Publications

Wang Y, Hilsman J, Li C, Morris M, Heider PM, Fu S, Kwak MJi, Wen A, Applegate JR, Wang L et al..  2025.  Development and Validation of Natural Language Processing Algorithms in the ENACT National Electronic Health Record Research Network.. medRxiv.

Xiao Y, Bi K, Yip PSiu-Fai, Cerel J, Brown TT, Peng Y, Pathak J, J Mann J.  2024.  Decoding Suicide Decedent Profiles and Signs of Suicidal Intent Using Latent Class Analysis.. JAMA Psychiatry. 81(6):595-605.

Holste G, Lin M, Zhou R, Wang F, Liu L, Yan Q, Van Tassel SH, Kovacs K, Chew EY, Lu Z et al..  2024.  Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.. NPJ Digit Med. 7(1):216.

Zhang G, Jin Q, McInerney DJered, Chen Y, Wang F, Cole CL, Yang Q, Wang Y, Malin BA, Peleg M et al..  2024.  Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness.. J Biomed Inform. 153:104640.

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.

Holste G, Zhou Y, Wang S, Jaiswal A, Lin M, Zhuge S, Yang Y, Kim D, Nguyen-Mau T-H, Tran M-T et al..  2024.  Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge.. Med Image Anal. 97:103224.

Holste G, Zhou Y, Wang S, Jaiswal A, Lin M, Zhuge S, Yang Y, Kim D, Nguyen-Mau T-H, Tran M-T et al..  2024.  Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge.. Med Image Anal. 97:103224.

Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J et al..  2023.  Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction.. BMC Med Res Methodol. 23(1):22.

Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J et al..  2023.  Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction.. BMC Med Res Methodol. 23(1):22.

Tong J, Luo C, Sun Y, Duan R, Saine E, Lin L, Peng Y, Lu Y, Batra A, Pan A et al..  2023.  Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints.. J Am Med Inform Assoc.

Lin M, Hou B, Mishra S, Yao T, Huo Y, Yang Q, Wang F, Shih G, Peng Y.  2023.  Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access.. Comput Biol Med. 159:106962.

Lin M, Hou B, Mishra S, Yao T, Huo Y, Yang Q, Wang F, Shih G, Peng Y.  2023.  Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access.. Comput Biol Med. 159:106962.

Lin M, Li T, Yang Y, Holste G, Ding Y, Van Tassel SH, Kovacs K, Shih G, Wang Z, Lu Z et al..  2023.  Improving model fairness in image-based computer-aided diagnosis.. Nat Commun. 14(1):6261.

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.

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.

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.

Yan K, Peng Y, Lu Z, Summers RM.  2019.  Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports. IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019). :285-288.

Yan K, Tang Y, Peng Y, Sandfort V, Bagheri M, Lu Z, Summers RM.  2019.  MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation. Medical Image Computing and Computer Assisted Intervention – MICCAI. 11769:194-202.

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).

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.

Peng Y, Yan S, Lu Z.  2019.  Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. Proceedings of the 18th BioNLP Workshop and Shared Task. :58–65.

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

Yan K, Peng Y, Sandfort V, Bagheri M, Lu Z, Summers RM.  0.  Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology. IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). :8523-8532.