Journal Publication

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

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

       Yu H, Kim W, Hatzivassiloglou V, and Wilbur J. 2007. Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. Journal of Biomedical Informatics (JBI) 40(2):150-9.

       Yu H, Lee M, Kaufman D, Ely J, Osheroff JA, Hripcsak G, and Cimino J. 2007. Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. Journal of Biomedical Informatics (JBI) 40(3):236-51.

       Zweigenbaum P, Demner-Fushman DD, Yu H, and Cohen KB. 2008. New frontiers for biomedical text mining: current progress. Briefing in Bioinformatics 8(5):358-75.

       Zhang Q and Yu H. 2009. Parsing citations in biomedical articles using conditional random fields. Computers in Biology and Medicine (in press).

       Cao YG, Li ZF, Liu FF, Agarwal S, Zhang Q, and Yu H. 2010. An IR-aided machine learning framework for the BioCreative II.5 Challenge. IEEE/ACM Transaction on Computational Biology and Bioinformatics. In press.

       Agarwal S and Yu H. 2010. Detecting hedge cues and their scope in biomedical literature with conditional random fields. Journal of Biomedical Informatics.

       Yu H, Cao YG, Cimino JJ, and Ely J. 2010. Automatically extracting information needs from complex clinical questions. Journal of Biomedical Informatics.

       Antieau L and Yu H. 2010. Towards consumer question answering: automatically separating questions posed by physicians from those posed by consumers. Journal of Biomedical Informatics. In revision.

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

       Agarwal S and Yu H. 2010. Biomedical negation scope detection with conditional random fields. Journal of American Medical Informatics Association.

       Liu FF, Kruse A, Hakkani-Tur D, Tur G, and Yu H. 2010. Towards spoken clinical question answering: evaluating automatic speech recognition systems for clinical spoken questions. Journal of American Informatics Association (in revision).

       Cao YG, Liu FF, Antieau L, Simpson P, Cimino JJ, Ely J, Yu H. 2010. AskHERMES: An online question answering system for complex clinical questions. Journal of Biomedical Informatics (in revision)

PEER-REVIEWED CONFERENCE PROCEEDINGS-Long Paper

       Yu H and Sable C. 2005. Being Erlang Shen: Identifying answerable questions. Nineteenth International Joint Conference of Artificial Intelligence (IJCAI) Workshop on Knowledge and Reasoning for Answering Questions, Edinburgh, Scotland.

       Yu H, Sable C, and Zhu HR. 2005. Classifying medical questions based on an evidence taxonomy. 20th National Conference on Artificial Intelligence Workshop on Question Answering in Restricted Domains, Pittsburgh, Pennsylvania.

       Yu H and Wei Y. 2006. The semantics of a definiendum constrains both the lexical semantics and the lexicosyntactic patterns in the definiens.  The Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL-HLT) Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis (BioNLP), New York.

       Lee M, Cimino J, Osheroff J, Ely J, and Yu H. 2006. Beyond information retrievalMedical question answering. American Medical Informatics Association (AMIA) Fall Symposium.

       Yu H. 2006. Towards answering biological questions with experimental evidence: Automatically identifying text that summarize image content in full-text articles. American Medical Informatics Association (AMIA) Fall Symposium, Washington, DC.

       Rafkind B, Lee M, Chang SF, and Yu H. 2006. Exploring text and image features to classify images in bioscience literature.  The Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL-HLT) Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis (BioNLP), New York.

       Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. 2007. New frontiers in biomedical text mining. Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii.

       Yu H and Kaufman D. 2007. A cognitive evaluation of four online information systems by physicians. Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii.

       Cohen KB, Yu H, Bourne PE, and Hirschman L. 2008. Translating biology: text mining tools that work. Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii.

       Yu H, Frid N, McRoy S, Simpson P, Prasad R, Lee A, and Joshi A. 2008. Exploring discourse connectivity in biomedical text for text mining. 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) Linking Literature, Information and Knowledge for Biology (BioLINK) SIG, Toronto, Canada.

       Yu H, Cao YG. 2008. Automatically extracting information needs from ad-hoc clinical questions. American Medical Informatics Association (AMIA) Fall Symposium, San Francisco, California.

       Yu H and Cao YG. 2009. Using the weighted keyword models to improve information retrieval for answering biomedical questions. American Medical Informatics Association (AMIA) Summit on Translational Bioinformatics, San Francisco, California.

       Kim D and Yu H. 2009. Hierarchical image classification in the bioscience literature. American Medical Informatics Association (AMIA) Fall Symposium, San Francisco, California.

       Zhang Q and Yu H. 2009. Parsing citations using conditional random fields. American Medical Informatics Association (AMIA) Fall Symposium, San Francisco, California.

       Yu H, Agarwal S, and Frid N. 2009. Investigating and annotating the role of citation in biomedical full-text articles. IEEE International Conference on Bioinformatics & Biomedicine Workshop NLP Approaches for Unmet Information Needs in Health Care, Washington, DC. Chen et al. Editor. 331-335.

       Cao YG, Ely J, and Yu H. 2009. Using weighted keywords to improve clinical question answering. IEEE International Conference on Bioinformatics & Biomedicine Workshop NLP Approaches for Unmet Information Needs in Health Care, Washington, DC. Chen et al. Editor, 308-313.

       Ramesh BP, Prasad R, Yu H. 2010. Identifying explicit discourse connective in biomedical text. American Medical Informatics Association (AMIA) Fall Symposium. In press.

       Agarwal S, Yu H. 2010. Automatically classifying role of citations in biomedical articles. American Medical Informatics Association (AMIA) Fall Symposium.

Poster Presentation

       Yu H, Frid N, McRoy S, Prasad R, Lee A, and Joshi A. 2008. A pilot annotation to investigate discourse connectivity in biomedical text. 46th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies (BioNLP), Columbus, Ohio.

       Cao YG, Ely J, Antieau L, and Yu H. 2009. Evaluation of the clinical question answering presentation. The North American Chapter of the Association for Computational

       Linguistics-Human Language Technologies (NAACL-HLT) Conference BioNLP, Boulder, Colorado.

       Agarwal S and Yu H. 2009. Adding automatically generated summaries to biomedical figures to improve literature search. American Medical Informatics Association (AMIA) Fall Symposium, San Francisco, California.

       Cao YG and Yu H. 2009. American Medical Informatics Association (AMIA) Fall Symposium, San Francisco, California.

       Zhang Q and Yu H. 2009. CitHit C An automatic citation recognition system. American Medical Informatics Association (AMIA) Fall Symposium, San Francisco, California.