Rui Zhang

Publication Activity (10 Years)

Years Active: 2012-2024
Publications (10 Years): 72

Top Topics

Natural Language Processing

Biomedical Literature

Clinical Trials

Top Venues

J. Am. Medical Informatics Assoc.

Publications

Mingchen Li, Anne H. Blaes, Steven Johnson, Hongfang Liu, Hua Xu, Rui Zhang
CancerLLM: A Large Language Model in Cancer Domain. CoRR (2024)
Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg M. Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, Rui Zhang
Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition. J. Am. Medical Informatics Assoc. 31 (2) (2024)
Le Peng, Gaoxiang Luo, Sicheng Zhou, Jiandong Chen, Ziyue Xu, Ju Sun, Rui Zhang
An in-depth evaluation of federated learning on biomedical natural language processing for information extraction. npj Digit. Medicine 7 (1) (2024)
Shuang Zhou, Sirui Ding, Jiashuo Wang, Mingquan Lin, Genevieve B. Melton, Rui Zhang
Interpretable Differential Diagnosis with Dual-Inference Large Language Models. CoRR (2024)
Mingchen Li, Zaifu Zhan, Han Yang, Yongkang Xiao, Jiatan Huang, Rui Zhang
Benchmarking Retrieval-Augmented Large Language Models in Biomedical NLP: Application, Robustness, and Self-Awareness. CoRR (2024)
Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang
BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine. CoRR (2024)
Shufan Ming, Rui Zhang, Halil Kilicoglu
Enhancing the coverage of SemRep using a relation classification approach. J. Biomed. Informatics 155 (2024)
Sunyang Fu, Liwei Wang, Huan He, Andrew Wen, Nansu Zong, Anamika Kumari, Feifan Liu, Sicheng Zhou, Rui Zhang, Chenyu Li, Yanshan Wang, Jennifer St Sauver, Hongfang Liu, Sunghwan Sohn
A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. J. Am. Medical Informatics Assoc. 31 (7) (2024)
Huixue Zhou, Greg M. Silverman, Zhongran Niu, Jenzi Silverman, Roni Evans, Robin Austin, Rui Zhang
Extracting Complementary and Integrative Health Approaches in Electronic Health Records. J. Heal. Informatics Res. 7 (3) (2023)
Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg M. Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, Rui Zhang
Complementary and Integrative Health Lexicon (CIHLex) and Entity Recognition in the Literature. CoRR (2023)
Benjamin C. Knoll, Melissa Gunderson, Geetanjali Rajamani, Elizabeth C. Wick, Alexis Colley, Elizabeth Lindemann, Rubina F. Rizvi, Molly Diethelm, Gretchen M. Hultman, Logan Pierce, Rui Zhang, Genevieve B. Melton
Advanced Care Planning Content Encoding with Natural Language Processing. MedInfo (2023)
Sicheng Zhou, Nan Wang, Liwei Wang, Ju Sun, Anne H. Blaes, Hongfang Liu, Rui Zhang
A Cross-institutional Evaluation on Breast Cancer Phenotyping NLP Algorithms on Electronic Health Records. CoRR (2023)
Vipina Kuttichi Keloth, Juan M. Banda, Michael J. Gurley, Paul M. Heider, Georgina Kennedy, Hongfang Liu, Feifan Liu, Timothy A. Miller, Karthik Natarajan, Olga V. Patterson, Yifan Peng, Kalpana Raja, Ruth M. Reeves, Masoud Rouhizadeh, Jianlin Shi, Xiaoyan Wang, Yanshan Wang, Wei-Qi Wei, Andrew E. Williams, Rui Zhang, Rimma Belenkaya, Christian G. Reich, Clair Blacketer, Patrick B. Ryan, George Hripcsak, Noémie Elhadad, Hua Xu
Representing and utilizing clinical textual data for real world studies: An OHDSI approach. J. Biomed. Informatics 142 (2023)
Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30 (12) (2023)
Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Halil Kilicoglu, You Chen, Hua Xu, William G. Mantyh, Rui Zhang
Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature. ICHI (2023)
Zhe He, Rui Zhang, Gayo Diallo, Zhengxing Huang, Benjamin S. Glicksberg
Editorial: Explainable artificial intelligence for critical healthcare applications. Frontiers Artif. Intell. 6 (2023)
Greg M. Silverman, Geetanjali Rajamani, Nicholas E. Ingraham, James K. Glover, Himanshu S. Sahoo, Michael Usher, Rui Zhang, Farha Ikramuddin, Tanya E. Melnik, Genevieve B. Melton, Christopher J. Tignanelli
A Symptom-Based Natural Language Processing Surveillance Pipeline for Post-COVID-19 Patients. MedInfo (2023)
Sicheng Zhou, Rui Zhang, Anne H. Blaes, Chetan Shenoy, György J. Simon
Predicting Cancer Treatments Induced Cardiotoxicity of Breast Cancer Patients. CoRR (2022)
Sicheng Zhou, Nan Wang, Liwei Wang, Hongfang Liu, Rui Zhang
CancerBERT: a cancer domain-specific language model for extracting breast cancer phenotypes from electronic health records. J. Am. Medical Informatics Assoc. 29 (7) (2022)
Zitao Shen, Dalton Schutte, Yoonkwon Yi, Anusha Bompelli, Fang Yu, Yanshan Wang, Rui Zhang
Classifying the lifestyle status for Alzheimer's disease from clinical notes using deep learning with weak supervision. BMC Medical Informatics Decis. Mak. (1) (2022)
Huixue Zhou, Greg M. Silverman, Zhongran Niu, Jenzi Silverman, Rui Zhang, Roni Evans, Robin Austin
Annotating Music Therapy, Chiropractic and Aquatic Exercise Using Electronic Health Record. ICHI (2022)
Benjamin C. Knoll, Reed McEwan, Raymond L. Finzel, Greg M. Silverman, Rui Zhang, Serguei V. S. Pakhomov, Genevieve B. Melton
MTAP - A Distributed Framework for NLP Pipelines. ICHI (2022)
Esha Singh, Anusha Bompelli, Ruyuan Wan, Jiang Bian, Serguei Pakhomov, Rui Zhang
A conversational agent system for dietary supplements use. BMC Medical Informatics Decis. Mak. (1) (2022)
Haozuo Zhao, Haitao Chu, Sicheng Zhou, Fang Yu, Xianghua Luo, Rui Zhang
Racial Disparities in Alzheimer's Disease and Alzheimer's Disease-Related Dementias from the Disease Progression Perspective. ICHI (2022)
Tanya Melnik, Joshua A. Thompson, Jake Vasilakes, Tucker Annis, Sicheng Zhou, Dalton Schutte, Genevieve Melton-Meaux, Susan Pleasants, Rui Zhang
Semi-automated Clinical Content Curation of COVID-19 Chatbot Remote Patient Monitoring Solution. AMIA (2022)
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. J. Biomed. Informatics 131 (2022)
Huixue Zhou, Robin Austin, Halil Kilicoglu, Sheng-Chieh Lu, Rui Zhang
CIHLex: Complementary and Integrative Health Lexicon. AMIA (2022)
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
Drug repurposing for COVID-19 via knowledge graph completion. J. Biomed. Informatics 115 (2021)
Esha Singh, Anusha Bompelli, Ruyuan Wan, Jiang Bian, Serguei Pakhomov, Rui Zhang
A Conversational Agent System for Dietary Supplements Use. CoRR (2021)
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature. CoRR (2021)
Zitao Shen, Yoonkwon Yi, Anusha Bompelli, Fang Yu, Yanshan Wang, Rui Zhang
Extracting Lifestyle Factors for Alzheimer's Disease from Clinical Notes Using Deep Learning with Weak Supervision. CoRR (2021)
Yadan Fan, Sicheng Zhou, Yifan Li, Rui Zhang
Deep learning approaches for extracting adverse events and indications of dietary supplements from clinical text. J. Am. Medical Informatics Assoc. 28 (3) (2021)
Greg M. Silverman, Himanshu S. Sahoo, Nicholas Ingraham, Monica Lupei, Michael A. Puskarich, Michael Usher, James Dries, Raymond L. Finzel, Eric Murray, John Sartori, György J. Simon, Rui Zhang, Genevieve B. Melton, Christopher J. Tignanelli, Serguei V. S. Pakhomov
NLP Methods for Extraction of Symptoms from Unstructured Data for Use in Prognostic COVID-19 Analytic Models. J. Artif. Intell. Res. 72 (2021)
Sicheng Zhou, Dalton Schutte, Aiwen Xing, Jiyang Chen, Julian Wolfson, Zhe He, Fang Yu, Rui Zhang
Identification of Dietary Supplement Use from Electronic Health Records Using Transformer-based Language Models. ICHI (2021)
Laura A. Barrett, Aiwen Xing, Elizabeth Steidley, Terrence J. Adam, Rui Zhang, Zhe He
Assessing the Use of Prescription Drugs in Obese Respondents in the National Health and Nutrition Examination Survey. AMIA (2021)
Anusha Bompelli, Yanshan Wang, Ruyuan Wan, Esha Singh, Yuqi Zhou, Lin Xu, David Oniani, Bhavani Singh Agnikula Kshatriya, Joyce E. Balls-Berry, Rui Zhang
Social determinants of health in the era of artificial intelligence with electronic health records: A systematic review. CoRR (2021)
Anusha Bompelli, Greg M. Silverman, Raymond L. Finzel, Jake Vasilakes, Benjamin Knoll, Serguei Pakhomov, Rui Zhang
Comparing NLP Systems to Extract Entities of Eligibility Criteria in Dietary Supplements Clinical Trials Using NLP-ADAPT. AIME (2020)
Xing He, Rui Zhang, Jordan Alpert, Sicheng Zhou, Terrence J. Adam, Aantaki Raisa, Yifan Peng, Hansi Zhang, Jiang Bian
When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information? CoRR (2020)
Zhe He, Cui Tao, Jiang Bian, Rui Zhang
Selected articles from the Fourth International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019). BMC Medical Informatics Decis. Mak. (4) (2020)
Hansi Zhang, Christopher Wheldon, Adam G. Dunn, Cui Tao, Jinhai Huo, Rui Zhang, Mattia C. F. Prosperi, Yi Guo, Jiang Bian
Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States. J. Am. Medical Informatics Assoc. 27 (2) (2020)
Yoonkwon Yi, Zitao Shen, Anusha Bompelli, Fang Yu, Yanshan Wang, Rui Zhang
Natural Language Processing Methods to Extract Lifestyle Exposures for Alzheimer's Disease from Clinical Notes. ICHI (2020)
Esha Singh, Anusha Bompelli, Andrew Yang, Andrew Wang, Serguei Pakhomov, Rui Zhang
A Prototype Conversational Agent for Dietary Supplements. ICHI (2020)
Anusha Bompelli, Jianfu Li, Yiqi Xu, Nan Wang, Yanshan Wang, Terrence J. Adam, Zhe He, Rui Zhang
Deep Learning Approach to Parse Eligibility Criteria in Dietary Supplements Clinical Trials Following OMOP Common Data Model. AMIA (2020)
Rubina F. Rizvi, Jake Vasilakes, Terrence J. Adam, Genevieve B. Melton, Jeffrey R. Bishop, Jiang Bian, Cui Tao, Rui Zhang
iDISK: the integrated DIetary Supplements Knowledge base. J. Am. Medical Informatics Assoc. 27 (4) (2020)
Jake Vasilakes, Anusha Bompelli, Jeffrey R. Bishop, Terrence J. Adam, Olivier Bodenreider, Rui Zhang
Assessing the enrichment of dietary supplement coverage in the Unified Medical Language System. J. Am. Medical Informatics Assoc. 27 (10) (2020)
Yadan Fan, Sicheng Zhou, Yifan Li, Rui Zhang
Deep Learning Approaches for Extracting Adverse Events and Indications of Dietary Supplements from Clinical Text. CoRR (2020)
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
Drug Repurposing for COVID-19 via Knowledge Graph Completion. CoRR (2020)
Xing He, Rui Zhang, Rubina F. Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, Mattia C. F. Prosperi, Jinhai Huo, Jordan Alpert, Jiang Bian
ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design. BMC Medical Informatics Decis. Mak. (4) (2019)
Rubina F. Rizvi, Yefeng Wang, Thao Nguyen, Jake Vasilakes, Jiang Bian, Zhe He, Rui Zhang
Analyzing Social Media Data to Understand Consumers' Information Needs on Dietary Supplements. CoRR (2019)
Sicheng Zhou, Yunpeng Zhao, Rubina F. Rizvi, Jiang Bian, Ann F. Haynos, Rui Zhang
Analysis of Twitter to Identify Topics Related to Eating Disorder Symptoms. ICHI (2019)
Hansi Zhang, Christopher Wheldon, Adam G. Dunn, Cui Tao, Jinhai Huo, Rui Zhang, Mattia C. F. Prosperi, Yi Guo, Jiang Bian
Mining Twitter to Assess the Determinants of Health Behavior towards Human Papillomavirus Vaccination in the United States. CoRR (2019)
Jake Vasilakes, Yadan Fan, Rubina F. Rizvi, Anusha Bompelli, Olivier Bodenreider, Rui Zhang
Normalizing Dietary Supplement Product Names Using the RxNorm Model. MedInfo (2019)
Rubina F. Rizvi, Yefeng Wang, Thao Nguyen, Jake Vasilakes, Jiang Bian, Zhe He, Rui Zhang
Analyzing Social Media Data to Understand Consumer Information Needs on Dietary Supplements. MedInfo (2019)
Zhe He, Laura A. Barrett, Rubina F. Rizvi, Seyedeh Neelufar Payrovnaziri, Rui Zhang
Exploring the Discrepancies in Actual and Perceived Benefits of Dietary Supplements Among Obese Patients. MedInfo (2019)
Zhe He, Jiang Bian, Cui Tao, Rui Zhang
Selected articles from the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018). BMC Medical Informatics Decis. Mak. (4) (2019)
Xing He, Rui Zhang, Rubina F. Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, Mattia C. F. Prosperi, Jiang Bian
Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. BIBM (2018)
Zhe He, Cui Tao, Jiang Bian, Rui Zhang, Jingshan Huang
Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017). BMC Medical Informatics Decis. Mak. 18 (S-2) (2018)
Yefeng Wang, Yunpeng Zhao, Jiang Bian, Rui Zhang
Detecting Signals of Associations Between Dietary Supplement Use and Mental Disorders from Twitter. ICHI Workshops (2018)
Yadan Fan, Rui Zhang
Using natural language processing methods to classify use status of dietary supplements in clinical notes. BMC Medical Informatics Decis. Mak. 18 (S-2) (2018)
Deyu Sun, Gopal Sarda, Steven J. Skube, Anne H. Blaes, Rui Zhang, Genevieve B. Melton
A Study on Phenotyping and Visualizing Black Box Warnings of Antineoplastic Breast Cancer Medications. CRI (2017)
Deyu Sun, Gopal Sarda, Steven J. Skube, Anne H. Blaes, Saif S. Khairat, Genevieve B. Melton, Rui Zhang
Phenotyping and Visualizing Infusion-Related Reactions for Breast Cancer Patients. MedInfo (2017)
Yadan Fan, Terrence J. Adam, Reed McEwan, Serguei V. S. Pakhomov, Genevieve B. Melton, Rui Zhang
Detecting Signals of Interactions Between Warfarin and Dietary Supplements in Electronic Health Records. MedInfo (2017)
Yadan Fan, Lu He, Rui Zhang
Evaluating automatic methods to extract patients' supplement use from clinical reports. BIBM (2017)
Rui Zhang, György J. Simon, Fang Yu
Advancing Alzheimer's research: A review of big data promises. Int. J. Medical Informatics 106 (2017)
Deyu Sun, György J. Simon, Steven J. Skube, Anne H. Blaes, Genevieve B. Melton, Rui Zhang
Causal Phenotyping for Susceptibility to Cardiotoxicity from Antineoplastic Breast Cancer Medications. AMIA (2017)
Yefeng Wang, Divya R. Gunashekar, Terrence J. Adam, Rui Zhang
Mining Adverse Events of Dietary Supplements from Product Labels by Topic Modeling. MedInfo (2017)
Yadan Fan, Lu He, Serguei V. S. Pakhomov, Genevieve B. Melton, Rui Zhang
Classifying Supplement Use Status in Clinical Notes. CRI (2017)
Rui Zhang, Serguei V. S. Pakhomov, Elliot G. Arsoniadis, Janet T. Lee, Yan Wang, Genevieve B. Melton
Detecting clinically relevant new information in clinical notes across specialties and settings. BMC Medical Informatics Decis. Mak. 17 (2) (2017)
Yadan Fan, Lu He, Rui Zhang
Classification of use status for dietary supplements in clinical notes. BIBM (2016)
Yefeng Wang, Rui Zhang, Terrence J. Adam
Term Coverage of Dietary Supplements Ingredients in Product Labels. AMIA (2016)
Nivedha Manohar, Terrence J. Adam, Serguei V. S. Pakhomov, Genevieve B. Melton, Rui Zhang
Evaluation of Herbal and Dietary Supplement Resource Term Coverage. MedInfo (2015)
Rui Zhang, Nivedha Manohar, Elliot G. Arsoniadis, Yan Wang, Terrence J. Adam, Serguei V. S. Pakhomov, Genevieve B. Melton
Evaluating Term Coverage of Herbal and Dietary Supplements in Electronic Health Records. AMIA (2015)
Rui Zhang, William R. Hersh, Genevieve B. Melton, Yang Huang, Laura K. Wiley, Julie Doberne, Nawanan Theera-Ampornpunt
Evolving Career Landscapes in Biomedical and Health Informatics. AMIA (2014)
Rui Zhang, Serguei V. S. Pakhomov, Janet T. Lee, Genevieve B. Melton
Using Language Models to Identify Relevant New Information in Inpatient Clinical Note. AMIA (2014)
Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Graciela Rosemblat, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. S. Pakhomov, Genevieve B. Melton
Using semantic predications to uncover drug-drug interactions in clinical data. J. Biomed. Informatics 49 (2014)
Nawanan Theera-Ampornpunt, Kai Zheng, Yang Gong, Jennifer J. Boehne, David C. Kaelber, Rui Zhang, Sashank Kaushik, Ryan Shaw, Tiffany Kelley, Saif S. Khairat
Preparing for Informatics Careers and Trends in the Age of Meaningful Use. AMIA (2013)
Rui Zhang, Serguei V. S. Pakhomov, Janet T. Lee, Genevieve B. Melton
Navigating Longitudinal Clinical Notes with an Automated Method for Detecting New Information. MedInfo (2013)
Rui Zhang, Serguei V. S. Pakhomov, Sophia Gladding, Michael Aylward, Emily Borman-Shoap, Genevieve B. Melton
Automated Assessment of Medical Training Evaluation Text. AMIA (2012)
Rui Zhang, Serguei V. S. Pakhomov, Genevieve B. Melton
Automated identification of relevant new information in clinical narrative. IHI (2012)