Publications

Idnay B, Xu Z, Adams WG, Adibuzzaman M, Anderson NR, Bahroos N, Bell DS, Bumgardner C, Campion T, Castro M et al..  2025.  Environment scan of generative AI infrastructure for clinical and translational science.. Npj Health Syst. 2(1):4.

Zhou Y, Newbury AM, Zhang G, Idnay BRoss, Liu H, Weng C, Peng Y.  2025.  EvidenceOutcomes: A Dataset of Clinical Trial Publications with Clinically Meaningful Outcomes.. Stud Health Technol Inform. 329:723-727.

Flanders AE, Wang X, Wu CC, Kitamura FC, Shih G, Mongan J, Peng Y.  2025.  The Evolution of Radiology Image Annotation in the Era of Large Language Models.. Radiol Artif Intell. 7(4):e240631.

Gautam N, Elhusseiny A, Mansour M, Mehta JL, Andersen OS, Peng Y, Al'Aref SJ.  2025.  Exploring the feasibility of using artificial intelligence to simulate the placebo arm of randomized clinical trials.. Postgrad Med J.

Bai Z, Xu Z, Sun C, Zang C, H Bunnell T, Sinfield C, Rutter J, Martinez AThomas, L Bailey C, Weiner M et al..  2025.  Extracting post-acute sequelae of SARS-CoV-2 infection symptoms from clinical notes via hybrid natural language processing.. Npj Health Syst. 2

Wang Z, Cao L, Jin Q, Chan J, Wan N, Afzali B, Cho H-J, Choi C-I, Emamverdi M, Gill MK et al..  2025.  A foundation model for human-AI collaboration in medical literature mining.. Nat Commun. 16(1):8361.

Peng Y, Malin BA, Rousseau JF, Wang Y, Xu Z, Xu X, Weng C, Bian J.  2025.  From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare.. J Biomed Inform. 163:104791.

Sun C, Teichman K, Zhou Y, Critelli B, Nauheim D, Keir G, Wang X, Zhong J, Flanders AE, Shih G et al..  2025.  Generative Large Language Models Trained for Detecting Errors in Radiology Reports.. Radiology. 315(2):e242575.

Zhang G, Xu Z, Jin Q, Chen F, Fang Y, Liu Y, Rousseau JF, Xu Z, Lu Z, Weng C et al..  2025.  Leveraging long context in retrieval augmented language models for medical question answering.. NPJ Digit Med. 8(1):239.

Zhang Y, Wei Y, Wang Y, Xiao Y, Poropatich CRet Ronald, Haas GL, Zhang Y, Weng C, Liu J, Brenner LA et al..  2025.  Machine learning applications related to suicide in military and Veterans: A scoping literature review.. J Biomed Inform. 167:104848.

Chen J, Su L, Li Y, Lin M, Peng Y, Sun C.  2025.  A multimodal approach for few-shot biomedical named entity recognition in low-resource languages.. J Biomed Inform. 161:104754.

Wang S, Wei Y, Ma H, Lovitt M, Deng K, Meng Y, Xu Z, Zhang J, Xiao Y, Ding Y et al..  2025.  A multi-stage large language model framework for extracting suicide-related social determinants of health.. Commun Med (Lond). 5(1):404.

Ma H, Xu Z, Chung W, Weng C, Peng Y.  2025.  A Pilot Meta-Research on Evolving Evidence Behind Genetic Variant (Re)Classification.. Stud Health Technol Inform. 329:108-112.

Liang Y, Zhang G, Sun E, Idnay B, Fang Y, Chen F, Ta C, Peng Y, Weng C.  2025.  Scalable scientific interest profiling using large language models.. J Biomed Inform. 172:104949.

Consoli B, Wang H, Wu X, Wang S, Zhao X, Wang Y, Rousseau J, Hartvigsen T, Shen L, Wu H et al..  2025.  SDoH-GPT: using large language models to extract social determinants of health.. J Am Med Inform Assoc.

Chen F, Zhang G, Fang Y, Peng Y, Weng C.  2025.  Semi-supervised learning from small annotated data and large unlabeled data for fine-grained Participants, Intervention, Comparison, and Outcomes entity recognition.. J Am Med Inform Assoc. 32(3):555-565.

Xu RLi, Wang S, Wang Z, Zhang Y, Xiao Y, Pathak J, Hodge D, Leng Y, S Watkins C, Ding Y et al..  2024.  Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups.. Proc (IEEE Int Conf Healthc Inform). 2024:189-199.

Zhang G, Jin Q, Zhou Y, Wang S, Idnay B, Luo Y, Park E, Nestor JG, Spotnitz ME, Soroush A et al..  2024.  Closing the gap between open source and commercial large language models for medical evidence summarization.. NPJ Digit Med. 7(1):239.

Xiao Y, Bi K, Yip PSiu-Fai, Cerel J, Brown TT, Peng Y, Pathak J, J Mann J.  2024.  Decoding Suicide Decedent Profiles and Signs of Suicidal Intent Using Latent Class Analysis.. JAMA Psychiatry. 81(6):595-605.

Wei Y, Deng Y, Sun C, Lin M, Jiang H, Peng Y.  2024.  Deep learning with noisy labels in medical prediction problems: a scoping review.. J Am Med Inform Assoc. 31(7):1596-1607.

Su L, Chen J, Peng Y, Sun C.  2024.  Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension.. J Biomed Inform. 159:104739.

Zhou Y, Ong H, Kennedy P, Wu CC, Kazam J, Hentel K, Flanders A, Shih G, Peng Y.  2024.  Evaluating GPT-V4 (GPT-4 with Vision) on Detection of Radiologic Findings on Chest Radiographs.. Radiology. 311(2):e233270.

Tam TYu Chow, Sivarajkumar S, Kapoor S, Stolyar AV, Polanska K, McCarthy KR, Osterhoudt H, Wu X, Visweswaran S, Fu S et al..  2024.  A framework for human evaluation of large language models in healthcare derived from literature review.. NPJ Digit Med. 7(1):258.

Holste G, Lin M, Zhou R, Wang F, Liu L, Yan Q, Van Tassel SH, Kovacs K, Chew EY, Lu Z et al..  2024.  Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.. NPJ Digit Med. 7(1):216.

Jin Q, Chen F, Zhou Y, Xu Z, Cheung JM, Chen R, Summers RM, Rousseau JF, Ni P, Landsman MJ et al..  2024.  Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine.. NPJ Digit Med. 7(1):190.