Publications

Bian J, Peng Y, Mendonca E, Banerjee I, Xu H.  2026.  Biomedical multimodal large language models: From model-centric development to clinically grounded evaluation and integration.. J Biomed Inform. :105023.

Song Y, Zhan Z, Xie F, Wang N, Peng Y, Zhang R, Lin M.  2026.  A cancer-type-aware framework for robust multimodal survival prediction under missing modalities.. Brief Bioinform. 27(2)

Xu Z, Lin M, Zhou Y, Xu Z, Orlow SJ, Meehan SA, Flamm A, Moshiri AS, Peng Y.  2026.  Establishing dermatopathology encyclopedia DermpathNet with Artificial Intelligence-Based Workflow.. Sci Data. 13(1)

Xu Z, Lin M, Zhou Y, Xu Z, Orlow SJ, Meehan SA, Flamm A, Moshiri AS, Peng Y.  2026.  Establishing dermatopathology encyclopedia DermpathNet with Artificial Intelligence-Based Workflow.. Sci Data. 13(1)

Cheng S, Wei Y, Zhou Y, Xu Z, Wright DN, Liu J, Peng Y.  2025.  Deciphering genomic codes using advanced natural language processing techniques: a scoping review.. J Am Med Inform Assoc.

Wang Y, Hilsman J, Li C, Morris M, Heider PM, Fu S, Kwak MJi, Wen A, Applegate JR, Wang L et al..  2025.  Development and Validation of Natural Language Processing Algorithms in the ENACT National Electronic Health Record Research Network.. medRxiv.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

Wang S, Zhou Y, Han Z, Tao C, Xiao Y, Ding Y, Ghosh J, Peng Y.  2024.  A natural language processing approach to detect inconsistencies in death investigation notes attributing suicide circumstances.. Commun Med (Lond). 4(1):199.

Zhang G, Zhou Y, Hu Y, Xu H, Weng C, Peng Y.  2024.  A span-based model for extracting overlapping PICO entities from randomized controlled trial publications.. J Am Med Inform Assoc. 31(5):1163-1171.