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A Clinical Decision Support System of Pressure Ulcers Tissue Classification 21

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A Clinical Decision Support System of Pressure Ulcers Tissue...

5th International Conference on Medical and Health informatics, ICMHI 2021

作者： Chang, Dun-Hao Chu, Po-Jui Li, Yi-Jhen Ning, Chun-Kai Chien, Ting-Ying Department of Information Management Yuan Ze University Taoyuan City Taiwan Department of Plastic and Aesthetic Surgery Far Eastern Memorial Hospital Taiwan Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan

ISBN: (纸本)9781450389846

Pressure ulcers (PUs) are a common problem associated with great morbidity and cost. Because of the lack of professional personnel in the institutions or home care system, the diagnosis and treatment of PUs were sometimes delayed. We aim to develop an automatic tissue classification and severity evaluation system of PUs using AI technology. All PU images were collected from patients in the Far Eastern Memorial Hospital (FEMH) in recent 3 years and labeled according to different tissue types. The labeled images were used to train the tissue segmentation model with U-net convolutional neural network (CNN). The percentage of the different tissue can be calculated automatically and would be compared with the manually labeled one. The output of tissue classification was transformed to a clinical decision support system (CDSS) with a rule-base formula. Our study showed that proposed system can classify each tissue automatically and reach an accuracy about 93.6%. However, the CDSS's accuracy rate was only 64% for the referral suggestion and 62% for the care recommendation. Hence, the system should be modified with more data and information. © 2021 ACM.

关键词： Tissue

Population simulation modeling of disparities in US breast cancer mortality

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Journal of the National Cancer Institute - Monographs 2023年第62期2023卷 178-187页

作者： Mandelblatt, Jeanne S. Schechter, Clyde B. Stout, Natasha K. Huang, Hui Stein, Sarah Hunter Chapman, Christina Trentham-Dietz, Amy Jayasekera, Jinani Gangnon, Ronald E. Hampton, John M. Abraham, Linn O’Meara, Ellen S. Sheppard, Vanessa B. Lee, Sandra J. Department of Oncology Georgetown University Medical Center and Cancer Prevention and Control Program at Georgetown Lombardi Comprehensive Cancer Center WA United States Departments of Family and Social Medicine and of Epidemiology and Population Health Albert Einstein College of Medicine Bronx NY United States Department of Population Sciences Harvard Medical School and Harvard Pilgrim Health Care Institute Boston MA United States Department of Data Science Dana-Farber Cancer Institute and Harvard Medical School Boston MA United States Department of Radiation Oncology Section of Health Services Research Baylor College of Medicine and Health Policy Quality and Informatics Program at the Center for Innovations in Quality Effectiveness and Safety Michael E. DeBakey VA Medical Center Houston TX United States Department of Population Health Sciences and Carbone Cancer Center University of Wisconsin-Madison Madison WI United States Health Equity and Decision Sciences Research Lab National Institute on Minority Health and Health Disparities Intramural Research Program National Institutes of Health Bethesda MD United States Departments of Population Health Sciences and of Biostatistics and Medical Informatics and Carbone Cancer Center University of Wisconsin-Madison Madison WI United States Kaiser Permanente Washington Health Research Institute Seattle WA United States Department of Health Behavior and Policy and Massey Cancer Center Virginia Commonwealth University Richmond VA United States

BACKGROUND: Populations of African American or Black women have persistently higher breast cancer mortality than the overall US population, despite having slightly lower age-adjusted incidence. METHODS: Three Cancer Intervention and Surveillance Modeling Network simulation teams modeled cancer mortality disparities between Black female populations and the overall US population. Model inputs used racial group-specific data from clinical trials, national registries, nationally representative surveys, and observational studies. Analyses began with cancer mortality in the overall population and sequentially replaced parameters for Black populations to quantify the percentage of modeled breast cancer morality disparities attributable to differences in demographics, incidence, access to screening and treatment, and variation in tumor biology and response to therapy. RESULTS: Results were similar across the 3 models. In 2019, racial differences in incidence and competing mortality accounted for a net ‒1% of mortality disparities, while tumor subtype and stage distributions accounted for a mean of 20% (range across models = 13%-24%), and screening accounted for a mean of 3% (range = 3%-4%) of the modeled mortality disparities. Treatment parameters accounted for the majority of modeled mortality disparities: mean = 17% (range = 16%-19%) for treatment initiation and mean = 61% (range = 57%-63%) for real-world effectiveness. CONCLUSION: Our model results suggest that changes in policies that target improvements in treatment access could increase breast cancer equity. The findings also highlight that efforts must extend beyond policies targeting equity in treatment initiation to include high-quality treatment completion. This research will facilitate future modeling to test the effects of different specific policy changes on mortality disparities. © The Author(s) 2023. Published by Oxford University Press. All rights reserved. For permissions, please email: ***

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What we should learn from pandemic publishing

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arXiv 2024年

作者： Sikdar, Satyaki Venturini, Sara Charpignon, Marie-Laure Kumar, Sagar Rinaldi, Francesco Tudisco, Francesco Fortunato, Santo Majumder, Maimuna S. Luddy School of Informatics Computing and Engineering Indiana University BloomingtonIN United States Department of Computer Science Loyola University Chicago ChicagoIL United States Senseable City Laboratory Massachusetts Institute of Technology CambridgeMA United States Department of Mathematics "Tullio Levi-Civita" University of Padova Padova Italy Institute for Data Systems and Society Massachusetts Institute of Technology CambridgeMA United States Network Science Institute Northeastern University BostonMA United States School of Mathematics The University of Edinburgh Edinburgh United Kingdom School of Mathematics Gran Sasso Science Institute L’Aquila Italy Department of Pediatrics Harvard Medical School BostonMA United States Computational Health Informatics Program Boston Children’s Hospital BostonMA United States

Since the emergence of COVID-19, discussions of ongoing pandemic-related research have accounted for an unprecedented share of media coverage and debate in the public sphere1. The urgency of the pandemic forced researchers to operate on an accelerated timeline, as both policymakers and the public relied on the most current evidence to guide their decisions and behaviors. With high demand for rapid pandemic-related insights and lower barriers to entry via preprint servers, the volume of COVID-19 articles skyrocketed2. The pressing need for research triggered the participation of many researchers with expertise in the science of infectious disease outbreaks (‘outbreak scientists’), who were joined by researchers from other disciplines (‘bellwethers’) and more junior researchers still in training (‘newcomers’) with the common goal of advancing the frontiers of pandemic science and informing policy decisions3. Please see Box 1 for details of this taxonomy. © 2024, CC BY-NC-ND.

关键词： COVID-19

Improved Prediction Of Ligand-Protein Binding Affinities By Meta-Modeling

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arXiv 2023年

作者： Lee, Ho-Joon Emani, Prashant S. Gerstein, Mark B. Dept. of Genetics and Yale University New HavenCT06510 United States Yale Center for Genome Analysis Yale University New HavenCT06510 United States Dept. of Molecular Biophysics & Biochemistry Yale University New HavenCT06520 United States Program in Computational Biology & Bioinformatics Yale University New HavenCT06520 United States Dept. of Computer Science Yale University New HavenCT06520 United States Dept. of Statistics & Data Science Yale University New HavenCT06520 United States Dept. of Biomedical Informatics & Data Science Yale University New HavenCT06520 United States

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity between ligands and proteins. Many computational models for binding affinity prediction have been developed, but with varying results across targets. Given that ensembling or meta-modeling approaches have shown great promise in reducing model-specific biases, we develop a framework to integrate published force-field-based empirical docking and sequence-based deep learning models. In building this framework, we evaluate many combinations of individual base models, training databases, and several meta-modeling approaches. We show that many of our meta-models significantly improve affinity predictions over base models. Our best meta-models achieve comparable performance to state-of-the-art deep learning tools exclusively based on 3D structures, while allowing for improved database scalability and flexibility through the explicit inclusion of features such as physicochemical properties or molecular descriptors. We further demonstrate improved generalization capability by our models using a large-scale benchmark of affinity prediction as well as a virtual screening application benchmark. Overall, we demonstrate that diverse modeling approaches can be ensembled together to gain meaningful improvement in binding affinity prediction. © 2023, CC BY-NC-SA.

关键词： Prediction models

How Does ChatGPT Perform on the United States Medical Licensing Examination? The Implications of Large Language Models for Medical Education and Knowledge Assessment

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JMIR Medical Education 2023年 9卷 e45312页

作者： Gilson, Aidan Safranek, Conrad W. Huang, Thomas Socrates, Vimig Chi, Ling Taylor, Richard Andrew Chartash, David Section for Biomedical Informatics and Data Science Yale University School of Medicine New Haven CT United States Department of Emergency Medicine Yale University School of Medicine New Haven CT United States Program of Computational Biology and Bioinformatics Yale University New Haven CT United States School of Medicine University College Dublin National University of Ireland Dublin Ireland

Background: Chat Generative Pre-trained Transformer (ChatGPT) is a 175-billion-parameter natural language processing model that can generate conversation-style responses to user input. Objective: This study aimed to evaluate the performance of ChatGPT on questions within the scope of the United States Medical Licensing Examination Step 1 and Step 2 exams, as well as to analyze responses for user interpretability. Methods: We used 2 sets of multiple-choice questions to evaluate ChatGPT’s performance, each with questions pertaining to Step 1 and Step 2. The first set was derived from AMBOSS, a commonly used question bank for medical students, which also provides statistics on question difficulty and the performance on an exam relative to the user base. The second set was the National Board of Medical Examiners (NBME) free 120 questions. ChatGPT’s performance was compared to 2 other large language models, GPT-3 and InstructGPT. The text output of each ChatGPT response was evaluated across 3 qualitative metrics: logical justification of the answer selected, presence of information internal to the question, and presence of information external to the question. Results: Of the 4 data sets, AMBOSS-Step1, AMBOSS-Step2, NBME-Free-Step1, and NBME-Free-Step2, ChatGPT achieved accuracies of 44% (44/100), 42% (42/100), 64.4% (56/87), and 57.8% (59/102), respectively. ChatGPT outperformed InstructGPT by 8.15% on average across all data sets, and GPT-3 performed similarly to random chance. The model demonstrated a significant decrease in performance as question difficulty increased (P=.01) within the AMBOSS-Step1 data set. We found that logical justification for ChatGPT’s answer selection was present in 100% of outputs of the NBME data sets. Internal information to the question was present in 96.8% (183/189) of all questions. The presence of information external to the question was 44.5% and 27% lower for incorrect answers relative to correct answers on the NBME-Free-Step1 (P<.001

关键词： artificial intelligence chatbot ChatGPT conversational agent education technology generative pre-trained transformer GPT machine learning medical education MedQA natural language processing NLP

Herb compounds screening as meningitis inhibitor candidates using neural network and random forest methods

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AIP Conference Proceedings 2025年第1期3250卷

作者： Riska Aprilia Mohammad Hamim Zajuli Al Faroby Muhammad Adib Kamali Muhammad Dzulfikar Fauzi Information Technology Study Program Faculty of Information Technology and Business Institut Teknologi Telkom Surabaya Surabaya Indonesia Data Science Study Program Faculty of Information Technology and Business Institut Teknologi Telkom Surabaya Surabaya Indonesia Informatics Study Program Faculty of Information Technology and Business Institut Teknologi Telkom Surabaya Surabaya Indonesia

Meningitis is an inflammation of the meninges that occurs in the protective lining of the brain and spinal cord caused by bacterial, viral, or fungal infections. This disease is difficult to recognize because it has initial symptoms like the flu where the patient has a fever and headache. Current efforts to prevent the disease by strengthening antibodies. Meanwhile, drug candidates for the treatment of this disease still have not found optimal results in reducing mortality due to meningitis. This study aims to find and analyses herbal compound candidates that might be inhibitors of meningitis. Compound data was acquired from a validated open database. The data acquired are smiles of the chemical bond structure of the compounds. In the data processing process, compound feature extraction is required by applying the concept of molecular fingerprint. The results of feature extraction are used as datasets to build classification models by applying the Multilayer Perceptron (MLP) and Random Forest algorithms. The two models are compared, and a more robust model is selected to be used as a prediction model for herbal compound search. The MLP model has a better accuracy of 0.97 compared to the Random Forest model. The results of screening using the MLP learning model obtained Symphytine, cis-Linalool oxide, and 3-O-Methylcalopocarpin compounds have the highest probability compared to thousands of other herbal compounds. This candidate compound can be used as a recommendation for drug discovery to treat patients who contract Meningitis.

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A Foundational Multimodal Vision Language AI Assistant for Human Pathology

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arXiv 2023年

作者： Lu, Ming Y. Chen, Bowen Williamson, Drew F.K. Chen, Richard J. Ikamura, Kenji Gerber, Georg Liang, Ivy Phi Le, Long Ding, Tong Parwani, Anil V. Mahmood, Faisal Department of Pathology Brigham and Women's Hospital Harvard Medical School BostonMA United States Department of Pathology Massachusetts General Hospital Harvard Medical School BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States Cancer Data Science Program Dana-Farber Cancer Institute BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States CambridgeMA United States Harvard John A. Paulson School of Engineering And Applied Sciences Harvard University CambridgeMA United States Department of Pathology Wexner Medical Center Ohio State University ColumbusOH United States Harvard Data Science Initiative Harvard University CambridgeMA United States

The field of computational pathology has witnessed remarkable progress in the development of both taskspecific predictive models and task-agnostic self-supervised vision encoders. However, despite the explosive growth of generative artificial intelligence (AI), there has been limited study on building general purpose, multimodal AI assistants tailored to pathology. Here we present PathChat, a vision-language generalist AI assistant for human pathology using an in-house developed foundational vision encoder pretrained on 100 million histology images from over 100,000 patient cases and 1.18 million pathology image-caption pairs. The vision encoder is then combined with a pretrained large language model and the whole system is finetuned on over 250,000 diverse disease agnostic visual language instructions. We compare PathChat against several multimodal vision language AI assistants as well as GPT4V, which powers the commercially available multimodal general purpose AI assistant ChatGPT-4. When relevant clinical context is provided with the histology image, PathChat achieved a diagnostic accuracy of 87% on multiple-choice questions based on publicly available cases of diverse tissue origins and disease models. Additionally, using open-ended questions and human expert evaluation, we found that overall PathChat produced more accurate and pathologist-preferable responses to diverse queries related to pathology. As an interactive and general vision language AI assistant that can flexibly handle both visual and natural language inputs, PathChat can potentially find impactful applications in pathology education, research, and human-in-the-loop clinical decision making. © 2023, CC BY-NC-ND.

关键词： Pathology

A General-Purpose Self-Supervised Model for Computational Pathology

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arXiv 2023年

作者： Chen, Richard J. Ding, Tong Lu, Ming Y. Williamson, Drew F.K. Jaume, Guillaume Chen, Bowen Zhang, Andrew Shao, Daniel Song, Andrew H. Shaban, Muhammad Williams, Mane Vaidya, Anurag Sahai, Sharifa Oldenburg, Lukas Weishaupt, Luca L. Wang, Judy J. Williams, Walt Le, Long Phi Gerber, Georg Mahmood, Faisal Department of Pathology Brigham and Women’s Hospital Harvard Medical School BostonMA United States Department of Pathology Massachusetts General Hospital Harvard Medical School BostonMA United States Cancer Program Broad Institute of Harvard MIT CambridgeMA United States Cancer Data Science Program Dana-Farber Cancer Institute BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States CambridgeMA United States Health Sciences and Technology Harvard-MIT CambridgeMA United States Harvard John A. Paulson School of Engineering And Applied Sciences Harvard University CambridgeMA United States Department of Systems Biology Harvard University CambridgeMA United States Harvard Data Science Initiative Harvard University CambridgeMA United States

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology. Copyright © 2023, The Authors. All rights reserved.

关键词： Pathology

Xenoestrogen effects on the gut microbiome

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Current Opinion in Endocrine and Metabolic Research 2021年 19卷 41-45页

作者： Rosenfeld, Cheryl S. Christopher S Bond Life Sciences Center University of Missouri Columbia 65211 MO United States Biomedical Sciences University of Missouri Columbia 65211 MO United States MU Institute for Data Science and Informatics (MU IDSI) University of Missouri Columbia 65211 MO United States Thompson Center for Autism and Neurobehavioral Disorders University of Missouri Columbia 65211 MO United States Genetics Area Program University of Missouri Columbia 65211 MO United States

Endocrine disrupting chemicals (EDCs) that act as xenoestrogens are natural and synthetic chemicals widely present in food products, industrial products, and the environment. Such compounds can activate or inhibit normal hormonal pathways by binding to steroid and non-steroid receptors. It is becomingly apparent that resident bacteria in the gut and elsewhere in the body can dramatically influence host responses. As such, increasing number of studies have examined how EDCs affect the gut microbiome in a range of animal species. This review article will examine what is known about how various xenoestrogens, including bisphenol A (BPA), phthalates, and phytoestrogens, affect the gut microbiome in vertebrate species, any known secondary host effects, such as through alteration of gut metabolites, and future directions in the field. © 2021 Elsevier Ltd

关键词： Bisphenol A Genistein Phytoestrogens Rodent models Xenoestrogens