Publications

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

Peng Y, Rousseau JF, Shortliffe EH, Weng C.  2023.  AI-generated text may have a role in evidence-based medicine.. Nat Med.

Peng Y, Arighi C, Wu CH,.Vijay-Shanker K.  2015.  Extended dependency graph for BioC-compatible protein-protein interaction (PPI) passage detection in full-text articles. Proceedings of the BioCreative V Workshop. :30-35.

Peng Y, Wang X, Lu L, Bagheri M, Summers R, Lu Z.  2018.  NegBio: a high-performance tool for negation and uncertainty detection in radiology reports. AMIA Jt Summits Transl Sci Proc. 2017:188-196.

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

Paul A, Shen TC, Peng Y, Lu Z, Summers RM.  2021.  Learning few-shot chest X-ray diagnosis using images from the published scientific literature. IEEE International Symposium on Biomedical Imaging (ISBI).

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.

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.

Patra BGopal, Sun Z, Cheng Z, Kumar PKasi Reddy, Altammami A, Liu Y, Joly R, Jedlicka C, Delgado D, Pathak J et al..  2023.  Automated classification of lay health articles using natural language processing: a case study on pregnancy health and postpartum depression.. Front Psychiatry. 14:1258887.

Oniani D, Hilsman J, Peng Y, Poropatich RK, Pamplin JC, Legault GL, Wang Y.  2023.  Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare.. NPJ Digit Med. 6(1):225.

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.

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.

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.

Mathai TSudharshan, Lee S, Elton DC, Shen TC, Peng Y, Lu Z, Summers RM.  2022.  Lymph node detection in T2 MRI with transformers. SPIE Medical Imaging. :120333B.

Ma H, Xu Z, Chung W, Weng C, Peng Y.  2025.  A Pilot Meta-Research on Evolving Evidence Behind Genetic Variant (Re)Classification.. Stud Health Technol Inform. 329:108-112.

Lu Z, Peng Y, Cohen T, Ghassemi M, Weng C, Tian S.  2024.  Large language models in biomedicine and health: current research landscape and future directions.. J Am Med Inform Assoc. 31(9):1801-1811.

Lovitt M, Ma H, Wang S, Peng Y.  2024.  Suicide Risk Assessment on Social Media with Semi-Supervised Learning.. Proc IEEE Int Conf Big Data. 2024:8541-8549.

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

Liu H, Soroush A, Nestor JG, Park E, Idnay B, Fang Y, Pan J, Liao S, Bernard M, Peng Y et al..  2024.  Retrieval augmented scientific claim verification.. JAMIA Open. 7(1):ooae021.

Lin M, Hou B, Liu L, Gordon M, Kass M, Wang F, Van Tassel SH, Peng Y.  2022.  Automated diagnosing primary open-angle glaucoma from fundus image by simulating human's grading with deep learning.. Sci Rep. 12(1):14080.

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.

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, 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, Liu L, Gorden M, Kass M, Van Tassel S, Wang F, Peng Y.  2022.  Multi-scale Multi-structure Siamese Network (MMSNet) for Primary Open-Angle Glaucoma Prediction.. Mach Learn Med Imaging. 13583:436-445.

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.