Publications

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

Han Y, Holste G, Ding Y, Tewfik A, Peng Y, Wang Z.  2022.  Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays.. IEEE Trans Med Imaging. PP

Wang S, Lin M, Ding Y, Shih G, Lu Z, Peng Y.  2022.  Radiology Text Analysis System (RadText): Architecture and Evaluation.. IEEE Int Conf Healthc Inform. 2022:288-296.

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.

Wang S, Tang L, Lin M, Shih G, Ding Y, Peng Y.  2022.  Prior Knowledge Enhances Radiology Report Generation.. AMIA Annu Symp Proc. 2022:486-495.

Adekkanattu P, Rasmussen LV, Pacheco JA, Kabariti J, Stone DJ, Yu Y, Jiang G, Luo Y, Brandt PS, Xu Z et al..  2023.  Prediction of left ventricular ejection fraction changes in heart failure patients using machine learning and electronic health records: a multi-site study.. Sci Rep. 13(1):294.

Peng Y, Keenan TD, Chen Q, Agrón E, Allot A, Wong WT, Chew EY, Lu Z.  2020.  Predicting risk of late age-related macular degeneration using deep learning. NPJ Digit Med. 3:111.

Lee J, Wanyan T, Chen Q, Keenan TDL, Glicksberg BS, Chew EY, Lu Z, Wang F, Peng Y.  2022.  Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning.. Mach Learn Med Imaging. 13583:11-20.

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).

Ma H, Xu Z, Chung W, Weng C, Peng Y.  2025.  A Pilot Meta-Research on Evolving Evidence Behind Genetic Variant (Re)Classification.. Stud Health Technol Inform. 329:108-112.

Dong H, Lin Y, Zhou P, Feng XZhong, Legasto AClint, Lin M, Chen H, Yang Y, Shih G, Peng Y.  2026.  OVERVIEW OF THE CXR-LT 2026 CHALLENGE: MULTI-CENTER LONG-TAILED AND ZERO SHOT CHEST X-RAY CLASSIFICATION.. Proc IEEE Int Symp Biomed Imaging. 2026

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.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM et al..  2018.  Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 15(141)

Wang S, Dang Y, Sun Z, Ding Y, Pathak J, Tao C, Xiao Y, Peng Y.  2023.  An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives.. J Am Med Inform Assoc.

Islamaj R, Leaman R, Kim S, Kwon D, Wei C-H, Comeau DC, Peng Y, Cissel D, Coss C, Fisher C et al..  2021.  NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature.. Sci Data. 8(1):91.

Wangyan T, Sun Q, Grizzard P, Liu J, Peng Y.  2023.  A new deep learning framework to process Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI-MSI) data of Tissue Microarrays (TMAs).. AMIA Jt Summits Transl Sci Proc. 2023:554-561.

Zhang G, Fang Y, Chen F, Ta C, Hripcsak G, Ryan P, Peng Y, Weng C.  2026.  A neural-symbolic AI agent system for biomedical concept mapping.. NPJ Digit Med. 9(1)

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.

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.

Wang S, Zhou Y, Han Z, Tao C, Xiao Y, Ding Y, Ghosh J, Peng Y.  2024.  A natural language processing approach to detect inconsistencies in death investigation notes attributing suicide circumstances.. Commun Med (Lond). 4(1):199.

Ghahramani G, Brendel M, Lin M, Chen Q, Keenan T, Chen K, Chew E, Lu Z, Peng Y, Wang F.  2021.  Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.. AMIA Annu Symp Proc. 2021:506-515.

Chen Q, Peng Y, Keenan T, Dharssi S, N EAgro, Wong WT, Chew EY, Lu Z.  2019.  A multi-task deep learning model for the classification of Age-related Macular Degeneration. AMIA Jt Summits Transl Sci Proc. 2019:505-514.

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.

Lin M, Liu L, Gorden M, Kass M, Van Tassel S, Wang F, Peng Y.  2022.  Multi-scale Multi-structure Siamese Network (MMSNet) for Primary Open-Angle Glaucoma Prediction.. Mach Learn Med Imaging. 13583:436-445.

Chen Q, Keenan TDL, Allot A, Peng Y, Agrón E, Domalpally A, Klaver CCW, Luttikhuizen DT, Colyer MH, Cukras CA et al..  2021.  Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration.. J Am Med Inform Assoc.