Publications

Zhou Y, Newbury AM, Zhang G, Idnay BRoss, Liu H, Weng C, Peng Y.  2025.  EvidenceOutcomes: A Dataset of Clinical Trial Publications with Clinically Meaningful Outcomes.. Stud Health Technol Inform. 329:723-727.

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.

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.

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

Bai Z, Xu Z, Sun C, Zang C, H Bunnell T, Sinfield C, Rutter J, Martinez AThomas, L Bailey C, Weiner M et al..  2025.  Extracting post-acute sequelae of SARS-CoV-2 infection symptoms from clinical notes via hybrid natural language processing.. Npj Health Syst. 2

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.

Wang Z, Cao L, Jin Q, Chan J, Wan N, Afzali B, Cho H-J, Choi C-I, Emamverdi M, Gill MK et al..  2025.  A foundation model for human-AI collaboration in medical literature mining.. Nat Commun. 16(1):8361.

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.

Sun C, Teichman K, Zhou Y, Critelli B, Nauheim D, Keir G, Wang X, Zhong J, Flanders AE, Shih G et al..  2025.  Generative Large Language Models Trained for Detecting Errors in Radiology Reports.. Radiology. 315(2):e242575.

Wang S, Zhu Y, Lee S, Elton DC, Shen TC, Tang Y, Peng Y, Lu Z, Summers RM.  2022.  Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images.. Med Image Anal. 77:102345.

Holste G, Lin M, Zhou R, Wang F, Liu L, Yan Q, Van Tassel SH, Kovacs K, Chew EY, Lu Z et al..  2024.  Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.. NPJ Digit Med. 7(1):216.

Jin Q, Chen F, Zhou Y, Xu Z, Cheung JM, Chen R, Summers RM, Rousseau JF, Ni P, Landsman MJ et al..  2024.  Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine.. NPJ Digit Med. 7(1):190.

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.

Liu H, Peng Y, Weng C.  2023.  How Good Is ChatGPT for Medication Evidence Synthesis? Stud Health Technol Inform. 302:1062-1066.

Benda NC, Rogers C, Sharma M, Narain W, Diamond LC, Ancker J, Seier K, Stetson PD, Sulieman L, Armstrong M et al..  2022.  Identifying Nonpatient Authors of Patient Portal Secure Messages in Oncology: A Proof-of-Concept Demonstration of Natural Language Processing Methods.. JCO Clin Cancer Inform. 6:e2200071.

Armstrong M, Benda NC, Seier K, Rogers C, Ancker J, Stetson PD, Peng Y, Diamond L.  2023.  Improving Cancer Care Communication: Identifying Sociodemographic Differences in Patient Portal Secure Messages Not Authored by the Patient.. Appl Clin Inform.

Peng Y, Wei C-H, Lu Z.  2016.  Improving chemical disease relation extraction with rich features and weakly labeled data. J Cheminform. 8:53.

Lin M, Li T, Sun Z, Holste G, Ding Y, Wang F, Shih G, Peng Y.  2024.  Improving Fairness of Automated Chest Radiograph Diagnosis by Contrastive Learning.. Radiol Artif Intell. 6(5):e230342.

Lin M, Li T, Yang Y, Holste G, Ding Y, Van Tassel SH, Kovacs K, Shih G, Wang Z, Lu Z et al..  2023.  Improving model fairness in image-based computer-aided diagnosis.. Nat Commun. 14(1):6261.

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K.  2014.  iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database (Oxford). 2014

Wang S, Lin M, Ghosal T, Ding Y, Peng Y.  2022.  Knowledge Graph Applications in Medical Imaging Analysis: A Scoping Review.. Health Data Sci. 2022

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.