Yifan Peng Contact Information
BG 38A RM 10N1003E
8600 Rockville Pike
Bethesda, MD 20894-3825
Tel: 301-594-3218
Fax: 301-480-0814

Yifan Peng

Research Fellow
Biomedical Text Mining Group (with Zhiyong Lu, Ph.D.)
Computational Biology Branch

Research Interests

  • Bio Text Mining/Bio Natural Language Processing
  • Clinical Natural Language Processing
  • Deep Learning for Healthcare
  • Biomedical Image Processing


  • 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., Sginal and Information Processing, Peking University, China, 2010
  • B.S.E., Computer Science and Technology, Beijing University of Technology, China, 2007

Professional Activities

  • Academic Editor: PLoS ONE
  • Program Committee: The IEEE International Conference on Biomedical and Health Informatics, 2016-Present; ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), 2015
  • Reviewer: Bioinformatics, BMC Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Journal of Biomedical Semantics, Database (Oxford), PLoS One, IEEE Transactions on Knowledge and Data Engineering, Journal of Digital Imaging, AMIA Annual Symposium, AMIA Informatics Summit, Computer Methods and Programs in Biomedicine, Knowledge-Based Systems
  • Poster judge: Annual Graudate Student Research Symposium, NIH, 2017-Present

Work Experience

  • Research Fellow, NCBI, NIH, Bethesda, MD, 2017-Present
  • 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

Selected Recent Publications

* co-first author.

Journal articles

Conference proceedings


  • A Deep Learning Approach for Automated Detection and Quantification of Geographic Atrophy from Color Fundus Photographs. Dharssi S*, Peng Y*, Chen Q, Agron E, Wong W, Chew E, Lu Z. In AAO 2018. 2018. (talk)
  • Literature Mining to Improve the Prioritization, Curation, and Integration of Knowledge for Clinically Relevant Variants. Wei CH, Phan L, Allot A, Peng Y, Lee K, Maiti R, Hefferon T, Feltz J, Lu Z. In ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). 2018. (talk)
  • Discovering drug and retinal disease association patterns from electronic medical records: a text mining approach. Dharssi S, Peng Y, Leaman R, Chew EY, Lu Z. In ARVO Annual Meeting. 2018:59. ARVO E-Abstract 2924709. (poster)
  • Text Mining Radiology Reports for Deep Learning Radiology Images. Peng Y, Wang X, Lu L, Bagheri M, Summers R, Lu Z. In AMIA 2017 Annual Symposium. 2017, 157-158. (talk).
  • Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiograph. Wang X, Peng Y, Lu L, Bagheri M, Lu Z, Summers R. In RSNA Annual Meeting. 2018. (talk)
  • A semantic search engine for linking genomic variant data in PubMed and PMC. Allot A, Peng Y, Wei CH, Lee K, Phan L, Lu Z. In International Society for Computational Biology. 2018. (poster)
  • Text mining tools for biocuration in iProLINK web portal. 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. In Biocuration. 2015. (poster)



  • 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.
  • 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 National Library of Medicine, NIH, 2018
  • NIH Clinical Center CEO Awards, NIH, 2017
  • NIH Employee Awards, NIH, 2016-2017
  • CHEMPROT-Elsevier Prize, BioCreative VI, 2017
  • BioCreative Workshop Travel Award, 2015
  • Professional Development Award, University of Delaware, 2015


Support Center

Last updated: 2018-09-26T03:20:39Z