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Cardiology Cardiology

Electrocardiography (ECG) analysis and a new feature extraction method using wavelet transform with scalogram analysis.

In Biomedizinische Technik. Biomedical engineering

Electrocardiography (ECG) signals and the information obtained through the analysis of these signals constitute the main source of diagnosis for many cardiovascular system diseases. Therefore, accurate analyses of ECG signals are very important for correct diagnosis. In this study, an ECG analysis toolbox together with a user-friendly graphical user interface, which contains the all ECG analysis steps between the recording unit and the statistical investigation, is developed. Furthermore, a new feature calculation methodology is proposed for ECG analysis, which carries distinct information than amplitudes and durations of ECG main waves and can be used in artificial intelligence studies. Developed toolbox is tested using both Massachusetts Institute of Technology-Beth Israel Hospital (MIT-BIH) Arrhythmia ECG Database and an experimentally collected dataset for performance evaluation. The results show that ECG analysis toolbox presented in this study increases the accuracy and reliability of the ECG main wave detection analysis, highly fasten the process duration compared to manual ones and the new feature set can be used as a new parameter for decision support systems about ECG based on artificial intelligence.

Yanık Hüseyin, Değirmenci Evren, Büyükakıllı Belgin, Karpuz Derya, Kılınç Olgu Hallıoğlu, Gürgül Serkan


denoising, electrocardiography, feature extraction, pulmonary arterial hypertension, scalogram

General General

Distinguishing Obstructive Versus Central Apneas in Infrared Video of Sleep Using Deep Learning: Validation Study.

In Journal of medical Internet research ; h5-index 88.0

BACKGROUND : Sleep apnea is a respiratory disorder characterized by an intermittent reduction (hypopnea) or cessation (apnea) of breathing during sleep. Depending on the presence of a breathing effort, sleep apnea is divided into obstructive sleep apnea (OSA) and central sleep apnea (CSA) based on the different pathologies involved. If the majority of apneas in a person are obstructive, they will be diagnosed as OSA or otherwise as CSA. In addition, as it is challenging and highly controversial to divide hypopneas into central or obstructive, the decision about sleep apnea type (OSA vs CSA) is made based on apneas only. Choosing the appropriate treatment relies on distinguishing between obstructive apnea (OA) and central apnea (CA).

OBJECTIVE : The objective of this study was to develop a noncontact method to distinguish between OAs and CAs.

METHODS : Five different computer vision-based algorithms were used to process infrared (IR) video data to track and analyze body movements to differentiate different types of apnea (OA vs CA). In the first two methods, supervised classifiers were trained to process optical flow information. In the remaining three methods, a convolutional neural network (CNN) was designed to extract distinctive features from optical flow and to distinguish OA from CA.

RESULTS : Overnight sleeping data of 42 participants (mean age 53, SD 15 years; mean BMI 30, SD 7 kg/m2; 27 men and 15 women; mean number of OA 16, SD 30; mean number of CA 3, SD 7; mean apnea-hypopnea index 27, SD 31 events/hour; mean sleep duration 5 hours, SD 1 hour) were collected for this study. The test and train data were recorded in two separate laboratory rooms. The best-performing model (3D-CNN) obtained 95% accuracy and an F1 score of 89% in differentiating OA vs CA.

CONCLUSIONS : In this study, the first vision-based method was developed that differentiates apnea types (OA vs CA). The developed algorithm tracks and analyses chest and abdominal movements captured via an IR video camera. Unlike previously developed approaches, this method does not require any attachment to a user that could potentially alter the sleeping condition.

Akbarian Sina, Montazeri Ghahjaverestan Nasim, Yadollahi Azadeh, Taati Babak


central apnea, computer vision, deep learning, machine learning, motion analysis, noncontact monitoring, obstructive apnea, sleep apnea

General General

Integrating data mining and transmission theory in the ecology of infectious diseases.

In Ecology letters

Our understanding of ecological processes is built on patterns inferred from data. Applying modern analytical tools such as machine learning to increasingly high dimensional data offers the potential to expand our perspectives on these processes, shedding new light on complex ecological phenomena such as pathogen transmission in wild populations. Here, we propose a novel approach that combines data mining with theoretical models of disease dynamics. Using rodents as an example, we incorporate statistical differences in the life history features of zoonotic reservoir hosts into pathogen transmission models, enabling us to bound the range of dynamical phenomena associated with hosts, based on their traits. We then test for associations between equilibrium prevalence, a key epidemiological metric and data on human outbreaks of rodent-borne zoonoses, identifying matches between empirical evidence and theoretical predictions of transmission dynamics. We show how this framework can be generalized to other systems through a rubric of disease models and parameters that can be derived from empirical data. By linking life history components directly to their effects on disease dynamics, our mining-modelling approach integrates machine learning and theoretical models to explore mechanisms in the macroecology of pathogen transmission and their consequences for spillover infection to humans.

Han Barbara A, O’Regan Suzanne M, Paul Schmidt John, Drake John M


Boosted regression, disease dynamics, disease macroecology, pathogen transmission, random forest, statistical learning, zoonosis, zoonotic spillover

General General

How to Be Helpful to Multiple People at Once.

In Cognitive science

When someone hosts a party, when governments choose an aid program, or when assistive robots decide what meal to serve to a family, decision-makers must determine how to help even when their recipients have very different preferences. Which combination of people's desires should a decision-maker serve? To provide a potential answer, we turned to psychology: What do people think is best when multiple people have different utilities over options? We developed a quantitative model of what people consider desirable behavior, characterizing participants' preferences by inferring which combination of "metrics" (maximax, maxsum, maximin, or inequality aversion [IA]) best explained participants' decisions in a drink-choosing task. We found that participants' behavior was best described by the maximin metric, describing the desire to maximize the happiness of the worst-off person, though participant behavior was also consistent with maximizing group utility (the maxsum metric) and the IA metric to a lesser extent. Participant behavior was consistent across variation in the agents involved and  tended to become more maxsum-oriented when participants were told they were players in the task (Experiment 1). In later experiments, participants maintained maximin behavior across multi-step tasks rather than shortsightedly focusing on the individual steps therein (Experiment 2, Experiment 3). By repeatedly asking participants what choices they would hope for in an optimal, just decision-maker, and carefully disambiguating which quantitative metrics describe these nuanced choices, we help constrain the space of what behavior we desire in leaders, artificial intelligence systems helping decision-makers, and the assistive robots and decision-makers of the future.

Gates Vael, Griffiths Thomas L, Dragan Anca D


Assistive artificial intelligence, Fairness, Maximin, Modeling, Preferences

General General

High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery.

In SLAS discovery : advancing life sciences R & D

Esophageal adenocarcinoma (EAC) is a highly heterogeneous disease, dominated by large-scale genomic rearrangements and copy number alterations. Such characteristics have hampered conventional target-directed drug discovery and personalized medicine strategies, contributing to poor outcomes for patients. We describe the application of a high-content Cell Painting assay to profile the phenotypic response of 19,555 compounds across a panel of six EAC cell lines and two tissue-matched control lines. We built an automated high-content image analysis pipeline to identify compounds that selectively modified the phenotype of EAC cell lines. We further trained a machine-learning model to predict the mechanism of action of EAC selective compounds using phenotypic fingerprints from a library of reference compounds. We identified a number of phenotypic clusters enriched with similar pharmacological classes, including methotrexate and three other antimetabolites that are highly selective for EAC cell lines. We further identify a small number of hits from our diverse chemical library that show potent and selective activity for EAC cell lines and that do not cluster with the reference library of compounds, indicating they may be selectively targeting novel esophageal cancer biology. Overall, our results demonstrate that our EAC phenotypic screening platform can identify existing pharmacologic classes and novel compounds with selective activity for EAC cell phenotypes.

Hughes Rebecca E, Elliott Richard J R, Munro Alison F, Makda Ashraff, O’Neill J Robert, Hupp Ted, Carragher Neil O


esophageal adenocarcinoma, high content, machine learning, mechanism of action, phenotypic

General General

Evaluation of the diagnostic value of joint PET myocardial perfusion and metabolic imaging for vascular stenosis in patients with obstructive coronary artery disease.

In Journal of nuclear cardiology : official publication of the American Society of Nuclear Cardiology

BACKGROUND : To investigate the diagnostic value of joint PET myocardial perfusion and metabolic imaging for vascular stenosis in patients with suspected obstructive coronary artery disease (CAD).

METHODS : Eighty-eight patients (53 and 35 applied for training and validation, respectively) with suspected obstructive CAD were referred to 13N-NH3 PET/CT myocardial perfusion imaging (MPI) and 18F-FDG PET/CT myocardial metabolic imaging (MMI) with available coronary angiography for analysis. One semi-quantitative indicator summed rest score (SRS) and five quantitative indicators, namely, perfusion defect extent (EXT), total perfusion deficit (TPD), myocardial blood flow (MBF), scar degree (SCR), and metabolism-perfusion mismatch (MIS), were extracted from the PET rest MPI and MMI scans. Different combinations of indicators and seven machine learning methods were used to construct diagnostic models. Diagnostic performance was evaluated using the sum of four metrics (noted as sumScore), namely, area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity.

RESULTS : In univariate analysis, MIS outperformed other individual indicators in terms of sumScore (2.816-3.042 vs 2.138-2.908). In multivariate analysis, support vector machine (SVM) consisting of three indicators (MBF, SCR, and MIS) achieved the best performance (AUC 0.856, accuracy 0.810, sensitivity 0.838, specificity 0.757, and sumScore 3.261). This model consistently achieved significantly higher AUC compared with the SRS method for four specific subgroups (0.897, 0.839, 0.875, and 0.949 vs 0.775, 0.606, 0.713, and 0.744; P = 0.041, 0.005, 0.034 0.003, respectively).

CONCLUSIONS : The joint evaluation of PET rest MPI and MMI could improve the diagnostic performance for obstructive CAD. The multivariate model (MBF, SCR, and MIS) combined with SVM outperformed other methods.

Wang Fanghu, Xu Weiping, Lv Wenbing, Du Dongyang, Feng Hui, Zhang Xiaochun, Wang Shuxia, Chen Wufan, Lu Lijun


Myocardial perfusion imaging, coronary artery disease, machine learning, myocardial metabolic imaging