Publications

Peng Y, Arighi C, Wu CH, Vijay-Shanker K.  2016.  BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database (Oxford). 2016

Comeau DC, Batista-Navarro RTheresa, Dai H-J, Doğan RIslamaj, Yepes AJimeno, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M et al..  2014.  BioC interoperability track overview. Database (Oxford). 2014

Comeau DC, Doğan RIslamaj, Ciccarese P, Cohen KBretonnel, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M et al..  2013.  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013:bat064.

Chen Q, Rankine A, Peng Y, Aghaarabi E, Lu Z.  2021.  Benchmarking Effectiveness and Efficiency of Deep Learning Models for Semantic Textual Similarity in the Clinical Domain: Validation Study.. JMIR Med Inform. 9(12):e27386.

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.

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.

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.

Jaiswal A, Chen T, Rousseau JF, Peng Y, Ding Y, Wang Z.  2023.  Attend Who is Weak: Pruning-assisted Medical Image Localization under Sophisticated and Implicit Imbalances.. IEEE Winter Conf Appl Comput Vis. 2023:4976-4985.

Wei C-H, Peng Y, Leaman R, Davis APeter, Mattingly CJ, Li J, Wiegers TC, Lu Z.  2016.  Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database (Oxford). 2016

Xu RLi, Wang S, Wang Z, Zhang Y, Xiao Y, Pathak J, Hodge D, Leng Y, S Watkins C, Ding Y et al..  2024.  Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups.. Proc (IEEE Int Conf Healthc Inform). 2024:189-199.

Wu P, Lin M, Chen Q, Chew EY, Lu Z, Peng Y, Dong H.  2025.  AMD-Mamba: A Phenotype-Aware Multi-Modal Framework for Robust AMD Prognosis.. ArXiv.

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

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.

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.

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.

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).

Jaiswal A, Li T, Zander C, Han Y, Rousseau JF, Peng Y, Ding Y.  2021.  SCALP - Supervised Contrastive Learning for Cardiopulmonary Disease Classification and Localization in Chest X-rays using Patient Metadata. The IEEE International Conference on Data Mining (ICDM).

Jaiswal A, Tang L, Ghosh M, Rousseau J, Peng Y, Ding Y.  2021.  RadBERT-CL: Factually-Aware Contrastive Learning for Radiology Report Classification. Machine Learning for Health (ML4H). :196-208.

Han Y, Chen C, Tewfik AH, Ding Y, Peng Y.  2021.  Pneumonia Detection on Chest X-ray using Radiomic Features and Contrastive Learning. IEEE International Symposium on Biomedical Imaging (ISBI).

Wei C-H, Peng Y, Leaman R, Davis APeter, Mattingly CJ, Li J, Wiegers TC, Lu Z.  2015.  Overview of the Biocreative V chemical disease relation (CDR) task. Proceedings of the BioCreative V Workshop. :154-166.

Yeganova L, Islamaj R, Chen Q, Leaman R, Allot A, Wei C-H, Comeau DC, Kim W, Peng Y, W. Wilbur J et al..  2020.  Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. KDD AI for COVID.

Yan K, Tang Y, Peng Y, Sandfort V, Bagheri M, Lu Z, Summers RM.  2019.  MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation. Medical Image Computing and Computer Assisted Intervention – MICCAI. 11769:194-202.

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.

Lee HGi, Scholle E, Al'Aref S, Beecy A, Peng Y.  2021.  Leveraging Deep Representations of Radiology Reports in Survival Analysis for Predicting Heart Failure Patient Mortality. NAACL.

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).