Publications

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.

Schmeelk S, Dogo MSamuel, Peng Y, Patra BGopal.  2022.  Classifying Cyber-Risky Clinical Notes by Employing Natural Language Processing.. Proc Annu Hawaii Int Conf Syst Sci. 2022:4140-4146.

Song Y, Zhan Z, Xie F, Wang N, Peng Y, Zhang R, Lin M.  2026.  A cancer-type-aware framework for robust multimodal survival prediction under missing modalities.. Brief Bioinform. 27(2)

Song Y, Zhang Y, Orengo-Nania S, Wang N, Ma F, Zhang R, Peng Y, Lin M.  2026.  Two-Stage Decoupling Framework for Variable-Length Glaucoma Prognosis.. Learn Longitud Med Images Data (2025). 16184:91-101.

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.

Sun Z, Lin M, Zhu Q, Xie Q, Wang F, Lu Z, Peng Y.  2023.  A scoping review on multimodal deep learning in biomedical images and texts.. J Biomed Inform. 146:104482.

Sun Q, Peng Y, Liu J.  2021.  A reference-free approach for cell type classification with scRNA-seq.. iScience. 24(8):102855.

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.

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.

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.

Tang Y-X, Tang Y-B, Peng Y, Yan K, Bagheri M, Redd BA, Brandon CJ, Lu Z, Han M, Xiao J et al..  2020.  Automated abnormality classification of chest radiographs using deep convolutional neural networks. NPJ Digit Med. 3:70.

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.

Tang L, Sun Z, Idnay B, Nestor JG, Soroush A, Elias PA, Xu Z, Ding Y, Durrett G, Rousseau JF et al..  2023.  Evaluating large language models on medical evidence summarization.. NPJ Digit Med. 6(1):158.

Tang L, Peng Y, Wang Y, Ding Y, Durrett G, Rousseau JF.  2023.  Less Likely Brainstorming: Using Language Models to Generate Alternative Hypotheses.. Proc Conf Assoc Comput Linguist Meet. 2023:12532-12555.

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.

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.

Wang X, Peng Y, Lu L, Lu Z, Summers RM.  2019.  Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiographs. Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Advances in Computer Vision and Pattern Recognition. :393-412.

Wang X, Peng Y, Lu L, Lu Z, Summers RM.  2018.  TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays. IEEE/CVF Conference on Computer Vision and Pattern Recognition. :9049-9058.

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.

Wang X, Peng Y, Lu L, Lu Z, Bagheri M, Summers RM.  2019.  ChestX-ray: Hospital-Scale Chest X-ray Database and Benchmarks on Weakly Supervised Classification and Localization of Common Thorax Diseases. Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. :369-392.

Wang X, Peng Y, Lu L, Lu Z, Bagheri M, Summers RM.  2017.  ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). :2097-2106.

Wang S, Wei Y, Ma H, Lovitt M, Deng K, Meng Y, Xu Z, Zhang J, Xiao Y, Ding Y et al..  2025.  A multi-stage large language model framework for extracting suicide-related social determinants of health.. Commun Med (Lond). 5(1):404.