Publications

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  Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints..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

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.

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.

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.

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.

Peng Y, Chen Q, Lu Z.  2020.  An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing.

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.

Wei Y, Wang X, Ong H, Zhou Y, Flanders A, Shih G, Peng Y.  2025.  Enhancing Disease Detection in Radiology Reports Through Fine-tuning Lightweight LLM on Weak Labels.. AMIA Jt Summits Transl Sci Proc. 2025:614-623.

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K.  2013.  Enhancing the interoperability of iSimp by using the BioC format. Proceedings of the BioCreative IV Workshop. :5-9.

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.