Publications

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.

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.

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)

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.

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.

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.

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)

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

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.

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.

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.

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.

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.

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.

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

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

Wei Y, Lin Y, Flanders A, Shih G, Peng Y.  2026.  Reinforcement learning improves LLM accuracy and reasoning in disease classification from radiology reports.. NPJ Digit Med.

Keloth VK, Banda JM, Gurley M, Heider PM, Kennedy G, Liu H, Liu F, Miller T, Natarajan K, Patterson OV et al..  2023.  Representing and Utilizing Clinical Textual Data for Real World Studies: An OHDSI Approach.. J Biomed Inform. :104343.

Lin Y, Yang Y, Shih G, Peng Y.  2026.  Rethinking radiology AI benchmarks.. Radiol Adv. 3(3):umag022.

Liu H, Soroush A, Nestor JG, Park E, Idnay B, Fang Y, Pan J, Liao S, Bernard M, Peng Y et al..  2024.  Retrieval augmented scientific claim verification.. JAMIA Open. 7(1):ooae021.

Jaiswal A, Ashutosh K, Rousseau JF, Peng Y, Wang Z, Ding Y.  2022.  RoS-KD: A Robust Stochastic Knowledge Distillation Approach for Noisy Medical Imaging.. Proc IEEE Int Conf Data Min. 2022:981-986.

Liang Y, Zhang G, Sun E, Idnay B, Fang Y, Chen F, Ta C, Peng Y, Weng C.  2025.  Scalable scientific interest profiling using large language models.. J Biomed Inform. 172:104949.

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.

Consoli B, Wang H, Wu X, Wang S, Zhao X, Wang Y, Rousseau J, Hartvigsen T, Shen L, Wu H et al..  2025.  SDoH-GPT: using large language models to extract social determinants of health.. J Am Med Inform Assoc.

Chen F, Zhang G, Fang Y, Peng Y, Weng C.  2025.  Semi-supervised learning from small annotated data and large unlabeled data for fine-grained Participants, Intervention, Comparison, and Outcomes entity recognition.. J Am Med Inform Assoc. 32(3):555-565.