Publications

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.

Tong J, Luo C, Sun Y, Duan R, Saine E, Lin L, Peng Y, Lu Y, Batra A, Pan A et al..  2023.  Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints.. J Am Med Inform Assoc.

Peng Y, Tang Y, Lee S, Zhu Y, Summers RM, Lu Z.  2021.  COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature. IEEE Transactions on Big Data. 7(1):3-12.

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.

Xiao Y, Bi K, Yip PSiu-Fai, Cerel J, Brown TT, Peng Y, Pathak J, J Mann J.  2024.  Decoding Suicide Decedent Profiles and Signs of Suicidal Intent Using Latent Class Analysis.. JAMA Psychiatry. 81(6):595-605.

Keenan TDL, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT et al..  2020.  Deep Learning Automated Detection of Reticular Pseudodrusen from Fundus Autofluorescence Images or Color Fundus Photographs in AREDS2. Ophthalmology.

Wei Y, Deng Y, Sun C, Lin M, Jiang H, Peng Y.  2024.  Deep learning with noisy labels in medical prediction problems: a scoping review.. J Am Med Inform Assoc. 31(7):1596-1607.

Su L, Chen J, Peng Y, Sun C.  2024.  Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension.. J Biomed Inform. 159:104739.

Brandt PS, Pacheco JA, Adekkanattu P, Sholle ET, Abedian S, Stone DJ, Knaack DM, Xu J, Xu Z, Peng Y et al..  2022.  Design and validation of a FHIR-based EHR-driven phenotyping toolbox.. J Am Med Inform Assoc. 29(9):1449-1460.

Teran F, Owyang CG, Wray TC, Hipskind JE, Lessard J, Michel WBédard, Lanthier C, Nazerian P, de Villa E, Nogueira J et al..  2025.  Development and Implementation of a Multicenter Registry for Resuscitation-Focused Transesophageal Echocardiography.. Ann Emerg Med. 85(2):147-162.

Tang L, Kooragayalu S, Wang Y, Ding Y, Durrett G, Rousseau JF, Peng Y.  2022.  EchoGen: A New Benchmark Study on Generating Conclusions from Echocardiogram Notes.. Proc Conf Assoc Comput Linguist Meet. 2022:359-368.

Lin M, Wang S, Ding Y, Zhao L, Wang F, Peng Y.  2025.  An empirical study of using radiology reports and images to improve intensive care unit mortality prediction.. JAMIA Open. 8(1):ooae137.

Lin M, Hou B, Mishra S, Yao T, Huo Y, Yang Q, Wang F, Shih G, Peng Y.  2023.  Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access.. Comput Biol Med. 159:106962.

Idnay B, Xu Z, Adams WG, Adibuzzaman M, Anderson NR, Bahroos N, Bell DS, Bumgardner C, Campion T, Castro M et al..  2025.  Environment scan of generative AI infrastructure for clinical and translational science.. Npj Health Syst. 2(1):4.

Lin M, Xiao Y, Hou B, Wanyan T, Sharma MManoj, Wang Z, Wang F, Van Tassel S, Peng Y.  2023.  Evaluate underdiagnosis and overdiagnosis bias of deep learning model on primary open-angle glaucoma diagnosis in under-served populations.. AMIA Jt Summits Transl Sci Proc. 2023:370-377.

Sun Z, Ong H, Kennedy P, Tang L, Chen S, Elias J, Lucas E, Shih G, Peng Y.  2023.  Evaluating GPT4 on Impressions Generation in Radiology Reports.. Radiology. 307(5):e231259.

Zhou Y, Ong H, Kennedy P, Wu CC, Kazam J, Hentel K, Flanders A, Shih G, Peng Y.  2024.  Evaluating GPT-V4 (GPT-4 with Vision) on Detection of Radiologic Findings on Chest Radiographs.. Radiology. 311(2):e233270.

Tang L, Sun Z, Idnay B, Nestor JG, Soroush A, Elias PA, Xu Z, Ding Y, Durrett G, Rousseau JF et al..  2023.  Evaluating large language models on medical evidence summarization.. NPJ Digit Med. 6(1):158.

Kang T, Sun Y, Kim JHyun, Ta C, Perotte A, Schiffer K, Wu M, Zhao Y, Moustafa-Fahmy N, Peng Y et al..  2023.  EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension.. J Am Med Inform Assoc.

Peng Y, Rios A, Kavuluru R, Lu Z.  2018.  Extracting chemical-protein relations with ensembles of SVM and deep learning models. Database (Oxford). 2018

Moukheiber D, Mahindre S, Moukheiber L, Moukheiber M, Wang S, Ma C, Shih G, Peng Y, Gao M.  2022.  Few-Shot Learning Geometric Ensemble for Multi-label Classification of Chest X-Rays.. Data Augment Label Imperfections (2022). 13567:112-122.

Tam TYu Chow, Sivarajkumar S, Kapoor S, Stolyar AV, Polanska K, McCarthy KR, Osterhoudt H, Wu X, Visweswaran S, Fu S et al..  2024.  A framework for human evaluation of large language models in healthcare derived from literature review.. NPJ Digit Med. 7(1):258.

Peng Y, Malin BA, Rousseau JF, Wang Y, Xu Z, Xu X, Weng C, Bian J.  2025.  From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare.. J Biomed Inform. 163:104791.

Peng Y, Torii M, Wu CH, Vijay-Shanker K.  2014.  A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems. BMC Bioinformatics. 15:285.

Paul A, Shen TC, Lee S, Balachandar N, Peng Y, Lu Z, Summers RM.  2021.  Generalized Zero-shot Chest X-ray Diagnosis through Trait-Guided Multi-view Semantic Embedding with Self-training.. IEEE Trans Med Imaging.