Publications

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

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.

Yan K, Peng Y, Lu Z, Summers RM.  2019.  Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports. IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019). :285-288.

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.

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.

Yan K, Peng Y, Sandfort V, Bagheri M, Lu Z, Summers RM.  0.  Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology. IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). :8523-8532.

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.

Yu Z, Peng C, Yang X, Dang C, Adekkanattu P, Patra BGopal, Peng Y, Pathak J, Wilson DL, Chang C-Y et al..  2024.  Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias.. J Biomed Inform. 153:104642.

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.

Ji Z, Shaikh MAbuzar, Moukheiber D, Srihari SN, Peng Y, Gao M.  2021.  Improving Joint Learning of Chest X-Ray and Radiology Report by Word Region Alignment. International Workshop on Machine Learning in Medical Imaging.

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..  2012.  iSimp: A sentence simplification system for biomedicail text. IEEE International Conference on Bioinformatics and Biomedicine. :211-216.

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