Yifan Peng

Research Interests

Biomedical / Clinical Natural Language Processing
Deep Learning for Healthcare
Biomedical Image Processing (by courtesy)

Education

Ph.D., Computer Science, University of Delaware, 2016 (supervisors: Dr. Cathy H. Wu and Dr. Vijay K. Shanker)
M.S., Computer Science, University of Delaware, 2013
M.Eng., Signal and Information Processing, Peking University, China, 2010
B.S.E., Computer Science and Technology, Beijing University of Technology, China, 2007

Teaching

HINF 5016 Natural Language Processing in Health (2021-present)
CTIV 5057 Introduction to GPT & LLMs in Clinical & Translational Research (2025-present)
SYSEN 5630: Clinical Natural Language Processing and Large Language Models (2025-present)

Professional Activities

Associate Editor: Radiology Advances (2024-present), JMIR AI (2025-present)
Editorial Board: Journal of Biomedical Informatics (2023-2027)
Area Chair: NeurIPS (2025)
NIH/NSF Grant Reviewer: 2025/4 Neurological Sciences and Disorders C Study Section, 2025/5 ZLM1 AS-C (01), 2025/3 NSF SCH Panel P250914
Austrian Science Fund Grant Reviewer: 2025

Work Experience

Assistant Professor, Population Health Sciences, Weill Cornell Medicine, New York, NY, 2020-2024
Research Fellow, NCBI, NIH, Bethesda, MD, 2016-2020
Intern/Visiting scholar, NCBI, NIH, Bethesda, MD, 2015
Intern, Google Inc., Mountain View, CA, 2014
Intern, Natural Language Processing Research Group, Sogou Corp., Beijing, China, 2009
Intern, China Research Lab, IBM Corp., Beijing, China, 2009
Editor and Reporter, Programmer Magazine and CSDN, Beijing, China, 2008

Research Support

PI/MPI: 1R01CA289249, 1R01LM014306, 1R01LM014344, 1R01LM014573, 1R21EY035296, NSF CAREER 2145640
co-I: 1OT2HL161847, 1R01NS140142, 2UL1TR002384, 75N92020D00021, ME-2020C3-21199, ME-2023C3-35934, NSF SCH 2306556

Honors and Awards

Fellow (FACMI), American College of Medical Informatics (ACMI), 2024
AMIA New Investigator Award, 2023
Fellow (FAMIA), AMIA, 2023

Mentoring

Shohom Chakraborty, 2025
Kelly Deng, 2024-present
Ertan Dogan, 2024, 2025
Xuan Zhong Feng, 2025-present
Haotian Ma, 2024-present
Geoffrey Martin, 2025-present
Jiahe Qian, 2025-present
Song Wang, 2020-present
Yishu Wei, 2024-present
Kunyu Yu, 2025-present
Jingze Zhang, 2024-present

Publications

* co-first author. Google Scholar

Journal articles

Yu K, Yang R, Liao J, Li S, Li H, Li I, Peng Y, Kamaleswaran R, Liu N. Benchmarking Foundation Models with Multimodal Public Electronic Health Records. IEEE J Biomed Health Inform. 2025 Dec 16;PP. doi: 10.1109/JBHI.2025.3645076. Epub ahead of print. PMID: 41406283.
Liang Y, Zhang G, Sun E, Idnay B, Fang Y, Chen F, Ta C, Peng Y, Weng C. Scalable scientific interest profiling using large language models. J Biomed Inform. 2025 Oct 31:104949. doi: 10.1016/j.jbi.2025.104949. Epub ahead of print. PMID: 41177243.
Wang S, Wei Y, Ma H, Lovitt M, Deng K, Meng Y, Xu Z, Zhang J, Xiao Y, Ding Y, Xu X, Ghosh J, Peng Y. A multi-stage large language model framework for extracting suicide-related social determinants of health. Commun Med (Lond). 2025 Sep 29;5(1):404. doi: 10.1038/s43856-025-01114-z. PMID: 41023090; PMCID: PMC12480878.
Wang Z, Cao L, Jin Q, Chan J, Wan N, Afzali B, Cho HJ, Choi CI, Emamverdi M, Gill MK, Kim SH, Li Y, Liu Y, Luo Y, Ong H, Rousseau JF, Sheikh I, Wei JJ, Xu Z, Zallek CM, Kim K, Peng Y, Lu Z, Sun J. A foundation model for human-AI collaboration in medical literature mining. Nat Commun. 2025 Sep 24;16(1):8361. doi: 10.1038/s41467-025-62058-5. PMID: 40993125; PMCID: PMC12460617.
Bai Z, Xu Z, Sun C, Zang C, Bunnell HT, Sinfield C, Rutter J, Martinez AT, Bailey LC, Weiner M, Campion TR, Carton TW, Forrest CB, Kaushal R, Wang F, Peng Y. Extracting post-acute sequelae of SARS-CoV-2 infection symptoms from clinical notes via hybrid natural language processing. Npj Health Syst. 2025 Aug 21;2:10.1038/s44401-025-00033-4. doi: 10.1038/s44401-025-00033-4. Epub ahead of print. PMID: 40958972; PMCID: PMC12435580.
Wang Y, Hilsman J, Li C, Morris M, Heider PM, Fu S, Kwak MJ, Wen A, Applegate JR, Wang L, Bernstam E, Liu H, Chang J, Harris DR, Corbeau A, Henderson D, Osborne J, Kennedy RE, Garduno-Rapp NE, Rousseau JF, Yan C, Chen Y, Patel MB, Murphy TJ, Malin BA, Park CM, Fan JW, Sohn S, Pagali S, Peng Y, Pathak A, Wu Y, Xia Z, Loguercio S, Reis SE, Visweswaran S. Development and validation of natural language processing algorithms in the national ENACT network. J Clin Transl Sci. 2025 Aug 22;9(1):e199. doi: 10.1017/cts.2025.10116. PMID: 40979101; PMCID: PMC12444719.
Lin M, Holste G, Wang S, Zhou Y, Wei Y, Banerjee I, Chen P, Dai T, Du Y, Dvornek NC, Ge Y, Guo Z, Hanaoka S, Kim D, Messina P, Lu Y, Parra D, Son D, Soto Á, Urooj A, Vidal R, Yamagishi Y, Yan P, Yang Z, Zhang R, Zhou Y, Celi LA, Summers RM, Lu Z, Chen H, Flanders A, Shih G, Wang Z, Peng Y. CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray. Med Image Anal. 2025 Dec;106:103739. doi: 10.1016/j.media.2025.103739. Epub 2025 Jul 29. PMID: 40795541; PMCID: PMC12396843.
Fang Y, Zhang G, Chen F, Hripcsak G, Peng Y, Ryan P, Weng C. CLEAR: A vision to support clinical evidence lifecycle with continuous learning. J Biomed Inform. 2025 Jul 29;169:104884. doi: 10.1016/j.jbi.2025.104884. Epub ahead of print. PMID: 40744316; PMCID: PMC12339056.
Gautam N, Elhusseiny A, Mansour M, Mehta JL, Andersen OS, Peng Y, Al'Aref SJ. Exploring the feasibility of using artificial intelligence to simulate the placebo arm of randomized clinical trials. Postgrad Med J. 2025 Jun 19:qgaf095. doi: 10.1093/postmj/qgaf095. Epub ahead of print. PMID: 40577492.
Consoli B, Wang H, Wu X, Wang S, Zhao X, Wang Y, Rousseau J, Hartvigsen T, Shen L, Wu H, Peng Y, Long Q, Chen T, Ding Y. SDoH-GPT: using large language models to extract social determinants of health. J Am Med Inform Assoc. 2025 Jun 10:ocaf094. doi: 10.1093/jamia/ocaf094. Epub ahead of print. PMID: 40493530.
Sun C, Teichman K, Zhou Y, Critelli B, Nauheim D, Keir G, Wang X, Zhong J, Flanders AE, Shih G, Peng Y. Generative Large Language Models Trained for Detecting Errors in Radiology Reports. Radiology. 2025 May;315(2):e242575. doi: 10.1148/radiol.242575. PMID: 40392090; PMCID: PMC12130665. Press release AuntMinnie
Zhang Y, Wei Y, Wang Y, Xiao Y, Poropatich CRRK, Haas GL, Zhang Y, Weng C, Liu J, Brenner LA, Bjork JM, Peng Y. Machine learning applications related to suicide in military and Veterans: A scoping literature review. J Biomed Inform. 2025 Jul;167:104848. doi: 10.1016/j.jbi.2025.104848. Epub 2025 May 13. PMID: 40373934.
Zhang G, Xu Z, Jin Q, Chen F, Fang Y, Liu Y, Rousseau JF, Xu Z, Lu Z, Weng C, Peng Y. Leveraging long context in retrieval augmented language models for medical question answering. NPJ Digit Med. 2025 May 2;8(1):239. doi: 10.1038/s41746-025-01651-w. PMID: 40316710; PMCID: PMC12048518.
Flanders AE, Wang X, Wu CC, Kitamura FC, Shih G, Mongan J, Peng Y. The Evolution of Radiology Image Annotation in the Era of Large Language Models. Radiol Artif Intell. 2025 Jul;7(4):e240631. doi: 10.1148/ryai.240631. PMID: 40304582; PMCID: PMC12319696.
Peng Y, Chen Q, Shih G. DeepSeek is open-access and the next AI disrupter for radiology. Radiol Adv. 2025 Jan;2(1):umaf009. doi: 10.1093/radadv/umaf009. Epub 2025 Feb 18. PMID: 40837590; PMCID: PMC12363671.
Cheng S, Wei Y, Zhou Y, Xu Z, Wright DN, Liu J, Peng Y. Deciphering genomic codes using advanced natural language processing techniques: a scoping review. J Am Med Inform Assoc. 2025 Apr 1;32(4):761-772. doi: 10.1093/jamia/ocaf029. PMID: 39998912; PMCID: PMC12005631.
Lin M, Wang S, Ding Y, Zhao L, Wang F, Peng Y. An empirical study of using radiology reports and images to improve intensive care unit mortality prediction. JAMIA Open. 2025 Feb 20;8(1):ooae137. doi: 10.1093/jamiaopen/ooae137. PMID: 39980476; PMCID: PMC11841685.
Peng Y, Malin BA, Rousseau JF, Wang Y, Xu Z, Xu X, Weng C, Bian J. From GPT to DeepSeek: Significant gaps remains in realizing AI in healthcare. J Biomed Inform. 2025 Mar;163:104791. doi: 10.1016/j.jbi.2025.104791. Epub 2025 Feb 10. PMID: 39938624; PMCID: PMC12188495.
Idnay B, Xu Z, Adams WG, Adibuzzaman M, Anderson NR, Bahroos N, Bell DS, Bumgardner C, Campion T, Castro M, Cimino JJ, Cohen IG, Dorr D, Elkin PL, Fan JW, Ferris T, Foran DJ, Hanauer DA, Hogarth M, Huang K, Kalpathy-Cramer J, Kandpal M, Karnik NS, Katoch A, Lai AM, Lambert CG, Li L, Lindsell C, Liu J, Lu Z, Luo Y, McGarvey P, Mendonca EA, Mirhaji P, Murphy S, Osborne JD, Paschalidis IC, Harris PA, Prior F, Shaheen NJ, Shara N, Sim I, Tachinardi U, Waitman LR, Wright RJ, Zai AH, Zheng K, Lee SS, Malin BA, Natarajan K, Price II WN, Zhang R, Zhang Y, Xu H, Bian J, Weng C, Peng Y. Environment scan of generative AI infrastructure for clinical and translational science. npj Health Syst. 2025;2(1):4. doi: 10.1038/s44401-024-00009-w. Epub 2025 Jan 25. PMID: 39872195; PMCID: PMC11762411.
Chen F, Zhang G, Fang Y, Peng Y, Weng C. 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. 2025 Mar 1;32(3):555-565. doi: 10.1093/jamia/ocae326. PMID: 39823371; PMCID: PMC11833487.
Chen J, Su L, Li Y, Lin M, Peng Y, Sun C. A multimodal approach for few-shot biomedical named entity recognition in low-resource languages. J Biomed Inform. 2025 Jan;161:104754. doi: 10.1016/j.jbi.2024.104754. Epub 2024 Nov 30. PMID: 39622400.

Conference proceedings

Wu P, Lin M, Chen Q, Chew EY, Lu Z, Peng Y, Dong H. AMD-Mamba: A Phenotype-Aware Multi-Modal Framework for Robust AMD Prognosis. Machine Learning in Medical Imaging. PMID: 40969487; PMCID: PMC12443226.
Song Y, Zhang Y, Orengo-Nania S, Wang N, Ma F, Zhang R, Peng Y, Lin M. Two-Stage Decoupling Framework for Variable-Length Glaucoma Prognosis. Learning with Longitudinal Medical Images and Data. 2025 Sep 15.
Zhang J, Qian J, Zhou Y, Peng Y. Enhancing Health Fact-Checking with LLM-Generated Synthetic Data. Proceedings of the BioCreative IX Challenge and Workshop (BC9). 2025 Aug 14; 1-7.
Ma H, Xu Z, Chung W, Weng C, Peng Y. A Pilot Meta-Research on Evolving Evidence Behind Genetic Variant (Re)Classification. Stud Health Technol Inform. 2025 Aug 7;329:108-112. doi: 10.3233/SHTI250811. PMID: 40775829.
Zhou Y, Newbury AB, Zhang G, Idnay BR, Liu H, Weng C, Peng Y. EvidenceOutcomes: a Dataset of Clinical Trial Publications with Clinically Meaningful Outcomes. Stud Health Technol Inform. 2025 Aug 7;329:723-727. doi: 10.3233/SHTI250935. PMID: 40775953.
Xu Z, Ma H, Zhang G, Ding Y, Weng C, Peng Y. Natural Language Processing in Support of Evidence-based Medicine: A Scoping Review. Find ACL ACL. 2025 Jul;2025:21421-21443. doi: 10.18653/v1/2025.findings-acl.1103. PMID: 41328283; PMCID: PMC12665387.
Tang F, Liu C, Xu Z, Hu M, Huang Z, Xue H, Chen Z, Peng Z, Yang Z, Zhou S, Li W, Li Y, Song W, Su S, Feng W, Su J, Lin M, Peng Y, Cheng X, Razzak I, Ge Z. Seeing Far and Clearly: Mitigating Hallucinations in MLLMs with Attention Causal Decoding. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2025 Jun;2025:26147-26159. doi: 10.1109/cvpr52734.2025.02435. Epub 2025 Aug 13. PMID: 40951258; PMCID: PMC12425127.
Wei Y, Wang X, Ong H, Zhou Y, Flanders A, Shih G, Peng Y. Enhancing disease detection in radiology reports through fine-tuning lightweight LLM on weak labels. AMIA Jt Summits Transl Sci Proc. 2025 Jun 10;2025:614-623. PMID: 40502255; PMCID: PMC12150749.
Morris JX, Campion TR, Nutheti SL, Peng Y, Raj A, Zabih R, Cole CL. DIRI: Adversarial Patient Reidentification with Large Language Models for Evaluating Clinical Text Anonymization. AMIA Jt Summits Transl Sci Proc. 2025 Jun 10;2025:355-364. PMID: 40502277; PMCID: PMC12150728.

Abstracts

Deng R, Wu X, Wang T, Rap EG, Yang Q, Wang Y, Rousseau JF, Peng Y, Wang Y. CPGPrompt: Translating Clinical Guidelines into LLM-Executable Decision Support - A Pilot Study. AMIA Annual Symposium. 2025
Wu X, Rousseau J, Peng Y, Wang Y. Embedding clinical guidelines into large language models for headache diagnosis decision support. AMIA 2025 Informatics Summit. 2025

Book chapters

Mukherjee S, Peng Y, Chen Q, Keenan TDL, Chew EL, Lu Z. Artificial Intelligence in Age-Related Macular Degeneration (AMD). Artificial Intelligence in Ophthalmology. Cham: Springer Nature Switzerland. 2025, 121-135. doi:10.1007/978-3-031-83756-2_8.

Talks

Ophthalmology Grand Rounds, Weill Cornell Medicine. 11/6/2025
Ezra Systems Seminar. Systems Engineering, Cornell Engineering. 9/12/2025
Department of Electrical Engineering. National Kaohsiung University of Science and Technology. 8/14/2025
Statistical Methods Talk. Centre for Quantitative Medicine. Duke-NUS Medical School. 7/21/2025
Keynote speech. Mayo Clinic AI Summit. 7/12/2025
Short course: Biomedical Large Language Models – Development and Application. Pharmaceutical Data Science (PharmaDS) Conference 2025. 4/7/2025
BMI Seminar Series, Ohio State University College of Medicine. 2/14/2025
PQHS Research Methods Meetings, UMass Chan Medical School. 2/6/2025