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Pathology Pathology

Deep learning for computer-assisted diagnosis of hereditary diffuse gastric cancer.

In Journal of pathology and translational medicine

Background : Patients with hereditary diffuse gastric cancer often undergo prophylactic gastrectomy to minimize cancer risk. Because intramucosal poorly cohesive carcinomas in this setting are typically not grossly visible, many pathologists assess the entire gastrectomy specimen microscopically. With 150 or more slides per case, this is a major time burden for pathologists. This study utilizes deep learning methods to analyze digitized slides and detect regions of carcinoma.

Materials and Methods : Prophylactic gastrectomy specimens from seven patients with germline CDH1 mutations were analyzed (five for training/validation and two for testing, with a total of 133 tumor foci). All hematoxylin and eosin slides containing cancer foci were digitally scanned, and patches of size 256×256 pixels were randomly extracted from regions of cancer as well as from regions of normal background tissue, resulting in 15,851 images for training/validation and 970 images for testing. A model with DenseNet-169 architecture was trained for 150 epochs, then evaluated on images from the test set. External validation was conducted on 814 images scanned at an outside institution.

Results : On individual patches, the trained model achieved a receiver operating characteristic (ROC) area under the curve (AUC) of 0.9986. This enabled it to maintain a sensitivity of 90% with a false-positive rate of less than 0.1%. On the external validation dataset, the model achieved a similar ROC AUC of 0.9984. On whole slide images, the network detected 100% of tumor foci and correctly eliminated an average of 99.9% of the non-cancer slide area from consideration.

Conclusion : Overall, our model shows encouraging progress towards computer-assisted diagnosis of hereditary diffuse gastric cancer.

Rasmussen Sean A, Arnason Thomas, Huang Weei-Yuarn

2021-Jan-22

Computer-assisted diagnosis, Deep learning, Machine learning, Pathology, Stomach neoplasms

General General

Use of Artificial Intelligence to understand adults' thoughts and behaviours relating to COVID-19.

In Perspectives in public health

AIMS : The outbreak of severe acute respiratory syndrome coronavirus 2 (COVID-19) is a global pandemic that has had substantial impact across societies. An attempt to reduce infection and spread of the disease, for most nations, has led to a lockdown period, where people's movement has been restricted resulting in a consequential impact on employment, lifestyle behaviours and wellbeing. As such, this study aimed to explore adults' thoughts and behaviours in response to the outbreak and resulting lockdown measures.

METHODS : Using an online survey, 1126 adults responded to invitations to participate in the study. Participants, all aged 18 years or older, were recruited using social media, email distribution lists, website advertisement and word of mouth. Sentiment and personality features extracted from free-text responses using Artificial Intelligence methods were used to cluster participants.

RESULTS : Findings demonstrated that there was varied knowledge of the symptoms of COVID-19 and high concern about infection, severe illness and death, spread to others, the impact on the health service and on the economy. Higher concerns about infection, illness and death were reported by people identified at high risk of severe illness from COVID-19. Behavioural clusters, identified using Artificial Intelligence methods, differed significantly in sentiment and personality traits, as well as concerns about COVID-19, actions, lifestyle behaviours and wellbeing during the COVID-19 lockdown.

CONCLUSIONS : This time-sensitive study provides important insights into adults' perceptions and behaviours in response to the COVID-19 pandemic and associated lockdown. The use of Artificial Intelligence has identified that there are two behavioural clusters that can predict people's responses during the COVID-19 pandemic, which goes beyond simple demographic groupings. Considering these insights may improve the effectiveness of communication, actions to reduce the direct and indirect impact of the COVID-19 pandemic and to support community recovery.

Flint S W, Piotrkowicz A, Watts K

2021-Jan-21

Artificial Intelligence, COVID-19, attitudes, behaviours, lockdown

General General

Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus)

bioRxiv Preprint

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. Based on 6,324 viral genome sequences, we create a spreadsheet dataset of point mutations that can facilitate the investigation of SARS-CoV-2 in many perspectives, especially in tracing the evolution and worldwide spread of the virus. Our analysis results also show that coding genes E, M, ORF6, ORF7a, ORF7b and ORF10 are most stable, potentially suitable to be targeted for vaccine and drug development.

Nguyen, T. T.; Pathirana, P. N.; Nguyen, T.; Nguyen, Q. V. H.; Bhatti, A.; Nguyen, D. C.; Nguyen, D. T.; Nguyen, N. D.; Creighton, D.; Abdelrazek, M.

2021-01-22

General General

A multi-perspective combined recall and rank framework for Chinese procedure terminology normalization

ArXiv Preprint

Medical terminology normalization aims to map the clinical mention to terminologies come from a knowledge base, which plays an important role in analyzing Electronic Health Record(EHR) and many downstream tasks. In this paper, we focus on Chinese procedure terminology normalization. The expression of terminologies are various and one medical mention may be linked to multiple terminologies. Previous study explores some methods such as multi-class classification or learning to rank(LTR) to sort the terminologies by literature and semantic information. However, these information is inadequate to find the right terminologies, particularly in multi-implication cases. In this work, we propose a combined recall and rank framework to solve the above problems. This framework is composed of a multi-task candidate generator(MTCG), a keywords attentive ranker(KAR) and a fusion block(FB). MTCG is utilized to predict the mention implication number and recall candidates with semantic similarity. KAR is based on Bert with a keywords attentive mechanism which focuses on keywords such as procedure sites and procedure types. FB merges the similarity come from MTCG and KAR to sort the terminologies from different perspectives. Detailed experimental analysis shows our proposed framework has a remarkable improvement on both performance and efficiency.

Ming Liang, Kui Xue, Tong Ruan

2021-01-22

Radiology Radiology

Machine learning combining CT findings and clinical parameters improves prediction of length of stay and ICU admission in torso trauma.

In European radiology ; h5-index 62.0

OBJECTIVE : To develop machine learning (ML) models capable of predicting ICU admission and extended length of stay (LOS) after torso (chest, abdomen, or pelvis) trauma, by using clinical and/or imaging data.

MATERIALS AND METHODS : This was a retrospective study of 840 adult patients admitted to a level 1 trauma center after injury to the torso over the course of 1 year. Clinical parameters included age, sex, vital signs, clinical scores, and laboratory values. Imaging data consisted of any injury present on CT. The two outcomes of interest were ICU admission and extended LOS, defined as more than the median LOS in the dataset. We developed and tested artificial neural network (ANN) and support vector machine (SVM) models, and predictive performance was evaluated by area under the receiver operating characteristic (ROC) curve (AUC).

RESULTS : The AUCs of SVM and ANN models to predict ICU admission were up to 0.87 ± 0.03 and 0.78 ± 0.02, respectively. The AUCs of SVM and ANN models to predict extended LOS were up to 0.80 ± 0.04 and 0.81 ± 0.05, respectively. Predictions based on imaging alone or imaging with clinical parameters were consistently more accurate than those based solely on clinical parameters.

CONCLUSIONS : The best performing models incorporated imaging findings and outperformed those with clinical findings alone. ML models have the potential to help predict outcomes in trauma by integrating clinical and imaging findings, although further research may be needed to optimize their performance.

KEY POINTS : • Artificial neural network and support vector machine-based models were used to predict the intensive care unit admission and extended length of stay after trauma to the torso. • Our input data consisted of clinical parameters and CT imaging findings derived from radiology reports, and we found that combining the two significantly enhanced the prediction of both outcomes with either model. • The highest accuracy (83%) and highest area under the receiver operating characteristic curve (0.87) were obtained for artificial neural networks and support vector machines, respectively, by combining clinical and imaging features in the prediction of intensive care unit admission.

Staziaki Pedro Vinícius, Wu Di, Rayan Jesse C, Santo Irene Dixe de Oliveira, Nan Feng, Maybury Aaron, Gangasani Neha, Benador Ilan, Saligrama Venkatesh, Scalera Jonathan, Anderson Stephan W

2021-Jan-21

Accidental injuries, diagnostic imaging, Artificial intelligence, Length of stay, Machine learning, Multidetector computed tomography

General General

Regulatory genes identification within functional genomics experiments for tissue classification into binary classes via machine learning techniques.

In JPMA. The Journal of the Pakistan Medical Association

OBJECTIVE : The aim of this study is to filter out the most informative genes that mainly regulate the target tissue class, increase classification accuracy, reduce the curse of dimensionality, and discard redundant and irrelevant genes.

Method : This paper presented the idea of gene selection using bagging sub-forest (BSF). The proposed method provided genes importance grounded on the idea specified in the standard random forest algorithm. The new method is compared with three state-of-the art methods, i.e., Wilcoxon, masked painter and proportional overlapped score (POS). These methods were applied on 5 data sets, i.e. Colon, Lymph node breast cancer, Leukaemia, Serrated colorectal carcinomas, and Breast Cancer. Comparison was done by selecting top 20 genes by applying the gene selection methods and applying random forest (RF) and support vector machine (SVM) classifiers to assess their predictive performance on the datasets with selected genes. Classification accuracy, Brier score, and sensitivity have been used as performance measures.

RESULTS : The proposed method gave better results than the other methods using both random forest and SVM classifiers on all the datasets among all the feature selection methods.

CONCLUSIONS : The proposed method showed improved performance in terms of classification accuracy, Brier score and sensitivity, and hence, could be used as a novel method for gene selection to classify tissue samples into their correct classes.

Wazir Bushra, Khan Dost Muhammad, Khalil Umair, Hamraz Muhammad, Gul Naz, Khan Zardad

2020-Dec

** Gene selection, classification, random forest, cancer, microarray gene expression \n\n**