For a complete and up-to-date list, please visit Google Scholar.
Machine-readable resources for AI agents and citation tools: BibTeX collection · structured JSON · LLM-readable index. Each publication also has an individual [cite] page with copy and download options.
2026
BRIDGE: Benchmarking Large Language Models for Understanding Real-World Clinical Practice Texts. Jiageng Wu, Bowen Gu, Ren Zhou, Kevin Xie, Doug Snyder, Yixing Jiang, Valentina Carducci, Richard Wyss, Rishi J Desai, Emily Alsentzer, Leo Anthony Celi, Adam Rodman, Sebastian Schneeweiss, Jonathan H Chen, Santiago Romero-Brufau, Kueiyu Joshua Lin, Jie Yang. Nature Biomedical Engineering. [cite]
Large Language Models Generate Stigmatizing Language During Reasoning Over Real-World Clinical Data. Yutong Yang, Bowen Gu, David B Hathaway, Richard Wyss, Laura Marengo, Jason B Gibbons, Stanley Lyndon, Jiageng Wu, Qingyu Chen, Nan Liu, Philip S Wang, Leo Anthony Celi, David W Bates, Kueiyu Joshua Lin, Li Zhou, Jie Yang. medRxiv preprint. [cite]
An Expedited Chart Review Process for Large Database Studies Using Natural Language Processing and Multiwave Adaptive Sampling. Shirley V Wang, Georg Hahn, Sreedhara Sushama Kattinakere, Mufaddal Mahesri, Haritha S Pillai, Rajendra Aldis, Joyce Lii, Sarah K Dutcher, Rhoda Eniafe, Jamal T Jones, Keewan Kim, Jiwei He, Hana Lee, Sengwee Toh, Rishi J Desai, Jie Yang. Epidemiology. [cite]
DT-Transformer: A Foundation Model for Disease Trajectory Prediction on a Real-World Health System. Yunying Zhu, Andrew R Weckstein, Kueiyu Joshua Lin, Jie Yang. arXiv preprint. [cite]
Trustworthy Classification for Complex Social Surveys: A Memory-Enhanced Hierarchical Framework with Calibrated Uncertainty. Zeqiang Wang, Rebecca Oldroyd, Yuqi Wang, Jiageng Wu, Jie Yang, Wei Wang, Nishanth R Sastry, Jon Johnson, Suparna De. Proceedings of the AAAI Conference on Artificial Intelligence. [cite]
Linguistic Effects of Ambient AI on Clinical Documentation: A Matched Pre-Post Study. Yiming Li, Huiyuan Zhou, Suzanne Blackley, Joseph M Plasek, Zhuoyang Lyu, Wei Zhang, Jacqueline You, Amanda Centi, Rebecca Mishuris, Jie Yang, Li Zhou. medRxiv preprint. [cite]
Transcranial Magnetic Stimulation Retreatment for Recurrent Depression: A Large Real-World Multisite Cohort Study. Stanley Lyndon, Jason B Gibbons, Loreen Straub, Meekang Sung, Jacob C Jameson, David B Hathaway, Denise H Mulcahy, Cason Elliott, Rachel Wood, Matthew Ruble, Alejandro G Szmulewicz, Jie Yang, Rajendra Aldis, Richard Wyss, Philip S Wang, Shan H Siddiqi. Acta Psychiatrica Scandinavica. [cite]
Predicting Deprescribing of High-Risk Medications Using Provider EHR Use and Patient Characteristics. Bowen Gu, Katharina Tabea Jungo, Julie Lauffenburger, Niteesh Choudhry, Thomas Isaac, John Zambrano, Jie Yang. medRxiv preprint. [cite]
Using Natural Language Processing of Clinical Notes to Supplement Structured Electronic Health Record Data for Phenotyping Smoking and Obesity in a Healthcare System. Jie Yang, Bowen Gu, Haritha Pillai, Joyce Lii, David Cronkite, Keith A Marsolo, Rishi J Desai. Pharmacoepidemiology and Drug Safety. [cite]
Scalable Medication Extraction and Discontinuation Identification from Electronic Health Records Using Large Language Models. Chong Shao, Douglas Snyder, Chiran Li, Bowen Gu, Kerry Ngan, Chun-Ting Yang, Jiageng Wu, Richard Wyss, Kueiyu Joshua Lin, Jie Yang. Journal of Clinical Epidemiology. [cite]
Efficacy of Cognitive Behavioral Therapy-Based Smartphone App for Smoking Cessation in China: A Randomized Controlled Trial. Jinsong Tang, Xiaocong Liu, Shanshan Chen, Yunkai Sun, Minzhe Zhu, Zitang Zhou, Yueheng Liu, Jie Yang, Wei Chen, Yanhui Liao. Addiction. [cite]
MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graph. Duzhen Zhang, Zixiao Wang, Zhong-Zhi Li, Yahan Yu, Shuncheng Jia, Jiahua Dong, Haotian Xu, Xing Wu, Yingying Zhang, Tielin Zhang, Jie Yang, Xiuying Chen, Le Song. npj Digital Medicine. [cite]
FinTruthQA: A Benchmark for AI-Driven Financial Disclosure Quality Assessment in Investor-Firm Interactions. Peilin Zhou, Ziyue Xu, Xinyu Shi, Jiageng Wu, Yikang Jiang, Dading Chong, Wang Dong, Jun Chen, Bin Ke, Jie Yang. Proceedings of the AAAI Symposium Series. [cite]
2025
The Impact of Low EHR-Continuity on Effect Estimates: Evidence from Two EHR-Medicare Linked Databases. Yinzhu Jin, Angela Y Tong, Richard Wyss, Jie Yang, Kueiyu Joshua Lin. Clinical Epidemiology. [cite]
Validation of Treatment Discontinuation in Claims Data Using NLP and Electronic Health Records. Chun-Ting Yang, Kerry Ngan, Dae Hyun Kim, Jie Yang, Jun Liu, Kueiyu Joshua Lin. Innovation in Aging. [cite]
Clinical Pathway-Aware Large Language Models for Reliable and Transparent Medical Dialogue. Jiageng Wu, Xian Wu, Yefeng Zheng, Jie Yang. Journal of Biomedical Informatics. [cite]
Why Chain of Thought Fails in Clinical Text Understanding. Jiageng Wu, Kevin Xie, Bowen Gu, Nils Krüger, Kueiyu Joshua Lin, Jie Yang. arXiv preprint. [cite]
Generative Artificial Intelligence for Fundus Fluorescein Angiography Interpretation and Human Expert Evaluation. An Shao, Xiaocong Liu, Wenyue Shen, Yingyu Li, Hongkang Wu, Xiangji Pan, Zexin Yang, Yufeng Xu, Tiepei Zhu, Yao Wang, Jie Yang, Yih Chung Tham, Jian Wu, Kai Jin, Juan Ye. npj Digital Medicine. [cite]
Comparative Ranking of Marginal Confounding Impact of Natural Language Processing-Derived versus Structured Features in Pharmacoepidemiology. Joseph M Plasek, Richard D Wyss, Janick G Weberpals, Jie Yang, Thomas Deramus, Theodore N Tsacogianis, Kerry Ngan, Lily G Bessette, Kueiyu Joshua Lin, Li Zhou. Computers in Biology and Medicine. [cite]
Electronic Health Record (EHR) Enhanced Signal Detection Using Tree-Based Scan Statistic Methods. Massimiliano Russo, Sushama Kattinakere Sreedhara, Joshua Smith, Sharon E Davis, Judith C Maro, Thomas Deramus, Joyce Lii, Jie Yang, Rishi Desai, José J Hernández-Muñoz. American Journal of Epidemiology. [cite]
Cognitive Assessment of Dementia Patients Using Large Language Models. Jiageng Wu, Richard Wyss, Kueiyu Joshua Lin, Jie Yang. Alzheimer’s & Dementia. [cite]
Large Language Model for Predicting Altered Mental Status in Dementia Patients Using Electronic Health Records. Jiageng Wu, Richard Wyss, Kueiyu Joshua Lin, Jie Yang. Alzheimer’s & Dementia. [cite]
Establishing a Validation Framework of Treatment Discontinuation in Claims Data Using Natural Language Processing and Electronic Health Records. Chun-Ting Yang, Kerry Ngan, Dae Hyun Kim, Jie Yang, Jun Liu, Kueiyu Joshua Lin. Clinical Pharmacology & Therapeutics. [cite]
Natural Language Processing for Scalable Feature Engineering and Ultra-High-Dimensional Confounding Adjustment in Healthcare Database Studies. Richard Wyss, Jie Yang, Sebastian Schneeweiss, Joseph M Plasek, Li Zhou, Thomas Deramus, Janick G Weberpals, Kerry Ngan, Kueiyu Joshua Lin. Journal of Biomedical Informatics. [cite]
Scalable Information Extraction from Free Text Electronic Health Records Using Large Language Models. Bowen Gu, Vivian Shao, Ziqian Liao, Valentina Carducci, Santiago Romero-Brufau, Jie Yang, Rishi Desai. BMC Medical Research Methodology. [cite]
Analysis of Longitudinal Social Media for Monitoring Symptoms During a Pandemic. Shixu Lin, Lucas Garay, Yining Hua, Zhijiang Guo, Wanxin Li, Minghui Li, Yujie Zhang, Xiaolin Xu, Jie Yang. Journal of Biomedical Informatics. [cite]
Identification of an ANCA-Associated Vasculitis Cohort Using Deep Learning and Electronic Health Records. Liqin Wang, John Novoa-Laurentiev, Claire Cook, Shruthi Srivatsan, Yining Hua, Jie Yang, Eli Miloslavsky, Hyon K Choi, Li Zhou, Zachary S Wallace. International Journal of Medical Informatics. [cite]
Characterizing Public Sentiments and Drug Interactions during COVID-19: A Pretrained Language Model and Network Analysis of Social Media Discourse. Wanxin Li, Yining Hua, Peilin Zhou, Li Zhou, Xin Xu, Jie Yang. Journal of Medical Internet Research. [cite]
2024
Probabilistic Medical Predictions of Large Language Models. Bowen Gu, Rishi J. Desai, Kueiyu Joshua Lin, Jie Yang. npj Digital Medicine. [cite]
Enhancing Postmarketing Surveillance of Medical Products with Large Language Models. Michael E Matheny, Jie Yang, Joshua C Smith, Colin G Walsh, Mohammed A Al-Garadi, Sharon E Davis, Keith Marsolo, Daniel Fabbri, Ruth Reeves, Kevin Johnson, Gerald Dal Pan, Robert Ball, Rishi Desai. JAMA Network Open. [cite]
Clinical Text Datasets for Medical Artificial Intelligence and Large Language Models — A Systematic Review. Jiageng Wu, Xiaocong Liu, Minghui Li, Wanxin Li, Zichang Su, Lucas Garay, Zhiyun Zhang, Yujie Zhang, Qingcheng Zeng, Jie Shen, Changzheng Yuan, Jie Yang. New England Journal of Medicine AI. Included by AMIA Informatics Year in Review. [cite]
Streamlining Social Media Information Retrieval for Public Health Research with Deep Learning. Yining Hua, Jiageng Wu, Shixu Lin, Minghui Li, Yujie Zhang, Dinah Foer, Siwen Wang, Peilin Zhou, Jie Yang, Li Zhou. Journal of the American Medical Informatics Association. [cite]
Guiding Clinical Reasoning with Large Language Models via Knowledge Seeds. Jiageng Wu, Xian Wu, Jie Yang. International Joint Conference on Artificial Intelligence (IJCAI). [cite]
Large Language Models Leverage External Knowledge to Extend Clinical Insight Beyond Language Boundaries. Jiageng Wu, Xian Wu, Zhaopeng Qiu, Minghui Li, Shixu Lin, Yingying Zhang, Yefeng Zheng, Changzheng Yuan, Jie Yang. Journal of the American Medical Informatics Association. Included by AMIA Informatics Year in Review. [cite]
Revealing COVID-19’s Social Dynamics: Diachronic Semantic Analysis of Vaccine and Symptom Discourse on Twitter. Zeqiang Wang, Jiageng Wu, Yuqi Wang, Wei Wang, Jie Yang, Nishanth R Sastry, Jon Johnson, Suparna De. Conference on Empirical Methods in Natural Language Processing (EMNLP), Findings. [cite]
MedJourney: Benchmark and Evaluation of Large Language Models over Patient Clinical Journey. Xian Wu, Yutian Zhao, Yunyan Zhang, Jiageng Wu, Zhihong Zhu, Yingying Zhang, Yi Ouyang, Ziheng Zhang, Huimin Wang, Zhenxi Lin, Jie Yang. Conference on Neural Information Processing Systems (NeurIPS). [cite]
The Sexual and Gender-Diverse Face More Health Challenges During COVID-19: A Large-Scale Social Media Analysis with Natural Language Processing. Zhiyun Zhang, Yining Hua, Peilin Zhou, Shixu Lin, Minghui Li, Yujie Zhang, Li Zhou, Yanhui Liao, Jie Yang. Health Data Science. [cite]
Uncovering Language Disparity of ChatGPT on Retinal Vascular Disease Classification: Cross-Sectional Study. Xiaocong Liu, Jiageng Wu, An Shao, Wenyue Shen, Panpan Ye, Yao Wang, Juan Ye, Kai Jin, Jie Yang. Journal of Medical Internet Research. [cite]
2023
GreenPLM: Cross-Lingual Transfer of Monolingual Pre-Trained Language Models at Almost No Cost. Qingcheng Zeng, Lucas Garay, Peilin Zhou, Dading Chong, Yining Hua, Jiageng Wu, Yikang Pan, Han Zhou, Rob Voigt, Jie Yang. International Joint Conference on Artificial Intelligence (IJCAI). [cite]
Efficacy of WeChat-Based Online Smoking Cessation Intervention (‘WeChat WeQuit’) in China: A Randomised Controlled Trial. Jinsong Tang, Jie Yang, Yi Liu, Xiaocong Liu, Ling Li, Yunkai Sun, Jieyin Jin, Yehong Fang, Zitang Zhou, Yunfei Wang, Yueheng Liu, Wei Chen, Ann McNeill, Brian Kelly, Joanna E Cohen, Yanhui Liao. eClinicalMedicine. [cite]
Exploring Social Media for Early Detection of Depression in COVID-19 Patients. Jiageng Wu, Xian Wu, Yining Hua, Shixu Lin, Yefeng Zheng, Jie Yang. The Web Conference (WWW). [cite]
Trend and Co-occurrence Network of COVID-19 Symptoms Through Large-Scale Social Media: Infoveillance Study. Jiageng Wu, Lumin Wang, Yining Hua, Minghui Li, Li Zhou, David W Bates, Jie Yang. Journal of Medical Internet Research. [cite]
Better Pay Attention Whilst Fuzzing. Shunkai Zhu, Jingyi Wang, Jun Sun, Jie Yang, Xingwei Lin, Liyi Zhang, Peng Cheng. IEEE Transactions on Software Engineering. [cite]
Transforming Retinal Vascular Disease Classification: A Comprehensive Analysis of ChatGPT’s Performance and Inference Abilities. Xiaocong Liu, Jiageng Wu, An Shao, Wenyue Shen, Panpan Ye, Yao Wang, Juan Ye, Kai Jin, Jie Yang. American Medical Informatics Association Annual Symposium (AMIA). [cite]
YATO: Yet Another Deep Learning Based Text Analysis Open Toolkit. Zeqiang Wang, Yile Wang, Jiageng Wu, Zhiyang Teng, Jie Yang. Conference on Empirical Methods in Natural Language Processing (EMNLP), Demo. [cite]
2022
Genetically Predicted Sex Hormone Levels and Health Outcomes: Phenome-Wide Mendelian Randomization Investigation. Shuai Yuan, Lijuan Wang, Jing Sun, Lili Yu, Xuan Zhou, Jie Yang, Yimin Zhu, Dipender Gill, Stephen Burgess, Joshua C Denny. International Journal of Epidemiology. [cite]
METS-CoV: A Dataset of Medical Entity and Targeted Sentiment on COVID-19 Related Tweets. Peilin Zhou, Zeqiang Wang, Dading Chong, Zhijiang Guo, Yining Hua, Zichang Su, Zhiyang Teng, Jiageng Wu, Jie Yang. Conference on Neural Information Processing Systems (NeurIPS). [cite]
Tracking the Impact of COVID-19 and Lockdown Policies on Public Mental Health Using Social Media: Infoveillance Study. Minghui Li, Yining Hua, Yanhui Liao, Li Zhou, Xue Li, Ling Wang, Jie Yang. Journal of Medical Internet Research. [cite]
Low-resource Accent Classification in Geographically-Proximate Settings: A Forensic and Sociophonetics Perspective. Qingcheng Zeng, Dading Chong, Peilin Zhou, Jie Yang. Annual Conference of the International Speech Communication Association (INTERSPEECH). [cite]
Natural Language Processing to Identify Abnormal Breast, Lung, and Cervical Cancer Screening Test Results from Unstructured Reports to Support Timely Follow-up. Courtney J Diamond, John Laurentiev, Jie Yang, Amy Wint, Kimberly A Harris, Tin H Dang, Amrita Mecker, Emily B Carpenter, Anna N Tosteson, Adam Wright. Studies in Health Technology and Informatics. [cite]
Using Twitter Data to Understand Public Perceptions of Approved versus Off-label Use for COVID-19-related Medications. Yining Hua, Hang Jiang, Shixu Lin, Jie Yang, Joseph M Plasek, David W Bates, Li Zhou. Journal of the American Medical Informatics Association. [cite]
2021
Development and Validation of a Deep Learning Model for Earlier Detection of Cognitive Decline from Clinical Notes in Electronic Health Records. Liqin Wang, John Laurentiev, Jie Yang, Ying-Chih Lo, Rebecca E. Amariglio, Deborah Blacker, Reisa A. Sperling, Gad A. Marshall, Li Zhou. JAMA Network Open. [cite]
Assessing the Prognostic Significance of Tumor-Infiltrating Lymphocytes in Patients With Melanoma Using Pathologic Features Identified by Natural Language Processing. Jie Yang, John Lian, Yen Po Chin, Liqin Wang, Anna Lian, George F. Murphy, Li Zhou. JAMA Network Open. [cite]
Sentiment Correlation in Financial News Networks and Associated Market Movements. Xingchen Wan*, Jie Yang*, Slavi Marinov, Jan-Peter Calliess, Stefan Zohren, Xiaowen Dong. Scientific Reports. [cite]
Multilevel Follow-up of Cancer Screening (mFOCUS): Protocol for a Multilevel Intervention to Improve the Follow-up of Abnormal Cancer Screening Test Results. Jennifer S Haas, Steven J Atlas, Adam Wright, E John Orav, David G Aman, Erica S Breslau, Timothy E Burdick, Emily Carpenter, Frank Chang, Tin Dang, Jie Yang, Li Zhou, Anna Tosteson. Contemporary Clinical Trials. [cite]
2020
Development and Validation of a Deep Learning Model for Detection of Allergic Reactions Using Safety Event Reports Across Hospitals. Jie Yang, Liqin Wang, Neelam A. Phadke, Paige G. Wickner, Christian M. Mancini, Kimberly G. Blumenthal, Li Zhou. JAMA Network Open. [cite]
Deep Learning to Detect Allergy Events from Hospital Safety Reports. Jie Yang, Liqin Wang, Neelam A Phadke, Paige G Wickner, Christian M Mancini, Kimberly G Blumenthal, Li Zhou. American Medical Informatics Association Annual Symposium (AMIA). [cite]
Implementing an IT-Based Intervention to Improve Follow-up Rates of Abnormal Cancer Screening Results: the mFOCUS Trial. Courtney Diamond, Steven Atlas, Tin Dang, Jie Yang, Li Zhou, Sanja Percac-Lima, Amy Wint, Kimberly Harris, John Orav, Erica Breslau, Shoshana Hort, Anna Tosteson, Jennifer Haas, Adam Wright. American Medical Informatics Association Annual Symposium (AMIA). [cite]
Allergic Reactions in Two Academic Medical Centers. Neelam A. Phadke, Li Zhou, Christian M. Mancini, Jie Yang, Liqin Wang, Paige Wickner, Xiaoqing Fu, Kimberly G. Blumenthal. Journal of General Internal Medicine. [cite]
Disparities in Outpatient Visits for Mental Health and/or Substance Use Disorders During the COVID-19 Surge and Partial Reopening in Massachusetts. Jie Yang, Mary B. Landrum, Li Zhou, Alisa B Busch. General Hospital Psychiatry. [cite]
Lattice LSTM for Chinese Sentence Representation. Yue Zhang, Yile Wang, Jie Yang. IEEE/ACM Transactions on Audio, Speech, and Language Processing. [cite]
2019
Subword Encoding in Lattice LSTM for Chinese Word Segmentation. Jie Yang, Yue Zhang, Shuailong Liang. Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL). [cite]
Mining Clinical Phrases from Nursing Notes to Discover Risk Factors of Patient Deterioration. Zfania T. Korach, Jie Yang, Sarah Collins Rossetti, Kenrick D. Cato, Min-Jeoung Kang, Christopher Knaplund, Kumiko O. Schnock, Jose P. Garcia, Haomiao Jia, Jessica M. Schwartz, Li Zhou. International Journal of Medical Informatics. [cite]
From Genesis to Creole Language: Transfer Learning for Singlish Universal Dependencies Parsing and POS Tagging. Hongming Wang, Jie Yang, Yue Zhang. ACM Transactions on Asian and Low-Resource Language Information Processing. [cite]
2018
Design Challenges and Misconceptions in Neural Sequence Labeling. Jie Yang, Shuailong Liang, Yue Zhang. International Conference on Computational Linguistics (COLING). Best Paper Award. [cite]
NCRF++: An Open-source Neural Sequence Labeling Toolkit. Jie Yang, Yue Zhang. Annual Meeting of the Association for Computational Linguistics (ACL), Demo. [cite]
Chinese NER Using Lattice LSTM. Yue Zhang*, Jie Yang*. Annual Meeting of the Association for Computational Linguistics (ACL). [cite]
YEDDA: A Lightweight Collaborative Text Span Annotation Tool. Jie Yang, Yue Zhang, Linwei Li, Xingxuan Li. Annual Meeting of the Association for Computational Linguistics (ACL), Demo. Best Demo Paper Nomination. [cite]
2017
Neural Word Segmentation with Rich Pretraining. Jie Yang, Yue Zhang, Fei Dong. Annual Meeting of the Association for Computational Linguistics (ACL). [cite]
Universal Dependencies Parsing for Colloquial Singaporean English. Hongmin Wang, Yue Zhang, Guang Yow Leonard Chan, Jie Yang, Hai Leong Chieu. Annual Meeting of the Association for Computational Linguistics (ACL). [cite]
Attention-based Recurrent Convolutional Neural Network for Automatic Essay Scoring. Fei Dong, Yue Zhang, Jie Yang. Conference on Computational Natural Language Learning (CoNLL). [cite]
Neural Reranking for Named Entity Recognition. Jie Yang, Yue Zhang, Fei Dong. Recent Advances in Natural Language Processing (RANLP). [cite]
2016
Combining Discrete and Neural Features for Sequence Labeling. Jie Yang, Zhiyang Teng, Meishan Zhang, Yue Zhang. International Conference on Intelligent Text Processing and Computational Linguistics (CICLing). [cite]
LibN3L: A Lightweight Package for Neural NLP. Meishan Zhang, Jie Yang, Zhiyang Teng, Yue Zhang. Language Resources and Evaluation Conference (LREC). [cite]
2015 and Earlier
Effects of Defects and Thermal Treatment on the Properties of Graphene. Kunpeng Jia, Yajuan Su, Yang Chen, Jun Luo, Jie Yang, Peng Lv, Zihan Zhang, Huilong Zhu, Chao Zhao, Tianchun Ye. Vacuum, 2015. [cite]
Hysteresis Analysis of Graphene Transistor Under Repeated Test and Gate Voltage Stress. Jie Yang, Kunpeng Jia, Yajuan Su, Yang Chen, Chao Zhao. Journal of Semiconductors, 2014. [cite]
Stability Analysis of a Back-gate Graphene Transistor in Air Environment. Kunpeng Jia, Jie Yang, Yajuan Su, Pengfei Nie, Jian Zhong, Qingqing Liang, Huilong Zhu. Journal of Semiconductors, 2013. [cite]