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

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

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

R01LM014573, NIH/NLM, PI (2024-2029)
R01CA289249, NIH/NCI, MPI (2024-2029)
R01LM014306, NIH/NLM, PI (2023-2028), Public Press Release
R01LM014344, NIH/NLM, MPI (2023-2028)
R21EY035296, NIH/NEI, PI (2023-2025)
AIM-AHEAD OT2OD032581, MPI (2023-2025), Public Press Release
2306556, NSF Smart and Connected Health, NSF, co-I (2023-2027)
2145640, NSF CAREER Award, PI (2022-2026)
75N92020D00021, NIBIB, co-I (2024-present)
1OT2HL161847, NIH/NHLBI, co-I (2021-2025)
1R01AG080624, NIH/NIA, co-I (2023-2026)
2UL1TR002384-06, NIH/NCATS, co-I (2023-2027)
ME-2020C3-21199, Eugene Washington PCORI Engagement Award, site PI (2024)

Honors and Awards

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

Mentoring

Kelly Deng, 2024-present
Haotian Ma, 2024-present
Geoffrey Martin, 2025-present
Jiahe Qian, 2025-present
Cong Sun, 2023-present
Song Wang, 2020-present
Yishu Wei, 2024-present
Puzhen Wu, 2024-present
Jingze Zhang, 2024-present

Publications

* co-first author. Google Scholar

Journal articles

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 May 13:104848. doi: 10.1016/j.jbi.2025.104848. Epub ahead of print. 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 Apr 30:e240631. doi: 10.1148/ryai.240631. Epub ahead of print. PMID: 40304582.
Peng Y, Chen Q, Shih G. DeepSeek is open-access and the next AI disrupter for radiology. Radiology Advances. Published online February 18, 2025. doi: 10.1093/radadv/umaf009.
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 Feb 25:ocaf029. doi: 10.1093/jamia/ocaf029. Epub ahead of print. PMID: 39998912.
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 Feb 10:104791. doi: 10.1016/j.jbi.2025.104791. Epub ahead of print. PMID: 39938624.
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 Jan 17:ocae326. doi: 10.1093/jamia/ocae326. Epub ahead of print. PMID: 39823371.
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.
Su L, Chen J, Peng Y, Sun C. Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension. J Biomed Inform. 2024 Oct 25:104739. doi: 10.1016/j.jbi.2024.104739. Epub ahead of print. PMID: 39490610.
Wang S, Zhou Y, Han Z, Tao C, Xiao Y, Ding Y, Ghosh J, Peng Y. A natural language processing approach to detect inconsistencies in death investigation notes attributing suicide circumstances. Commun Med (Lond). 2024 Oct 14;4(1):199. doi: 10.1038/s43856-024-00631-7. PMID: 39397053; PMCID: PMC11471859.
Teran F, Owyang CG, Wray TC, Hipskind JE, Lessard J, Bédard Michel W, Lanthier C, Nazerian P, de Villa E, Nogueira J, Doynow D, Clinton M, Myslik F, Prager R, Arntfield R, Salinas PD, Dieiev V, Woo MY, Thavanathan R, Puskas G, Singh K, Bhat P, Horn J, Buchanan BM, Baig N, Burns KM, Kennedy K, Haines L, Naraghi L, Singh H, Secko M, Singer D, Taylor M, Joyce JM, DeMasi S, Jafry ZM, Phan T, Truong N, Robinson E, Haycock KH, Hansen A, Derr C, West FM, Narasimhan M, Horowitz J, Usman A, Anderson KL, Peng Y, Rola P, Andrus P, Razzak J, Hemmings HC, Panchamia R, Palasz J, Kaviyarasu A, Sands NA, Sutton RM, Abella BS; Resuscitative TEE Collaborative Registry (rTEECoRe) Investigators. Development and Implementation of a Multicenter Registry for Resuscitation-Focused Transesophageal Echocardiography. Ann Emerg Med. 2024 Oct 15:S0196-0644(24)00448-7. doi: 10.1016/j.annemergmed.2024.08.004. Epub ahead of print. PMID: 39412464.
Tam TYC, Sivarajkumar S, Kapoor S, Stolyar AV, Polanska K, McCarthy KR, Osterhoudt H, Wu X, Visweswaran S, Fu S, Mathur P, Cacciamani GE, Sun C, Peng Y, Wang Y. A framework for human evaluation of large language models in healthcare derived from literature review. NPJ Digit Med. 2024 Sep 28;7(1):258. doi: 10.1038/s41746-024-01258-7. PMID: 39333376; PMCID: PMC11437138.
Zhang G, Jin Q, Zhou Y, Wang S, Idnay B, Luo Y, Park E, Nestor JG, Spotnitz ME, Soroush A, Campion TR Jr, Lu Z, Weng C, Peng Y. Closing the gap between open source and commercial large language models for medical evidence summarization. NPJ Digit Med. 2024 Sep 9;7(1):239. doi: 10.1038/s41746-024-01239-w. PMID: 39251804; PMCID: PMC11383939.
Lin M, Li T, Sun Z, Holste G, Ding Y, Wang F, Shih G, Peng Y. Fairness of Automated Chest Radiograph Diagnosis by Contrastive Learning. Radiol Artif Intell. 2024 Aug 21:e230342. doi: 10.1148/ryai.230342. PMID: 39166973; PMCID: PMC11449211.
Lu Z, Peng Y, Cohen T, Ghassemi M, Weng C, Tian S. Large language models in biomedicine and health: current research landscape and future directions. J Am Med Inform Assoc. 2024 Sep 1;31(9):1801-1811. doi: 10.1093/jamia/ocae202. PMID: 39169867; PMCID: PMC11339542.
Holste G, Lin M, Zhou R, Wang F, Liu L, Yan Q, Van Tassel SH, Kovacs K, Chew EY, Lu Z, Wang Z, Peng Y. Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. NPJ Digit Med. 2024 Aug 16;7(1):216. doi: 10.1038/s41746-024-01207-4. PMID: 39152209; PMCID: PMC11329720.
Jin Q, Chen F, Zhou Y, Xu Z, Cheung JM, Chen R, Summers RM, Rousseau JF, Ni P, Landsman MJ, Baxter SL, Al'Aref SJ, Li Y, Chen A, Brejt JA, Chiang MF, Peng Y, Lu Z. Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. NPJ Digit Med. 2024 Jul 23;7(1):190. doi: 10.1038/s41746-024-01185-7. PMID: 39043988; PMCID: PMC11266508.
Holste G, Zhou Y, Wang S, Jaiswal A, Lin M, Zhuge S, Yang Y, Kim D, Nguyen-Mau TH, Tran MT, Jeong J, Park W, Ryu J, Hong F, Verma A, Yamagishi Y, Kim C, Seo H, Kang M, Celi LA, Lu Z, Summers RM, Shih G, Wang Z, Peng Y. Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. Med Image Anal. 2024 May 31;97:103224. doi: 10.1016/j.media.2024.103224. Epub 2024 May 31. PMID: 38850624; PMCID: PMC11365790.
Wei Y, Deng Y, Sun C, Lin M, Jiang H, Peng Y. Deep learning with noisy labels in medical prediction problems: a scoping review. J Am Med Inform Assoc. 2024 Jun 20;31(7):1596-1607. doi: 10.1093/jamia/ocae108. PMID: 38814164; PMCID: PMC11187424.
Zhou Y, Ong H, Kennedy P, Wu CC, Kazam J, Hentel K, Flanders A, Shih G, Peng Y. GPT-4V (GPT-4 with Vision) on Detection of Radiologic Findings on Chest Radiographs. Radiology. 2024 May;311(2):e233270. doi: 10.1148/radiol.233270. PMID: 38713028.
Yang Y, Lin M, Zhao H, Peng Y, Huang F, Lu Z. A survey of recent methods for addressing AI fairness and bias in biomedicine. J Biomed Inform. 2024 Jun;154:104646. doi: 10.1016/j.jbi.2024.104646. Epub 2024 Apr 25. PMID: 38677633; PMCID: PMC11129918.
Zhang G, Jin Q, Jered McInerney D, Chen Y, Wang F, Cole CL, Yang Q, Wang Y, Malin BA, Peleg M, Wallace BC, Lu Z, Weng C, Peng Y. Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness. J Biomed Inform. 2024 May;153:104640. doi: 10.1016/j.jbi.2024.104640. Epub 2024 Apr 10. PMID: 38608915; PMCID: PMC11217921.
Zhang G, Zhou Y, Hu Y, Xu H, Weng C, Peng Y. A span-based model for extracting overlapping PICO entities from RCT publications. J Am Med Inform Assoc. 2024 Apr 19;31(5):1163-1171. doi: 10.1093/jamia/ocae065. PMID: 38471120; PMCID: PMC11031223.
Xiao Y, Bi K, Yip PS, Cerel J, Brown TT, Peng Y, Pathak J, Mann JJ. Decoding Suicide Decedent Profiles and Signs of Suicidal Intent Using Latent Class Analysis. JAMA Psychiatry. 2024 Mar 20. doi: 10.1001/jamapsychiatry.2024.0171. PMID: 38506817; PMCID: PMC10955339.
Liu H, Soroush A, Nestor JG, Park E, Idnay B, Fang Y, Pan J, Liao S, Bernard M, Peng Y, Weng C. Retrieval augmented scientific claim verification. JAMIA Open. 2024 Feb 21;7(1):ooae021. doi: 10.1093/jamiaopen/ooae021. PMID: 38455840; PMCID: PMC10919922.
Yu Z, Peng C, Yang X, Dang C, Adekkanattu P, Gopal Patra B, Peng Y, Pathak J, Wilson DL, Chang CY, Lo-Ciganic WH, George TJ, Hogan WR, Guo Y, Bian J, Wu Y. Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias. J Biomed Inform. 2024 May;153:104642. doi: 10.1016/j.jbi.2024.104642. Epub 2024 Apr 14. PMID: 38621641; PMCID: PMC11141428.
Zhou R, Miller JP, Gordon M, Kass M, Lin M, Peng Y, Li F, Feng J, Liu L. Deep learning models to predict primary open-angle glaucoma. Stat (Int Stat Inst). 2024;13(1):e649. doi: 10.1002/sta4.649. Epub 2024 Feb 7. PMID: 39220673; PMCID: PMC11364364.

Conference proceedings

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 2025 Informatics Summit. 2025.
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 2025 Informatics Summit. 2025.
Lovitt M, Ma H, Wang S, Peng Y. Suicide Risk Assessment on Social Media with Semi-Supervised Learning. Proc IEEE Int Conf Big Data. 2024 Dec;2024:8541-8549. doi: 10.1109/bigdata62323.2024.10825422. PMID: 39896202; PMCID: PMC11786971.
Xu RL, Wang S, Wang Z, Zhang Y, Xiao Y, Pathak J, Hodge D, Leng Y, Watkins SC, Ding Y, Peng Y. Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups. Proc (IEEE Int Conf Healthc Inform). 2024 Jun;2024:189-199. doi: 10.1109/ichi61247.2024.00032. Epub 2024 Aug 22. PMID: 39372906; PMCID: PMC11450796.
Leng H, Deng R, Bao S, Fang D, Millis BA, Tang Y, Yang H, Wang X, Peng Y, Wan L, Huo Y. High-performance data management for whole slide image analysis in digital pathology. In Proc. SPIE 12933, Medical Imaging 2024: Digital and Computational Pathology. 2024 Apr;12933:238-244. doi: 10.1117/12.3006273.

Abstracts

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 Prediction of late stage AMD based on deep learning models using multimodal AREDS data. Investigative Ophthalmology & Visual Science. 2024 Jun 17;65(7):OD50.
Xu Z, Lin M, Zhou Y, Xu Z, Orlow S, Meehan S, Flamm A, Moshiri A, Peng Y. Establishment of dermatopathology image encyclopedia DermpathNet using Artificial Intelligence Empowered Workflow. ASDP 61st Annual Meeting. 2024 Nov 4.
Zhang Q, Yan Q, Peng Y, Lin M, Schuman JS, Haller JA, Chew EY. Prediction of late stage AMD based on deep learning models using multimodal AREDS data. Investigative Ophthalmology & Visual Science. 2024 Jun 17;65(7):OD50.

Book chapters

Peng Y, Chen Q, Keenan TDL, Chew EL, Lu Z. Artificial Intelligence in Age-Related Macular Degeneration (AMD). Artificial Intelligence in Ophthalmology. Grzybowski A. (eds.). Springer, Cham. 2021, 101-112. doi:10.1016/10.1007/978-3-030-78601-4_8.
Peng Y, Zhang Z, Wang X, Yang L, Lu L. Text Mining and Deep Learning for Disease Classification. Handbook of Medical Image Computing and Computer Assisted Intervention. Zhou et al. (eds.). Elsevier. 2019, 109-136. doi:10.1016/B978-0-12-816176-0.00010-7.
Wang X, Peng Y, Lu L, Lu Z, Summers RM. ChestX-ray: Hospital-Scale Chest X-ray Database and Benchmarks on Weakly Supervised Classification and Localization of Common Thorax Diseases. Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Lu et al. (eds.). Springer. 2019, 369-392. doi:10.1007/978-3-030-13969-8_18.
Wang X, Peng Y, Lu L, Lu Z, Summers RM. Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiographs. Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Lu et al. (eds.). Springer. 2019, 393-412. doi:10.1007/978-3-030-13969-8_19.

Patents

Chew E, Lu Z, Lenaghan D, Tiarnan K, Wong WT, Peng Y, Chen Q, Agrón E, inventors; The United States of America, as represented by the Secretary, Dept. of Health, assignee. METHODS AND SYSTEMS FOR PREDICTING RATES OF PROGRESSION OF AGE-RELATED MACULAR DEGENERATION. United States patent application US 17/904,573. 2023 Mar 23.
Wang X, Peng Y, Lu L, Bagheri M, Lu Z, Summers R. Method and system of building hospital-scale chest x-ray database for entity extraction and weakly-supervised classification and localization of common thorax diseases. WO2018176035A1, filed 03/24/2017

Talks

BMI Seminar Series, Ohio State University College of Medicine. 2/14/2025
PQHS Research Methods Meetings, UMass Chan Medical School. 2/6/2025
2nd TAI4H workshop, IJCAI 2024
Statistical Methods in Imaging Conference. 5/31/2024
Machine Learning in Medicine Seminar, Boston Univ/Univ Toronto/Univ Pitt/. 4/19/2024
Public Health Coalition Research Symposium, UT Austin. 4/1/2024