Publications

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.

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.

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.

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.

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.

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.

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.

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.

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