Publications

Holste G, Jiang Z, Jaiswal A, Hanna M, Minkowitz S, Legasto AC, Escalon JG, Steinberger S, Bittman M, Shen TC et al..  2023.  How Does Pruning Impact Long-Tailed Multi-label Medical Image Classifiers? Med Image Comput Comput Assist Interv. 14224:663-673.

He S, Nie Y, Wang H, Yang S, Wang Y, Cai Z, Chen Z, Xu Y, Wu L, Cheng NShing et al..  2026.  Towards generalizable AI in medicine via Generalist-Specialist Collaboration.. Nat Biomed Eng.

He X, Zhang R, Alpert J, Zhou S, Adam TJ, Raisa A, Peng Y, Zhang H, Guo Y, Bian J.  2021.  When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information? JAMIA Open. 4(1):ooab026.

Han Y, Chen C, Tewfik A, Glicksberg B, Ding Y, Peng Y, Wang Z.  2022.  Knowledge-Augmented Contrastive Learning for Abnormality Classification and Localization in Chest X-rays with Radiomics using a Feedback Loop.. IEEE Winter Conf Appl Comput Vis. 2022:1789-1798.

Han Y, Holste G, Ding Y, Tewfik A, Peng Y, Wang Z.  2022.  Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays.. IEEE Trans Med Imaging. PP

Han Y, Chen C, Tewfik AH, Ding Y, Peng Y.  2021.  Pneumonia Detection on Chest X-ray using Radiomic Features and Contrastive Learning. IEEE International Symposium on Biomedical Imaging (ISBI).

Han Y, Chen C, Tang L, Lin M, Jaiswal A, Wang S, Tewfik A, Shih G, Ding Y, Peng Y.  2021.  Using Radiomics as Prior Knowledge for Thorax Disease Classification and Localization in Chest X-rays.. AMIA Annu Symp Proc. 2021:546-555.

Han Z, Shen M, Liu H, Peng Y.  2022.  Topical and emotional expressions regarding extreme weather disasters on social media: a comparison of posts from official media and the public.. Humanit Soc Sci Commun. 9(1):421.

Ghahramani G, Brendel M, Lin M, Chen Q, Keenan T, Chen K, Chew E, Lu Z, Peng Y, Wang F.  2021.  Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.. AMIA Annu Symp Proc. 2021:506-515.

Ghahramani GC, Brendel M, Chen Q, Keenan TD, Chen K, Chew EY, Lu Z, Peng Y, Wang F.  2021.  Deep learning survival analysis on the progression to late AMD in the Age-Related Eye Disease Study. Investigative Ophthalmology & Visual Science.

Gautam N, Elhusseiny A, Mansour M, Mehta JL, Andersen OS, Peng Y, Al'Aref SJ.  2025.  Exploring the feasibility of using artificial intelligence to simulate the placebo arm of randomized clinical trials.. Postgrad Med J.

Flanders AE, Peng Y, Prevedello L, Ball R, Colak E, Menon P, Shih G, Lin H-M, Lakhani P.  2026.  A multi-agent large language model framework to automatically assess performance of a clinical AI Triage tool.. Npj Health Syst. 3

Flanders AE, Wang X, Wu CC, Kitamura FC, Shih G, Mongan J, Peng Y.  2025.  The Evolution of Radiology Image Annotation in the Era of Large Language Models.. Radiol Artif Intell. 7(4):e240631.

Fang Y, Zhang G, Chen F, Peng Y, Weng C.  2026.  A critical evaluation of generative query expansion on biomedical literature retrieval.. J Am Med Inform Assoc. 33(6):1121-1133.

Fang Y, Zhang G, Chen F, Hripcsak G, Peng Y, Ryan P, Weng C.  2025.  CLEAR: A vision to support clinical evidence lifecycle with continuous learning.. J Biomed Inform. 169:104884.

Du J, Chen Q, Peng Y, Xiang Y, Tao C, Lu Z.  2019.  ML-Net: multi-label classification of biomedical texts with deep neural networks. J Am Med Inform Assoc. 26(11):1279-1285.

Dong H, Lin Y, Zhou P, Feng XZhong, Legasto AClint, Lin M, Chen H, Yang Y, Shih G, Peng Y.  2026.  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

Doğan RIslamaj, Chatr-aryamontri A, Kim S, Wei C-H, Peng Y, Comeau D, Lu Z.  2017.  BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017. :171–175.

Deng R, Martin G, Wang T, Zhang G, Liu Y, Weng C, Wang Y, Rousseau JF, Peng Y.  2026.  CPGPrompt: translating clinical guidelines into large language model-executable decision support.. J Am Med Inform Assoc.

Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J et al..  2023.  Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction.. BMC Med Res Methodol. 23(1):22.

Consoli B, Wang H, Wu X, Wang S, Zhao X, Wang Y, Rousseau J, Hartvigsen T, Shen L, Wu H et al..  2025.  SDoH-GPT: using large language models to extract social determinants of health.. J Am Med Inform Assoc.

Comeau DC, Doğan RIslamaj, Ciccarese P, Cohen KBretonnel, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M et al..  2013.  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013:bat064.

Comeau DC, Batista-Navarro RTheresa, Dai H-J, Doğan RIslamaj, Yepes AJimeno, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M et al..  2014.  BioC interoperability track overview. Database (Oxford). 2014

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM et al..  2018.  Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 15(141)

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.