Publications

Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K.  2015.  miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput Biol. 11(9):e1004391.

Du J, Chen Q, Peng Y, Xiang Y, Tao C, Lu Z.  2019.  ML-Net: multi-label classification of biomedical texts with deep neural networks. J Am Med Inform Assoc. 26(11):1279-1285.

Chen J, Su L, Li Y, Lin M, Peng Y, Sun C.  2025.  A multimodal approach for few-shot biomedical named entity recognition in low-resource languages.. J Biomed Inform. 161:104754.

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.

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, 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.

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.

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.

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)

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.

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.

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.

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.