Professional Activities (before 2023)
- Section Editor: PLOS Digital Health (2023-2024)
- Guest Editor: JAMIA (2023)
- Chair:
HealthNLP 2023
- Area Chair:
NeurIPS Track Datasets and Benchmarks (2021-present)
- Publication Chair:
HealthNLP 2021
- Organizing Committee:
Interpretable Machine Learning in Healthcare at ICML (2021-2023)
- Academic Editor:
PLoS ONE (2018-2023)
- Senior Program Committee:
IJCAI (2021), AMIA Informatics Summit (2023), AMIA Symposium (2023)
- Program Committee:
ACL,
Clinical NLP Workshop,
MICCAI,
AAAI,
Workshop on NLP for Medical Conversations (NLPMC),
Semantic Indexing and Information Retrieval for Health, 42nd European Conference on Information Retrieval (SIIRH-ECIR),
BioNLP Workshop,
ICCV Visual Recognition for Medical Image Workshop,
ICHI,
The IEEE International Conference on Biomedical and Health Informatics,
ACM-BCB
- 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
- NIH Grant Reviewer:
2025/5 ZLM1 AS-C (01),
2024/10 ZRG1 NV-P 81S,
2023/10 BDMA,
2023/10 ZNS1 SRB-S(15)1,
ZAG1 ZIJ-4(C1),
2023/01 ZRG1 HSS-J(90S),
2020/10 ZAG1 ZIJ-7(O1),
- Swiss National Science Foundation (SNSF) Grant Reviewer: 2022
Research Support (Finished)
Honors and Awards (before 2020)
- 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
- Graduate Student Fellowship, Peking University, 2007-2009
- Intel Fellowship, 2007
- Graduation Honors, Beijing Municipal Education Commission, 2007
- Excellent Student Award, Beijing University of Technology, 2004-2006
Past Lab Members
- Shohom Chakraborty, 2025
- Kelly Deng, 2024-2025
- Ertan Dogan 2024, 2025 (AMIA 2025 Annual Symposium High School Scholars)
- Gregory Holste, 2023
- Hyun Gi Lee, 2020-2021
- Eric Zhewen Li, 2021-2022
- Mingquan Lin, 2021-2024
- Max Lovitt, 2024 (AMIA 2024 Annual Symposium High School Scholars)
- Akash Majety, 2021-2022
- Shreya Patel, 2021-2022
- Flora Yu Shen, 2021-2022
- Ziyu Song, 2021-2022
- Cong Sun, 2023-2025
- Zhaoyi Sun, 2022-2023
- Liyan Tang, 2021-2023
- Altria Wang, 2023-2024
- Song Wang, 2020-2025
- Tingyi Wanyan, 2022-2023
- Puzhen Wu, 2024-2025
- Tianyou Xiao, 2021-2022
- Richard Xu, 2023 (AMIA 2023 Annual Symposium High School Scholars)
- Zhongxing Xu, 2024
- Zihan Xu, 2024-2025
- Jingze Zhang, 2024-2025
- Yuhan Zhang, 2023-2024
- Yiliang Zhou, 2023-2024
Publications (before 2025)
Journal articles
- Su L, Chen J, Peng Y, Sun C.
Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension.
J Biomed Inform. 2024 Nov;159:104739. doi: 10.1016/j.jbi.2024.104739. Epub 2024 Oct 25. PMID: 39490610.
- Wang S, Zhou Y, Han Z, Tao C, Xiao Y, Ding Y, Ghosh J, Peng Y.
A natural language processing approach to detect inconsistencies in death investigation notes attributing suicide circumstances.
Commun Med (Lond). 2024 Oct 14;4(1):199. doi: 10.1038/s43856-024-00631-7. PMID: 39397053; PMCID: PMC11471859.
- 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. 2025 Feb;85(2):147-162. doi: 10.1016/j.annemergmed.2024.08.004. Epub 2024 Oct 16. PMID: 39412464.
- Tam TYC, Sivarajkumar S, Kapoor S, Stolyar AV, Polanska K, McCarthy KR, Osterhoudt H, Wu X, Visweswaran S, Fu S, Mathur P, Cacciamani GE, Sun C, Peng Y, Wang Y.
A framework for human evaluation of large language models in healthcare derived from literature review.
NPJ Digit Med. 2024 Sep 28;7(1):258. doi: 10.1038/s41746-024-01258-7. PMID: 39333376; PMCID: PMC11437138.
- Zhang G, Jin Q, Zhou Y, Wang S, Idnay B, Luo Y, Park E, Nestor JG, Spotnitz ME, Soroush A, Campion TR Jr, Lu Z, Weng C, Peng Y.
Closing the gap between open source and commercial large language models for medical evidence summarization.
NPJ Digit Med. 2024 Sep 9;7(1):239. doi: 10.1038/s41746-024-01239-w. PMID: 39251804; PMCID: PMC11383939.
- Lin M, Li T, Sun Z, Holste G, Ding Y, Wang F, Shih G, Peng Y.
Fairness of Automated Chest Radiograph Diagnosis by Contrastive Learning.
Radiol Artif Intell. 2024 Aug 21:e230342. doi: 10.1148/ryai.230342. PMID: 39166973; PMCID: PMC11449211.
- Lu Z, Peng Y, Cohen T, Ghassemi M, Weng C, Tian S.
Large language models in biomedicine and health: current research landscape and future directions.
J Am Med Inform Assoc. 2024 Sep 1;31(9):1801-1811. doi: 10.1093/jamia/ocae202. PMID: 39169867; PMCID: PMC11339542.
- Holste G, Lin M, Zhou R, Wang F, Liu L, Yan Q, Van Tassel SH, Kovacs K, Chew EY, Lu Z, Wang Z, Peng Y.
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.
NPJ Digit Med. 2024 Aug 16;7(1):216. doi: 10.1038/s41746-024-01207-4. PMID: 39152209; PMCID: PMC11329720.
- 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; PMCID: PMC11266508.
- 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 2024 May 31. PMID: 38850624; PMCID: PMC11365790.
- Wei Y, Deng Y, Sun C, Lin M, Jiang H, Peng Y.
Deep learning with noisy labels in medical prediction problems: a scoping review.
J Am Med Inform Assoc. 2024 Jun 20;31(7):1596-1607. doi: 10.1093/jamia/ocae108. PMID: 38814164; PMCID: PMC11187424.
- Zhou Y, Ong H, Kennedy P, Wu CC, Kazam J, Hentel K, Flanders A, Shih G, Peng Y.
GPT-4V (GPT-4 with Vision) on Detection of Radiologic Findings on Chest Radiographs.
Radiology. 2024 May;311(2):e233270. doi: 10.1148/radiol.233270. PMID: 38713028.
- Yang Y, Lin M, Zhao H, Peng Y, Huang F, Lu Z.
A survey of recent methods for addressing AI fairness and bias in biomedicine.
J Biomed Inform. 2024 Jun;154:104646. doi: 10.1016/j.jbi.2024.104646. Epub 2024 Apr 25. PMID: 38677633; PMCID: PMC11129918.
- Zhang G, Jin Q, Jered McInerney D, Chen Y, Wang F, Cole CL, Yang Q, Wang Y, Malin BA, Peleg M, Wallace BC, Lu Z, Weng C, Peng Y.
Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness.
J Biomed Inform. 2024 May;153:104640. doi: 10.1016/j.jbi.2024.104640. Epub 2024 Apr 10. PMID: 38608915; PMCID: PMC11217921.
- Zhang G, Zhou Y, Hu Y, Xu H, Weng C, Peng Y.
A span-based model for extracting overlapping PICO entities from RCT publications.
J Am Med Inform Assoc. 2024 Apr 19;31(5):1163-1171. doi: 10.1093/jamia/ocae065. PMID: 38471120; PMCID: PMC11031223.
- Xiao Y, Bi K, Yip PS, Cerel J, Brown TT, Peng Y, Pathak J, Mann JJ.
Decoding Suicide Decedent Profiles and Signs of Suicidal Intent Using Latent Class Analysis.
JAMA Psychiatry. 2024 Mar 20. doi: 10.1001/jamapsychiatry.2024.0171. PMID: 38506817; PMCID: PMC10955339.
- 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.
- Yu Z, Peng C, Yang X, Dang C, Adekkanattu P, Gopal Patra B, Peng Y, Pathak J, Wilson DL, Chang CY, Lo-Ciganic WH, George TJ, Hogan WR, Guo Y, Bian J, Wu Y.
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias.
J Biomed Inform. 2024 May;153:104642. doi: 10.1016/j.jbi.2024.104642. Epub 2024 Apr 14. PMID: 38621641; PMCID: PMC11141428.
- 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.
- Peng Y, Rousseau JF, Shortliffe EH, Weng C.
AI-generated text may have a role in evidence-based medicine.
Nat Med. 2023 Jul;29(7):1593-1594. doi: 10.1038/s41591-023-02366-9. PMID: 37221382; PMCID: PMC11193148.
- 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.
- Sun Z, Lin M, Zhu Q, Xie Q, Wang F, Lu Z, Peng Y.
A scoping review on multimodal deep learning in biomedical images and texts.
J Biomed Inform. 2023 Aug 29:104482. doi: 10.1016/j.jbi.2023.104482. Epub 2023 Aug 29. PMID: 37652343; PMCID: PMC10591890.
- 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.
- Benda NC, Rogers C, Sharma M, Narain W, Diamond LC, Ancker J, Seier K, Stetson PD, Sulieman L, Armstrong M, Peng Y.
Identifying Nonpatient Authors of Patient Portal Secure Messages in Oncology: A Proof-of-Concept Demonstration of Natural Language Processing Methods.
JCO Clin Cancer Inform. 2023 Jul;7:e2300029. doi: 10.1200/CCI.23.00029. PMID: 36542818; PMCID: PMC10476725.
- Sun Z, Ong H, Kennedy P, Tang L, Chen S, Elias J, Lucas E, Shih G, Peng Y.
Evaluating GPT4 on Impressions Generation in Radiology Reports.
Radiology. 2023 Jun;307(5):e231259. doi: 10.1148/radiol.231259. PMID: 37367439; PMCID: PMC10534271.
- Lin M, Hou B, Mishra S, Yao T, Huo Y, Yang Q, Wang F, Shih G, Peng Y.
Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access.
Comput Biol Med. 2023 Jun;159:106962. doi: 10.1016/j.compbiomed.2023.106962. Epub 2023 Apr 20. PMID: 37094464; PMCID: PMC10349296.
- Wang S, Dang Y, Sun Z, Ding Y, Pathak J, Tao C, Xiao Y*, Peng Y*.
An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives.
J Am Med Inform Assoc. 2023 Jul 19;30(8):1408-1417. doi: 10.1093/jamia/ocad068. PMID: 37040620; PMCID: PMC10354765.
- Kang T, Sun Y, Kim JH, Ta C, Perotte A, Schiffer K, Wu M, Zhao Y, Moustafa-Fahmy N, Peng Y, Weng C.
EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension.
J Am Med Inform Assoc. 2023 May 19;30(6):1022-1031. doi: 10.1093/jamia/ocad036. PMID: 36921288; PMCID: PMC10198523.
- Patra BG, Sun Z, Cheng Z, Kumar PKRJ, Altammami A, Liu Y, Joly R, Jedlicka C, Delgado D, Pathak J, Peng Y, Zhang Y.
Automated classification of lay health articles using natural language processing: a case study on pregnancy health and postpartum depression. Front Psychiatry. 2023 Nov 20;14:1258887. doi: 10.3389/fpsyt.2023.1258887. PMID: 38053538; PMCID: PMC10694448.
- Tong J, Luo C, Sun Y, Duan R, Saine E, Lin L, Peng Y, Lu Y, Batra A, Pan A, Wang O, Li R, Marks-Anglin A, Yang Y, Zuo X, Liu Y, Bian J, Kimmel SE, Hamilton K, Cuker A, Hubbard RA, Xu H, Chen Y.
Confidence Score: A Data-Driven Measure for Inclusive Systematic Reviews Considering Unpublished Preprints.
J Am Med Inform Assoc. 2023 Dec 8:ocad248. doi: 10.1093/jamia/ocad248. PMID: 38065694; PMCID: PMC10990515.
- Xu J, Wang F, Zang C, Zhang H, Niotis K, Liberman AL, Stonnington CM, Ishii M, Adekkanattu P, Luo Y, Mao C, Rasmussen LV, Xu Z, Brandt P, Pacheco JA, Peng Y, Jiang G, Isaacson R, Pathak J.
Comparing the effects of four common drug classes on the progression of mild cognitive impairment to dementia using electronic health records.
Sci Rep. 2023 May 19;13(1):8102. doi: 10.1038/s41598-023-35258-6. PMID: 37208478; PMCID: PMC10199021.
- Oniani D, Hilsman J, Peng Y, Poropatich RK, Pamplin JC, Legault GL, Wang Y.
Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare.
NPJ Digit Med. 2023 Dec 2;6(1):225. doi: 10.1038/s41746-023-00965-x. PMID: 38042910; PMCID: PMC10693640.
- 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.
- Xie Q, Hu J, Zhou J, Peng Y, Wang F.
Factreranker: Fact-guided reranker for faithful radiology report summarization.
arXiv preprint arXiv:2303.08335. 2023 Mar 15.
- Deng Y, Liu L, Jiang H, Peng Y, Wei Y, Zhou Z, Zhong Y, Zhao Y, Yang X, Yu J, Lu Z, Kho A, Ning H, Allen NB, Wilkins JT, Liu K, Lloyd-Jones DM, Zhao L.
Comparison of State-of-the-Art Neural Network Survival Models with the Pooled Cohort Equations for Cardiovascular Disease Risk Prediction. BMC Med Res Methodol. 2023 Jan 24;23(1):22. doi: 10.1186/s12874-022-01829-w. PMID: 36694118; PMCID: PMC9872364.
- Armstrong M, Benda NC, Seier K, Rogers C, Ancker J, Stetson PD, Peng Y, Diamond L.
Improving Cancer Care Communication: Identifying Sociodemographic Differences in Patient Portal Secure Messages Not Authored by the Patient.
Appl Clin Inform. 2023 Mar;14(2):296-299. doi: 10.1055/a-2015-8679. Epub 2023 Jan 19. PMID: 36657471; PMCID: PMC10115514.
- Adekkanattu P, Rasmussen LV, Pacheco JA, Kabariti J, Stone DJ, Yu Y, Jiang G, Luo Y, Brandt PS, Xu Z, Vekaria V, Xu J, Wang F, Benda NC, Peng Y, Goyal P, Ahmad FS, Pathak J.
Prediction of left ventricular ejection fraction changes in heart failure patients using machine learning and electronic health records: a multi-site study.
Sci Rep. 2023 Jan 6;13(1):294. doi: 10.1038/s41598-023-27493-8. PMID: 36609415; PMCID: PMC9822934.
- Han Z, Shen M, Liu H, Peng Y.
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. 2022;9(1):421. doi: 10.1057/s41599-022-01457-1. Epub 2022 Nov 28. PMID: 36466706; PMCID: PMC9703438.
- Lin M, Hou B, Liu L, Gordon M, Kass M, Wang F, Van Tassel SH, Peng Y.
Automated diagnosing primary open-angle glaucoma from fundus image by simulating human's grading with deep learning.
Sci Rep. 2022 Aug 18;12(1):14080. doi: 10.1038/s41598-022-17753-4. PMID: 35982106; PMCID: PMC9388536.
- Lin M, Liu L, Gordon M, Kass M, Wang F, Van Tassel SH, Peng Y.
Primary open-angle glaucoma diagnosis from optic disc photographs using Siamese network.
Ophthalmol Sci. 2022 Aug 13;2(4):100209. doi: 10.1016/j.xops.2022.100209. PMID: 36531584; PMCID: PMC9754976.
- Wang S, Tang L, Majety A, Rousseau JF, Shih G, Ding Y, Peng Y.
Trustworthy assertion classification through prompting.
J Biomed Inform. 2022 Aug;132:104139. doi: 10.1016/j.jbi.2022.104139. Epub 2022 Jul 8. PMID: 35811026; PMCID: PMC9378721.
- Wang S, Lin M, Ghosal T, Ding Y, Peng Y.
Knowledge Graph Applications in Medical Imaging Analysis: A Scoping Review.
Health Data Sci. 2022;2022:9841548. doi: 10.34133/2022/9841548. Epub 2022 Jun 14. PMID: 35800847; PMCID: PMC9259200.
- Han Y, Holste G, Ding Y, Tewfik A, Peng Y, Wang Z.
Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays.
IEEE Trans Med Imaging. 2023 Mar;42(3):750-761. doi: 10.1109/TMI.2022.3217218. Epub 2023 Mar 2. PMID: 36288235; PMCID: PMC10081959.
- Shi X, Peng Y, Chen Q, Keenan T, Thavikulwat AT, Lee S, Tang Y, Chew EY, Summers RM, Lu Z.
Robust convolutional neural networks against adversarial attacks on medical images.
Pattern Recognition. 2022;132:108923. doi: 10.1016/j.patcog.2022.108923
- Wang S, Zhu Y, Lee S, Elton DC, Shen TC, Tang Y, Peng Y, Lu Z, Summers RM.
Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images.
Medical Image Analysis. 2022 Apr;77:102345. doi: 10.1016/j.media.2021.102345. Epub 2022 Jan 8. PMID: 35051899; PMCID: PMC8988884.
- 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.
- Chen Q, Rankine A, Peng Y, Aghaarabi E, Lu Z.
Benchmarking effectiveness and efficiency of deep learning models for semantic textual similarity in the clinical domain: validation study.
JMIR Med Inform. 2021 Dec 30;9(12):e27386. doi: 10.2196/27386. PMID: 34967748; PMCID: PMC8759018.
- Sun Q, Peng Y, Liu J.
A reference-free approach for cell type classification with scRNA-seq.
iScience. 2021 Jul 14;24(8):102855. doi: 10.1016/j.isci.2021.102855. PMID: 34381979; PMCID: PMC8335627.
- He X, Zhang R, Alpert J, Zhou S, Adam TJ, Raisa A, Peng Y, Zhang H, Guo Y, Bian J.
When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information?.
JAMIA Open. 2021 Apr 4;4(1):ooab026. doi: 10.1093/jamiaopen/ooab026. PMID: 33855274; PMCID: PMC8029346.
- 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.
- Paul A, Shen TC, Lee S, Balachandar N, Peng Y, Lu Z, Summers RM.
Generalized zero-shot chest x-ray diagnosis through trait-guided multi-view semantic embedding with self-training.
IEEE Transactions on Medical Imaging. 2021 Oct;40(10):2642-2655. doi: 10.1109/TMI.2021.3054817. Epub 2021 Sep 30. PMID: 33523805; PMCID: PMC8591713.
- Chen Q, Keenan TDL, Allot A, Peng Y, Agrón E, Domalpally A, Klaver CCW, Luttikhuizen DT, Colyer MH, Cukras CA, Wiley HE, Teresa Magone M, Cousineau-Krieger C, Wong WT, Zhu Y, Chew EY, Lu Z.
Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration.
Journal of the American Medical Informatics Association (JAMIA). 2021 Jun 12;28(6):1135-1148. doi: 10.1093/jamia/ocaa302. PMID: 33792724; PMCID: PMC8200273.
- Peng Y, Tang YX, Lee S, Zhu Y, Summers RM, Lu Z.
COVID-19-CT-CXR: a freely accessible and weakly labeled chest X-ray and CT image collection on COVID-19 from the biomedical literature.
IEEE Trans Big Data. 2021 Mar 1;7(1):3-12. doi: 10.1109/tbdata.2020.3035935. Epub 2020 Nov 4. PMID: 33997112; PMCID: PMC8117951.
data
- Peng Y, Keenan T, Chen Q, Agrón E, Allot A, Wong W, Chew E, Lu Z.
Predicting risk of late age-related macular degeneration using deep learning.
NPJ Digit Med. 2020 Aug 27;3:111. doi: 10.1038/s41746-020-00317-z. PMID: 32904246; PMCID: PMC7453007.
- Keenan TD, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT, Lu Z, Chew EY.
Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images or color fundus photographs in AREDS2.
Ophthalmology. 2020 Dec;127(12):1674-1687. doi: 10.1016/j.ophtha.2020.05.036. Epub 2020 May 21. PMID: 32447042.
- Tang YX, Tang YB, Peng Y, Yan K, Bagher M, Redd BA, Brandon CJ, Lu Z, Han M, Xiao J, Summers RM.
Automated abnormality classification of chest radiographs using deep convolutional neural networks.
NPJ Digit Med. 2020 May 14;3:70. doi: 10.1038/s41746-020-0273-z. PMID: 32435698; PMCID: PMC7224391.
github
- Peng Y*, Dharssi S*, Chen Q, Keenan T, Agrón E, Wong W, Chew E, Lu Z.
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs.
Ophthalmology. 2019 Apr;126(4):565-575. doi: 10.1016/j.ophtha.2018.11.015. Epub 2018 Nov 22. PMID: 30471319; PMCID: PMC6435402.
github
2019 NIH National Library of Medicine Honor Awards
- Du J, Chen Q, Peng Y, Xiang Y, Tao C, Lu Z.
ML-Net: multi-label classification of biomedical texts with deep neural networks.
Journal of the American Medical Informatics Association (JAMIA). 2019 Nov 1;26(11):1279-1285. doi: 10.1093/jamia/ocz085. PMID: 31233120; PMCID: PMC7647240.
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A deep learning approach for automated detection of geographic atrophy from color fundus photographs.
Ophthalmology. 2019 Nov;126(11):1533-1540. doi: 10.1016/j.ophtha.2019.06.005. Epub 2019 Jun 11. PMID: 31358385; PMCID: PMC6810830.
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arXiv preprint arXiv:1901.07042. 2019.
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Extracting chemical-protein relations with ensembles of SVM and deep learning models.
Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay073. PMID: 30020437; PMCID: PMC6051439.
Top Performance in the BioCreative VI Chemical-Protein relation extraction track
2017 ChemProt-Elsevier Award
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LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.
Nucleic Acids Research. 2018 Jul 2;46(W1):W530-W536. doi: 10.1093/nar/gky355. PMID: 29762787; PMCID: PMC6030971.
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2018 NIH National Library of Medicine Honor Awards
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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.
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Journal of Cheminformatics. 2016;8:53. doi: 10.1186/s13321-016-0165-z. eCollection 2016. PMID: 28316651; PMCID: PMC5054544.
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BioC-compatible full-text passage detection for protein-protein interactions using Extended Dependency Graph.
Database (Oxford). 2016;2016. doi: 10.1093/database/baw072. Print 2016. PMID: 27170286; PMCID: PMC4915133.
- Wei C*, Peng Y*, Leaman R, Davis AP, Mattingly CJ, Li J, Wiegers TC, Lu Z.
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.
Database (Oxford). 2016;2016. doi: 10.1093/database/baw032. Print 2016. PMID: 26994911; PMCID: PMC4799720.
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BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database (Oxford). 2016;2016. doi: 10.1093/database/baw121. Print 2016. PMID: 27589962; PMCID: PMC5009341.
- Li G, Ross K, Arighi C, Peng Y, Wu CH, Vijay-Shanker K.
miRTex: A text mining system for miRNA-Gene relation extraction.
PLOS Computational Biology. 2015;11(9):e1004391. doi: 10.1371/journal.pcbi.1004391. eCollection 2015. PMID: 26407127; PMCID: PMC4583433.
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A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.
BMC Bioinformatics. 2014 Aug 23;15:285. doi: 10.1186/1471-2105-15-285. PMID: 25149151; PMCID: PMC4262219.
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iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.
Database (Oxford). 2014;2014. doi: 10.1093/database/bau038. Print 2014. PMID: 24850848; PMCID: PMC4028706.
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BioC interoperability track overview.
Database (Oxford). 2014;2014. doi: 10.1093/database/bau053. Print 2014. Review. PMID: 24980129; PMCID: PMC4074764.
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BioC: a minimalist approach to interoperability for biomedical text processing.
Database (Oxford). 2013;2013:bat064. doi: 10.1093/database/bat064. Print 2013. PMID: 24048470; PMCID: PMC3889917.
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Suicide Risk Assessment on Social Media with Semi-Supervised Learning.
Proc IEEE Int Conf Big Data. 2024 Dec;2024:8541-8549. doi: 10.1109/bigdata62323.2024.10825422. PMID: 39896202; PMCID: PMC11786971.
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Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups.
Proc (IEEE Int Conf Healthc Inform). 2024 Jun;2024:189-199. doi: 10.1109/ichi61247.2024.00032. Epub 2024 Aug 22. PMID: 39372906; PMCID: PMC11450796.
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High-performance Data Management for Whole Slide Image Analysis in Digital Pathology.
Proc SPIE Int Soc Opt Eng. 2024 Feb;12933:129330Y. doi: 10.1117/12.3006273. Epub 2024 Apr 3. PMID: 40343079; PMCID: PMC12061081.
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Identification of Offensive Language in Social Media Using Prompt Learning.
Proc (IEEE Int Conf Healthc Inform). 2023 Jun;2023:690-691. doi: 10.1109/ichi57859.2023.00122. Epub 2023 Dec 11. PMID: 39935530; PMCID: PMC11811837.
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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.
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Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology Reports.
Med Image Comput Comput Assist Interv. 2023 Oct;14224:189-198. doi: 10.1007/978-3-031-43904-9_19. Epub 2023 Oct 1. PMID: 38501075; PMCID: PMC10947431.
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Less Likely Brainstorming: Using Language Models to Generate Alternative Hypotheses.
Annual Meeting of the Association for Computational Linguistics (ACL). 2023 Jul;2023:12532-12555. doi: 10.18653/v1/2023.findings-acl.794. PMID: 37701928; PMCID: PMC10494958.
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Faithful AI in Medicine: A Systematic Review with Large Language Models and Beyond.
medRxiv [Preprint]. 2023 Jul 1:2023.04.18.23288752. doi: 10.1101/2023.04.18.23288752. PMID: 37398329; PMCID: PMC10312867.
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A new deep learning framework to process Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI-MSI) data of Tissue Microarrays (TMAs).
AMIA Jt Summits Transl Sci Proc. 2023 Jun 16;2023:554-561. PMID: 37350928; PMCID: PMC10283129.
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Evaluate underdiagnosis and overdiagnosis bias of deep learning model on primary open-angle glaucoma diagnosis in under-served populations.
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How Good Is ChatGPT for Medication Evidence Synthesis?
Stud Health Technol Inform. 2023 May 18;302:1062-1066. doi: 10.3233/SHTI230347. PMID: 37203581; PMCID: PMC11192029.
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Attend Who is Weak: Pruning-assisted Medical Image Localization under Sophisticated and Implicit Imbalances.
In IEEE Winter Conf Appl Comput Vis. 2023 Jan;2023:4976-4985. doi: 10.1109/wacv56688.2023.00496. Epub 2023 Feb 6. PMID: 37051561; PMCID: PMC10089697.
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In 2022 IEEE International Conference on Data Mining (ICDM). 2022 Nov-Dec;2022:981-986. doi: 10.1109/icdm54844.2022.00118. Epub 2023 Feb 1. PMID: 37038389; PMCID: PMC10082964.
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Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning.
In International Workshop on Machine Learning in Medical Imaging (MLMI). 2022 Sep;13583:11-20. doi: 10.1007/978-3-031-21014-3_2. Epub 2022 Dec 16. PMID: 36656604; PMCID: PMC9842432.
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IEEE Int Conf Healthc Inform. 2022 Jun;2022:288-296. doi: 10.1109/ichi54592.2022.00050. Epub 2022 Sep 8. PMID: 36128510; PMCID: PMC9484781.
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The IEEE International Conference on Data Mining (ICDM). 2021:1132-1137. doi: 10.1109/icdm51629.2021.00134. PMID: 35574510; PMCID: PMC9103376.
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Circulation. 2023 Nov 6;148(Suppl_1):A349-A349. doi: 10.1161/circ.148.suppl_1.349
- 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.
In RSNA. 2022. (poster).
- Wang S, Tang L, Majety A, Rousseau JF, Shih G, Ding Y, Peng Y.
Prompt-based Learning for Assertion Classification in Clinical Notes.
In AMIA 2022 Annual Symposium. 2022. (poster)
- Lee J, Wangyan T, Chen Q, Chen Q, Keenan TD, Chew E, Lu Z, Wang F, Peng Y.
Predicting 2-year and 5-year Late AMD Progression using Deep Learning with Longitudinal Fundus Images.
In Investigative Ophthalmology & Visual Science. 2022;63, 3003 - F0273. (poster)
- Ghahramani GC, Brendel M, Chen Q, Keenan TD, Chen K, Chew E, Lu Z, Peng Y*, Wang F*.
Deep learning survival analysis on the progression to late AMD in the Age-Related Eye Disease Study.
In Investigative Ophthalmology & Visual Science. 2021 June;62(8):92. (talk)
- Chen Q, Keenan TD, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT, Chew E, Lu Z.
Detection of reticular pseudodrusen using deep learning.
In AMIA 2020 Annual Symposium. 2020. (talk)
- Keenan TD, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT, Lu Z, Chew E.
Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images and color fundus photographs in the Age-Related Eye Disease Study 2 (AREDS2).
In Investigative Ophthalmology & Visual Science. 2020 June;61(7):1644. (talk)
- Peng Y, Keenan T, Chen Q, Agrón E, Wong W, Chew E, Lu Z.
A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs.
In AMIA 2019 Annual Symposium. 2019. (talk)
- 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)
- Keenan TD, Peng Y, Chen Q, Agrón E, Wong WT, Lu Z, Chew EY.
Deep learning prediction of progression to late age-related macular degeneration in the Age-Related Eye Disease Study (AREDS) using deep feature extraction and survival analysis.
In Investigative Ophthalmology & Visual Science. 2019 July;60(9):1491. (poster)
- 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, Leaman R, Chew EY, Lu Z.
Discovering drug and retinal disease association patterns from electronic medical records: a text mining approach.
Investigative Ophthalmology & Visual Science. 2018, 59(9), 4149. (ARVO E-Abstract 2924709)
- Wang X, Peng Y, Lu L, Bagheri M, Lu Z, Summers RM.
Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiograph.
In RSNA Annual Meeting. 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)
- Peng Y, Wang X, Lu L, Bagheri M, Summers R, Lu Z.
Text mining radiology reports for deep learning radiology images.
In AMIA 2017 Annual Symposium. 2017, 157-158. (talk)
- 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)
Book chapters
- Peng Y, Chen Q, Keenan TDL, Chew EL, Lu Z.
Artificial Intelligence in Age-Related Macular Degeneration (AMD).
Artificial Intelligence in Ophthalmology. Grzybowski A. (eds.). Springer, Cham. 2021, 101-112. doi:10.1007/978-3-030-78601-4_8.
- 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, Lu Z, Summers RM.
ChestX-ray: Hospital-Scale Chest X-ray Database and Benchmarks on Weakly Supervised Classification and Localization of Common Thorax Diseases.
Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Lu et al. (eds.). Springer. 2019, 369-392. doi:10.1007/978-3-030-13969-8_18.
- Wang X, Peng Y, Lu L, Lu Z, Summers RM.
Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiographs.
Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Lu et al. (eds.). Springer. 2019, 393-412. doi:10.1007/978-3-030-13969-8_19.
Patents
- Chew E, Lu Z, Lenaghan D, Tiarnan K, Wong WT, Peng Y, Chen Q, Agrón E, inventors;
The United States of America, as represented by the Secretary, Dept. of Health, assignee. METHODS AND SYSTEMS FOR PREDICTING RATES OF PROGRESSION OF AGE-RELATED MACULAR DEGENERATION. United States patent application US 17/904,573. 2023 Mar 23.
- 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 (before 2025)