Publications

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.

Zhang G, Jin Q, Zhou Y, Wang S, Idnay B, Luo Y, Park E, Nestor JG, Spotnitz ME, Soroush A et al..  2024.  Closing the gap between open source and commercial large language models for medical evidence summarization.. NPJ Digit Med. 7(1):239.

Paul A, Shen TC, Balachandar N, Tang Y, Peng Y, Lu Z, Summers RM.  2020.  COMe-SEE: Cross-modality Semantic Embedding Ensemble for Generalized Zero-Shot Diagnosis of Chest Radiographs. Procceddings of the Workshop on Medical Image Learning with Less Labels and Imperfect Data (MIL3ID). :103-111.

Xu J, Wang F, Zang C, Zhang H, Niotis K, Liberman AL, Stonnington CM, Ishii M, Adekkanattu P, Luo Y et al..  2023.  Comparing the effects of four common drug classes on the progression of mild cognitive impairment to dementia using electronic health records.. Sci Rep. 13(1):8102.

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  Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints..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.

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.

Karabulut MEfruz, Vijay-Shanker K., Peng Y.  2021.  CU-UD: text-mining drug and chemical-proteininteractions with ensembles of BERT-based models. BioCreative VII. :45-48.

Lin M, Holste G, Wang S, Zhou Y, Wei Y, Banerjee I, Chen P, Dai T, Du Y, Dvornek NC et al..  2025.  CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray.. Med Image Anal. 106:103739.

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.

Keenan TDL, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat ATherese, Lee DHana, Li D, Wong WT et al..  2020.  Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images and color fundus photographs in the Age-Related Eye Disease Study 2 (AREDS2) . Investigative Ophthalmology & Visual Science. 61:1644.

Peng Y, Lu Z.  2017.  Deep learning for extracting protein-protein interactions from biomedical literature. BioNLP 2017. :29–38.

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.

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.

Zhou Z, Deng Y, Liu L, Jiang H, Peng Y, Yang X, Zhao Y, Ning H, Allen NB, Wilkins JT et al..  2026.  Deep Neural Network With a Smooth Monotonic Output Layer for Dynamic Risk Prediction.. Stat Med. 45(3-5):e70401.

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.

Mathai TSudharshan, Lee S, Elton DC, Shen TC, Peng Y, Lu Z, Summers RM.  2021.  Detection of lymph nodes in T2 MRI using neural network ensembles. Learning in Medical Imaging (MLMI). :682-691.

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.

Wang Y, Hilsman J, Li C, Morris M, Heider PM, Fu S, Kwak MJi, Wen A, Applegate JR, Wang L et al..  2025.  Development and Validation of Natural Language Processing Algorithms in the ENACT National Electronic Health Record Research Network.. medRxiv.

Morris JX, Campion TR, Nutheti SLaasya, Peng Y, Raj A, Zabih R, Cole CL.  2025.  DIRI: Adversarial Patient Reidentification with Large Language Models for Evaluating Clinical Text Anonymization.. AMIA Jt Summits Transl Sci Proc. 2025:355-364.

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.