Yifan Peng

Deputy Director, Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine

Associate Professor, Department of Population Health Sciences, Weill Cornell Medicine

Affiliated Faculty, Department of Radiology, Weill Cornell Medicine

Faculty Member, Systems Engineering, Cornell University

Research Interests

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

Education

Ph.D., Computer Science, University of Delaware (Advisors: Dr. Cathy H. Wu and Dr. Vijay K. Shanker). 2016.
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

Deputy Editor, Radiology Advances (2025–Present)
Associate Editor, Radiology Advances (2024-2026), JMIR AI (2025–Present)
Guest Editor: npj Health Systems (Advances in Software-Powered Healthcare), Digital Health (Tele-emergency and Disaster Informatics), Journal of Biomedical Informatics (Biomedical Multimodal Large Language Models — Novel Approaches and Applications)
Editorial Board: Journal of Biomedical Informatics (2023-2027)
Area Chair: NeurIPS (2025-present), EMNLP (2027)
NIH/NSF Grant Reviewer: 2026/5 ZRG1 BBBT-K (86), 2026/1 ZRG1 HSS-Y (10), 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: R01EY037701, R01HD120978, R01NS148533, 1R01NS140142, 1R01AG080624, 2UL1TR002384, 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), American Medical Informatics Association (AMIA), 2023

Mentoring

Hexing Dong, 2025-present
Xuan Zhong Feng, 2025-present
Aryan Kumar, 2026-present
Yi Lin, 2025-present
Will H. Lu, 2026-present
Haotian Ma, 2024-present
Geoffrey Martin, 2025-present
Max Lovitt, 2024, 2026
Jiahe Qian, 2025-present
Zhaolong Su, 2026-present
Yufan Wang, 2026-present
Yishu Wei, 2024-present
Kunyu Yu, 2025-present

Publications

Google Scholar

Journal articles

Wang Z, Chen Z, Yang Z, Wang X, Jin Q, Peng Y, Lu Z, Sun J. Empowering biomedical evidence exploration and synthesis with deep knowledge graph research. Nat Mach Intell. Published online July 2, 2026:1-15. doi: 10.1038/s42256-026-01266-0.
Wu L, Nie Y, He S, Zhuang J, Luo L, Li T, Xie Z, Chen D, Zhao Y, Mahboobani N, Vardhanabhuti V, Chan RCK, Peng Y, Rajpurkar P, Chen H. A universal foundation model for grounded biomedical image interpretation. Nat Commun. 2026 Jun 4. doi: 10.1038/s41467-026-73986-1. Epub ahead of print. PMID: 42243102.
Flanders AE, Peng Y, Prevedello L, Ball R, Colak E, Menon P, Shih G, Lin HM, Lakhani P. A multi-agent large language model framework to automatically assess performance of a clinical AI Triage tool. Npj Health Syst. 2026;3:35. doi: 10.1038/s44401-026-00100-4. Epub 2026 May 25. PMID: 42245913; PMCID: PMC13233039.
He S, Nie Y, Wang H, Yang S, Wang Y, Cai Z, Chen Z, Xu Y, Wu L, Cheng NS, Luo L, Xiang H, Lin X, Wu M, Peng Y, Shih G, Xu Z, Wu X, Wang Q, Chan RCK, Vardhanabhuti V, Duan X, Chu WCW, Zheng Y, Rajpurkar P, Zhang K, Chen H. Towards generalizable AI in medicine via Generalist-Specialist Collaboration. Nat Biomed Eng. 2026 May 1. doi: 10.1038/s41551-026-01653-3. Epub ahead of print. PMID: 42067582.
Wei Y, Lin Y, Flanders A, Shih G, Peng Y. Reinforcement learning improves LLM accuracy and reasoning in disease classification from radiology reports. NPJ Digit Med. 2026 Apr 30;9(1):515. doi: 10.1038/s41746-026-02685-4. PMID: 42062541; PMCID: PMC13338140.
Lin Y, Yang Y, Shih G, Peng Y. Rethinking Radiology AI Benchmarks. Radiol Adv. 2026 Apr 11;3(3):umag022. doi: 10.1093/radadv/umag022. PMID: 42131312; PMCID: PMC13163161.
Zhang G, Fang Y, Chen F, Ta C, Hripcsak G, Ryan P, Peng Y, Weng C. A neural-symbolic AI agent system for biomedical concept mapping. NPJ Digit Med. 2026 Apr 4;9(1):425. doi: 10.1038/s41746-026-02594-6. PMID: 41935204; PMCID: PMC13230558.
Fang Y, Zhang G, Chen F, Peng Y, Weng C. A critical evaluation of generative query expansion on biomedical literature retrieval. J Am Med Inform Assoc. 2026 Jun 1;33(6):1121-1133. doi: 10.1093/jamia/ocag037. PMID: 41921511; PMCID: PMC13197180.
Bian J, Peng Y, Mendonca E, Banerjee I, Xu H. Biomedical multimodal large language models: From model-centric development to clinically grounded evaluation and integration. J Biomed Inform. 2026 May;177:105023. doi: 10.1016/j.jbi.2026.105023. Epub 2026 Mar 26. PMID: 41903641; PMCID: PMC13329790.
Yang R, Li H, Heng Wong MY, Ke Y, Li X, Yu K, Liao J, Kai Liew JC, Nair SV, Ong JCL, Li I, Teodoro D, Hong C, Peng Y, Ting DSW, Liu N. The evolving landscape of large language models and non-large language models in health care. Npj Health Syst. 2026;3:22. doi: 10.1038/s44401-026-00076-1. Epub 2026 Mar 9. PMID: 41924194; PMCID: PMC13038296.
Song Y, Zhan Z, Xie F, Wang N, Peng Y, Zhang R, Lin M. A cancer-type-aware framework for robust multimodal survival prediction under missing modalities. Brief Bioinform. 2026 Mar 1;27(2):bbag124. doi: 10.1093/bib/bbag124. PMID: 41870128; PMCID: PMC13006980.
Deng R, Martin G, Wang T, Zhang G, Liu Y, Weng C, Wang Y, Rousseau JF, Peng Y. CPGPrompt: translating clinical guidelines into large language model-executable decision support. J Am Med Inform Assoc. 2026 Apr 1;33(4):855-862. doi: 10.1093/jamia/ocag026. PMID: 41746783; PMCID: PMC13089456.
Zhou Z, Deng Y, Liu L, Jiang H, Peng Y, Yang X, Zhao Y, Ning H, Allen NB, Wilkins JT, Liu K, Lloyd-Jones DM, Zhao L. Deep Neural Network With a Smooth Monotonic Output Layer for Dynamic Risk Prediction. Stat Med. 2026 Feb;45(3-5):e70401. doi: 10.1002/sim.70401. PMID: 41640287; PMCID: PMC12873558.
Xu Z, Lin M, Zhou Y, Xu Z, Orlow SJ, Meehan SA, Flamm A, Moshiri AS, Peng Y. Establishing dermatopathology encyclopedia DermpathNet with Artificial Intelligence-Based Workflow. Sci Data. 2026 Feb 6;13(1):368. doi: 10.1038/s41597-026-06715-4. PMID: 41651886; PMCID: PMC12987945.
Lei Y, Cao Y, Wang WK, Dong Y, Yin C, Cao W, Zhang P, Yang J, Yao B, Peng Y, Weng C, Auerbach R, Mamykina L, Wang D, Wang Y, Xu X. Watchguardian: Enabling user-defined personalized just-in-time intervention on smartwatch. ACM Trans. Comput. Healthcare. 2026 Jan. doi: 10.1145/3788689
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. 2026 Jan 1;33(1):67-78. doi: 10.1093/jamia/ocaf094. PMID: 40493530; PMCID: PMC12758468.
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:10.1109/JBHI.2025.3645076. doi: 10.1109/JBHI.2025.3645076. Epub ahead of print. PMID: 41406283; PMCID: PMC13030920.
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 Dec;172:104949. doi: 10.1016/j.jbi.2025.104949. Epub 2025 Nov 1. PMID: 41177243; PMCID: PMC12705189.
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.
Cheng J, Zhang Y, Zhang H, Peng Y, Lu M. An Interpretable Complex Knowledge Multi-Hop Reasoning Model for Predicting Synthetic Lethality in Human Cancers. IEEE Trans Comput Biol Bioinform. 2025 Nov-Dec;22(6):3386-3398. doi: 10.1109/TCBBIO.2025.3626526. PMID: 41150233.
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 Sep;169:104884. doi: 10.1016/j.jbi.2025.104884. Epub 2025 Jul 29. 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 Nov 18;101(1202):1239-1241. doi: 10.1093/postmj/qgaf095. Erratum in: Postgrad Med J. 2025 Nov 18;101(1202):1333. doi: 10.1093/postmj/qgaf158. PMID: 40577492; PMCID: PMC12624531.
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 RSNA News 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. Best of Radiology Advances 2025
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

Lin Y, Ding Y, Wu Y, Peng Y. MARCH: Multi-Agent Radiology Clinical Hierarchy for CT Report Generation. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers). 2026 Jul; 273-285. doi: 10.18653/v1/2026.acl-short.24.
Qureshi K, Martin G, Peng Y. Budget-aware routing for long clinical text. Findings of the Association for Computational Linguistics: ACL 2026. 2026 Jul; 42583-42598. doi: 10.18653/v1/2026.findings-acl.2114.
Ding Y, Luo S, Dai Y, Jiang Y, Li Z, Sun Q, Martin G, Liu W, Peng Y. A survey on MLLM-based visually rich document understanding: Methods, challenges, and emerging trends. Findings of the Association for Computational Linguistics: ACL 2026. 2026 Jul; 13319–13340. doi: 10.18653/v1/2026.findings-acl.652.
Zhang G, Peng Y, Weng C. Improving Retrieval-Augmented Generation without Taxonomy-based Error Categorization. Proc Conf Assoc Comput Linguist Meet. 2026 Jul;2026:155-165. doi: 10.18653/v1/2026.acl-short.14. PMID: 42382679; PMCID: PMC13317761.
Xu Z, Wang Z, Qian Z, Shi D, Tang F, Hu M, Su S, Zou X, Feng W, Mahapatra D, Peng Y, Lin M, Ge Z. Thinking in Uncertainty: Mitigating Hallucinations in MLRMs with Latent Entropy-Aware Decoding. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2026 Mar;2025:11064-11075.
Dong H, Lin Y, Zhou P, Feng XZ, Legasto AC, Lin M, Chen H, Yang Y, Shih G, Peng Y. OVERVIEW OF THE CXR-LT 2026 CHALLENGE: MULTI-CENTER LONG-TAILED AND ZERO SHOT CHEST X-RAY CLASSIFICATION. Proc IEEE Int Symp Biomed Imaging. 2026 Apr;2026:10.1109/isbi61048.2026.11515307. doi: 10.1109/isbi61048.2026.11515307. Epub 2026 May 20. PMID: 42222662; PMCID: PMC13220745.
Wu P, Dong H, Lin Y, Ding Y, Peng Y. Disease-Aware Dual-Stage Framework for Chest X-ray Report Generation. Proc AAAI Conf Artif Intell. 2026 Mar 14;40(40):33953-61. doi: 10.1609/aaai.v40i40.40688. Epub 2026 Mar 14. PMID: 41930268; PMCID: PMC13042579.
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. Mach Learn Med Imaging. 2026;16241:150-160. doi: 10.1007/978-3-032-09513-8_15. Epub 2026 Jan 2. PMID: 41527550; PMCID: PMC12790706.
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. Learn Longitud Med Images Data (2025). 2026;16184:91–101. doi: 10.1007/978-3-032-16128-4_9. Epub 2026 Apr 1. PMID: 42222134; PMCID: PMC13222103.
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. doi: 10.5281/zenodo.16875756.
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; PMCID: PMC12976955.
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; PMCID: PMC12976956.
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.

Preprint

Le D, Correa-Medero R, Tariq A, Joshi VP, Murlidhar F, Dong H, Peng Y, Shih G, Wang ZJ, Pannala R, Yano M, Banerjee I. From Routine Imaging to Risk Stratification: Multimodal Vision–Language Survival Modeling for Pancreatic Cancer. IEEE ICHI. 2026 Apr 8.
Jin Q, Wan N, Leaman R, Tian S, Wang Z, Yang Y, Wang Z, Xiong G, Lai P-T, Zhu Q, Hou B, Sarfo-Gyamfi M, Zhang G, Gilson A, Bhasuran B, He Z, Zhang A, Sun J, Weng C, Summers RM, Chen Q, Peng Y, Lu Z. Demystifying large language models for medicine: A primer. Nature Protocols. Published online November 20, 2024. doi: 10.48550/arXiv.2410.18856. PMID: 39801619. PMCID: PMC11722506.
Wang Z, Xu Z, Wei Y, Chary M, Peng Y. Curation and Extraction of Drug-Related Entities from Reddit Platform. IEEE ICHI. 2026 Apr 8.
Martin G, Feng XZ, Peng Y. Comparing LLM and Fine-Tuned Model Performance on NVDRS Circumstance Extraction with Varying Prompt Complexity. IEEE ICHI. 2026 May 21.
Dogan E, Yu K, Peng Y. Using reasoning LLMs to extract SDOH events from clinical notes. IEEE ICHI. 2026 Apr 15.
Wei Y, Flanders AE, Colak E, Mongan J, Prevedello LM, Chen PH, Lee HM, Szarf G, Shoji H, Sho J, Andriole K, Cook T, Adams LC, Chu LC, Chung M, Brusca-Augello G, Deva DP, Singh N, Tijmes FS, Alpert JB, Nguyen ET, Torigian DA, Hanneman K, Groner LK, Phan A, Islam A, Callejas MF, Teles GB da S, Jamal F, Vazirabad M, Tejani A, Trivedi H, Kuriki P, Bhayana R, Benishay ET, Lin Y, Peng Y, Shih G. RSNA Large Language Model Benchmark Dataset for Chest Radiographs of Cardiothoracic Disease: Radiologist Evaluation and Validation Enhanced by AI Labels (REVEAL-CXR). arXiv preprint arXiv:2601.15129. 2026 Jan 21. doi: 10.48550/arXiv.2601.15129.

Abstracts/Posters

Le D, Correa-Medero R, Tariq A, Joshi VP, Murlidhar F, Dong H, Peng Y, Shih G, Wang ZJ, Pannala R, Yano M, Banerjee I. Pre-diagnostic imaging and radiology report–based risk modeling for pancreatic ductal adenocarcinoma. J Clin Oncol. 2026;44:e16017. doi: 10.1200/JCO.2026.44.16_suppl.e16017.
Qureshi K, Martin G, Peng Y. Budget-Aware Routing for Long Clinical Text. AMIA Annual Symposium. 2026.
Wei Y, Dong H, Lin Y, Qian J, Liu Y, Peng Y. Optimizing LLMs for censoring-aware survival analysis. AMIA Annual Symposium. 2026.
Lin Y, Ding Y, Benishay E, Trikantzopoulos E, Nauheim D, Ong H, Bian J, Xu H, Yang Y, Shih G, Peng Y. MonteRET: AI agent enhancing multimodal LLMs with multi-granularity knowledge retrieval for chest CT report generation. AMIA Annual Symposium. 2026.
Ma H, Lin Y, Godschall E, Matuck B, Byrd K, Peng Y, Liu J. Understanding channel complementarity for multiplex cell segmentation. AMIA Annual Symposium. 2026.
Yang R, Li H, Wong MYH, Yu K, Li X, Liew JCK, Liao J, Peng Y, Teodoro D, Liu N. Evaluating large language models for global health. AMIA Annual Symposium. 2026.
Le D, Correa-Medero R, Tariq A, Peng Y, Shih G, Wang Z, Patel B, Yano M, Banerjee I. Prognostic modeling for pancreatic ductal adenocarcinoma using pre-diagnostic CT imaging, radiomic features, and free-text reports. RSNA. 2025.
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

Wu SW, Davatzikos C, Peng Y. Artificial Intelligence Research in Radiology: Team, Approach, and Direction. In: Wu S, Ko HS, Seng NY, eds. Clinical Artificial Intelligence in Radiology. American Roentgen Ray Society; 2026:146-151. ISBN: 978-1-890705-13-8.
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

Innovation and Precision Eye Health Webinar, National Univeristy of Singapore. 8/11/2026
SAPA Science and Career Symposium. 5/2/2026
UMass Lowell CS Colloquium. 4/17/2026
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 Speaker, 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