Publications

Tang L, Kooragayalu S, Wang Y, Ding Y, Durrett G, Rousseau JF, Peng Y.  2022.  EchoGen: A New Benchmark Study on Generating Conclusions from Echocardiogram Notes.. Proc Conf Assoc Comput Linguist Meet. 2022:359-368.

Brandt PS, Pacheco JA, Adekkanattu P, Sholle ET, Abedian S, Stone DJ, Knaack DM, Xu J, Xu Z, Peng Y et al..  2022.  Design and validation of a FHIR-based EHR-driven phenotyping toolbox.. J Am Med Inform Assoc. 29(9):1449-1460.

Keenan TDL, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT et al..  2020.  Deep Learning Automated Detection of Reticular Pseudodrusen from Fundus Autofluorescence Images or Color Fundus Photographs in AREDS2. Ophthalmology.

Peng Y, Tang Y, Lee S, Zhu Y, Summers RM, Lu Z.  2021.  COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature. IEEE Transactions on Big Data. 7(1):3-12.

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  Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints..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.

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.

Xu J, Wang F, Zang C, Zhang H, Niotis K, Liberman AL, Stonnington CM, Ishii M, Adekkanattu P, Luo Y et al..  2023.  Comparing the effects of four common drug classes on the progression of mild cognitive impairment to dementia using electronic health records.. Sci Rep. 13(1):8102.

Schmeelk S, Dogo MSamuel, Peng Y, Patra BGopal.  2022.  Classifying Cyber-Risky Clinical Notes by Employing Natural Language Processing.. Proc Annu Hawaii Int Conf Syst Sci. 2022:4140-4146.

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Peng Y, Arighi C, Wu CH, Vijay-Shanker K.  2016.  BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database (Oxford). 2016

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

Comeau DC, Doğan RIslamaj, Ciccarese P, Cohen KBretonnel, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M et al..  2013.  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013:bat064.

Chen Q, Rankine A, Peng Y, Aghaarabi E, Lu Z.  2021.  Benchmarking Effectiveness and Efficiency of Deep Learning Models for Semantic Textual Similarity in the Clinical Domain: Validation Study.. JMIR Med Inform. 9(12):e27386.

Lin M, Hou B, Liu L, Gordon M, Kass M, Wang F, Van Tassel SH, Peng Y.  2022.  Automated diagnosing primary open-angle glaucoma from fundus image by simulating human's grading with deep learning.. Sci Rep. 12(1):14080.

Patra BGopal, Sun Z, Cheng Z, Kumar PKasi Reddy, Altammami A, Liu Y, Joly R, Jedlicka C, Delgado D, Pathak J et al..  2023.  Automated classification of lay health articles using natural language processing: a case study on pregnancy health and postpartum depression.. Front Psychiatry. 14:1258887.

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.

Jaiswal A, Chen T, Rousseau JF, Peng Y, Ding Y, Wang Z.  2023.  Attend Who is Weak: Pruning-assisted Medical Image Localization under Sophisticated and Implicit Imbalances.. IEEE Winter Conf Appl Comput Vis. 2023:4976-4985.

Wei C-H, Peng Y, Leaman R, Davis APeter, Mattingly CJ, Li J, Wiegers TC, Lu Z.  2016.  Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database (Oxford). 2016

Peng Y, Rousseau JF, Shortliffe EH, Weng C.  2023.  AI-generated text may have a role in evidence-based medicine.. Nat Med.

Oniani D, Hilsman J, Peng Y, Poropatich RK, Pamplin JC, Legault GL, Wang Y.  2023.  Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare.. NPJ Digit Med. 6(1):225.

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.

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.

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).

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).

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.