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arXiv 2025年

作者： Sufriyana, Herdiantri Su, Emily Chia-Yu Institute of Biomedical Informatics College of Medicine National Yang Ming Chiao Tung University Taipei Taiwan Graduate Institute of Biomedical Informatics College of Medical Science and Technology Taipei Medical University Taipei Taiwan Clinical Big Data Research Center Taipei Medical University Hospital Taipei Taiwan Institute of Biomedical Informatics College of Medicine National Yang Ming Chiao Tung University 155 Section 2 Linong Street Beitou District Taipei112304 Taiwan

Background: Current nomogram can only be created for regression algorithm. Providing nomogram for any machine learning (ML) algorithms may accelerate model deployment in clinical settings or improve model availability. We developed an R package and web application to construct nomogram with model explainability of any ML algorithms. Methods: We formulated a function to transform an ML prediction model into a nomogram, requiring datasets with: (1) all possible combinations of predictor values;(2) the corresponding outputs of the model;and (3) the corresponding explainability values for each predictor (optional). Web application was also created. Results: Our R package could create 5 types of nomograms for categorical predictors and binary outcome without probability (1), categorical predictors and binary outcome with probability (2) or continuous outcome (3), and categorical with single numerical predictors and binary outcome with probability (4) or continuous outcome (5). Respectively, the first and remaining types optimally allowed maximum 15 and 5 predictors with maximum 3,200 combinations. Web application is provided with such limits. The explainability values were possible for types 2 to 5. Conclusions: Our R package and web application could construct nomogram with model explainability of any ML algorithms using a fair number of predictors. © 2025, CC BY-NC-SA.

关键词： Adversarial machine learning

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Improving Entity Recognition Using Ensembles of Deep Learning and Fine-tuned Large Language Models: A Case Study on Adverse Event Extraction from Multiple Sources

arXiv

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arXiv 2024年

作者： Li, Yiming Viswaroopan, Deepthi He, William Li, Jianfu Zuo, Xu Xu, Hua Tao, Cui McWilliams School of Biomedical Informatics The University of Texas Health Science Center at Houston HoustonTX77030 United States Department of Electrical & Computer Engineering Pratt School of Engineering Duke University 305 Tower Engineering Building DurhamNC27708 United States Department of Artificial Intelligence and Informatics Mayo Clinic JacksonvilleFL32224 United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT06510 United States

Objective Adverse event (AE) extraction following COVID-19 vaccines from text data is crucial for monitoring and analyzing the safety profiles of immunizations, identifying potential risks and ensuring the safe use of these products. Traditional deep learning models are adept at learning intricate feature representations and dependencies in sequential data, but often require extensive labeled data. In contrast, large language models (LLMs) excel in understanding contextual information, but exhibit unstable performance on named entity recognition (NER) tasks, possibly due to their broad but unspecific training. This study aims to evaluate the effectiveness of LLMs and traditional deep learning models in AE extraction, and to assess the impact of ensembling these models on performance. Methods In this study, we utilized reports and posts from the Vaccine Adverse Event Reporting System (VAERS) (n=621), Twitter (n=9,133), and Reddit (n=131) as our corpora. Our goal was to extract three types of entities: vaccine, shot, and adverse event (ae). We explored and fine-tuned (except GPT-4) multiple LLMs, including GPT-2, GPT-3.5, GPT-4, Llama-2 7b, and Llama-2 13b, as well as traditional deep learning models like Recurrent neural network (RNN) and Bidirectional Encoder Representations from Transformers for biomedical Text Mining (BioBERT). To enhance performance, we created ensembles of the three models with the best performance. For evaluation, we used strict and relaxed F1 scores to evaluate the performance for each entity type, and micro-average F1 was used to assess the overall performance. Results The ensemble model achieved the highest performance in "vaccine," "shot," and "ae," with strict F1-scores of 0.878, 0.930, and 0.925, respectively, along with a micro-average score of 0.903. These results underscore the significance of fine-tuning models for specific tasks and demonstrate the effectiveness of ensemble methods in enhancing performance. Conclusion In conclusion,

关键词： Vaccines

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Kamino: A Scalable Architecture to Support Medical AI Research Using Large Real World data

Kamino: A Scalable Architecture to Support Medical AI Resear...

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IEEE International Conference on Healthcare informatics (ICHI)

作者： Fongci Lin Patrick Young Huan He Jimin Huang Roger Gagne Daniel Rice Nathan Price Will Byron Yan Hu Donn Felker Will Button Deniella Meeker Allen Hsiao Hua Xu Charles Torre Wade Schulz Section of Biomedical Informatics and Data Science School of Medicine Yale University New Haven CT USA Department of Laboratory Medicine School of Medicine Yale University New Haven CT USA Digital & Technology Solutions Yale New Haven Hospital New Haven CT USA Mcwilliam School of Biomedical Informatics University of Texas Health Science at Houston Houston TX USA Pediatrics and of Emergency Medicine at Yale School of Medicine Yale University New Haven CT USA

ISBN: (数字)9798350383737

ISBN: (纸本)9798350383744

Electronic Health Records (EHRs) represent a crucial data source for real-world evidence generation. To facilitate biomedical studies using EHRs, standard data models like the OMOP CDM have been developed. Nevertheless, recent advancements in biomedical AI research that leverage EHRs have introduced new challenges, encompassing security considerations, large-scale data retrieval, and computational resource management, including GPUs. This paper introduces Kamino, an innovative architectural solution tailored to support biomedical AI research using EHR data. Kamino offers a user-friendly interface with features designed for efficient team access management in accordance with regulatory requirements. It facilitates direct data retrieval from an OMOP CDM instance and includes a resource allocation system based on Kubernetes orchestration. Here, we demonstrate the practical application and utility of Kamino through a clinical natural language processing task. We firmly believe that such a tool will significantly expedite AI research conducted with EHR data within academic institutions.

关键词： Soft sensors Medical services data models Natural language processing Resource management Security Artificial intelligence

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Relation Extraction Using Large Language Models: A Case Study on Acupuncture Point Locations

arXiv

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arXiv 2024年

作者： Li, Yiming Peng, Xueqing Li, Jianfu Zuo, Xu Peng, Suyuan Pei, Donghong Tao, Cui Xu, Hua Hong, Na McWilliams School of Biomedical Informatics The University of Texas Health Science Center at Houston HoustonTX77030 United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT06510 United States Department of Artificial Intelligence and Informatics Mayo Clinic JacksonvilleFL32224 United States Institute of Information on Traditional Chinese Medicine China Academy of Chinese Medical Sciences Beijing100010 China The University of Texas MD Anderson Cancer Center HoustonTX77030 United States

In acupuncture therapy, the accurate location of acupoints is essential for its effectiveness. The advanced language understanding capabilities of large language models (LLMs) like Generative Pre-trained Transformers (GPT) present a significant opportunity for extracting relations related to acupoint locations from textual knowledge sources. This study aims to compare the performance of GPT with traditional deep learning models (Long Short-Term Memory (LSTM) and Bidirectional Encoder Representations from Transformers for biomedical Text Mining (BioBERT)) in extracting acupoint-related location relations and assess the impact of pretraining and fine-tuning on GPT's performance. Materials and Methods We utilized the World Health Organization Standard Acupuncture Point Locations in the Western Pacific Region (WHO Standard) as our corpus, which consists of descriptions of 361 acupoints. Five types of relations ('direction_of,' 'distance_of,' 'part_of,' 'near_acupoint,' and 'located_near') (n= 3,174) between acupoints were annotated. Five models were compared: BioBERT, LSTM, pre-trained GPT-3.5, fine-tuned GPT-3.5, as well as pre-trained GPT-4. Performance metrics included micro-average exact match precision, recall, and F1 scores. Results Our results demonstrate that fine-tuned GPT-3.5 consistently outperformed other models in F1 scores across all relation types. Overall, it achieved the highest micro-average F1 score of 0.92. Conclusion This study underscores the effectiveness of LLMs like GPT in extracting relations related to acupoint locations, with implications for accurately modeling acupuncture knowledge and promoting standard implementation in acupuncture training and practice. The findings also contribute to advancing informatics applications in traditional and complementary medicine, showcasing the potential of LLMs in natural language processing. Copyright © 2024, The Authors. All rights reserved.

关键词： Acupuncture

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BiomedRAG: A Retrieval augmented Large Language Model for Biomedicine

arXiv

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arXiv 2024年

作者： Li, Mingchen Kilicoglu, Halil Xu, Hua Zhang, Rui Division of Computational Health Sciences Department of Surgery University of Minnesota MinneapolisMN United States School of Information Sciences University of Illinois at Urbana-Champaign Champaign United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT United States

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains;however, these models encounter issues such as generating inaccurate information or hallucinations. Retrieval-augmented generation provided a solution for these models to update knowledge and enhance their performance. In contrast to previous retrieval-augmented LMs, which utilize specialized cross-attention mechanisms to help LLM encode retrieved text, BiomedRAG adopts a simpler approach by directly inputting the retrieved chunk-based documents into the LLM. This straightforward design is easily applicable to existing retrieval and language models, effectively bypassing noise information in retrieved documents, particularly in noise-intensive tasks. Moreover, we demonstrate the potential for utilizing the LLM to supervise the retrieval model in the biomedical domain, enabling it to retrieve the document that assists the LM in improving its predictions. Specifically, BIOMEDRAG retrieves relevant documents from a specifically curated, diverse chunk database through a unique, purpose-built chunk scoring mechanism by a tunable scorer. This retrieval process then integrates the selected information directly into the LLM's input, facilitating the generation of expected output, such as structured knowledge. Our experiments reveal that with the tuned scorer, BIOMEDRAG attains superior performance across 4 biomedical NLP tasks, encompassing information extraction (triple extraction, relation extraction), text classification, and link prediction leveraging over 8 datasets. For instance, in the triple extraction task, BIOMEDRAG outperforms other triple extraction systems with micro-F1 scores of 81.42 and 88.83 on GIT and ChemProt corpora, respectively. The outstanding performance underscores the potential of BIOMEDRAG in constructing effective biomedical intervention systems for various tasks. © 2024, CC BY.

关键词： Classification (of information)

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Harnessing Artificial Intelligence for Innovation in Interventional Cardiovascular Care

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Journal of the Society for Cardiovascular Angiography and Interventions 2025年第3期4卷 102562-102562页

作者： Aminorroaya, Arya Biswas, Dhruva Pedroso, Aline F. Khera, Rohan Section of Cardiovascular Medicine Department of Internal Medicine Yale School of Medicine New Haven Connecticut United States Cardiovascular Data Science (CarDS) Lab Yale School of Medicine New Haven Connecticut United States Center for Outcomes Research and Evaluation (CORE) Yale New Haven Hospital New Haven Connecticut United States Section of Biomedical Informatics and Data Science Yale School of Medicine New Haven Connecticut United States Section of Health Informatics Department of Biostatistics Yale School of Public Health New Haven Connecticut United States

Artificial intelligence (AI) serves as a powerful tool that can revolutionize how personalized, patient-focused care is provided within interventional cardiology. Specifically, AI can augment clinical care across the spectrum for acute coronary syndrome, coronary artery disease, and valvular heart disease, with applications in coronary and structural heart interventions. This has been enabled by the potential of AI to harness various types of health data. We review how AI-driven technologies can advance diagnosis, preprocedural planning, intraprocedural guidance, and prognostication in interventional cardiology. AI automates clinical tasks, increases efficiency, improves reliability and accuracy, and individualizes clinical care, establishing its potential to transform care. Furthermore, AI-enabled, community-based screening programs are yet to be implemented to leverage the full potential of AI to improve patient outcomes. However, to transform clinical practice, AI tools require robust and transparent development processes, consistent performance across various settings and populations, positive impact on clinical and care quality outcomes, and seamless integration into clinical workflows. Once these are established, AI can reshape interventional cardiology, improving precision, efficiency, and patient outcomes. © 2025 The Author(s)

关键词： artificial intelligence interventional cardiology percutaneous coronary intervention structural heart intervention

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Biomedrag: A Retrieval Augmented Large Language Model for Biomedicine

SSRN

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SSRN 2024年

作者： Li, Mingchen Kilicoglu, Halil Xu, Hua Zhang, Rui Division of Computational Health Sciences Department of Surgery University of Minnesota MinneapolisMN United States School of Information Sciences University of Illinois at Urbana-Champaign Champaign IL United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT United States

Retrieval-augmented generation (RAG) offers a solution by retrieving knowledge from an established database to avoid hallucination of large language models (LLM). However, these models utilize specialized cross-attention mechanisms to help LLMs encode the retrieved text, hindering the application of RAG in closed LLMs (such as GPT-4). Additionally, these models retrieve information at the sentence or paragraph level, potentially introducing noise and affecting the generation quality. To address these issues, we propose a novel BiomedRAG framework that directly feeds automatically retrieved chunk-based documents into the LLM. Our evaluation of BiomedRAG across four biomedical natural language processing tasks using eight datasets demonstrates that our proposed framework not only improves the performance of LLMs 12.12% averagely but also achieves state of-the-art results compared to various baseline models by 5.33%. The BiomedRAG paves the way for more accurate and adaptable LLM applications in the biomedical domain. © 2024, The Authors. All rights reserved.

关键词： Computational linguistics

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

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JMIR Medical Education 2024年 10卷 e57594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 Dublin Ireland Section for Biomedical Informatics and Data Science Yale University School of Medicine 300 George Street Suite 501 New Haven 06511 CT United States

In “How Does ChatGPT Perform on the United States Medical Licensing Examination (USMLE)? The Implications of Large Language Models for Medical Education and Knowledge” (MIR Med Educ 2023;9:e45312) three additions were made to enhance discoverability. The title originally appeared as: How Does ChatGPT Perform on the United States Medical Licensing Examination? The Implications of Large Language Models for Medical Education and Knowledge Assessment And has been changed to: How Does ChatGPT Perform on the United States Medical Licensing Examination (USMLE)? The Implications of Large Language Models for Medical Education and Knowledge In the “Objective” section of the Abstract, the following sentence: 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. Has been changed to read as: This study aimed to evaluate the performance of ChatGPT on questions within the scope of the United States Medical Licensing Examination (USMLE) Step 1 and Step 2 exams, as well as to analyze responses for user interpretability. Finally, the abbreviation “USMLE” has been added to the Keywords section. The correction will appear in the online version of the paper on the JMIR Publications website on February 27, 2024 together with the publication of this correction notice. Because this was made after submission to PubMed, PubMed Central, and other full-text repositories, the corrected article has also been resubmitted to those repositories. © 2024 JMIR Publications Inc.. All rights reserved.

关键词：

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Repurposing Drugs for Alzheimer's Diseases through Link Prediction on biomedical Literature 11

Repurposing Drugs for Alzheimer's Diseases through Link Pred...

引用

11th IEEE International Conference on Healthcare informatics, ICHI 2023

作者： Xiao, Yongkang Hou, Yu Zhou, Huixue Diallo, Gayo Fiszman, Marcelo Wolfson, Julian Kilicoglu, Halil Chen, You Xu, Hua Mantyh, William G. Zhang, Rui University of Minnesota Institute for Health Informatics MinneapolisMN United States University of Minnesota Department of Surgery MinneapolisMN United States University of Bordeaux Inria Sistm Team AHeaD Inserm 1219 Bordeaux Population Health F-33000 France Pontifical Catholic University of Rio de Janeiro Nites - Núcleo de Inovação e Tecnologia em Saúde Brazil University of Minnesota Division of Biostatistics School of Public Health MinneapolisMN United States University of Illinois Urbana-Champaign School of Information Sciences ChampaignIL United States Vanderbilt University Medical Center Department of Biomedical Informatics NashvilleTN United States Yale University Section of Biomedical Informatics and Data Science New HavenCT United States University of Minnesota Department of Neurology MinneapolisMN United States

ISBN: (纸本)9798350302639

Recently, computational drug repurposing has emerged as a promising method for identifying new interventions for diseases. This study predicts novel drugs for Alzheimer's disease (AD) through link prediction on our developed biomedical knowledge graph. We constructed a comprehensive knowledge graph containing AD concepts and various potential interventions, called ADInt, by integrating a dietary supplement (DS) domain knowledge graph, SuppKG, with semantic triples from SemMedDB database. Four knowledge graph embedding models (TransE, RotatE, DistMult and ComplEX) and two graph convolutional network models (R-GCN and CompGCN) were compared to learn the representation of ADInt. R-GCN outperformed other models by evaluating on the time slice test set and the clinical trial test set, and was used to generate the score tables for the link prediction task. According to the results of link prediction, we proposed candidate drugs for AD. In conclusion, we presented a novel methodology to extend an existing knowledge graph and discover novel drugs for AD. Our method can potentially be applied to other clinical problems, such as discovering drug adverse reactions and drug-drug interactions. © 2023 IEEE.

关键词： Knowledge graph

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53914 Association between Atopic Dermatitis and Peripheral Vascular Disease: A Cross-sectional Study in the All of Us Research Program

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Journal of the American Academy of Dermatology 2024年第3期91卷 AB19-AB19页

作者： Spaulding, Sarah, BS Chen, Gloria, BA Craver, Andrew, BA Cohen, Jeffrey, MD Yale School of Medicine Department of Dermatology Yale School of Medicine Section of Biomedical Informatics and Data Science Yale School of Medicine

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