Contact Information
575 Lexington Ave RM 651
New York, NY 10022

Tel: +1 646-967-5117
yip4002@med.cornell.edu

Peng Lab
VIVO
Github

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)
• SYSEN 5630: Clinical Natural Language Processing and Large Language Models (2025)

Professional Activities

• Editorial Board: Journal of Biomedical Informatics (2023-2027)
• Section Editor: PLOS Digital Health (2023-present)
• Guest Editor: JAMIA (2023)
• Chair: HealthNLP 2023
• Area Chair: NeurIPS Track Datasets and Benchmarks (2021-present)
• Publication Chair: HealthNLP 2021
• Organizing Committee: Interpretable Machine Learning in Healthcare at ICML (2021-2023)
• Academic Editor: PLoS ONE (2018-2023)
• Senior Program Committee: IJCAI (2021), AMIA Informatics Summit (2023), AMIA Symposium (2023)
• Program Committee: ACL (2021-present), Clinical NLP Workshop (2020-present), MICCAI (2019-present), AAAI (2020-present), Workshop on NLP for Medical Conversations (NLPMC, 2021), Semantic Indexing and Information Retrieval for Health, 42nd European Conference on Information Retrieval (SIIRH-ECIR, 2020), BioNLP Workshop (2019-present), ICCV Visual Recognition for Medical Image Workshop (2019-2020), ICHI (2019-present), The IEEE International Conference on Biomedical and Health Informatics (ICBHI, 2016-2021), ACM-BCB (2015-present)
• Reviewer: ACM Transactions on Computing for Healthcare, AMIA, Artificial Intelligence in Medicine, Bioinformatics, BMC Bioinformatics, Computational Biology and Chemistry, Computer Methods and Programs in Biomedicine, Database (Oxford), IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE Journal of Biomedical and Health Informatics (JBHI), IEEE Transactions on Knowledge and Data Engineering, IEEE Transactions on Medical Imaging (TMI), IEEE Transactions on Neural Networks and Learning Systems, IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), Journal of Biomedical Informatics (JBI), Journal of Biomedical Semantics, Journal of Digital Imaging, Knowledge-Based Systems, Nature Communications, Nature Computational Science, Nature Medicine, Ophthalmology
• NIH Grant Reviewer: 2024/10 ZRG1 NV-P 81S, 2023/10 BDMA, 2023/10 ZNS1 SRB-S(15)1, ZAG1 ZIJ-4(C1), 2023/01 ZRG1 HSS-J(90S), 2020/10 ZAG1 ZIJ-7(O1),
• Swiss National Science Foundation (SNSF) Grant Reviewer: 2022

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)

Finished

Honors and Awards

• Fellow (FACMI), American College of Medical Informatics (ACMI), 2024
• AMIA New Investigator Award, 2023
• Fellow (FAMIA), AMIA, 2023
• NIH Fellows Award for Research Excellence (FARE), NIH, 2020
• NIH National Library of Medicine Honor Awards, NIH, 2019
• NIH Summer Research Mentor Award, NIH, 2019
• NIH National Library of Medicine Honor Awards, NIH, 2018
• NIH Clinical Center CEO Awards, NIH, 2017
• NIH Employee Awards, NIH, 2016-2018
• CHEMPROT-Elsevier Prize, BioCreative VI, 2017
• BioCreative Workshop Travel Award, 2015
• Professional Development Award, University of Delaware, 2015
• Graduate Student Fellowship, Peking University, 2007-2009
• Intel Fellowship, 2007
• Graduation Honors, Beijing Municipal Education Commission, 2007
• Excellent Student Award, Beijing University of Technology, 2004-2006

Mentoring

• Kelly Deng, Specialization project, 2024-present
• Haotian Ma, Research Assistant, 2024-present
• Cong Sun, Postdoc Associate, 2023-present
• Song Wang, PhD student at UT Austin, 2020-present
• Yishu Wei, Postdoc Associate, 2024-present
• Puzhen Wu, Research Assistant, 2024-present
• Zihan Xu, Research Assistant, 2024-present
• Jingze Zhang, Research Assistant, 2024-present

Past Lab Members

Publications

* co-first author. Google Scholar

Journal articles

• 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.
• 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. Epub ahead of print. PMID: 39166973.
• 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.
• 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.
• 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.
• 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 ahead of print. PMID: 38850624.
• 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. Epub ahead of print. 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.

Other journal articles

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.

Other conference proceedings

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.
• 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.
• Teran F, Peng Y, 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 K, 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, Andrus P, Razzak J, Palasz J, Kaviyarasu A, Sands NA, Lin M, Abella BS. Deep Learning Detection of Chest Compression Location Using Transesophageal Echocardiography. Circulation. 2023 Nov 6;148(Suppl_1):A349-A349. doi: 10.1161/circ.148.suppl_1.349
• Holste G, Wang S, Jiang Z, Shen TC, Shih G, Summers RM, Peng Y*, Wang Z*. Long-Tailed Classification of Thorax Diseases on Chest X-Ray. In RSNA. 2022. (poster).
• Wang S, Tang L, Majety A, Rousseau JF, Shih G, Ding Y, Peng Y. Prompt-based Learning for Assertion Classification in Clinical Notes. In AMIA 2022 Annual Symposium. 2022. (poster)
• Lee J, Wangyan T, Chen Q, Chen Q, Keenan TD, Chew E, Lu Z, Wang F, Peng Y. Predicting 2-year and 5-year Late AMD Progression using Deep Learning with Longitudinal Fundus Images. In Investigative Ophthalmology & Visual Science. 2022;63, 3003 - F0273. (poster)
• Ghahramani GC, Brendel M, Chen Q, Keenan TD, Chen K, Chew E, Lu Z, Peng Y*, Wang F*. Deep learning survival analysis on the progression to late AMD in the Age-Related Eye Disease Study. In Investigative Ophthalmology & Visual Science. 2021 June;62(8):92. (talk)
• Chen Q, Keenan TD, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT, Chew E, Lu Z. Detection of reticular pseudodrusen using deep learning. In AMIA 2020 Annual Symposium. 2020. (talk)
• Keenan TD, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT, Lu Z, Chew E. Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images and color fundus photographs in the Age-Related Eye Disease Study 2 (AREDS2). In Investigative Ophthalmology & Visual Science. 2020 June;61(7):1644. (talk)
• Peng Y, Keenan T, Chen Q, Agrón E, Wong W, Chew E, Lu Z. A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs. In AMIA 2019 Annual Symposium. 2019. (talk)
• Yan K, Peng Y, Standfort V, Bagheri M, Lu Z, Summers RM. Comprehensive Lesion Tagging on Diverse CT Images: Learning from Radiology Reports and Label Ontology. In RSNA Annual Meeting. 2019. (talk)
• Yan K, Tang Y, Peng Y, Standfort V, Bagheri M, Lu Z, Summers RM. MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation in CT Images. In RSNA Annual Meeting. 2019. (talk)
• Keenan TD, Peng Y, Chen Q, Agrón E, Wong WT, Lu Z, Chew EY. Deep learning prediction of progression to late age-related macular degeneration in the Age-Related Eye Disease Study (AREDS) using deep feature extraction and survival analysis. In Investigative Ophthalmology & Visual Science. 2019 July;60(9):1491. (poster)
• Phan L, Ward M, Allot A, Peng Y, Wei CH, Lee K, Lu Z, Wang J, Youkharibache P, Zhang D, Lanczycki C, Geer L, Geer R, Marchler-Bauer A, Madej T, Lu S, Marchler G, Wang Y, Bryant S, Rose P, Holmes JB, Kattman BL. Integrative Analyses of dbSNP For Variant Prioritization and Interpretation. In Biological Data Science. 2018.
• Wei CH, Phan L, Allot A, Peng Y, Lee K, Maiti R, Hefferon T, Feltz J, Lu Z. Literature Mining to Improve the Prioritization, Curation, and Integration of Knowledge for Clinically Relevant Variants. In ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). 2018. (talk)
• Dharssi S, Peng Y, Leaman R, Chew EY, Lu Z. Discovering drug and retinal disease association patterns from electronic medical records: a text mining approach. Investigative Ophthalmology & Visual Science. 2018, 59(9), 4149. (ARVO E-Abstract 2924709)
• Wang X, Peng Y, Lu L, Bagheri M, Lu Z, Summers RM. Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiograph. In RSNA Annual Meeting. 2018. (talk)
• Dharssi S*, Peng Y*, Chen Q, Agron E, Wong W, Chew E, Lu Z. A Deep Learning Approach for Automated Detection and Quantification of Geographic Atrophy from Color Fundus Photographs. In AAO 2018. 2018. (talk)
• Wei CH, Phan L, Allot A, Peng Y, Lee K, Maiti R, Hefferon T, Feltz J, Lu Z. Literature Mining to Improve the Prioritization, Curation, and Integration of Knowledge for Clinically Relevant Variants. In ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). 2018. (talk)
• Allot A, Peng Y, Wei CH, Lee K, Phan L, Lu Z. A semantic search engine for linking genomic variant data in PubMed and PMC. In International Society for Computational Biology. 2018. (poster)
• Peng Y, Wang X, Lu L, Bagheri M, Summers R, Lu Z. Text mining radiology reports for deep learning radiology images. In AMIA 2017 Annual Symposium. 2017, 157-158. (talk)
• Arighi C, Ding R, Gupta S, Li G, Mahmood AA, Peng Y, Ren J, Ross K, Tudor CO, Huang H, Schimidt C, Wu CH, Vijay-Shanker K. Text mining tools for biocuration in iProLINK web portal. In Biocuration. 2015. (poster)

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
• University of Washington. 12/7/2023.
• Columbia University. 11/20/2023.
• Univeristy of Delaware. 9/25/2023.
• Health Day @ The Web Conference 2023. 5/1/2023.
• University of Hong Kong (HKU). 4/26/2023.
• University of Minnesota Twin Cities. 12/14/2022.
• Virginia Commonwealth University. 5/6/2022.
• NSF EPSCoR Workshop on Artificial Intelligence & NBT. 4/3/2022.
• NIC-ASA and ICSA Midwest Chapter Joint Fall Meeting. 10/22/2021.
• AIME tutorial on Methods and Applications of Natural Language Processing in Medicine (AIME'20). 8/25/2020.
• MICCAI tutorial on Medical Informatics in Medical Image Analytics (MIMIA'19). 10/18/2019.
• NIH.AI Workshop on Natural Language Processing. 05/09/2019.
• NCI Center for Biomedical Informatics and Information Technology (CBIIT) Cancer Data Science workshop. 01/24/2019.
• ICSA 2018 Applied Statistics Symposium. 06/17/2018.
• Computer and Information Science Department, University of Delaware. 06/25/2018.
• NIH-CSSA Symposium. 06/02/2017.
• ABCC-Imaging and Visualization Group, Frederick National Laboratory for Cancer Research. 06/23/2017.