Publications

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.

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 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.

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.

Chen Q, Peng Y, Lu Z.  2019.  BioSentVec: creating sentence embeddings for biomedical texts. IEEE International Conference on Healthcare Informatics (ICHI).

Doğan RIslamaj, Chatr-aryamontri A, Kim S, Wei C-H, Peng Y, Comeau D, Lu Z.  2017.  BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017. :171–175.

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

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.

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.

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.

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.