Yifan Peng

Research Interests

Biomedical / Clinical Natural Language Processing
Deep Learning for Healthcare
Biomedical Image Processing (by courtesy)

Education

Ph.D., Computer Science, University of Delaware, 2016 (supervisors: Dr. Cathy H. Wu and Dr. Vijay K. Shanker)
M.S., Computer Science, University of Delaware, 2013
M.Eng., Signal and Information Processing, Peking University, China, 2010
B.S.E., Computer Science and Technology, Beijing University of Technology, China, 2007

Teaching

HINF 5016 Natural Language Processing in Health (2021-present)

Professional Activities

Academic Editor: PLoS ONE
Editorial Board: Journal of Biomedical Informatics (2023-2027)
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-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,
NIH Grant Reviewer: 2020/10 ZAG1 ZIJ-7(O1), 2023/01 ZRG1 HSS-J(90S), ZAG1 ZIJ-4(C1)
Swiss National Science Foundation (SNSF) Grant Reviewer: 2022

Work Experience

Research Fellow, NCBI, NIH, Bethesda, MD, 2016-2020
Intern/Visiting scholar, NCBI, NIH, Bethesda, MD, 2015
Intern, Google Inc., Mountain View, CA, 2014
Intern, Natural Language Processing Research Group, Sogou Corp., Beijing, China, 2009
Intern, China Research Lab, IBM Corp., Beijing, China, 2009
Editor and Reporter, Programmer Magazine and CSDN, Beijing, China, 2008

Research Support

2145640, NSF CAREER Award, NSF, PI (2022-2026)
4R00LM013001, NIH/NLM, PI (2019-2023)
1OT2HL161847, PASC EHR/ORWD Phase II Proposal (RECOVER), NIH/NHLBI, co-I (2021-2025)
1R01AG080624, Disparities of Alzheimer's disease progression in sexual and gender minorities, NIH/NIA, co-I (2023-2026)
Amazon Research Award (Fall 2021)
Multi-Investigator Seed Grant, Cornell (2022)
AWS Diagnostic Development Initiative Support, Amazon (2022)
NVIDIA Academic Hardware Grant Award, NVIDIA (2022)
Google COVID-19 Research, Google (2020)

Publications

* co-first author. Google Scholar

Journal articles

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 Mar 14:ocad036. doi: 10.1093/jamia/ocad036. Epub ahead of print. PMID: 36921288.
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.
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 Jan 19. doi: 10.1055/a-2015-8679. Epub ahead of print. PMID: 36657471.
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.
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. 2022 Dec;6:e2200071. doi: 10.1200/CCI.22.00071. PMID: 36542818.
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. 2022 Oct 26;PP. doi: 10.1109/TMI.2022.3217218. Epub ahead of print. PMID: 36288235.
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. preprint
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. preprint
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. preprint
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 preprint
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. preprint
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 preprint 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. github preprint
Keenan T*, Dharssi S*, Peng Y*, Chen Q, Agrón E, Wong W, Lu Z, Chew E. 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. github preprint
Peng Y, Rios A, Kavuluru R, Lu Z. 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
Allot A*, Peng Y*, Wei CH, Lee K, Phan L, Lu Z. 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. service 2018 NIH National Library of Medicine Honor Awards
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 bioRxiv
Peng Y, Wei C, Lu Z. Improving chemical disease relation extraction with rich features and weakly labeled data. Journal of Cheminformatics. 2016;8:53. doi: 10.1186/s13321-016-0165-z. eCollection 2016. PMID: 28316651; PMCID: PMC5054544.
Peng Y, Arighi C, Wu CH, Vijay-Shanker K. 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.
Kim S, Islamaj Doğan R, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S, Santos A, Campos D, Oliveira JL, Singh O, Jonnagaddala J, Dai HJ, Su EC, Chang YC, Su YC, Chu CH, Chen CC, Hsu WL, Peng Y, Arighi C, Wu CH, Vijay-Shanker K, Aydın F, Hüsünbeyi ZM, Özgür A, Shin SY, Kwon D, Dolinski K, Tyers M, Wilbur WJ, Comeau DC. 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. service
Peng Y, Torii M, Wu CH, Vijay-Shanker K. 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.
Peng Y, Tudor CO, Torii M , Wu CH, Vijay-Shanker K. 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.
Comeau DC, Batista-Navarro RT, Dai HJ, Doğan RI, Yepes AJ, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RT, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC interoperability track overview. Database (Oxford). 2014;2014. doi: 10.1093/database/bau053. Print 2014. Review. PMID: 24980129; PMCID: PMC4074764.
Comeau DC, Doğan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia V, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. 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. github
Yi X, Peng Y. The design and implementation of a pipeline model machine based on Verilog HDL. Journal of Beijing University of Technology. 2007, 10, 1096-1101.

Conference proceedings

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. preprint
Wanyan T, Sung Q, Grizzard P, Liu J, Peng Y. A new deep learning framework to process Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI-MSI) data of Tissue Microarrays (TMAs). AMIA 2023 Informatics Summit. 2023 Jan 26.
Lin M, Xiao Y, Hou B, Wanyan T, Sharma MM, Wang Z, Wang F, Van Tassel S, Peng Y. Evaluate underdiagnosis and overdiagnosis bias of deep learning model on primary open-angle glaucoma diagnosis in under-served patient populations. AMIA 2023 Informatics Summit. 2023 Jan 26. preprint
Jaiswal A, Chen T, Rousseau JF, Peng Y, Ding Y, Wang Z. Attend Who is Weak: Pruning-assisted Medical Image Localization under Sophisticated and Implicit Imbalances. In IEEE/CVF Winter Conference on Applications of Computer Vision (WACV). 2023:4987-4996. preprint
Lee J, Wanyan T, Chen Q, Keenan TDL, Glicksberg BS, Chew YE, Lu Z, Wang F, Peng Y. 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.
Lin M, Liu L, Gorden M, Kass M, Tassel SV, Wang F, Peng Y. Multi-scale Multi-structure Siamese Network (MMSNet) for Primary Open-Angle Glaucoma Prediction. In International Workshop on Machine Learning in Medical Imaging (MLMI). 2022 Sep;13583:436-445. doi: 10.1007/978-3-031-21014-3_45. Epub 2022 Dec 16. PMID: 36656619; PMCID: PMC9844668.
Jaiswal A, Ashutosh K, Rousseau JF, Peng Y, Wang Z, Ding Y. RoS-KD: A Robust Stochastic Knowledge Distillation Approach for Noisy Medical Imaging. In 2022 IEEE International Conference on Data Mining (ICDM). 2022. preprint
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. preprint
Moukheiber D, Mahindre S, Moukheiber L, Moukheiber M, Wang S, Ma C, Shih G, Peng Y, Gao M. Few-Shot Learning Geometric Ensemble for Multi-label Classification of Chest X-Rays. In: Data Augmentation, Labelling, and Imperfections. 2022:112-122. doi: 10.1007/978-3-031-17027-0_12. Epub 2022 Sep 16. PMID: 36383493; PMCID: PMC9652771.
Wanyan T, Lin M, Klang E, Menon K, Gulamali F, Azad A, Zhang Y, Ding Y, Wang Z, Wang F, Glicksberg B, Peng Y. Supervised Pretraining through Contrastive Categorical Positive Samplings to Improve COVID-19 Mortality Prediction. In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB). 2022 Aug;9:1-9. doi: 10.1145/3535508.3545541. PMID: 35960866; PMCID: PMC9365529.
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.
Wang S, Lin M, Ding Y, Shih G, Lu Z, Peng Y. Radiology Text Analysis System (RadText): Architecture and Evaluation. IEEE Int Conf Healthc Inform. 2022 Jun;2022:288-296. doi: 10.1109/ichi54592.2022.00050. Epub 2022 Sep 8. PMID: 36128510; PMCID: PMC9484781. preprint
Wang S, Tang L, Lin M, Shih G, Ding Y, Peng Y. Prior knowledge enhances radiology report generation. AMIA Annu Symp Proc. 2022 May 23;2022:486-495. PMID: 35854760; PMCID: PMC9285179. preprint
Mathai TS, Lee S, Elton DC, Shen T, Peng Y, Lu Z, Summers RM. Lymph node detection in T2 MRI with transformers. In SPIE Medical Imaging. 2022:120333B. doi:10.1117/12.2613273. preprint
Han Y, Chen C, Tewfik A, Gicksberg B, Ying D, Peng Y, Wang Z. Knowledge-augmented contrastive learning for abnormality classification and localization in chest x-rays with radiomics using a feedback loop. The IEEE Winter Conference on Applications of Computer Vision (WACV). 2022 Jan;2022:2465-2474. doi: 10.1109/wacv51458.2022.00185. Epub 2022 Feb 15. PMID: 36300103; PMCID: PMC9594386. preprint
Schmeelk S, Dogo MS, Peng Y, Patra BG. Classifying cyber-risky clinical notes by employing natural language processing. Proceedings of the Hawaii International Conference on System Sciences (HICSS). 2022;2022:4140-4146. doi: 10.24251/hicss.2022.505. Epub 2022 Jan 4. PMID: 35528964; PMCID: PMC9076271.
Jaiswal A, Li T, Zander C, Han Y, Rousseau J, Peng Y, Ding Y. 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). 2021:1132-1137. doi: 10.1109/icdm51629.2021.00134. PMID: 35574510; PMCID: PMC9103376. preprint
Karabulut ME, Vijay-Shanker K*, Peng Y*. CU-UD: text-mining drug and chemical-proteininteractions with ensembles of BERT-based models. BioCreative VII. 2021:45-48. preprint github
Jaiswal A, Li T, Ghosh M, Rousseau J, Peng Y, Ding Y. RadBERT-CL: factually-aware contrastive learning for radiology report classification. Proceedings of Machine Learning for Health (ML4H). 22021 Dec;158:196-208. PMID: 35498230; PMCID: PMC9055736. preprint
Mathai TS, Lee S, Elton DC, Shen T, Peng Y, Lu Z, Summers RM. Detection of lymph nodes in T2 MRI using neural network ensembles. In International Workshop on Machine Learning in Medical Imaging (MLMI). 2021:682-691. doi:10.1007/978-3-030-87589-3_70
Ji Z, Shaikh MA, Moukheiber D, Srihari SN, Peng Y, Gao M. Improving joint learning of chest x-ray and radiology report by word region alignment. In Mach Learn Med Imaging. 2021:110-119. doi:10.1007/978-3-030-87589-3_12. Epub 2021 Sep 21. PMID: 35647616; PMCID: PMC9134785. preprint
Han Y, Chen C, Tang L, Lin M, Jaiswal A, Ding Y*, Peng Y*. Using radiomics as prior knowledge for thorax disease classification and localization in chest X-rays. In AMIA Annu Symp Proc. 2021:546-555. PMID: 35308939; PMCID: PMC8861661. preprint github
Ghahramani G, Brendel M, Lin M, Chen Q, Keenan T, Chen K, Chew E, Lu Z, Peng Y*, Wang F*. Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. In AMIA Annu Symp Proc. 2021:506-515. PMID: 35308963; PMCID: PMC8861665. github preprint
Lin M, Wang S, Ding Y, Zhao L, Wang F, Peng Y. An empirical study of using radiology reports and images to improve ICU-mortality prediction. In HealthNLP workshop. 2021 Aug;2021:497-498. doi: 10.1109/ichi52183.2021.00088. Epub 2021 Oct 15. PMID: 35531070; PMCID: PMC9076267.
Lee HG, Scholle E, Al'Aref S, Beecy A, Peng Y. Leveraging deep representations of radiology reports in survival analysis for predicting heart failure patient mortality. In NAACL. 2021;4533-4538. doi:10.18653/v1/2021.naacl-main.358. PMID: 35463193; PMCID: PMC9034454. preprint
Su P, Peng Y*, Vijay-Shanker K*. Improving BERT model using contrastive learning for biomedical relation extraction. In Proceedings of the Workshop on Biomedical Natural Language Processing (BioNLP). 2021;1-10. doi:10.18653/v1/2021.bionlp-1.1. preprint
Sun Q, Peng Y, Liu J. A reference-free approach for cell type classification with scRNA-seq. In RECOMB-SEQ. 2021. doi:10.1101/2021.05.29.446268.
Han Y, Chen C, Tewfik AH, Ding Y, Peng Y. Pneumonia detection on chest x-ray using radiomic features and contrastive learning. In IEEE International Symposium on Biomedical Imaging (ISBI). 2021;247-251. doi:10.1109/ISBI48211.2021.9433853. PMID: 35571507; PMCID: PMC9096898. preprint
Paul A, Shen TC, Peng Y, Lu Z, Summers RM. Learning few-shot chest X-ray diagnosis using images from the published scientific literature. In IEEE International Symposium on Biomedical Imaging (ISBI). 2021;344-348. doi:10.1109/ISBI48211.2021.9434059.
Peng Y, Lee S, Elton D, Shen T, Tang YX, Chen Q, Wang S, Zhu Y, Summers RM, Lu Z. Automatic recognition of abdominal lymph nodes from clinical text. In Proceedings of the ClinicalNLP Workshop. 2020;101-110. doi:10.18653/v1/2020.clinicalnlp-1.12.
Peng Y, Chen Q, Lu Z. An empirical study of multi-task learning on BERT for biomedical text mining. In Proceedings of the Workshop on Biomedical Natural Language Processing (BioNLP). 2020;205-214. doi:10.18653/v1/2020.bionlp-1.22. github preprint
Yeganova L, Islamaj R, Chen Q, Leaman R, Allot A, Wei CH, Comeau DC, Kim W, Peng Y, Wilbur WJ, Lu Z. Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. In KDD AI for COVID. 2020.
Paul A, Shen TC, Balachandar N, Tang YX, Peng Y, Lu Z, Summers RM. COMe-SEE: cross-modality semantic embedding ensemble for generalized zero-shot diagnosis of chest radiographs. In Procceddings of the Workshop on Medical Image Learning with Less Labels and Imperfect Data (MIL3ID). 2020;103-111. doi:10.1007/978-3-030-61166-8_11.
Peng Y, Yan S, Lu Z. Transfer learning in biomedical natural language processing: an evaluation of BERT and ELMo on ten benchmarking datasets. In Proceedings of the Workshop on Biomedical Natural Language Processing (BioNLP). 2019, 58-65. doi:10.18653/v1/W19-5006. data github preprint
Peng Y, Yan K, Standfort V, Summers RM, Lu Z. A self-attention based deep learning method for lesion attribute detection from CT reports. IEEE International Conference on Healthcare Informatics (ICHI). 2019. doi:10.1109/ICHI.2019.8904668. preprint
Yan K, Peng Y, Standfort V, Bagheri M, Lu Z, Summers RM. Holistic and comprehensive annotation of clinically significant findings on diverse CT images: learning from radiology reports and label ontology. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). 2019, 8523-8532. doi:10.1109/CVPR.2019.00872. preprint
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. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). 2019, 194-202. doi:10.1007/978-3-030-32226-7_22. github preprint
Chen Q*, Peng Y*, Lu Z. BioSentVec: creating sentence embeddings for biomedical texts. IEEE International Conference on Healthcare Informatics (ICHI). 2019. doi:10.1109/ICHI.2019.8904728. github preprint
Chen Q*, Peng Y*, Keenan T, Dharssi S, Agrón E, Wong WT, Chew EY, Lu Z. A multi-task deep learning framework for the classification of Age-related Macular Degeneration. AMIA 2019 Informatics Summit. 2019;2019:505-514. eCollection 2019. PMID: 31259005; PMCID: PMC6568069. preprint
Yan K, Peng Y, Lu Z, Summers R. Fine-grained lesion annotation in CT images with knowledge mined from radiology reports. IEEE International Symposium on Biomedical Imaging (ISBI). 2019, 285-288. doi:10.1109/ISBI.2019.8759336. Best paper award finalist preprint
Wang X*, Peng Y*, Lu L, Lu Z, Summers RM. TieNet: text-image embedding network for common thorax disease classification and reporting in chest x-rays. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). 2018, 9049-9058. doi:10.1109/cvpr.2018.00943. preprint
Peng Y, Wang X, Lu L, Bagheri M, Summers R, Lu Z. NegBio: a high-performance tool for negation and uncertainty detection in radiology reports. In AMIA 2018 Informatics Summit. 2018;2017:188-196. eCollection 2018. PMID: 29888070; PMCID: PMC596182 github Public Press Release preprint
Peng Y, Rios A, Kavuluru R, Lu Z. Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models. In Proceedings of the BioCreative VI Workshop. 2017, 148-151.
Peng Y, Lu Z. Deep learning for extracting protein-protein interactions from biomedical literature. In Proceedings of BioNLP workshop. 2017, 29-38. doi:10.18653/v1/W17-2304. github preprint
Dogan RI, Chatr-aryamontri A, Kim S, Wei C, Peng Y, Comeau D, Lu Z. BioCreative VI precision medicine track: creating a training corpus for mining protein-protein interactions affected by mutations. In Proceedings of BioNLP workshop. 2017, 171-175. doi:10.18653/v1/W17-2321.
Wang X, Peng Y, Lu L, Bagheri M, Lu Z, Summers R. Chestx-ray8: hospital-scale chest x-ray database and benchmarks on weakly-supervised classification and localization of common thorax diseases. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). 2017, 2097-2106. doi:10.1109/CVPR.2017.369. data 2017 NIH Clinical Center CEO Awards Public Press Release preprint
Peng Y, Gupta S, Wu CH, Vijay-Shanker K. An extended dependency graph for relation extraction in biomedical texts. In Proceedings of BioNLP workshop. 2015, 21-30. doi:10.18653/v1/W15-3803。
Peng Y, Arighi C, Wu CH, Vijay-Shanker K. Extended dependency graph for BioC-compatible protein-protein interaction (PPI) passage detection in full-text articles.In Proceedings of the BioCreative V Workshop. 2015, 30-35.
Wei C, Peng Y, Leaman R, Davis A, Mattingly C, Li J, Wiegers T, Lu Z. Overview of the Biocreative V chemical disease relation (CDR) task. In Proceedings of the BioCreative V Workshop. 2015, 154-166.
Peng Y, Tudor CO, Torii M , Wu CH, Vijay-Shanker K. Enhancing the interoperability of iSimp by using the BioC format. In Proceedings of the BioCreative IV Workshop. 2013, 5-9.
Peng Y*, Tudor CO*, Torii M , Wu CH, Vijay-Shanker K. iSimp: a sentence simplification system for biomedical text. IEEE International Conference on Bioinformatics and Biomedicine (BIBM2012). 2012, 211-216. doi:10.1109/BIBM.2012.6392671. data
Yi X, Peng Y, Song Q, Yang F, Li X. The schema and implementation of a model machine based on DFA theorem. International Symposium on Education and Computer Science (ECS2009). 2009, 2, 1038-1041. doi:10.1109/ETCS.2009.496.
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.
Peng Y, Chen W. A research of storing dynamical data structures based on XML. The 9th National Java Technology and Application Conference. 2006.

Preprint

Johnson A, Pollard T, Greenbaum N, Lungren M, Deng C, Peng Y, Lu Z, Mark R, Berkowitz S, Horng S. MIMIC-CXR-JPG, a large publicly available database of labeled chest radiographs. preprint preprint preprint:1901.07042. 2019. data

Abstracts

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:10.1016/10.1007/978-3-030-78601-4_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

Clinical NLP and deep learning in assisting medical image analysis. Invited talk at Virginia Commonwealth University. 5/6/2022.
Knowledge Enhances Radiology Report Generation. NSF EPSCoR Workshop on Artificial Intelligence & NBT. 4/3/2022.
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.
Clinical NLP and deep learning in assisting medical image analysis. Invited talk at MICCAI tutorial on Medical Informatics in Medical Image Analytics (MIMIA'19). 10/18/2019.
Transfer Learning in Biomedical NLP: A Case Study with BERT. NIH.AI Workshop on Natural Language Processing. 05/09/2019.
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
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

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