Organizing Committee:
Interpretable Machine Learning in Healthcare at ICML (2021-present)
Senior Program Committee:
IJCAI (2021), AMIA Informatics Summit (2023)
Program Committee:
ACL (2021-present),
Clinical NLP Workshop (2020-present),
MICCAI (2019-present),
AAAI (2020-present),
Workshop on NLP for Medical Conversations (NLPMC, 2021),
Semantic Indexing and Information Retrieval for Health, 42nd European Conference on Information Retrieval (SIIRH-ECIR, 2020),
BioNLP Workshop (2019-present),
ICCV Visual Recognition for Medical Image Workshop (2019-2020),
ICHI (2019-present),
The IEEE International Conference on Biomedical and Health Informatics (ICBHI, 2016-2021),
ACM-BCB (2015-present)
Reviewer:
ACM Transactions on Computing for Healthcare,
AMIA,
Artificial Intelligence in Medicine,
Bioinformatics,
BMC Bioinformatics,
Computational Biology and Chemistry,
Computer Methods and Programs in Biomedicine,
Database (Oxford),
IEEE/ACM Transactions on Computational Biology and Bioinformatics,
IEEE Journal of Biomedical and Health Informatics (JBHI),
IEEE Transactions on Knowledge and Data Engineering,
IEEE Transactions on Medical Imaging (TMI),
IEEE Transactions on Neural Networks and Learning Systems,
IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI),
Journal of Biomedical Informatics (JBI),
Journal of Biomedical Semantics,
Journal of Digital Imaging,
Knowledge-Based Systems,
Nature Communications,
Nature Computational Science,
Nature Medicine
Ophthalmology,
Keloth VK, Banda JM, Gurley M, Heider PM, Kennedy G, Liu H, Liu F, Miller T, Natarajan K, V Patterson O, Peng Y, Raja K, Reeves RM, Rouhizadeh M, Shi J, Wang X, Wang Y, Wei WQ, Williams AE, Zhang R, Belenkaya R, Reich C, Blacketer C, Ryan P, Hripcsak G, Elhadad N, Xu H.
Representing and Utilizing Clinical Textual Data for Real World Studies: An OHDSI Approach. J Biomed Inform. 2023 Mar 17:104343. doi: 10.1016/j.jbi.2023.104343. Epub ahead of print. PMID: 36935011.
Brandt PS, Pacheco JA, Adekkanattu P, Sholle ET, Abedian S, Stone DJ, Knaack DM, Xu J, Xu Z, Peng Y, Benda NC, Wang F, Luo Y, Jiang G, Pathak J, Rasmussen LV.
Design and validation of a FHIR-based EHR-driven phenotyping toolbox.
J Am Med Inform Assoc. 2022 Aug 16;29(9):1449-1460. doi: 10.1093/jamia/ocac063. PMID: 35799370; PMCID: PMC9382394.
Islamaj R, Leaman R, Wei CH, Kim S, Kwon D, Comeau D, Peng Y, Cissel D, Coss C, Carol F, Guzman R, Kochar P, Stella K, Trinh D, Sekiya K, Ward J, Whitman D, Schmidt S, Lu Z.
NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature.Scientific Data. 2021 Mar 25;8(1):91. doi: 10.1038/s41597-021-00875-1. PMID: 33767203; PMCID: PMC7994842.
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS.
Opportunities and obstacles for deep learning in biology and medicine.
Journal of The Royal Society Interface. 2018 Apr;15(141). doi: 10.1098/rsif.2017.0387. Review. PMID: 29618526; PMCID: PMC5938574.
githubbioRxiv
Tang L, Kooragayalu S, Wang Y, Ding Y, Durrett G, Rousseau JF, Peng Y.
EchoGen: A new benchmark study on generating conclusions from echocardiogram notes.
In Proceedings of the Workshop on Biomedical Natural Language Processing (BioNLP). 2022 May;2022:359-368. doi: 10.18653/v1/2022.bionlp-1.35. PMID: 36339656; PMCID: PMC9634991.
Zhang M, Peng Y, Fan Y, Li D, Lin X, Wu X.
Research on Chinese orientation analysis.
The First Chinese Opinion Analysis Evaluation (COAE 2008). 2008, 38-45.
Yan K, Peng Y, Standfort V, Bagheri M, Lu Z, Summers RM.
Comprehensive Lesion Tagging on Diverse CT Images: Learning from Radiology Reports and Label Ontology.
In RSNA Annual Meeting. 2019. (talk)
Yan K, Tang Y, Peng Y, Standfort V, Bagheri M, Lu Z, Summers RM.
MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation in CT Images.
In RSNA Annual Meeting. 2019. (talk)
Phan L, Ward M, Allot A, Peng Y, Wei CH, Lee K, Lu Z, Wang J, Youkharibache P, Zhang D, Lanczycki C, Geer L, Geer R, Marchler-Bauer A, Madej T, Lu S, Marchler G, Wang Y, Bryant S, Rose P, Holmes JB, Kattman BL.
Integrative Analyses of dbSNP For Variant Prioritization and Interpretation.
In Biological Data Science. 2018.
Wei CH, Phan L, Allot A, Peng Y, Lee K, Maiti R, Hefferon T, Feltz J, Lu Z.
Literature Mining to Improve the Prioritization, Curation, and Integration of Knowledge for Clinically Relevant Variants.
In ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). 2018. (talk)
Dharssi S*, Peng Y*, Chen Q, Agron E, Wong W, Chew E, Lu Z.
A Deep Learning Approach for Automated Detection and Quantification of Geographic Atrophy from Color Fundus Photographs.
In AAO 2018. 2018. (talk)
Wei CH, Phan L, Allot A, Peng Y, Lee K, Maiti R, Hefferon T, Feltz J, Lu Z.
Literature Mining to Improve the Prioritization, Curation, and Integration of Knowledge for Clinically Relevant Variants.
In ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). 2018. (talk)
Allot A, Peng Y, Wei CH, Lee K, Phan L, Lu Z.
A semantic search engine for linking genomic variant data in PubMed and PMC.
In International Society for Computational Biology. 2018. (poster)
Arighi C, Ding R, Gupta S, Li G, Mahmood AA, Peng Y, Ren J, Ross K, Tudor CO, Huang H, Schimidt C, Wu CH, Vijay-Shanker K.
Text mining tools for biocuration in iProLINK web portal.
In Biocuration. 2015. (poster)
Peng Y, Zhang Z, Wang X, Yang L, Lu L.
Text Mining and Deep Learning for Disease Classification.
Handbook of Medical Image Computing and Computer Assisted Intervention. Zhou et al. (eds.). Elsevier. 2019, 109-136. doi:10.1016/B978-0-12-816176-0.00010-7.
Wang X, Peng Y, Lu L, Bagheri M, Lu Z, Summers R.
Method and system of building hospital-scale chest x-ray database for entity extraction and weakly-supervised classification and localization of common thorax diseases.
WO2018176035A1, filed 03/24/2017
Talks
Clinical NLP and deep learning in assisting medical image analysis. Invited talk at Virginia Commonwealth University. 5/6/2022.
Leveraging longitudinal and multi-modal EHR in Clinical Predictions. Invited talk at NIC-ASA and ICSA Midwest Chapter Joint Fall Meeting. 10/22/2021.
Transfer Learning of NLP in Medicine. Invited talk at AIME tutorial on Methods and Applications of Natural Language Processing in Medicine (AIME'20). 8/25/2020.
Overview of natural language processing in biomedical and cancer research. Invited talk at NCI Center for Biomedical Informatics and Information Technology (CBIIT) Cancer Data Science workshop. 01/24/2019.
Clinical NLP and deep learning for disease classification and reporting in Chest X-rays. Invited talk at ICSA 2018 Applied Statistics Symposium. 06/17/2018.
Clinical NLP and deep learning for disease classification and reporting in Chest X-rays. Invited talk at Computer and Information Science Department, University of Delaware. 06/25/2018.
Deep learning for extracting protein-protein interactions from biomedical literature. NIH-CSSA Symposium. 06/02/2017.
Text Mining Radiology Reports for Deep Learning Radiology Images. Invited talk at ABCC-Imaging and Visualization Group, Frederick National Laboratory for Cancer Research. 06/23/2017.
Honors and Awards
NIH Fellows Award for Research Excellence (FARE), NIH, 2020
NIH National Library of Medicine Honor Awards, NIH, 2019
NIH Summer Research Mentor Award, NIH, 2019
NIH National Library of Medicine Honor Awards, NIH, 2018
NIH Clinical Center CEO Awards, NIH, 2017
NIH Employee Awards, NIH, 2016-2018
CHEMPROT-Elsevier Prize, BioCreative VI, 2017
BioCreative Workshop Travel Award, 2015
Professional Development Award, University of Delaware, 2015