Hong Yu

BioOHDSI Publications

Hong Yu, MS, MA, PhD, FACMI
Professor, Department of Quantitative Health Sciences
University of Massachusetts Medical School

Professor Yu’s research interests are in the areas of information retrieval, extraction, natural language processing, summarization, human-computer interaction, with a focus on biomedical applications. She has led the development of many systems, including the biomedical question answering system AskHERMES, the adverse drug event pharmacovigilance system, the innovative biomedical figure search system, and the NoteAid systems that help patients comprehend electronic medical records.

She is an elected fellow of American College of Medical Informatics. She has served as co-Chair in the biomedical natural language processing sections of the Pacific Symposium of Biocomputing and IEEE International Conference on Bioinformatics & Biomedicine. She is a member of the editorial board of the Journal of Biomedical Informatics, and is the PI of several National Institutes of Health and industry funded projects. Her papers and poster was nominated or awarded as best paper in major biomedical informatics conferences: AMIA, MedInfo, and ISMB. Her work is included as best paper in IMIA Yearbook of Medical Informatics, described in Translational Bioinformatics Year in Review, and featured in Science, Nature, BioInform, the Pulitzer-winning Milwaukee Journal Sentinel, and the Milwaukee Public Radio.

Yu H, Hripcsak G, and Friedman C. Mapping abbreviations to full forms in biomedical articles. Journal of American Medical Informatics Association (JAMIA) 9(3):262-272 (2002).

Lee M, Wang WQ, and Yu H. Exploring supervised and unsupervised methods to detect topics in biomedical text. BMC Bioinformatics 7(1):140 (2006).

Yu H, Kim W, Hatzivassiloglou V, and Wilbur J. Disambiguating biomedical abbreviations. ACM Transactions on Information Systems 24(3):380-404 (2006).

Agarwal S and Yu H. Detecting hedge cues and their scope in biomedical literature with conditional random fields. Journal of Biomedical Informatics. 43(6):953-61 (2010).

Yu H, Cao YG, Cimino JJ, and Ely J. Automatically extracting information needs from complex clinical questions. Journal of Biomedical Informatics. 43(6):962-71 (2010).

Li ZF, Liu FF, Antieau L, Yu H. Lancet: a high precision medication event extraction system for clinical text. Journal of American Medical Informatics Association. 17:563-567 (2010).

Agarwal S and Yu H. Biomedical negation scope detection with conditional random fields. Journal of American Medical Informatics Association. 17:696-701 (2010).

Cao YG, Liu FF, Antieau L, Simpson P, Cimino JJ, Ely J, and Yu H. AskHERMES: An online question answering system for complex clinical questions. Journal of Biomedical Informatics 44(2):277-288 (2011).

Prasad R, McRoy S, Frid N, Joshi A, and Yu H. The biomedical discourse relation bank. BMC Bioinformatics 2011, 12:188doi:10.1186/1471-2105-12-188 (2011).

Zhang Q, Cao YY, and Yu H. Parsing citations in biomedical articles using conditional random fields. Computers in Biology and Medicine. 41(4):190-4 (2011).

Agarwal S, Yu H and Kohane I. BioNOT: A searchable database of biomedical negated sentences. BMC Bioinformatics. 12:420doi:10.1186/1471-2105-12-420 (2011).

Ramesh BP, Prasad R, Miller T, Harrington B, and Yu H. Automatic discourse connective detection in biomedical text. Journal of American Medical Informatics Association. doi:10.1136/amiajnl-2011-000775 (2012).

Ramesh BP, Belknap S, Li ZF, Frid N, West D, Raisch D and Yu H. 2014. Automatically recognizing medication and adverse event information from FDA AERS Narratives. Journal of Medical Internet Research.

Zheng J, Yarzebski J, Ramesh BP, Goldberg RJ and Yu H. 2014. Automatically detecting Acute Myocardial Infarction events from EHR text. AMIA Fall Symposium.

Yu H, Ramesh B, Brandt C, Becker W, Kern R. 2015. Towards Mining Electronic Health Records for Opioid ADE Surveillance. The 2015 HSR&D/QUERI National Conference.

Jagannatha A, Chen J and Yu H. 2015. Representing clinical notes for adverse drug event detection. EMNLP workshop the sixth international workshop on health text mining and information analysis.