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
Teran F, Owyang CG, Wray TC, Hipskind JE, Lessard J, Bédard Michel W, Lanthier C, Nazerian P, de Villa E, Nogueira J, Doynow D, Clinton M, Myslik F, Prager R, Arntfield R, Salinas PD, Dieiev V, Woo MY, Thavanathan R, Puskas G, Singh K, Bhat P, Horn J, Buchanan BM, Baig N, Burns KM, Kennedy K, Haines L, Naraghi L, Singh H, Secko M, Singer D, Taylor M, Joyce JM, DeMasi S, Jafry ZM, Phan T, Truong N, Robinson E, Haycock KH, Hansen A, Derr C, West FM, Narasimhan M, Horowitz J, Usman A, Anderson KL, Peng Y, Rola P, Andrus P, Razzak J, Hemmings HC, Panchamia R, Palasz J, Kaviyarasu A, Sands NA, Sutton RM, Abella BS; Resuscitative TEE Collaborative Registry (rTEECoRe) Investigators.
Development and Implementation of a Multicenter Registry for Resuscitation-Focused Transesophageal Echocardiography.
Ann Emerg Med. 2024 Oct 15:S0196-0644(24)00448-7. doi: 10.1016/j.annemergmed.2024.08.004. Epub ahead of print. PMID: 39412464.
Jin Q, Chen F, Zhou Y, Xu Z, Cheung JM, Chen R, Summers RM, Rousseau JF, Ni P, Landsman MJ, Baxter SL, Al'Aref SJ, Li Y, Chen A, Brejt JA, Chiang MF, Peng Y, Lu Z.
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine.
NPJ Digit Med. 2024 Jul 23;7(1):190. doi: 10.1038/s41746-024-01185-7. PMID: 39043988.
Holste G, Zhou Y, Wang S, Jaiswal A, Lin M, Zhuge S, Yang Y, Kim D, Nguyen-Mau TH, Tran MT, Jeong J, Park W, Ryu J, Hong F, Verma A, Yamagishi Y, Kim C, Seo H, Kang M, Celi LA, Lu Z, Summers RM, Shih G, Wang Z, Peng Y.
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge.
Med Image Anal. 2024 May 31;97:103224. doi: 10.1016/j.media.2024.103224. Epub ahead of print. PMID: 38850624.
Liu H, Soroush A, Nestor JG, Park E, Idnay B, Fang Y, Pan J, Liao S, Bernard M, Peng Y, Weng C.
Retrieval augmented scientific claim verification.
JAMIA Open. 2024 Feb 21;7(1):ooae021. doi: 10.1093/jamiaopen/ooae021. PMID: 38455840; PMCID: PMC10919922.
Zhou R, Miller JP, Gordon M, Kass M, Lin M, Peng Y, Li F, Feng J, Liu L.
Deep learning models to predict primary open-angle glaucoma.
Stat (Int Stat Inst). 2024;13(1):e649. doi: 10.1002/sta4.649. Epub 2024 Feb 7. PMID: 39220673; PMCID: PMC11364364.
Lin M, Li T, Yang Y, Holste G, Ding Y, Van Tassel SH, Kovacs K, Shih G, Wang Z, Lu Z, Wang F, Peng Y.
Improving model fairness in image-based computer-aided diagnosis.
Nat Commun. 2023 Oct 6;14(1):6261. doi: 10.1038/s41467-023-41974-4. PMID: 37803009; PMCID: PMC10558498.
Tang L, Sun Z, Idnay B, Nestor JG, Soroush A, Elias PA, Xu Z, Ding Y, Durrett G, Rousseau J, Weng C, Peng Y.
Evaluating Large Language Models on Medical Evidence Summarization.
npj Digital Medicine. 2023 Aug 24;6(1):158. doi: 10.1038/s41746-023-00896-7. PMID: 37620423; PMCID: PMC10449915.
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 Jun;142:104343. doi: 10.1016/j.jbi.2023.104343. Epub 2023 Mar 17. PMID: 36935011; PMCID: PMC10428170.
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.
github
Holste G, Jiang Z, Jaiswal A, Hanna M, Minkowitz S, Legasto A, Escalon J, Steinberger S, Bittman M, Ding Y, Shih G, Peng Y, Wang Z.
How Does Pruning Impact Long-Tailed Multi-Label Medical Image Classifiers?Med Image Comput Comput Assist Interv. 2023 Oct;14224:663-673. doi: 10.1007/978-3-031-43904-9_64. Epub 2023 Oct 1. PMID: 37829549; PMCID: PMC10568970.
Zhu Q, Mathai TS, Mukherjee P, Peng Y, Summers RM, Lu Z.
Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology Reports.
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). 2023 Oct;14224:189-198. doi: 10.1007/978-3-031-43904-9_19. Epub 2023 Oct 1. PMID: 38501075; PMCID: PMC10947431.
Holste G, Wang S, Jiang Z, Shen TC, Shih G, Summers RM, Peng Y*, Wang Z*.
Long-Tailed Classification of Thorax Diseases on Chest X-Ray: A New Benchmark Study.
In The 2nd MICCAI workshop on Data Augmentation, Labeling, and Imperfections (DALI). 2022 Sep;13567:22-32. doi: 10.1007/978-3-031-17027-0_3. Epub 2022 Sep 16. PMID: 36318048; PMCID: PMC9618235.
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.
Teran F, Peng Y, Owyang CG, Wray TC, Hipskind JE, Lessard J, Bédard Michel W, Lanthier C, Nazerian P, de Villa E, Nogueira J, Doynow D, Clinton M, Myslik F, Prager R, Arntfield R, Salinas PD, Dieiev V, Woo MY, Thavanathan R, Puskas G, Singh K, Bhat P, Horn J, Buchanan BM, Baig N, Burns K, Kennedy K, Haines L, Naraghi L, Singh H, Secko M, Singer D, Taylor M, Joyce JM, DeMasi S, Jafry ZM, Phan T, Truong N, Robinson E, Haycock KH, Hansen A, Derr C, Andrus P, Razzak J, Palasz J, Kaviyarasu A, Sands NA, Lin M, Abella BS.
Deep Learning Detection of Chest Compression Location Using Transesophageal Echocardiography.
Circulation. 2023 Nov 6;148(Suppl_1):A349-A349. doi: 10.1161/circ.148.suppl_1.349
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