fourth, the public became bored with videos regarding daily new cases in the resolution stage. Finally, the main reason for the negative public sentiment was that the local government did not follow the central government's anti-epidemic policy.

CONCLUSION : Our results suggest that the methodology used in this study is feasible. Furthermore, our findings will help the Chinese government or PHAs improve the possible behaviors that displease the public in the anti-epidemic process.

Che ShaoPeng, Wang Xiaoke, Zhang Shunan, Kim Jang Hyun

2023-Jan-31

COVID-19, Crisis and Emergency Risk Communication, Daily new cases, Deep learning, Public health agency, Semantic network analysis

Public Health Public Health

Whale Optimization with Random Contraction and Rosenbrock Method for COVID-19 disease prediction.

In Biomedical signal processing and control

Coronavirus Disease 2019 (COVID-19), instigated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has hugely impacted global public health. To identify and intervene in critically ill patients early, this paper proposes an efficient, intelligent prediction model based on the machine learning approach, which combines the improved whale optimization algorithm (RRWOA) with the k-nearest neighbor (KNN) classifier. In order to improve the problem that WOA is prone to fall into local optimum, an improved version named RRWOA is proposed based on the random contraction strategy (RCS) and the Rosenbrock method. To verify the capability of the proposed algorithm, RRWOA is tested against nine classical metaheuristics, nine advanced metaheuristics, and seven well-known WOA variants based on 30 IEEE CEC2014 competition functions, respectively. The experimental results in mean, standard deviation, the Friedman test, and the Wilcoxon signed-rank test are considered, proving that RRWOA won first place on 18, 24, and 25 test functions, respectively. In addition, a binary version of the algorithm, called BRRWOA, is developed for feature selection problems. An efficient prediction model based on BRRWOA and KNN classifier is proposed and compared with seven existing binary metaheuristics based on 15 datasets of UCI repositories. The experimental results show that the proposed algorithm obtains the smallest fitness value in eleven datasets and can solve combinatorial optimization problems, indicating that it still performs well in discrete cases. More importantly, the model was compared with five other algorithms on the COVID-19 dataset. The experiment outcomes demonstrate that the model offers a scientific framework to support clinical diagnostic decision-making. Therefore, RRWOA is an effectively improved optimizer with efficient value.

Zhang Meilin, Wu Qianxi, Chen Huiling, Asghar Heidari Ali, Cai Zhennao, Li Jiaren, Md Abdelrahim Elsaid, Mansour Romany F

2023-Feb-01

COVID-19, Feature selection, Random contraction strategy, Rosenbrock method, Swarm intelligence, Whale optimization algorithm

General General

Prediction and comparison of psychological health during COVID-19 among Indian population and Rajyoga meditators using machine learning algorithms.

In Procedia computer science

Issues of providing mental health support to people with emerging or current mental health disorders are becoming a significant concern throughout the world. One of the biggest effects of digital psychiatry during COVID-19 is its capacity for early identification and forecasting of a person's mental health decline resulting in chronic mental health issues. Therefore, through this study aims at addressing the hological problems by identifying people who are more likely to acquire mental health issues induced by COVID-19 epidemic. To achieve this goal, this study includes 1) Rajyoga practitioners' perceptions of psychological effects, levels of anxiety, stress, and depression are compared to those of the non practitioners 2) Predictions of mental health disorders such as stress, anxiety and depression using machine learning algorithms using the online survey data collected from Rajyoga meditators and general the population. Decision tree, random forest, naive bayeBayespport vector machine and K nearest neighbor algorithms were used for the prediction as they have been shown to be more accurate for predicting psychological disorders. The support vector machine showed the highest accuracy among all other algorithms. The f1 score was also the highest for support vector machine.

Shobhika Kumar, Prashant Chandra

2023

COVID-19, DASS, Machine learning algorithms, mental health

General General

A Unified Framework for Monitoring Social Distancing and Face Mask Wearing Using Deep Learning: An Approach to Reduce COVID-19 Risk.

In Procedia computer science

Corona Virus Disease 2019 (COVID-19) is caused by Severe Acute Syndrome Corona Virus 2 (SARS-COV-2). It has become a pandemic disease of the 21st century, killing many lives. During this pandemic situation, precautious measures like social distancing and wearing face mask are being followed globally to break the COVID chain. A pre-programmed viewing system is needed to monitor whether these COVID-19 appropriate behaviours are being followed by the commoners and to ensure COVID-19 preventive measures are followed appropriately. In this work, a deep learning based predictive model and live risk analysis application has been proposed, which detects the high-risk prone areas based on social distancing measures among individuals and face mask wearing tendency of the commoners. The proposed system utilizes ImageNet-1000 dataset for human detection using You Only Look Once (YOLOv3) object detection algorithm; Residual Neural Network (ResNet50v2) uses Kaggle dataset and Real-World Masked Face Dataset (RMFD) for detecting if the persons are face masked or not. Detected human beings (in side-view) are transformed to top view using Top-View Transform Model (TVTM) followed by the calculation of interpersonal distance between the pedestrians and categorized them into three classes include high risk, medium risk, low risk. This unified predictive model provided an accuracy of 97.66%, precision of 97.84%, and F1-Score of 97.92%.

Kaviya P, Chitra P, Selvakumar B

2023

COVID-19, Deep Learning, Face Mask Detection, ResNet50v2, Social Distance Prediction, Top View Transform Model (TVTM), YOLOv3

General General

Coronavirus disease identification using Multi-subband feature analysis in DWT domain.

In Procedia computer science

Coronavirus disease early identification and differentiating it with other lung infections is a complex and time-consuming task. At present RT-PCR and Antigen tests are used for diagnosis, but the whole process is tedious, time exhausting and sometimes gives inaccurate results. Radiological scans like CT scan and X-rays are often considered for confirmation of infection, as it contains vital information about region of infection, disease state and severity, texture, size and opacity of infection. Automated machine learning techniques along with CXR (Chest X-ray) images can serve as alternative approach for Covid-19 diagnosis and differentiating it with other health conditions. In this work, Covid-19 disease identification is performed based on multi-subband feature extraction using 2D Discrete Wavelet Transform (DWT) on CX-Ray images. The CX-ray images are decomposed into multi-subbands of frequencies using DWT. The quarter-sized decomposed low and high frequency components are concatenated into single feature vector. In order to find suitable wavelet filter for extracting features from CX-ray images, a rigorous experimentation is carried out among various wavelet families such as Haar, Daubechies, Symlets, Biorthogonal and their respective members that have different vanishing moment and regularity properties. The feature vector is then used for training machine learning model based on support vector machine classifier. Experimental result shows that the classification model based on Haar wavelet feature extraction performs better as compared to other wavelet families with classification accuracy of 100%.

Ali Nikhat, Yadav Jyotsna

2023

Covid-19, Discrete wavelet transform (DWT), X-ray, classification, machine learning, multi-subband

General General

Data Mining Based Techniques for Covid-19 Predictions.

In Procedia computer science

COVID-19 is a pandemic that has resulted in numerous fatalities and infections in recent years, with a rising tendency in both the number of infections and deaths and the pace of recovery. Accurate forecasting models are important for making accurate forecasts and taking relevant actions. As a result, accurate short-term forecasting of the number of new cases that are contaminated and recovered is essential for making the best use of the resources at hand and stopping or delaying the spread of such illnesses. This paper shows the various techniques for forecasting the covid-19 cases. This paper classifies the various models according to their category and shows the merits and demerits of various fore-casting techniques. The research provides insight into potential issues that may arise during the forecasting of covid-19 instances for predicting the positive, negative, and death cases in this pandemic. In this paper, numerous forecasting techniques and their categories have been studied. The goal of this work is to aggregate the findings of several forecasting techniques to aid in the fight against the pandemic.

Rane Rahul, Dubey Aditya, Rasool Akhtar, Wadhvani Rajesh

2023

Deep Learning Models, Soft Computing-based Models, Stochastic Forecasting Models, Supervised ML Models

General General

SCS-Net: An efficient and practical approach towards Face Mask Detection.

In Procedia computer science

Much work has been done in the computer vision domain for the problem of facial mask detection to curb the spread of the Coronavirus disease (COVID-19). Preventive measures developed using deep learning-based models have got enormous attention. With the state-of-the-art results touching perfect accuracies on various models and datasets, two very practical problems are still not addressed - the deployability of the model in the real world and the crucial cases of incorrectly worn masks. To this end, our method proposes a lightweight deep learning model with just 0.12M parameters having up to 496 times reduction as compared to some of the existing models. Our novel architecture of the deep learning model is designed for practical implications in the real world. We also augment an existing dataset with a large set of incorrectly masked face images leading to a more balanced three-class classification problem. A large collection of 25296 synthetically designed incorrect face mask images are provided. This is the first of its kind of data to be proposed with equal diversity and quantity. The proposed model achieves a competitive accuracy of 95.41% on two class classification and 95.54% on the extended three class classification with minimum number of parameters in comparison. The performance of the proposed system is assessed with various state-of-the-art literature and experimental results indicate that our solution is more realistic and rational than many existing works which use overly massive models unsuitable for practical deployability.

Masud Umar, Siddiqui Momin, Sadiq Mohd, Masood Sarfaraz

2023

CNNs, cosine similarity, covid-19, deep learning, face mask detection, image classification

General General

VGG-COVIDNet: A Novel model for COVID detection from X-Ray and CT Scan images.

In Procedia computer science

In this research work, a new deep learning model named VGG-COVIDNet has been proposed which can classify COVID-19 cases from normal cases over X-Rays and CT scan images of lungs. Medical practitioners use the X-Rays and CT scan images of lungs to identify whether a person is infected from COVID or not. In present times, it is very important to give real time COVID prediction with high reliability of results. Deep learning models equipped with machine learning support have been found very influential in accurate prediction of COVID or Non-COVID cases in real time. However, there are some limitations associated with the performance of these model which are model size, achieving good balance of model size and accuracy, and making a single model fitting well for both X-Ray and CT Scan image datasets. Keeping in mind these performance constraints, this new model (VGG-COVIDNet) has been proposed for real time prediction of COVID cases with good balance of model size and accuracy working well for both type of datasets (CT Scan and X-Ray). In order to control model size, an improved version of VGG-16 architecture has been proposed which contains only 13 convolutional layers and 5 fully connected layers. Multiple dropout layers have been added in the proposed architecture which can drop some percentage of features and applies random transformations to decrease the model over-fitting issue. Keeping in mind the primary goal to increase the model accuracy the proposed model has been trained on different datasets with ReLU activation function which is one of the best non-linear activation functions. Four different capacity datasets with CT scan and X-Ray images have been used to validate the performance of proposed model. The proposed model gives an overall accuracy of more than 90% on both types of input datasets i.e. X-Ray and CT Scan.

Goyal Lakshay, Dhull Anuradha, Singh Akansha, Kukreja Sonal, Singh Krishna Kant

2023

Covid-19;Deep Learning, VGG-NET;Medical Iamging

Radiology Radiology

AMSFMap Methodology to improve prediction accuracy of CNN model for Covid19 using X-ray images.

In Procedia computer science

A serious medical issue reported at the center of media worldwide, Since December, 2019 is the Covid19 pandemic. As declared by World Health Organization, confirmed cases of Covid19 have been 579,893,790 including 6,415,070 deaths as of 29 July 2022. Even new cases reported in last 24 hours are 20,409 in India. This needs to diagnose and timely treatment of Covid-19 is essential to prevent hurdles including death. The author developed deep learning based Covid19 diagnosis and severity prediction models using x-ray images with hope that this technology can increase access to radiology expertise in remote places where availability of expert radiologist is limited. The researchers proposed and implemented Attentive Multi Scale Feature map based deep Network (AMSF-Net) for x- ray image classification with improved accuracy. In binary classification, x-ray images are classified as normal or Covid19. Multiclass classification classifies x-ray images into mild, moderate or severe infection of Covid19. The researchers utilized lower layers features in addition to features from highest level with different scale to increase ability of CNN to learn fine-grained features. Channel attention also incorporated to amplify features of important channels. ROI based cropping and AHE employed to enhance content of training image. Image augmentation utilized to increase dataset size. To address the issue of the class imbalance problem, focal loss has been applied. Sensitivity, precision, accuracy and F1 score metrics are used for performance evaluation. The author achieved 78% accuracy for binary classification. Precision, recall and F1 score values for positive class is 85, 67 and 75, respectively while 73, 88 and 80 for negative class. Classification accuracy of mild, moderate and sever class is 90, 97 and 96. Average accuracy of 95 % achieved with superior performance compared to existing methods.

Chauhan Hetal, Modi Kirit

2023

CNN, Channel Attention, Covid-19 Diagnosis, Deep Learning, Multi Scale Features, Severity Prediction

General General

COVID-19 Lung CT image segmentation using localization and enhancement methods with U-Net.

In Procedia computer science

Segmentation of pneumonia lesions from Lung CT images has become vital for diagnosing the disease and evaluating the severity of the patients during the COVID-19 pandemic. Several AI-based systems have been proposed for this task. However, some low-contrast abnormal zones in CT images make the task challenging. The researchers investigated image preprocessing techniques to accomplish this problem and to enable more accurate segmentation by the AI-based systems. This study proposes a COVID-19 Lung-CT segmentation system based on histogram-based non-parametric region localization and enhancement (LE) methods prior to the U-Net architecture. The COVID-19-infected lung CT images were initially processed by the LE method, and the infected regions were detected and enhanced to provide more discriminative features to the deep learning segmentation methods. The U-Net is trained using the enhanced images to segment the regions affected by COVID-19. The proposed system achieved 97.75%, 0.85, and 0.74 accuracy, dice score, and Jaccard index, respectively. The comparison results suggested that the use of LE methods as a preprocessing step in CT Lung images significantly improved the feature extraction and segmentation abilities of the U-Net model by a 0.21 dice score. The results might lead to implementing the LE method in segmenting varied medical images.

Ilhan Ahmet, Alpan Kezban, Sekeroglu Boran, Abiyev Rahib

2023

COVID-19, Enhancement, Localization, Lung CT, U-Net

General General

Simulating Federated Transfer Learning for Lung Segmentation using Modified UNet Model.

In Procedia computer science

Lung segmentation helps doctors in analyzing and diagnosing lung diseases effectively. Covid -19 pandemic highlighted the need for such artificial intelligence (AI) model to segment Lung X-ray images and diagnose patient covid conditions, in a short time, which was not possible due to huge number of patient influx at hospitals with the limited radiologist to diagnose based on test report in short time. AI models developed to assist doctors to diagnose faster, faces another challenge of data privacy. Such AI Models, for better performance, need huge data collected from multiple hospitals/diagnostic centres across the globe into single place to train the AI models. Federated Learning (FL) framework, using transfer learning approach addresses these concerns as FL framework doesn't need data to be shared to outside hospital ecosystem, as AI model get trained on local system and AI model get trained on distributed data. FL with Transfer learning doesn't need the parallel training of the model at all participants nodes like other FL. Paper simulates Federated Transfer learning for Image segmentation using transfer learning technique with few participating nodes and each nodes having different size dataset. The proposed method also leverages other healthcare data available at local system to train the proposed model to overcome lack of more data. Paper uses pre-trained weights of U-net Segmentation Model trained for MRI image segmentation to lung segmentation model. Paper demonstrates using such similar healthcare data available at local system helps improving the performance of the model. The paper uses Explainable AI approach to explain the result. Using above three techniques, Lung segmentation AI model gets near perfect segmentation accuracy.

Ambesange Sateesh, Annappa B, Koolagudi Shashidhar G

2023

Federated Learning, Federated Transfer Learning, Lung image segmentation, MRI image segmentation, Transfer Learning, U-net Architecture, X-ray Image segmentation, data privacy

General General

Impact on Air Quality Index of India Due to Lockdown.

In Procedia computer science

For the very first time, on 22-March-2020 the Indian government forced the only known method at that time to prevent the outburst of the COVID-19 pandemic which was restricting the social movements, and this led to imposing lockdown for a few days which was further extended for a few months. As the impact of lockdown, the major causes of air pollution were ceased which resulted in cleaner blue skies and hence improving the air quality standards. This paper presents an analysis of air quality particulate matter (PM)2.5, PM10, Nitrogen Dioxide (NO2), and Air quality index (AQI). The analysis indicates that the PM10 AQI value drops impulsively from (40-45%), compared before the lockdown period, followed by NO2 (27-35%), Sulphur Dioxide (SO2) (2-10%), PM2.5 (35-40%), but the Ozone (O3) rises (12-25%). To regulate air quality, many steps were taken at national and regional levels, but no effective outcome was received yet. Such short-duration lockdowns are against economic growth but led to some curative effects on AQI. So, this paper concludes that even a short period lockdown can result in significant improvement in Air quality.

Dubey Aditya, Rasool Akhtar

2023

Deep Learning Models, Soft Computing-based Models, Stochastic Forecasting Models, Supervised ML Models

General General

DapNet-HLA: Adaptive dual-attention mechanism network based on deep learning to predict non-classical HLA binding sites.

In Analytical biochemistry

Human leukocyte antigen (HLA) plays a vital role in immunomodulatory function. Studies have shown that immunotherapy based on non-classical HLA has essential applications in cancer, COVID-19, and allergic diseases. However, there are few deep learning methods to predict non-classical HLA alleles. In this work, an adaptive dual-attention network named DapNet-HLA is established based on existing datasets. Firstly, amino acid sequences are transformed into digital vectors by looking up the table. To overcome the feature sparsity problem caused by unique one-hot encoding, the fused word embedding method is used to map each amino acid to a low-dimensional word vector optimized with the training of the classifier. Then, we use the GCB (group convolution block), SENet attention (squeeze-and-excitation networks), BiLSTM (bidirectional long short-term memory network), and Bahdanau attention mechanism to construct the classifier. The use of SENet can make the weight of the effective feature map high, so that the model can be trained to achieve better results. Attention mechanism is an Encoder-Decoder model used to improve the effectiveness of RNN, LSTM or GRU (gated recurrent neural network). The ablation experiment shows that DapNet-HLA has the best adaptability for five datasets. On the five test datasets, the ACC index and MCC index of DapNet-HLA are 4.89% and 0.0933 higher than the comparison method, respectively. According to the ROC curve and PR curve verified by the 5-fold cross-validation, the AUC value of each fold has a slight fluctuation, which proves the robustness of the DapNet-HLA. The codes and datasets are accessible at https://github.com/JYY625/DapNet-HLA.

Jing Yuanyuan, Zhang Shengli, Wang Houqiang

2023-Feb-03

Bahdanau attention mechanism, Non-classical HLA binding sites, SENet attention mechanism, Word embedding

Public Health Public Health

Explainable artificial intelligence model for identifying COVID-19 gene biomarkers.

In Computers in biology and medicine

AIM : COVID-19 has revealed the need for fast and reliable methods to assist clinicians in diagnosing the disease. This article presents a model that applies explainable artificial intelligence (XAI) methods based on machine learning techniques on COVID-19 metagenomic next-generation sequencing (mNGS) samples.

METHODS : In the data set used in the study, there are 15,979 gene expressions of 234 patients with COVID-19 negative 141 (60.3%) and COVID-19 positive 93 (39.7%). The least absolute shrinkage and selection operator (LASSO) method was applied to select genes associated with COVID-19. Support Vector Machine - Synthetic Minority Oversampling Technique (SVM-SMOTE) method was used to handle the class imbalance problem. Logistics regression (LR), SVM, random forest (RF), and extreme gradient boosting (XGBoost) methods were constructed to predict COVID-19. An explainable approach based on local interpretable model-agnostic explanations (LIME) and SHAPley Additive exPlanations (SHAP) methods was applied to determine COVID-19- associated biomarker candidate genes and improve the final model's interpretability.

RESULTS : For the diagnosis of COVID-19, the XGBoost (accuracy: 0.930) model outperformed the RF (accuracy: 0.912), SVM (accuracy: 0.877), and LR (accuracy: 0.912) models. As a result of the SHAP, the three most important genes associated with COVID-19 were IFI27, LGR6, and FAM83A. The results of LIME showed that especially the high level of IFI27 gene expression contributed to increasing the probability of positive class.

CONCLUSIONS : The proposed model (XGBoost) was able to predict COVID-19 successfully. The results show that machine learning combined with LIME and SHAP can explain the biomarker prediction for COVID-19 and provide clinicians with an intuitive understanding and interpretability of the impact of risk factors in the model.

Yagin Fatma Hilal, Cicek İpek Balikci, Alkhateeb Abedalrhman, Yagin Burak, Colak Cemil, Azzeh Mohammad, Akbulut Sami

2023-Feb-01

COVID-19, Explainable artificial intelligence, LIME, SHAP, XGBoost

Radiology Radiology

Classification of COVID-19 from community-acquired pneumonia: Boosting the performance with capsule network and maximum intensity projection image of CT scans.

In Computers in biology and medicine

BACKGROUND : The coronavirus disease 2019 (COVID-19) and community-acquired pneumonia (CAP) present a high degree of similarity in chest computed tomography (CT) images. Therefore, a procedure for accurately and automatically distinguishing between them is crucial.

METHODS : A deep learning method for distinguishing COVID-19 from CAP is developed using maximum intensity projection (MIP) images from CT scans. LinkNet is employed for lung segmentation of chest CT images. MIP images are produced by superposing the maximum gray of intrapulmonary CT values. The MIP images are input into a capsule network for patient-level pred iction and diagnosis of COVID-19. The network is trained using 333 CT scans (168 COVID-19/165 CAP) and validated on three external datasets containing 3581 CT scans (2110 COVID-19/1471 CAP).

RESULTS : LinkNet achieves the highest Dice coefficient of 0.983 for lung segmentation. For the classification of COVID-19 and CAP, the capsule network with the DenseNet-121 feature extractor outperforms ResNet-50 and Inception-V3, achieving an accuracy of 0.970 on the training dataset. Without MIP or the capsule network, the accuracy decreases to 0.857 and 0.818, respectively. Accuracy scores of 0.961, 0.997, and 0.949 are achieved on the external validation datasets. The proposed method has higher or comparable sensitivity compared with ten state-of-the-art methods.

CONCLUSIONS : The proposed method illustrates the feasibility of applying MIP images from CT scans to distinguish COVID-19 from CAP using capsule networks. MIP images provide conspicuous benefits when exploiting deep learning to detect COVID-19 lesions from CT scans and the capsule network improves COVID-19 diagnosis.

Wu Yanan, Qi Qianqian, Qi Shouliang, Yang Liming, Wang Hanlin, Yu Hui, Li Jianpeng, Wang Gang, Zhang Ping, Liang Zhenyu, Chen Rongchang

2023-Jan-23

COVID-19, Capsule network, Community-acquired pneumonia, Computed tomography, Maximum intensity projection

General General

[CRISPR-based molecular diagnostics: a review].

In Sheng wu gong cheng xue bao = Chinese journal of biotechnology

Rapid and accurate detection technologies are crucial for disease prevention and control. In particular, the COVID-19 pandemic has posed a great threat to our society, highlighting the importance of rapid and highly sensitive detection techniques. In recent years, CRISPR/Cas-based gene editing technique has brought revolutionary advances in biotechnology. Due to its fast, accurate, sensitive, and cost-effective characteristics, the CRISPR-based nucleic acid detection technology is revolutionizing molecular diagnosis. CRISPR-based diagnostics has been applied in many fields, such as detection of infectious diseases, genetic diseases, cancer mutation, and food safety. This review summarized the advances in CRISPR-based nucleic acid detection systems and its applications. Perspectives on intelligent diagnostics with CRISPR-based nucleic acid detection and artificial intelligence were also provided.

Sun Wenjun, Huang Xingxu, Wang Xinjie

2023-Jan-25

CRISPR, CRISPR-based detection, gene editing, molecular detection, nucleic acid detection, point-of-care testing (POCT)

General General

Post-COVID-19 interstitial lung disease: Insights from a machine learning radiographic model.

In Frontiers in medicine

INTRODUCTION : Post-acute sequelae of COVID-19 seem to be an emerging global crisis. Machine learning radiographic models have great potential for meticulous evaluation of post-COVID-19 interstitial lung disease (ILD).

METHODS : In this multicenter, retrospective study, we included consecutive patients that had been evaluated 3 months following severe acute respiratory syndrome coronavirus 2 infection between 01/02/2021 and 12/5/2022. High-resolution computed tomography was evaluated through Imbio Lung Texture Analysis 2.1.

RESULTS : Two hundred thirty-two (n = 232) patients were analyzed. FVC% predicted was ≥80, between 60 and 79 and <60 in 74.2% (n = 172), 21.1% (n = 49), and 4.7% (n = 11) of the cohort, respectively. DLCO% predicted was ≥80, between 60 and 79 and <60 in 69.4% (n = 161), 15.5% (n = 36), and 15.1% (n = 35), respectively. Extent of ground glass opacities was ≥30% in 4.3% of patients (n = 10), between 5 and 29% in 48.7% of patients (n = 113) and <5% in 47.0% of patients (n = 109). The extent of reticulation was ≥30%, 5-29% and <5% in 1.3% (n = 3), 24.1% (n = 56), and 74.6% (n = 173) of the cohort, respectively. Patients (n = 13, 5.6%) with fibrotic lung disease and persistent functional impairment at the 6-month follow-up received antifibrotics and presented with an absolute change of +10.3 (p = 0.01) and +14.6 (p = 0.01) in FVC% predicted at 3 and 6 months after the initiation of antifibrotic.

CONCLUSION : Post-COVID-19-ILD represents an emerging entity. A substantial minority of patients presents with fibrotic lung disease and might experience benefit from antifibrotic initiation at the time point that fibrotic-like changes are "immature." Machine learning radiographic models could be of major significance for accurate radiographic evaluation and subsequently for the guidance of therapeutic approaches.

Karampitsakos Theodoros, Sotiropoulou Vasilina, Katsaras Matthaios, Tsiri Panagiota, Georgakopoulou Vasiliki E, Papanikolaou Ilias C, Bibaki Eleni, Tomos Ioannis, Lambiri Irini, Papaioannou Ourania, Zarkadi Eirini, Antonakis Emmanouil, Pandi Aggeliki, Malakounidou Elli, Sampsonas Fotios, Makrodimitri Sotiria, Chrysikos Serafeim, Hillas Georgios, Dimakou Katerina, Tzanakis Nikolaos, Sipsas Nikolaos V, Antoniou Katerina, Tzouvelekis Argyris

2022

antifibrotics, interstitial lung disease, long COVID, machine learning, post-COVID-19

Ophthalmology Ophthalmology

Tele-Glaucoma Using a New Smartphone-based Tool for Visual Field Assessment.

In Journal of glaucoma

PRECIS : Covid-19 underlines the importance of telemedical diagnostics. The Sb-C is a newly developed digital application allowing visual field testing using a head-mounted device and a smartphone. It enables visual field screening remotely from a clinic.

BACKGROUND : Smartphone-based campimetry (Sb-C) is a newly developed tool for functional ophthalmic diagnosis. This study aimed to examine the comparability of the Sb-C and Octopus 900 to ensure ophthalmologic care in times of social distancing.

METHODS : 93 eyes were included in the study. After an ophthalmological examination, the visual field was tested by the Octopus program G1 and by the smartphone-based campimeter. The Sb-C was performed using VR-glasses and an iPhone 6. The software Sb-C was downloaded and installed as SmartCampiTracker app and is examining the 30° visual field with 59 test positions corresponding to the G pattern of Octopus G1. Sensitivities were recorded and saved on the app. Additionally, test-retest reliability was tested on 6 ophthalmologically healthy participants.

RESULTS : The group comprised 48 women and 45 men (mean age: 62.52±12.2 y) including 19 controls, 17 patients with ocular hypertension, 11 preperimetric glaucomas, and 46 perimetric glaucomas. The mean sensitivity (MS) of all points of G1 perimetry was 23.13 dB (95% CI: 22.08-24.18). The MS of the Sb-C was 21.23 dB (95% CI: 20.37-22.08). The correlation between the mean MS measured by G1 perimetry and the Sb-C was strong (r=0.815, P<0.05). The test-retest reliability showed a correlation of r=0.591 (P<0.05.

CONCLUSION : With some technical adjustments, the Sb-C shows promise for screening glaucoma and monitoring disease progression remotely from an ophthalmologic clinic.

Grau Elisabeth, Andrae Stefan, Horn Folkert, Hohberger Bettina, Ring Matthias, Michelson Georg

2022-Nov-29

General General

Methodological and Quality Flaws in the Use of Artificial Intelligence in Mental Health Research: Systematic Review.

In JMIR mental health

BACKGROUND : Artificial intelligence (AI) is giving rise to a revolution in medicine and health care. Mental health conditions are highly prevalent in many countries, and the COVID-19 pandemic has increased the risk of further erosion of the mental well-being in the population. Therefore, it is relevant to assess the current status of the application of AI toward mental health research to inform about trends, gaps, opportunities, and challenges.

OBJECTIVE : This study aims to perform a systematic overview of AI applications in mental health in terms of methodologies, data, outcomes, performance, and quality.

METHODS : A systematic search in PubMed, Scopus, IEEE Xplore, and Cochrane databases was conducted to collect records of use cases of AI for mental health disorder studies from January 2016 to November 2021. Records were screened for eligibility if they were a practical implementation of AI in clinical trials involving mental health conditions. Records of AI study cases were evaluated and categorized by the International Classification of Diseases 11th Revision (ICD-11). Data related to trial settings, collection methodology, features, outcomes, and model development and evaluation were extracted following the CHARMS (Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies) guideline. Further, evaluation of risk of bias is provided.

RESULTS : A total of 429 nonduplicated records were retrieved from the databases and 129 were included for a full assessment-18 of which were manually added. The distribution of AI applications in mental health was found unbalanced between ICD-11 mental health categories. Predominant categories were Depressive disorders (n=70) and Schizophrenia or other primary psychotic disorders (n=26). Most interventions were based on randomized controlled trials (n=62), followed by prospective cohorts (n=24) among observational studies. AI was typically applied to evaluate quality of treatments (n=44) or stratify patients into subgroups and clusters (n=31). Models usually applied a combination of questionnaires and scales to assess symptom severity using electronic health records (n=49) as well as medical images (n=33). Quality assessment revealed important flaws in the process of AI application and data preprocessing pipelines. One-third of the studies (n=56) did not report any preprocessing or data preparation. One-fifth of the models were developed by comparing several methods (n=35) without assessing their suitability in advance and a small proportion reported external validation (n=21). Only 1 paper reported a second assessment of a previous AI model. Risk of bias and transparent reporting yielded low scores due to a poor reporting of the strategy for adjusting hyperparameters, coefficients, and the explainability of the models. International collaboration was anecdotal (n=17) and data and developed models mostly remained private (n=126).

CONCLUSIONS : These significant shortcomings, alongside the lack of information to ensure reproducibility and transparency, are indicative of the challenges that AI in mental health needs to face before contributing to a solid base for knowledge generation and for being a support tool in mental health management.

Tornero-Costa Roberto, Martinez-Millana Antonio, Azzopardi-Muscat Natasha, Lazeri Ledia, Traver Vicente, Novillo-Ortiz David

2023-Feb-02

artificial intelligence, health research, mental health, research methodology, research quality, review methodology, systematic review, trial methodology

Pathology Pathology

Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments.

In The Journal of clinical investigation ; h5-index 129.0

BACKGROUND : The role of host immunity in emergence of evasive SARS-CoV-2 Spike mutations under therapeutic monoclonal antibody (mAb) pressure remains to be explored.

METHODS : In a prospective, observational, monocentric ORCHESTRA cohort study, conducted between March 2021 and November 2022, mild-to-moderately ill COVID-19 patients (n=204) receiving bamlanivimab, bamlanivimab/etesevimab, casirivimab/imdevimab, or sotrovimab were longitudinally studied over 28 days for viral loads, de novo Spike mutations, mAb kinetics, seroneutralization against infecting variants of concern, and T-cell immunity. Additionally, a machine learning-based circulating immune-related (CIB) biomarker profile predictive of evasive Spike mutations was constructed and confirmed in an independent dataset (n=19) that included patients receiving sotrovimab or tixagevimab/cilgavimab.

RESULTS : Patients treated with various mAbs developed evasive Spike mutations with remarkable speed and high specificity to the targeted mAb-binding sites. Immunocompromised patients receiving mAb therapy not only continued to display significantly higher viral loads, but also showed higher likelihood of developing de novo Spike mutations. Development of escape mutants also strongly correlated with neutralizing capacity of the therapeutic mAbs and T-cell immunity, suggesting immune pressure as an important driver of escape mutations. Lastly, we showed that an anti-inflammatory and healing-promoting host milieu facilitates Spike mutations, where 4 CIBs identified patients at high risk of developing escape mutations against therapeutic mAbs with high accuracy.

CONCLUSIONS : Our data demonstrate that host-driven immune and non-immune responses are essential for development of mutant SARS-CoV-2. These data also support point-of-care decision-making in reducing the risk of mAb treatment failure and improving mitigation strategies for possible dissemination of escape SARS-CoV-2 mutants.

Gupta Akshita, Konnova Angelina, Smet Mathias, Berkell Matilda, Savoldi Alessia, Morra Matteo, Van Averbeke Vincent, De Winter Fien Hr, Peserico Denise, Danese Elisa, Hotterbeekx An, Righi Elda, De Nardo Pasquale, Tacconelli Evelina, Malhotra-Kumar Surbhi, Kumar-Singh Samir

2023-Feb-09

COVID-19, Cellular immune response

General General

Improving effectiveness of online learning for higher education students during the COVID-19 pandemic.

In Frontiers in psychology ; h5-index 92.0

During the COVID-19 pandemic, online learning has become one of the important ways of higher education because it is not confined by time and place. How to ensure the effectiveness of online learning has become the focus of education research, and the role of the "online learning community" cannot be ignored. In the context of the Internet of Things (IoT), we try to build up a new online learning community model: (1) First, we introduce the Kolb learning style theory to identify different online learning styles; (2) Second, we use a clustering algorithm to identify the nature of different learning style groups; and (3) Third, we introduce the group dynamics theory to design the dimensions of the questionnaire and combine the Analytic Hierarchy Process (AHP) method to identify the key influencing factors of the online learning community. We take business administration majors and students in universities as an example. The results show that (1) as a machine learning method, the clustering algorithm method is superior to the random construction method in identifying different learning style groups, and (2) our method can well judge the importance of each factor based on hierarchical analysis and clarify the different roles of factors in the process of knowledge transfer. This study can provide a useful reference for the sustainable development of online learning in higher education.

Li Xuelan, Pei Zhiqiang

2022

COVID-19, analytic hierarchy process, cluster analysis, group dynamics theory, online learning community

General General

Interacting with chatbots later in life: A technology acceptance perspective in COVID-19 pandemic situation.

In Frontiers in psychology ; h5-index 92.0

INTRODUCTION : Within the technological development path, chatbots are considered an important tool for economic and social entities to become more efficient and to develop customer-centric experiences that mimic human behavior. Although artificial intelligence is increasingly used, there is a lack of empirical studies that aim to understand consumers' experience with chatbots. Moreover, in a context characterized by constant population aging and an increased life-expectancy, the way aging adults perceive technology becomes of great interest. However, based on the digital divide (unequal access to technology, knowledge, and resources), and since young adults (aged between 18 and 34 years old) are considered to have greater affinity for technology, most of the research is dedicated to their perception. The present paper investigates the way chatbots are perceived by middle-aged and aging adults in Romania.

METHODS : An online opinion survey has been conducted. The age-range of the subjects is 40-78 years old, a convenience sampling technique being used (N = 235). The timeframe of the study is May-June 2021. Thus, the COVID-19 pandemic is the core context of the research. A covariance-based structural equation modelling (CB-SEM) has been used to test the theoretical assumptions as it is a procedure used for complex conceptual models and theory testing.

RESULTS : The results show that while perceived ease of use is explained by the effort, the competence, and the perceive external control in interacting with chatbots, perceived usefulness is supported by the perceived ease of use and subjective norms. Furthermore, individuals are likely to further use chatbots (behavioral intention) if they consider this interaction useful and if the others' opinion is in favor of using it. Gender and age seem to have no effect on behavioral intention. As studies on chatbots and aging adults are few and are mainly investigating reactions in the healthcare domain, this research is one of the first attempts to better understand the way chatbots in a not domain-specific context are perceived later in life. Likewise, judging from a business perspective, the results can help economic and social organizations to improve and adapt AI-based interaction for the aging customers.

Iancu Ioana, Iancu Bogdan

2022

behavioral intention, chatbots, middle-aged and aging adults, perceived ease of use, perceived usefulness, technology acceptance model

Public Health Public Health

Socioexposomics of COVID-19 across New Jersey: a comparison of geostatistical and machine learning approaches.

In Journal of exposure science & environmental epidemiology ; h5-index 34.0

BACKGROUND : Disparities in adverse COVID-19 health outcomes have been associated with multiple social and environmental stressors. However, research is needed to evaluate the consistency and efficiency of methods for studying these associations at local scales.

OBJECTIVE : To assess socioexposomic associations with COVID-19 outcomes across New Jersey and evaluate consistency of findings from multiple modeling approaches.

METHODS : We retrieved data for COVID-19 cases and deaths for the 565 municipalities of New Jersey up to the end of the first phase of the pandemic, and calculated mortality rates with and without long-term-care (LTC) facility deaths. We considered 84 spatially heterogeneous environmental, demographic and socioeconomic factors from publicly available databases, including air pollution, proximity to industrial sites/facilities, transportation-related noise, occupation and commuting, neighborhood and housing characteristics, age structure, racial/ethnic composition, poverty, etc. Six geostatistical models (Poisson/Negative-Binomial regression, Poison/Negative-Binomial mixed effect model, Poisson/Negative-Binomial Bersag-York-Mollie spatial model) and two Machine Learning (ML) methods (Random Forest, Extreme Gradient Boosting) were implemented to assess association patterns. The Shapley effects plot was established for explainable ML and change of support validation was introduced to compare performances of different approaches.

RESULTS : We found robust positive associations of COVID-19 mortality with historic exposures to NO2, population density, percentage of minority and below high school education, and other social and environmental factors. Exclusion of LTC deaths does not significantly affect correlations for most factors but findings can be substantially influenced by model structures and assumptions. The best performing geostatistical models involved flexible structures representing data variations. ML methods captured association patterns consistent with the best performing geostatistical models, and furthermore detected consistent nonlinear associations not captured by geostatistical models.

SIGNIFICANCE : The findings of this work improve the understanding of how social and environmental disparities impacted COVID-19 outcomes across New Jersey.

Ren Xiang, Mi Zhongyuan, Georgopoulos Panos G

2023-Feb-01

Bayesian geospatial modeling, COVID-19, Explainable machine learning, Exposome and socioexposome, Social/environmental health disparities

General General

Future trajectory of respiratory infections following the COVID-19 pandemic in Hong Kong.

In Chaos (Woodbury, N.Y.)

The accumulation of susceptible populations for respiratory infectious diseases (RIDs) when COVID-19-targeted non-pharmaceutical interventions (NPIs) were in place might pose a greater risk of future RID outbreaks. We examined the timing and magnitude of RID resurgence after lifting COVID-19-targeted NPIs and assessed the burdens on the health system. We proposed the Threshold-based Control Method (TCM) to identify data-driven solutions to maintain the resilience of the health system by re-introducing NPIs when the number of severe infections reaches a threshold. There will be outbreaks of all RIDs with staggered peak times after lifting COVID-19-targeted NPIs. Such a large-scale resurgence of RID patients will impose a significant risk of overwhelming the health system. With a strict NPI strategy, a TCM-initiated threshold of 600 severe infections can ensure a sufficient supply of hospital beds for all hospitalized severely infected patients. The proposed TCM identifies effective dynamic NPIs, which facilitate future NPI relaxation policymaking.

Cheng Weibin, Zhou Hanchu, Ye Yang, Chen Yifan, Jing Fengshi, Cao Zhidong, Zeng Daniel Dajun, Zhang Qingpeng

2023-Jan

General General

Recent Issues in Medical Journal Publishing and Editing Policies: Adoption of Artificial Intelligence, Preprints, Open Peer Review, Model Text Recycling Policies, Best Practice in Scholarly Publishing 4th Version, and Country Names in Titles.

In Neurointervention

In Korea, many editors of medical journal are also publishers; therefore, they need to not only manage peer review, but also understand current trends and policies in journal publishing and editing. This article aims to highlight some of these policies with examples. First, the use of artificial intelligence tools in journal publishing has increased, including for manuscript editing and plagiarism detection. Second, preprint publications, which have not been peer-reviewed, are becoming more common. During the COVID-19 pandemic, medical journals have been more willing to accept preprints to adjust rapidly changing pandemic health issues, leading to a significant increase in their use. Third, open peer review with reviewer comments is becoming more widespread, including the mandatory publication of peer-reviewed manuscripts with comments. Fourth, model text recycling policies provide guidelines for researchers and editors on how to appropriately recycle text, for example, in the background section of the Introduction or the Methods section. Fifth, journals should take into account the recently updated 4th version of the Principles of Transparency and Best Practice in Scholarly Publishing, released in 2022. This version includes more detailed guidelines on journal websites, peer review processes, advisory boards, and author fees. Finally, it recommends that titles of human studies include country names to clarify the cultural context of the research. Each editor must decide whether to adopt these six policies for their journals. Editor-publishers of society journals are encouraged to familiarize themselves with these policies so that they can implement them in their journals as appropriate.

Huh Sun

2023-Feb-01

Artificial intelligence, Culture, Peer review, Policy, Scholarly communication

Public Health Public Health

Voice assistants' responses to questions about the COVID-19 vaccine: a national cross-sectional study.

In JMIR formative research

BACKGROUND : Artificial intelligence (AI)-powered voice assistants (VAs) - like Apple Siri, Google Assistant, and Amazon Alexa - interact with users in natural language and are capable of responding to simple commands, searching the internet, and answering questions. Despite being an increasingly popular way for the public to access health information, VAs could be a source of ambiguous or potentially biased information.

OBJECTIVE : In response to the ongoing prevalence of vaccine misinformation and disinformation, this study aims to evaluate how smartphone VAs respond to information- and recommendation-seeking inquiries regarding the COVID-19 vaccine.

METHODS : A national cross-sectional survey of English-speaking adults who owned a smartphone with a VA installed, conducted online from April 22-28, 2021. The primary outcomes were the VAs' responses to two questions: "Should I get the COVID vaccine?" and "Is the COVID vaccine safe?". Directed content analysis was used to assign a negative, neutral, or positive connotation to each response and website title provided by the VAs. Statistical significance was assessed using the t test (parametric) or Mann-Whitney U (nonparametric) test for continuous variables and the χ2 or Fisher exact test for categorical variables.

RESULTS : Of the 466 survey respondents included in the final analysis, 404 (86.7%) used Apple Siri, 53 (11.4%) used Google Assistant, and 9 (1.9%) used Amazon Alexa. In response to the question "Is the COVID vaccine safe?" 89.9% of users received a direct response, of which 97.3% had a positive connotation encouraging users to get vaccinated. Of the websites presented, only 5.3% had a positive connotation and 94.7% had a neutral connotation. In response to the question "Should I get the COVID vaccine?" 93.1% of users received a list of websites, of which 91.5% had a neutral connotation. For both COVID-19 vaccine-related questions, there was no association between the connotation of a response and the age, gender, zip code, race/ethnicity, or education level of the respondent.

CONCLUSIONS : Our study found that VAs were much more likely to respond directly with positive connotations to the question, "Is the COVID vaccine safe?" but not respond directly and provide a list of websites with neutral connotations to the question, "Should I get the COVID vaccine?" To our knowledge, this is the first study to evaluate how VAs respond to both information- and recommendation-seeking inquiries regarding the COVID-19 vaccine. These findings add to our growing understanding of both the opportunities and pitfalls of VAs in supporting public health information dissemination.

Sossenheimer Philip, Hong Grace, Devon-Sand Anna, Lin Steven

2023-Jan-29

General General

PneuNet: deep learning for COVID-19 pneumonia diagnosis on chest X-ray image analysis using Vision Transformer.

In Medical & biological engineering & computing ; h5-index 32.0

A long-standing challenge in pneumonia diagnosis is recognizing the pathological lung texture, especially the ground-glass appearance pathological texture. One main difficulty lies in precisely extracting and recognizing the pathological features. The patients, especially those with mild symptoms, show very little difference in lung texture, neither conventional computer vision methods nor convolutional neural networks perform well on pneumonia diagnosis based on chest X-ray (CXR) images. In the meanwhile, the Coronavirus Disease 2019 (COVID-19) pandemic continues wreaking havoc around the world, where quick and accurate diagnosis backed by CXR images is in high demand. Rather than simply recognizing the patterns, extracting feature maps from the original CXR image is what we need in the classification process. Thus, we propose a Vision Transformer (VIT)-based model called PneuNet to make an accurate diagnosis backed by channel-based attention through X-ray images of the lung, where multi-head attention is applied on channel patches rather than feature patches. The techniques presented in this paper are oriented toward the medical application of deep neural networks and VIT. Extensive experiment results show that our method can reach 94.96% accuracy in the three-categories classification problem on the test set, which outperforms previous deep learning models.

Wang Tianmu, Nie Zhenguo, Wang Ruijing, Xu Qingfeng, Huang Hongshi, Xu Handing, Xie Fugui, Liu Xin-Jun

2023-Jan-31

COVID-19, Deep learning, Multi-head attention, Pneumonia diagnosis, Vision Transformer

General General

Data-driven analysis and predictive modeling on COVID-19.

In Concurrency and computation : practice & experience

The coronavirus (COVID-19) started in China in 2019, has spread rapidly in every single country and has spread in millions of cases worldwide. This paper presents a proposed approach that involves identifying the relative impact of COVID-19 on a specific gender, the mortality rate in specific age, investigating different safety measures adopted by each country and their impact on the virus growth rate. Our study proposes data-driven analysis and prediction modeling by investigating three aspects of the pandemic (gender of patients, global growth rate, and social distancing). Several machine learning and ensemble models have been used and compared to obtain the best accuracy. Experiments have been demonstrated on three large public datasets. The motivation of this study is to propose an analytical machine learning based model to explore three significant aspects of COVID-19 pandemic as gender, global growth rate, and social distancing. The proposed analytical model includes classic classifiers, distinctive ensemble methods such as bagging, feature based ensemble, voting and stacking. The results show a superior prediction performance comparing with the related approaches.

Sharma Sonam, Alsmadi Izzat, Alkhawaldeh Rami S, Al-Ahmad Bilal

2022-Dec-25

COVID‐19, gender of patients, global growth rate, predictive modeling, social distancing

General General

A face mask detection system: An approach to fight with COVID-19 scenario.

In Concurrency and computation : practice & experience

A new coronavirus has caused a pandemic crisis around the globe. According to the WHO, this is an infectious illness that spreads from person to person. Therefore, the only way to avoid this infection is to take precautions. Wearing a mask is the most critical COVID-19 protection method because it prevents the virus from spreading from an infected person to a healthy one. This study reflects a deep learning method to create a system for detecting Face Masks. The paper proposes a unique FMDRT (Face Mask Dataset in Real-Time) dataset to determine whether a person is wearing a mask or not. The RFMD and Face Mask datasets are also taken from the internet to evaluate the performance of the proposed method. The CLAHE preprocessing method is employed to enhance the image quality, then resizing and Image augmentation techniques are used to convert it into a standard format and increase the size of the dataset, respectively. The pretrained Caffe face detector model is used to detect the faces, and then the lightweight transfer learning-based Xception model is applied for the feature extraction process. This paper recommended a novel model that is, CL-SSDXcept to distinguish the Face Mask or no mask images. However, accession with the MobileNetV2, VGG16, VGG19, and InceptionV3 models with different hyperparameter settings has been tested on the FMDRT dataset. We have also compared the results of the synthesized dataset FMDRT to the existing Face Mask datasets. The experimental results attained 98% test accuracy on the suggested dataset 'FMDRT' using the CL-SSDXcept method. The empirical findings have been reported at 50 iterations with tuned hyperparameter values with an average accuracy 98% and a loss of 0.05.

Jayaswal Ruchi, Dixit Manish

2022-Dec-25

3D‐face masks, CL‐SSDXcept, COVID‐19, DNN models, face mask detection, hyperparameters, optimizers

General General

Rationing scarce healthcare capacity: A study of the ventilator allocation guidelines during the COVID-19 pandemic.

In Production and operations management

In the United States, even though national guidelines for allocating scarce healthcare resources are lacking, 26 states have specific ventilator allocation guidelines to be invoked in case of a shortage. While several states developed their guidelines in response to the recent COVID-19 pandemic, New York State developed these guidelines in 2015 as "pandemic influenza is a foreseeable threat, one that we cannot ignore." The primary objective of this study is to assess the existing procedures and priority rules in place for allocating/rationing scarce ventilator capacity and propose alternative (and improved) priority schemes. We first build machine learning models using inpatient records of COVID-19 patients admitted to New York-Presbyterian/Columbia University Irving Medical Center and an affiliated community health center to predict survival probabilities as well as ventilator length-of-use. Then, we use the resulting point estimators and their uncertainties as inputs for a multiclass priority queueing model with abandonments to assess three priority schemes: (i) SOFA-P (Sequential Organ Failure Assessment based prioritization), which most closely mimics the existing practice by prioritizing patients with sufficiently low SOFA scores; (ii) ISP (incremental survival probability), which assigns priority based on patient-level survival predictions; and (iii) ISP-LU (incremental survival probability per length-of-use), which takes into account survival predictions and resource use duration. Our findings highlight that our proposed priority scheme, ISP-LU, achieves a demonstrable improvement over the other two alternatives. Specifically, the expected number of survivals increases and death risk while waiting for ventilator use decreases. We also show that ISP-LU is a robust priority scheme whose implementation yields a Pareto-improvement over both SOFA-P and ISP in terms of maximizing saved lives after mechanical ventilation while limiting racial disparity in access to the priority queue.

Anderson David R, Aydinliyim Tolga, Bjarnadóttir Margrét V, Çil Eren B, Anderson Michaela R

2023-Jan-22

COVID‐19, fairness, machine learning, multiclass queueing with abandonments, priority scheduling, resource allocation, scarce ventilator capacity

General General

Federated learning based Covid-19 detection.

In Expert systems

The world is affected by COVID-19, an infectious disease caused by the SARS-CoV-2 virus. Tests are necessary for everyone as the number of COVID-19 affected individual's increases. So, the authors developed a basic sequential CNN model based on deep and federated learning that focuses on user data security while simultaneously enhancing test accuracy. The proposed model helps users detect COVID-19 in a few seconds by uploading a single chest X-ray image. A deep learning-aided architecture that can handle client and server sides efficiently has been proposed in this work. The front-end part has been developed using StreamLit, and the back-end uses a Flower framework. The proposed model has achieved a global accuracy of 99.59% after being trained for three federated communication rounds. The detailed analysis of this paper provides the robustness of this work. In addition, the Internet of Medical Things (IoMT) will improve the ease of access to the aforementioned health services. IoMT tools and services are rapidly changing healthcare operations for the better. Hopefully, it will continue to do so in this difficult time of the COVID-19 pandemic and will help to push the envelope of this work to a different extent.

Chowdhury Deepraj, Banerjee Soham, Sannigrahi Madhushree, Chakraborty Arka, Das Anik, Dey Ajoy, Dwivedi Ashutosh Dhar

2022-Nov-02

COVID‐19, CXR images, Internet of Medical Things (IoMT), Xception, cybersecurity, federated learning, privacy, transfer learning

General General

The RW3D: A multi-modal panel dataset to understand the psychological impact of the pandemic

ArXiv Preprint

Besides far-reaching public health consequences, the COVID-19 pandemic had a significant psychological impact on people around the world. To gain further insight into this matter, we introduce the Real World Worry Waves Dataset (RW3D). The dataset combines rich open-ended free-text responses with survey data on emotions, significant life events, and psychological stressors in a repeated-measures design in the UK over three years (2020: n=2441, 2021: n=1716 and 2022: n=1152). This paper provides background information on the data collection procedure, the recorded variables, participants' demographics, and higher-order psychological and text-based derived variables that emerged from the data. The RW3D is a unique primary data resource that could inspire new research questions on the psychological impact of the pandemic, especially those that connect modalities (here: text data, psychological survey variables and demographics) over time.

Isabelle van der Vegt, Bennett Kleinberg

2023-02-01

General General

Dissociating COVID-19 from other respiratory infections based on acoustic, motor coordination, and phonemic patterns.

In Scientific reports ; h5-index 158.0

In the face of the global pandemic caused by the disease COVID-19, researchers have increasingly turned to simple measures to detect and monitor the presence of the disease in individuals at home. We sought to determine if measures of neuromotor coordination, derived from acoustic time series, as well as phoneme-based and standard acoustic features extracted from recordings of simple speech tasks could aid in detecting the presence of COVID-19. We further hypothesized that these features would aid in characterizing the effect of COVID-19 on speech production systems. A protocol, consisting of a variety of speech tasks, was administered to 12 individuals with COVID-19 and 15 individuals with other viral infections at University Hospital Galway. From these recordings, we extracted a set of acoustic time series representative of speech production subsystems, as well as their univariate statistics. The time series were further utilized to derive correlation-based features, a proxy for speech production motor coordination. We additionally extracted phoneme-based features. These features were used to create machine learning models to distinguish between the COVID-19 positive and other viral infection groups, with respiratory- and laryngeal-based features resulting in the highest performance. Coordination-based features derived from harmonic-to-noise ratio time series from read speech discriminated between the two groups with an area under the ROC curve (AUC) of 0.94. A longitudinal case study of two subjects, one from each group, revealed differences in laryngeal based acoustic features, consistent with observed physiological differences between the two groups. The results from this analysis highlight the promise of using nonintrusive sensing through simple speech recordings for early warning and tracking of COVID-19.

Talkar Tanya, Low Daniel M, Simpkin Andrew J, Ghosh Satrajit, O’Keeffe Derek T, Quatieri Thomas F

2023-Jan-28

Radiology Radiology

Longitudinal changes in global structural brain connectivity and cognitive performance in former hospitalized COVID-19 survivors: an exploratory study.

In Experimental brain research

BACKGROUND : Long-term sequelae of COVID-19 can result in reduced functionality of the central nervous system and substandard quality of life. Gaining insight into the recovery trajectory of admitted COVID-19 patients on their cognitive performance and global structural brain connectivity may allow a better understanding of the diseases' relevance.

OBJECTIVES : To assess whole-brain structural connectivity in former non-intensive-care unit (ICU)- and ICU-admitted COVID-19 survivors over 2 months following hospital discharge and correlate structural connectivity measures to cognitive performance.

METHODS : Participants underwent Magnetic Resonance Imaging brain scans and a cognitive test battery after hospital discharge to evaluate structural connectivity and cognitive performance. Multilevel models were constructed for each graph measure and cognitive test, assessing the groups' influence, time since discharge, and interactions. Linear regression models estimated whether the graph measurements affected cognitive measures and whether they differed between ICU and non-ICU patients.

RESULTS : Six former ICU and six non-ICU patients completed the study. Across the various graph measures, the characteristic path length decreased over time (β = 0.97, p = 0.006). We detected no group-level effects (β = 1.07, p = 0.442) nor interaction effects (β = 1.02, p = 0.220). Cognitive performance improved for both non-ICU and ICU COVID-19 survivors on four out of seven cognitive tests 2 months later (p < 0.05).

CONCLUSION : Adverse effects of COVID-19 on brain functioning and structure abate over time. These results should be supported by future research including larger sample sizes, matched control groups of healthy non-infected individuals, and more extended follow-up periods.

Tassignon B, Radwan A, Blommaert J, Stas L, Allard S D, De Ridder F, De Waele E, Bulnes L C, Hoornaert N, Lacor P, Lathouwers E, Mertens R, Naeyaert M, Raeymaekers H, Seyler L, Van Binst A M, Van Imschoot L, Van Liedekerke L, Van Schependom J, Van Schuerbeek P, Vandekerckhove M, Meeusen R, Sunaert S, Nagels G, De Mey J, De Pauw K

2023-Jan-28

Magnetic resonance imaging, Recovery, SARS-CoV-2

Surgery Surgery

Virtual screening and molecular dynamics simulations provide insight into repurposing drugs against SARS-CoV-2 variants Spike protein/ACE2 interface.

In Scientific reports ; h5-index 158.0

After over two years of living with Covid-19 and hundreds of million cases worldwide there is still an unmet need to find proper treatments for the novel coronavirus, due also to the rapid mutation of its genome. In this context, a drug repositioning study has been performed, using in silico tools targeting Delta Spike protein/ACE2 interface. To this aim, it has been virtually screened a library composed by 4388 approved drugs through a deep learning-based QSAR model to identify protein-protein interactions modulators for molecular docking against Spike receptor binding domain (RBD). Binding energies of predicted complexes were calculated by Molecular Mechanics/Generalized Born Surface Area from docking and molecular dynamics simulations. Four out of the top twenty ranking compounds showed stable binding modes on Delta Spike RBD and were evaluated also for their effectiveness against Omicron. Among them an antihistaminic drug, fexofenadine, revealed very low binding energy, stable complex, and interesting interactions with Delta Spike RBD. Several antihistaminic drugs were found to exhibit direct antiviral activity against SARS-CoV-2 in vitro, and their mechanisms of action is still debated. This study not only highlights the potential of our computational methodology for a rapid screening of variant-specific drugs, but also represents a further tool for investigating properties and mechanisms of selected drugs.

Pirolli Davide, Righino Benedetta, Camponeschi Chiara, Ria Francesco, Di Sante Gabriele, De Rosa Maria Cristina

2023-Jan-27

General General

A survey of machine learning-based methods for COVID-19 medical image analysis.

In Medical & biological engineering & computing ; h5-index 32.0

The ongoing COVID-19 pandemic caused by the SARS-CoV-2 virus has already resulted in 6.6 million deaths with more than 637 million people infected after only 30 months since the first occurrences of the disease in December 2019. Hence, rapid and accurate detection and diagnosis of the disease is the first priority all over the world. Researchers have been working on various methods for COVID-19 detection and as the disease infects lungs, lung image analysis has become a popular research area for detecting the presence of the disease. Medical images from chest X-rays (CXR), computed tomography (CT) images, and lung ultrasound images have been used by automated image analysis systems in artificial intelligence (AI)- and machine learning (ML)-based approaches. Various existing and novel ML, deep learning (DL), transfer learning (TL), and hybrid models have been applied for detecting and classifying COVID-19, segmentation of infected regions, assessing the severity, and tracking patient progress from medical images of COVID-19 patients. In this paper, a comprehensive review of some recent approaches on COVID-19-based image analyses is provided surveying the contributions of existing research efforts, the available image datasets, and the performance metrics used in recent works. The challenges and future research scopes to address the progress of the fight against COVID-19 from the AI perspective are also discussed. The main objective of this paper is therefore to provide a summary of the research works done in COVID detection and analysis from medical image datasets using ML, DL, and TL models by analyzing their novelty and efficiency while mentioning other COVID-19-based review/survey researches to deliver a brief overview on the maximum amount of information on COVID-19-based existing researches.

Sailunaz Kashfia, Özyer Tansel, Rokne Jon, Alhajj Reda

2023-Jan-28

COVID-19, Computer tomography, Deep learning, Machine learning, Medical image analysis, Transfer learning

Public Health Public Health

Development of an Artificial Intelligence-Guided Citizen-Centric Predictive Model for the Uptake of Maternal Health Services Among Pregnant Women Living in Urban Slum Settings in India: Protocol for a Cross-sectional Study With a Mixed Methods Design.

In JMIR research protocols ; h5-index 26.0

BACKGROUND : Pregnant women are considered a "high-risk" group with limited access to health facilities in urban slums in India. Barriers to using health services appropriately may lead to maternal and child mortality, morbidity, low birth weight, and children with stunted growth. With the increase in the use of artificial intelligence (AI) and machine learning in the health sector, we plan to develop a predictive model that can enable substantial uptake of maternal health services and improvements in adverse pregnancy health care outcomes from early diagnostics to treatment in urban slum settings.

OBJECTIVE : The objective of our study is to develop and evaluate the AI-guided citizen-centric platform that will support the uptake of maternal health services among pregnant women seeking antenatal care living in urban slum settings.

METHODS : We will conduct a cross-sectional study using a mixed methods approach to enroll 225 pregnant women aged 18-44 years, living in the urban slums of Delhi for more than 6 months, seeking antenatal care, and who have smartphones. Quantitative and qualitative data will be collected using an Open Data Kit Android-based tool. Variables gathered will include sociodemographics, clinical history, pregnancy history, dietary history, COVID-19 history, health care facility data, socioeconomic status, and pregnancy outcomes. All data gathered will be aggregated into a common database. We will use AI to predict the early at-risk pregnancy outcomes (in terms of the type of delivery method, term, and related complications) depending on the needs of the beneficiaries translating into effective service-delivery improvements in enhancing the use of maternal health services among pregnant women seeking antenatal care. The proposed research will help policy makers to prioritize resource planning, resource allocation, and the development of programs and policies to enhance maternal health outcomes. The academic research study has received ethical approval from the University Research Ethics Committee of Dehradun Institute of Technology (DIT) University, Dehradun, India.

RESULTS : The study was approved by the University Research Ethics Committee of DIT University, Dehradun, on July 4, 2021. Enrollment of the eligible participants will begin by April 2022 followed by the development of the predictive model by October 2022 till January 2023. The proposed AI-guided citizen-centric tool will be designed, developed, implemented, and evaluated using principles of human-centered design that will help to predict early at-risk pregnancy outcomes.

CONCLUSIONS : The proposed internet-enabled AI-guided prediction model will help identify the potential risk associated with pregnancies and enhance the uptake of maternal health services among those seeking antenatal care for safer deliveries. We will explore the scalability of the proposed platform up to different geographic locations for adoption for similar and other health conditions.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) : PRR1-10.2196/35452.

Shrivastava Rahul, Singhal Manmohan, Gupta Mansi, Joshi Ashish

2023-Jan-27

artificial intelligence, citizen centric, development, evaluation, informatics, machine learning, maternal health, predictive model

Public Health Public Health

Application of artificial intelligence to the public health education.

In Frontiers in public health

With the global outbreak of coronavirus disease 2019 (COVID-19), public health has received unprecedented attention. The cultivation of emergency and compound professionals is the general trend through public health education. However, current public health education is limited to traditional teaching models that struggle to balance theory and practice. Fortunately, the development of artificial intelligence (AI) has entered the stage of intelligent cognition. The introduction of AI in education has opened a new era of computer-assisted education, which brought new possibilities for teaching and learning in public health education. AI-based on big data not only provides abundant resources for public health research and management but also brings convenience for students to obtain public health data and information, which is conducive to the construction of introductory professional courses for students. In this review, we elaborated on the current status and limitations of public health education, summarized the application of AI in public health practice, and further proposed a framework for how to integrate AI into public health education curriculum. With the rapid technological advancements, we believe that AI will revolutionize the education paradigm of public health and help respond to public health emergencies.

Wang Xueyan, He Xiujing, Wei Jiawei, Liu Jianping, Li Yuanxi, Liu Xiaowei

2022

algorithm, artificial intelligence, big data, curriculum, education, public health

Public Health Public Health

Entity and relation extraction from clinical case reports of COVID-19: a natural language processing approach.

In BMC medical informatics and decision making ; h5-index 38.0

BACKGROUND : Extracting relevant information about infectious diseases is an essential task. However, a significant obstacle in supporting public health research is the lack of methods for effectively mining large amounts of health data.

OBJECTIVE : This study aims to use natural language processing (NLP) to extract the key information (clinical factors, social determinants of health) from published cases in the literature.

METHODS : The proposed framework integrates a data layer for preparing a data cohort from clinical case reports; an NLP layer to find the clinical and demographic-named entities and relations in the texts; and an evaluation layer for benchmarking performance and analysis. The focus of this study is to extract valuable information from COVID-19 case reports.

RESULTS : The named entity recognition implementation in the NLP layer achieves a performance gain of about 1-3% compared to benchmark methods. Furthermore, even without extensive data labeling, the relation extraction method outperforms benchmark methods in terms of accuracy (by 1-8% better). A thorough examination reveals the disease's presence and symptoms prevalence in patients.

CONCLUSIONS : A similar approach can be generalized to other infectious diseases. It is worthwhile to use prior knowledge acquired through transfer learning when researching other infectious diseases.

Raza Shaina, Schwartz Brian

2023-Jan-26

Artificial intelligence, COVID-19, Data cohort, Named entity, Natural language processing, Relation extraction, Transfer learning

Public Health Public Health

Insights in paediatric virology during the COVID-19 era (Review).

In Medicine international

The present article provides an overview of the key messages of the topics discussed at the '7th Workshop on Paediatric Virology', which was organised virtually on December 20, 2021 by the Institute of Paediatric Virology, located on the Island of Euboea in Greece. The workshop's plenary lectures were on: i) viral pandemics and epidemics in the ancient Mediterranean; ii) the impact of obesity on the outcome of viral infections in children and adolescents; and iii) COVID-19 and artificial intelligence. Despite the scarcity of evidence from fossils and remnants, viruses have been recognised as significant causes of several epidemics in the ancient Mediterranean. Paediatric obesity, a modifiable critical health risk factor, has been shown to impact on the development, progression and severity of viral infections. Thus, the prevention of paediatric obesity should be included in formulating public health policies and decision-making strategies against emerging global viral threats. During the current COVID-19 pandemic, artificial intelligence has been used to facilitate the identification, monitoring and prevention of SARS-CoV-2. In the future, it will play a fundamental role in the surveillance of epidemic-prone infectious diseases, in the repurposing of older therapies and in the design of novel therapeutic agents against viral infections. The collaboration between different medical specialties and other diverse scientific fields, including archaeology, history, epidemiology, nutritional technologies, mathematics, computer technology, engineering, medical law and ethics is essential for the successful management of paediatric viral infections. The current COVID-19 pandemic has underscored this need, which should be further encouraged in modern medical education.

Mammas Ioannis N, Liston Maria, Koletsi Patra, Vitoratou Dimitra-Irinna, Koutsaftiki Chryssie, Papatheodoropoulou Alexia, Kornarou Helen, Theodoridou Maria, Kramvis Anna, Drysdale Simon B, Spandidos Demetrios A

2022

Institute of Paediatric Virology, ancient Mediterranean, artificial intelligence, coronavirus disease 2019, obesity, paediatric virology, severe acute respiratory syndrome coronavirus 2, viral infections, viral pandemics

General General

DeepMPF: deep learning framework for predicting drug-target interactions based on multi-modal representation with meta-path semantic analysis.

In Journal of translational medicine

BACKGROUND : Drug-target interaction (DTI) prediction has become a crucial prerequisite in drug design and drug discovery. However, the traditional biological experiment is time-consuming and expensive, as there are abundant complex interactions present in the large size of genomic and chemical spaces. For alleviating this phenomenon, plenty of computational methods are conducted to effectively complement biological experiments and narrow the search spaces into a preferred candidate domain. Whereas, most of the previous approaches cannot fully consider association behavior semantic information based on several schemas to represent complex the structure of heterogeneous biological networks. Additionally, the prediction of DTI based on single modalities cannot satisfy the demand for prediction accuracy.

METHODS : We propose a multi-modal representation framework of 'DeepMPF' based on meta-path semantic analysis, which effectively utilizes heterogeneous information to predict DTI. Specifically, we first construct protein-drug-disease heterogeneous networks composed of three entities. Then the feature information is obtained under three views, containing sequence modality, heterogeneous structure modality and similarity modality. We proposed six representative schemas of meta-path to preserve the high-order nonlinear structure and catch hidden structural information of the heterogeneous network. Finally, DeepMPF generates highly representative comprehensive feature descriptors and calculates the probability of interaction through joint learning.

RESULTS : To evaluate the predictive performance of DeepMPF, comparison experiments are conducted on four gold datasets. Our method can obtain competitive performance in all datasets. We also explore the influence of the different feature embedding dimensions, learning strategies and classification methods. Meaningfully, the drug repositioning experiments on COVID-19 and HIV demonstrate DeepMPF can be applied to solve problems in reality and help drug discovery. The further analysis of molecular docking experiments enhances the credibility of the drug candidates predicted by DeepMPF.

CONCLUSIONS : All the results demonstrate the effectively predictive capability of DeepMPF for drug-target interactions. It can be utilized as a useful tool to prescreen the most potential drug candidates for the protein. The web server of the DeepMPF predictor is freely available at http://120.77.11.78/DeepMPF/ , which can help relevant researchers to further study.

Ren Zhong-Hao, You Zhu-Hong, Zou Quan, Yu Chang-Qing, Ma Yan-Fang, Guan Yong-Jian, You Hai-Ru, Wang Xin-Fei, Pan Jie

2023-Jan-25

Drug–protein interactions, Joint learning, Meta-path, Multi-modal, Natural language processing, Sequence analysis

General General

An open-source molecular builder and free energy preparation workflow.

In Communications chemistry

Automated free energy calculations for the prediction of binding free energies of congeneric series of ligands to a protein target are growing in popularity, but building reliable initial binding poses for the ligands is challenging. Here, we introduce the open-source FEgrow workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations. For a given ligand core and receptor structure, FEgrow enumerates and optimises the bioactive conformations of the grown functional group(s), making use of hybrid machine learning/molecular mechanics potential energy functions where possible. Low energy structures are optionally scored using the gnina convolutional neural network scoring function, and output for more rigorous protein-ligand binding free energy predictions. We illustrate use of the workflow by building and scoring binding poses for ten congeneric series of ligands bound to targets from a standard, high quality dataset of protein-ligand complexes. Furthermore, we build a set of 13 inhibitors of the SARS-CoV-2 main protease from the literature, and use free energy calculations to retrospectively compute their relative binding free energies. FEgrow is freely available at https://github.com/cole-group/FEgrow , along with a tutorial.

Bieniek Mateusz K, Cree Ben, Pirie Rachael, Horton Joshua T, Tatum Natalie J, Cole Daniel J

2022-Oct-27

General General

DeepGpgs: a novel deep learning framework for predicting arginine methylation sites combined with Gaussian prior and gated self-attention mechanism.

In Briefings in bioinformatics

Protein arginine methylation is an important posttranslational modification (PTM) associated with protein functional diversity and pathological conditions including cancer. Identification of methylation binding sites facilitates a better understanding of the molecular function of proteins. Recent developments in the field of deep neural networks have led to a proliferation of deep learning-based methylation identification studies because of their fast and accurate prediction. In this paper, we propose DeepGpgs, an advanced deep learning model incorporating Gaussian prior and gated attention mechanism. We introduce a residual network channel to extract the evolutionary information of proteins. Then we combine the adaptive embedding with bidirectional long short-term memory networks to form a context-shared encoder layer. A gated multi-head attention mechanism is followed to obtain the global information about the sequence. A Gaussian prior is injected into the sequence to assist in predicting PTMs. We also propose a weighted joint loss function to alleviate the false negative problem. We empirically show that DeepGpgs improves Matthews correlation coefficient by 6.3% on the arginine methylation independent test set compared with the existing state-of-the-art methylation site prediction methods. Furthermore, DeepGpgs has good robustness in phosphorylation site prediction of SARS-CoV-2, which indicates that DeepGpgs has good transferability and the potential to be extended to other modification sites prediction. The open-source code and data of the DeepGpgs can be obtained from https://github.com/saizhou1/DeepGpgs.

Zhou Haiwei, Tan Wenxi, Shi Shaoping

2023-Jan-24

Gaussian prior, gated attention mechanism, methylation, residual network, weighted joint loss function

General General

Executive protocol designed for new review study called: systematic review and artificial intelligence network meta-analysis (RAIN) with the first application for COVID-19.

In Biology methods & protocols

Artificial intelligence (AI) as a suite of technologies can complement systematic review and meta-analysis studies and answer questions that cannot be typically answered using traditional review protocols and reporting methods. The purpose of this protocol is to introduce a new protocol to complete systematic review and meta-analysis studies. In this work, systematic review, meta-analysis, and meta-analysis network based on selected AI technique, and for P < 0.05 are followed, with a view to responding to questions and challenges that the global population is facing in light of the COVID-19 pandemic. Finally, it is expected that conducting reviews by following the proposed protocol can provide suitable answers to some of the research questions raised due to COVID-19.

Salari Nader, Shohaimi Shamarina, Kiaei Aliakbar, Hosseinian-Far Amin, Mansouri Kamran, Ahmadi Arash, Mohammadi Masoud

2023

COVID-19, artificial intelligence, meta-analysis, network meta-analysis, protocol, systematic review

Public Health Public Health

Conspiracy beliefs and COVID-19 guideline adherence in adolescent psychiatric outpatients: the predictive role of adverse childhood experiences.

In Child and adolescent psychiatry and mental health

BACKGROUND : Conspiracy beliefs have become widespread throughout the COVID-19 pandemic. Previous studies have shown that endorsing conspiracy beliefs leads to lower protective guideline adherence (i.e., wearing face masks), posing a threat to public health measures. The current study expands this research across the lifespan, i.e., in a sample of adolescents with mental health problems. Here, we investigated the association between conspiracy beliefs and guideline adherence while also exploring the predictors of conspiracy beliefs.

METHODS : N = 93 adolescent psychiatric outpatients (57% female, mean age: 15.8) were assessed using anonymous paper-pencil questionnaires. Endorsement of generic and COVID-19 conspiracy beliefs was assessed, in addition to items measuring adherence to protective guidelines and mental health (stress, depressive symptoms, emotional/behavioral problems, and adverse childhood experiences). Multiple regressions and supervised machine learning (conditional random forests) were used for analyses.

RESULTS : Fourteen percent of our sample fully endorsed at least one COVID-19 conspiracy theory, while protective guidelines adherence was relatively high (M = 4.92, on a scale from 1 to 7). The endorsement of COVID-19 conspiracy beliefs-but not of generic conspiracy beliefs-was associated with lower guideline adherence (β = - 0.32, 95% CI - 0.53 to - 0.11, p < .001). Conditional random forests suggested that adverse childhood experiences and peer and conduct problems were relevant predictors of both conspiracy belief categories.

CONCLUSION : While a significant proportion of our sample of adolescents in psychiatric treatment endorsed conspiracy beliefs, the majority did not. Furthermore, and to some degree, contrary to public perception, we found that adolescents show relatively good adherence to public health measures-even while experiencing a high degree of mental distress. The predictive value of adverse childhood experiences and peer/conduct problems for conspiracy beliefs might be explained by compensatory mechanisms to ensure the safety, structure, and inclusion that conspiracies provide.

Goreis Andreas, Pfeffer Bettina, Zesch Heidi Elisabeth, Klinger Diana, Reiner Tamara, Bock Mercedes M, Ohmann Susanne, Sackl-Pammer Petra, Werneck-Rohrer Sonja, Eder Harald, Skala Katrin, Czernin Klara, Mairhofer Dunja, Rohringer Bernhard, Bedus Carolin, Lipp Ronja, Vesely Christine, Plener Paul L, Kothgassner Oswald D

2023-Jan-24

Adolescents, Adverse childhood experiences, COVID-19, Childhood Trauma, Conspiracy beliefs, Guideline adherence, Mental health

Public Health Public Health

Generating simple classification rules to predict local surges in COVID-19 hospitalizations.

In Health care management science

Low rates of vaccination, emergence of novel variants of SARS-CoV-2, and increasing transmission relating to seasonal changes and relaxation of mitigation measures leave many US communities at risk for surges of COVID-19 that might strain hospital capacity, as in previous waves. The trajectories of COVID-19 hospitalizations differ across communities depending on their age distributions, vaccination coverage, cumulative incidence, and adoption of risk mitigating behaviors. Yet, existing predictive models of COVID-19 hospitalizations are almost exclusively focused on national- and state-level predictions. This leaves local policymakers in urgent need of tools that can provide early warnings about the possibility that COVID-19 hospitalizations may rise to levels that exceed local capacity. In this work, we develop a framework to generate simple classification rules to predict whether COVID-19 hospitalization will exceed the local hospitalization capacity within a 4- or 8-week period if no additional mitigating strategies are implemented during this time. This framework uses a simulation model of SARS-CoV-2 transmission and COVID-19 hospitalizations in the US to train classification decision trees that are robust to changes in the data-generating process and future uncertainties. These generated classification rules use real-time data related to hospital occupancy and new hospitalizations associated with COVID-19, and when available, genomic surveillance of SARS-CoV-2. We show that these classification rules present reasonable accuracy, sensitivity, and specificity (all ≥ 80%) in predicting local surges in hospitalizations under numerous simulated scenarios, which capture substantial uncertainties over the future trajectories of COVID-19. Our proposed classification rules are simple, visual, and straightforward to use in practice by local decision makers without the need to perform numerical computations.

Yaesoubi Reza, You Shiying, Xi Qin, Menzies Nicolas A, Tuite Ashleigh, Grad Yonatan H, Salomon Joshua A

2023-Jan-24

COVID-19, Decision tree, Machine learning, Prediction, Simulation, Surveillance

General General

Deep learning identified genetic variants for COVID-19-related mortality among 28,097 affected cases in UK Biobank.

In Genetic epidemiology

Analysis of host genetic components provides insights into the susceptibility and response to viral infection such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). To reveal genetic determinants of susceptibility to COVID-19 related mortality, we train a deep learning model to identify groups of genetic variants and their interactions that contribute to the COVID-19 related mortality risk using the UK Biobank data (28,097 affected cases and 1656 deaths). We refer to such groups of variants as super variants. We identify 15 super variants with various levels of significance as susceptibility loci for COVID-19 mortality. Specifically, we identify a super variant (odds ratio [OR] = 1.594, p = 5.47 × 10-9 ) on Chromosome 7 that consists of the minor allele of rs76398985, rs6943608, rs2052130, 7:150989011_CT_C, rs118033050, and rs12540488. We also discover a super variant (OR = 1.353, p = 2.87 × 10-8 ) on Chromosome 5 that contains rs12517344, rs72733036, rs190052994, rs34723029, rs72734818, 5:9305797_GTA_G, and rs180899355.

Liu Zihuan, Dai Wei, Wang Shiying, Yao Yisha, Zhang Heping

2023-Jan-24

COVID-19, SARS-CoV-2, TAS2R1, UK Biobank, deep learning

General General

Deep learning approach to security enforcement in cloud workflow orchestration.

In Journal of cloud computing (Heidelberg, Germany)

Supporting security and data privacy in cloud workflows has attracted significant research attention. For example, private patients' data managed by a workflow deployed on the cloud need to be protected, and communication of such data across multiple stakeholders should also be secured. In general, security threats in cloud environments have been studied extensively. Such threats include data breaches, data loss, denial of service, service rejection, and malicious insiders generated from issues such as multi-tenancy, loss of control over data and trust. Supporting the security of a cloud workflow deployed and executed over a dynamic environment, across different platforms, involving different stakeholders, and dynamic data is a difficult task and is the sole responsibility of cloud providers. Therefore, in this paper, we propose an architecture and a formal model for security enforcement in cloud workflow orchestration. The proposed architecture emphasizes monitoring cloud resources, workflow tasks, and the data to detect and predict anomalies in cloud workflow orchestration using a multi-modal approach that combines deep learning, one class classification, and clustering. It also features an adaptation scheme to cope with anomalies and mitigate their effect on the workflow cloud performance. Our prediction model captures unsupervised static and dynamic features as well as reduces the data dimensionality, which leads to better characterization of various cloud workflow tasks, and thus provides better prediction of potential attacks. We conduct a set of experiments to evaluate the proposed anomaly detection, prediction, and adaptation schemes using a real COVID-19 dataset of patient health records. The results of the training and prediction experiments show high anomaly prediction accuracy in terms of precision, recall, and F1 scores. Other experimental results maintained a high execution performance of the cloud workflow after applying adaptation strategy to respond to some detected anomalies. The experiments demonstrate how the proposed architecture prevents unnecessary wastage of resources due to anomaly detection and prediction.

El-Kassabi Hadeel T, Serhani Mohamed Adel, Masud Mohammad M, Shuaib Khaled, Khalil Khaled

2023

Anomaly detection, Cloud, Cloud workflow, Covid-19, Deep learning, Prediction, Security enforcement

General General

Protein-ligand binding affinity prediction with edge awareness and supervised attention.

In iScience

Accurate prediction of protein-ligand binding affinity is crucial in structure-based drug design but remains some challenges even with recent advances in deep learning: (1) Existing methods neglect the edge information in protein and ligand structure data; (2) current attention mechanisms struggle to capture true binding interactions in the small dataset. Herein, we proposed SEGSA_DTA, a SuperEdge Graph convolution-based and Supervised Attention-based Drug-Target Affinity prediction method, where the super edge graph convolution can comprehensively utilize node and edge information and the multi-supervised attention module can efficiently learn the attention distribution consistent with real protein-ligand interactions. Results on the multiple datasets show that SEGSA_DTA outperforms current state-of-the-art methods. We also applied SEGSA_DTA in repurposing FDA-approved drugs to identify potential coronavirus disease 2019 (COVID-19) treatments. Besides, by using SHapley Additive exPlanations (SHAP), we found that SEGSA_DTA is interpretable and further provides a new quantitative analytical solution for structure-based lead optimization.

Gu Yuliang, Zhang Xiangzhou, Xu Anqi, Chen Weiqi, Liu Kang, Wu Lijuan, Mo Shenglong, Hu Yong, Liu Mei, Luo Qichao

2023-Jan-20

Biocomputational method, Classification of proteins, Molecular interaction

General General

Estimation of the unemployment rate in Turkey: A comparison of the ARIMA and machine learning models including Covid-19 pandemic periods.

In Heliyon

The article focuses on analyzing the robustness of Auto Regressive Integrated Moving Average (ARIMA) and Artificial Neural Networks (ANN) methods in unemployment rate estimation. In this context, a stochastic trend in the unemployment rate was determined by using monthly data in Turkey. The oil price, real exchange rate, interest rate and unemployment rate variables are imported into the ARIMA and ANN models with 176 data samples for the period of 01.01.2008-31.08.2022. The results of the conventional linear ARIMA and nonlinear ANN regressor models are compared. The comparison results show that the ARMA (2,1) model is the most suitable model for the unemployment rate estimation. This conclusion was reached based on ARMA (2,1) and ANN's RMSE, MAE, MAPE and R2 parameters. From the results of the specified criteria, it was found that both models gave results close to the actual unemployment rate however ARMA (2,1) was the more appropriate model for the current data set. The actual unemployment data and the estimated values are also given verifying the better modeling of the developed ARMA (2,1) model. In addition, there are meaningful relationships between month variables and the employment rate. This result supports that the unemployment possesses chronic reasons in Turkey. On the other side, the unemployment rate forecasting error of the ARMA (2,1) is higher than the ANN model for the 2020-2021 period during the intense pandemic. This result is important because it shows that during the times of the economic uncertainty caused by the Covid-19 pandemic, forecasts employing the neural network model is observed to have lower errors than the results of autoregressive moving average model. Therefore, under an economic uncertainty, it is shown that modeling the unemployment rate using artificial neural network provides novel insights for economic forecasting.

Yamacli Dilek Surekci, Yamacli Serhan

2023-Jan

ANN, ARIMA, Estimation, Unemployment rate

Internal Medicine Internal Medicine

Statistical Analysis of Mortality Rates of Coronavirus Disease 2019 (COVID-19) Patients in Japan Across the 4C Mortality Score Risk Groups, Age Groups, and Epidemiological Waves: A Report From the Nationwide COVID-19 Cohort.

In Open forum infectious diseases

BACKGROUND : The mortality rates of coronavirus disease 2019 (COVID-19) have been changed across the epidemiological waves. The aim was to investigate the differences in mortality rates of COVID-19 patients in Japan across the 6 epidemiological waves stratified by age group and Coronavirus Clinical Characterisation Consortium (4C) mortality score risk group.

METHODS : A total of 56 986 COVID-19 patients in the COVID-19 Registry Japan from 2 March 2020 to 1 February 2022 were enrolled. These patients were categorized into 4 risk groups based on their 4C mortality score. Mortality rates of each risk group were calculated separately for different age groups: 18-64, 65-74, 75-89, and ≥90 years. In addition, mortality rates across the wave periods were calculated separately in 2 age groups: <75 and ≥75 years. All calculated mortality rates were compared with reported data from the United Kingdom (UK) during the early epidemic.

RESULTS : The mortality rates of patients in Japan were significantly lower than in the UK across the board, with the exception of patients aged ≥90 years at very high risk. The mortality rates of patients aged ≥75 years at very high risk in the fourth and fifth wave periods showed no significant differences from those in the UK, whereas those in the sixth wave period were significantly lower in all age groups and in all risk groups.

CONCLUSIONS : The present analysis showed that COVID-19 patients had a lower mortality rate in the most recent sixth wave period, even among patients ≥75 years old at very high risk.

Baba Hiroaki, Ikumi Saori, Aoyama Shotaro, Ishikawa Tetsuo, Asai Yusuke, Matsunaga Nobuaki, Ohmagari Norio, Kanamori Hajime, Tokuda Koichi, Ueda Takuya, Kawakami Eiryo

2023-Jan

4C mortality score, COVID-19, Japan, elderly, epidemic wave

General General

CovidExpert: A Triplet Siamese Neural Network framework for the detection of COVID-19.

In Informatics in medicine unlocked

Patients with the COVID-19 infection may have pneumonia-like symptoms as well as respiratory problems which may harm the lungs. From medical images, coronavirus illness may be accurately identified and predicted using a variety of machine learning methods. Most of the published machine learning methods may need extensive hyperparameter adjustment and are unsuitable for small datasets. By leveraging the data in a comparatively small dataset, few-shot learning algorithms aim to reduce the requirement of large datasets. This inspired us to develop a few-shot learning model for early detection of COVID-19 to reduce the post-effect of this dangerous disease. The proposed architecture combines few-shot learning with an ensemble of pre-trained convolutional neural networks to extract feature vectors from CT scan images for similarity learning. The proposed Triplet Siamese Network as the few-shot learning model classified CT scan images into Normal, COVID-19, and Community-Acquired Pneumonia. The suggested model achieved an overall accuracy of 98.719%, a specificity of 99.36%, a sensitivity of 98.72%, and a ROC score of 99.9% with only 200 CT scans per category for training data.

Ornob Tareque Rahman, Roy Gourab, Hassan Enamul

2023

COVID-19 diagnosis, CT scan images, Ensemble CNN, Few-shot learning, Triplet siamese network

General General

ELUCNN for explainable COVID-19 diagnosis.

In Soft computing

COVID-19 is a positive-sense single-stranded RNA virus caused by a strain of coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several noteworthy variants of SARS-CoV-2 were declared by WHO as Alpha, Beta, Gamma, Delta, and Omicron. Till 13/Dec/2022, it has caused 6.65 million death tolls, and over 649 million confirmed positive cases. Based on the convolutional neural network (CNN), this study first proposes a ten-layer CNN as the backbone model. Then, the exponential linear unit (ELU) is introduced to replace ReLU, and the traditional convolutional block is now transformed into conv-ELU. Finally, an ELU-based CNN (ELUCNN) model is proposed for COVID-19 diagnosis. Besides, the MDA strategy is used to enhance the size of the training set. We develop a mobile app integrating ELUCNN, and this web app is run on a client-server modeled structure. Ten runs of the tenfold cross-validation experiment show our model yields a sensitivity of 94.41 ± 0.98 , a specificity of 94.84 ± 1.21 , an accuracy of 94.62 ± 0.96 , and an F1 score of 94.61 ± 0.95 . The ELUCNN model and mobile app are effective in COVID-19 diagnosis and give better results than 14 state-of-the-art COVID-19 diagnosis models concerning accuracy.

Wang Shui-Hua, Satapathy Suresh Chandra, Xie Man-Xia, Zhang Yu-Dong

2023-Jan-13

COVID-19, Cloud computing, Convolutional neural network, Cross validation, Deep learning, Exponential linear unit, Mobile app, Multiple-way data augmentation, SARS-CoV-2

General General

Assessment of the digital competencies of university instructors through use of the machine learning method.

In SN social sciences

The explosion of COVID-19 has brought new challenges to the education industry, especially higher education. Digital competency is becoming an essential competency for higher education instructors, and how to assess instructors' digital competency is attracting increasing attention in higher education. However, most studies have used self-report questionnaires or manual reviews to assess digital competencies, which are time-consuming and potentially biased, and there is a current need for valid and effective assessment methods. To address this issue, this study uses machine learning to analyze syllabi to assess the extent to which university instructors have incorporated digital competency into their courses. The results show that not only is the proposed method feasible, but the results of the assessment using machine learning are highly consistent with those of the human assessment. This approach contributes to the assessment of digital competency in higher education institutions and provides evidence that can be used as a reference for future research on the development of digital competency in higher education institutions.

Yang Tzu-Chi

2023

Digital competence, Higher education, Machine learning, Syllabus analysis

General General

COVID-19-The Role of Artificial Intelligence, Machine Learning, and Deep Learning: A Newfangled.

In Archives of computational methods in engineering : state of the art reviews

The absolute previously infected novel coronavirus (COVID-19) was found in Wuhan, China, in December 2019. The COVID-19 epidemic has spread to more than 220 nations and territories globally and has altogether influenced each part of our day-to-day lives. As of 9th March 2022, a total aggregate of 44,78,82,185 (60,07,317) contaminated (dead) COVID-19 cases were accounted for all over the world. The quantities of contaminated cases passing despite everything increment essentially and do not indicate a controlled circumstance. The scope of this paper is to address this issue by presenting a comprehensive and comparative analysis of the existing Machine Learning (ML), Deep Learning (DL) and Artificial Intelligence (AI) based approaches used in significance in reacting to the COVID-19 epidemic and diagnosing the severe impacts. The paper provides, firstly, an overview of COVID-19 infection and highlights of this article; Secondly, an overview of exploring various executive innovations by utilizing different resources to stop the spread of COVID-19; Thirdly, a comparison of existing predicting methods of COVID-19 in the literature, with focus on ML, DL and AI-driven techniques with performance metrics; and finally, a discussion on the results of the work as well as future scope.

Vinod Dasari Naga, Prabaharan S R S

2023-Jan-17

General General

Development of a Fast Fourier Transform-based Analytical Method for COVID-19 Diagnosis from Chest X-Ray Images Using GNU Octave.

In Journal of medical physics

PURPOSE : Many artificial intelligence-based computational procedures are developed to diagnose COVID-19 infection from chest X-ray (CXR) images, as diagnosis by CXR imaging is less time consuming and economically cheap compared to other detection procedures. Due to unavailability of skilled computer professionals and high computer architectural resource, majority of the employed methods are difficult to implement in rural and poor economic settings. Majority of such reports are devoid of codes and ignores related diseases (pneumonia). The absence of codes makes limitation in applying them widely. Hence, validation testing followed by evidence-based medical practice is difficult. The present work was aimed to develop a simple method that requires a less computational expertise and minimal level of computer resource, but with statistical inference.

MATERIALS AND METHODS : A Fast Fourier Transform-based (FFT) method was developed with GNU Octave, a free and open-source platform. This was employed to the images of CXR for further analysis. For statistical inference, two variables, i.e., the highest peak and number of peaks in the FFT distribution plot were considered.

RESULTS : The comparison of mean values among different groups (normal, COVID-19, viral, and bacterial pneumonia [BP]) showed statistical significance, especially when compared to normal, except between viral and BP groups.

CONCLUSION : Parametric statistical inference from our result showed high level of significance (P < 0.001). This is comparable to the available artificial intelligence-based methods (where accuracy is about 94%). Developed method is easy, availability with codes, and requires a minimal level of computer resource and can be tested with a small sample size in different demography, and hence, be implemented in a poor socioeconomic setting.

Majumder Durjoy

2022

COVID-19, Chest X-ray image, Fourier analysis, image analysis, pneumonia

Surgery Surgery

Machine learning-based integration develops biomarkers initial the crosstalk between inflammation and immune in acute myocardial infarction patients.

In Frontiers in cardiovascular medicine

Great strides have been made in past years toward revealing the pathogenesis of acute myocardial infarction (AMI). However, the prognosis did not meet satisfactory expectations. Considering the importance of early diagnosis in AMI, biomarkers with high sensitivity and accuracy are urgently needed. On the other hand, the prevalence of AMI worldwide has rapidly increased over the last few years, especially after the outbreak of COVID-19. Thus, in addition to the classical risk factors for AMI, such as overwork, agitation, overeating, cold irritation, constipation, smoking, and alcohol addiction, viral infections triggers have been considered. Immune cells play pivotal roles in the innate immunosurveillance of viral infections. So, immunotherapies might serve as a potential preventive or therapeutic approach, sparking new hope for patients with AMI. An era of artificial intelligence has led to the development of numerous machine learning algorithms. In this study, we integrated multiple machine learning algorithms for the identification of novel diagnostic biomarkers for AMI. Then, the possible association between critical genes and immune cell infiltration status was characterized for improving the diagnosis and treatment of AMI patients.

Li Hongyu, Sun Xinti, Li Zesheng, Zhao Ruiping, Li Meng, Hu Taohong

2022

acute myocardial infarction, bioinformatics, immune infiltration, machine learning, prognosis

General General

Analysis of individual characteristics influencing user polarization in COVID-19 vaccine hesitancy.

In Computers in human behavior ; h5-index 125.0

During the COVID-19 pandemic, vaccine hesitancy proved to be a major obstacle in efforts to control and mitigate the negative consequences of COVID-19. This study centered on the degree of polarization on social media about vaccine use and contributing factors to vaccine hesitancy among social media users. Examining the discussion about COVID-19 vaccine on the Weibo platform, a relatively comprehensive system of user features was constructed based on psychological theories and models such as the curiosity-drive theory and the big five model of personality. Then machine learning methods were used to explore the paramount impacting factors that led users into polarization. Findings revealed that factors reflecting the activity and effectiveness of social media use promoted user polarization. In contrast, features reflecting users' information processing ability and personal qualities had a negative impact on polarization. This study hopes to help healthcare organizations and governments understand and curb social media polarization around vaccine development in the face of future surges of pandemics.

Xie Lei, Wang Dandan, Ma Feicheng

2023-Jan-17

Big five model of personality, COVID-19 pandemic, Curiosity-drive theory, User polarization, Vaccine hesitancy

General General

Safety, Tolerability and Pharmacokinetics of Half-Life Extended SARS-CoV-2 Neutralizing Monoclonal Antibodies AZD7442 (Tixagevimab/Cilgavimab) in Healthy Adults.

In The Journal of infectious diseases ; h5-index 82.0

BACKGROUND : AZD7442 is a combination of extended half-life, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific neutralizing monoclonal antibodies (tixagevimab/cilgavimab).

METHODS : This phase 1, first-in-human, randomized, double-blind, placebo-controlled, dose-escalation study evaluated AZD7442 administered intramuscularly (300 mg) or intravenously (300, 1000, 3000 mg) in healthy adults (aged 18-55 years). The primary endpoint was safety and tolerability. Secondary endpoints included pharmacokinetics and anti-drug antibodies.

RESULTS : Between August 18-October 16, 2020, 60 participants enrolled; 50 received AZD7442 and 10 received placebo. Adverse events (all of mild/moderate intensity) occurred in 26 (52.0%) and 8 (80.0%) participants (AZD7442 and placebo groups, respectively). No infusion- or injection-site, or hypersensitivity reactions occurred. Tixagevimab and cilgavimab had mean half-lives of approximately 90 days (range: 87.0-95.3 [tixagevimab], 79.8--91.1 [cilgavimab]) and similar pharmacokinetic profiles over the 361-day study period. SARS-CoV-2-specific neutralizing antibody titers provided by AZD7442 were maintained above those in plasma from convalescent coronavirus disease-19 (COVID-19) patients.

CONCLUSIONS : AZD7442 was well tolerated in healthy adults, showing a favorable safety profile across all doses. Depending on the SARS-CoV-2 variant, pharmacokinetic analyses suggest AZD7442 could offer protection for at least 6 months against symptomatic COVID-19 following a single 300 mg intramuscular administration.

CLINICAL TRIALS REGISTRATION : NCT04507256 (https://clinicaltrials.gov/ct2/show/NCT04507256).

Forte-Soto Pablo, Albayaty Muna, Brooks Dennis, Arends Rosalinda H, Tillinghast John, Aksyuk Anastasia A, Bouquet Jerome, Chen Cecil, Gebre Asfiha, Kubiak Robert J, Pilla Reddy Venkatesh, Seegobin Seth, Streicher Katie, Templeton Alison, Esser Mark T

2023-Jan-23

COVID-19, SARS-CoV-2, monoclonal antibody, pharmacokinetics, phase 1, safety, tolerability

Surgery Surgery

Essential elements of weight loss apps for a multi-ethnic population with high BMI: a qualitative study with practical recommendations.

In Translational behavioral medicine

Smartphone weight loss apps are constantly being developed but the essential elements needed by a multi-ethnic population with overweight and obesity remains unclear. Purpose: To explore the perceptions of an Asian multi-ethnic population with overweight and obesity on the essential elements of weight loss apps. Twenty two participants were purposively sampled from a specialist weight management clinic in Singapore from 13 April to 30 April 2021. Recorded interviews were conducted using face-to-face and videoconferencing modalities. Data saturation was reached at the 18th participant. Data analysis was performed using inductive content analysis with constant comparison between and within transcripts. Findings: Three themes and eight subthemes on the essential app components emerged-(a) comprehensive and flexible calorie counters; (b) holistic, gradual and individualized behavior change recommendations tailored for people with overweight and obesity, and (c) just-in-time reminders of future consequences. There was a need to incorporate flexible options for food logging; break down general recommendations into small steps towards sustainable changes; tailor app contents for people with overweight and obesity; and evoke one's considerations of future consequences. Future weight loss apps should be designed to meet the needs of those with overweight and obesity, the very population that needs assistance with weight loss. Future apps could consider leveraging the capacity of artificial intelligence to provide personalized weight management in terms of sustaining self-regulation behaviors, optimizing goal-setting and providing personalized and timely recommendations for weight loss.

Chew Han Shi Jocelyn, Lim Su Lin, Kim Guowei, Kayambu Geetha, So Bok Yan Jimmy, Shabbir Asim, Gao Yujia

2023-Jan-23

App, BMI, Behavior, Perceptions, Weight management, mHealth

Dermatology Dermatology

The role of mobile teledermoscopy in skin cancer triage and management during the COVID-19 pandemic.

In Indian journal of dermatology, venereology and leprology

The unprecedented onset of the COVID-19 crisis poses a significant challenge to all fields of medicine, including dermatology. Since the start of the coronavirus outbreak, a stark decline in new skin cancer diagnoses has been reported by countries worldwide. One of the greatest challenges during the pandemic has been the reduced access to face-to-face dermatologic evaluation and non-urgent procedures, such as biopsies or surgical excisions. Teledermatology is a well-integrated alternative when face-to-face dermatological assistance is not available. Teledermoscopy, an extension of teledermatology, comprises consulting dermoscopic images to improve the remote assessment of pigmented and non-pigmented lesions when direct visualisation of lesions is difficult. One of teledermoscopy's greatest strengths may be its utility as a triage and monitoring tool, which is critical in the early detection of skin cancer, as it can reduce the number of unnecessary referrals, wait times, and the cost of providing and receiving dermatological care. Mobile teledermoscopy may act as a communication tool between medical practitioners and patients. By using their smartphone (mobile phone) patients can monitor a suspicious skin lesion identified by their medical practitioner, or alternatively self-detect concerning lesions and forward valuable dermoscopic images for remote medical evaluation. Several mobile applications that allow users to photograph suspicious lesions with their smartphones and have them evaluated using artificial intelligence technology have recently emerged. With the growing popularity of mobile apps and consumer-involved healthcare, this will likely be a key component of skin cancer screening in the years to come. However, most of these applications apply artificial intelligence technology to assess clinical images rather than dermoscopic images, which may lead to lower diagnostic accuracy. Incorporating the direct-to-consumer mobile dermoscopy model in combination with mole-scanning artificial intelligence as a mobile app may be the future of skin cancer detection.

Lee Claudia, Witkowski Alexander, Żychowska Magdalena, Ludzik Joanna

2022-Dec-08

COVID-19, Dermoscopy, melanoma, skin cancer, smartphone, teledermoscopy

General General

A framework for designing AI systems that support community wellbeing.

In Frontiers in psychology ; h5-index 92.0

INTRODUCTION : Designing artificial intelligence (AI) to support health and wellbeing is an important and broad challenge for technologists, designers, and policymakers. Drawing upon theories of AI and cybernetics, this article offers a design framework for designing intelligent systems to optimize human wellbeing. We focus on the production of wellbeing information feedback loops in complex community settings, and discuss the case study of My Wellness Check, an intelligent system designed to support the mental health and wellbeing needs of university students and staff during the COVID-19 pandemic.

METHODS : The basis for our discussion is the community-led design of My Wellness Check, an intelligent system that supported the mental health and wellbeing needs of university students and staff during the COVID-19 pandemic. Our system was designed to create an intelligent feedback loop to assess community wellbeing needs and to inform community action. This article provides an overview of our longitudinal assessment of students and staff wellbeing (n = 20,311) across two years of the COVID-19 pandemic.

RESULTS : We further share the results of a controlled experiment (n = 1,719) demonstrating the enhanced sensitivity and user experience of our context-sensitive wellbeing assessment.

DISCUSSION : Our approach to designing "AI for community wellbeing," may generalize to the systematic improvement of human wellbeing in other human-computer systems for large-scale governance (e.g., schools, businesses, NGOs, platforms). The two main contributions are: 1) showcasing a simple way to draw from AI theory to produce more intelligent human systems, and 2) introducing a human-centered, community-led approach that may be beneficial to the field of AI.

van der Maden Willem, Lomas Derek, Hekkert Paul

2022

artificial intelligence, community wellbeing, cybernetics, feedback loop, human values, human-centered design, wellbeing economy

General General

An Artificial Intelligence-as-a-Service Architecture for deep learning model embodiment on low-cost devices: A case study of COVID-19 diagnosis.

In Applied soft computing

Coronavirus Disease-2019 (COVID-19) causes Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) and has opened several challenges for research concerning diagnosis and treatment. Chest X-rays and computed tomography (CT) scans are effective and fast alternatives to detect and assess the damage that COVID causes to the lungs at diff