Publications

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)

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.

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).

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.

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, 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.

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).

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.

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).

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.

Zhang G, Zhou Y, Hu Y, Xu H, Weng C, Peng Y.  2024.  A span-based model for extracting overlapping PICO entities from randomized controlled trial publications.. J Am Med Inform Assoc. 31(5):1163-1171.

Lovitt M, Ma H, Wang S, Peng Y.  2024.  Suicide Risk Assessment on Social Media with Semi-Supervised Learning.. Proc IEEE Int Conf Big Data. 2024:8541-8549.

Wanyan T, Lin M, Klang E, Menon KM, Gulamali FF, Azad A, Zhang Y, Ding Y, Wang Z, Wang F et al..  2022.  Supervised Pretraining through Contrastive Categorical Positive Samplings to Improve COVID-19 Mortality Prediction.. ACM BCB. 2022

Yang Y, Lin M, Zhao H, Peng Y, Huang F, Lu Z.  2024.  A survey of recent methods for addressing AI fairness and bias in biomedicine.. J Biomed Inform. 154:104646.

Peng Y, Zhang Z, Wang X, Yang L, Lu L.  2019.  Text Mining and Deep Learning for Disease Classification. Handbook of Medical Image Computing and Computer Assisted Intervention. :109-136.

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.

Han Z, Shen M, Liu H, Peng Y.  2022.  Topical and emotional expressions regarding extreme weather disasters on social media: a comparison of posts from official media and the public.. Humanit Soc Sci Commun. 9(1):421.