Publications

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

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.

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.

Peng Y, Yan K, Sandfort V, Summers RM, Lu Z.  2019.  A self-attention based deep learning method for lesion attribute detection from CT reports. 2019 IEEE International Conference on Healthcare Informatics (ICHI).

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K..  2012.  iSimp: A sentence simplification system for biomedicail text. IEEE International Conference on Bioinformatics and Biomedicine. :211-216.

Peng Y, Zhang Z, Wang X, Yang L, Lu L.  2019.  Text Mining and Deep Learning for Disease Classification. Handbook of Medical Image Computing and Computer Assisted Intervention. :109-136.

Peng Y, Lee S, Elton DC, Shen T, Tang Y-xing, Chen Q, Wang S, Zhu Y, Summers R, Lu Z.  2020.  Automatic recognition of abdominal lymph nodes from clinical text. Proceedings of the 3rd Clinical Natural Language Processing Workshop.

Peng Y, Gupta S, Wu C, Shanker V.  2015.  An extended dependency graph for relation extraction in biomedical texts. Proceedings of BioNLP 15. :21–30.

Peng Y, Yan S, Lu Z.  2019.  Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. Proceedings of the 18th BioNLP Workshop and Shared Task. :58–65.

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, Rios A, Kavuluru R, Lu Z.  2017.  Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models. Proceedings of the BioCreative VI Workshop. :148-151.

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

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, 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.

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

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.