My UWM homepage is here

My research interests are text-mining, knowledge representation, and user-centric systems.

I co-chair the PSB 2008 Translating Biology: Text Mining Tools that Work that CFP Utility, Usability, Portability, and Robustness of text mining systems.

I serve as a founding Scientific Program Committee member for AMIA Summit on Translational Bioinformatics 2008

I serve as a program committee member for ACL07-BioNLP, ISMB BioLINK 2007, LBM 2007 and IEEE-BIBM KDMHI 2007

I co-chair the PSB 2007 New Frontiers in Biomedical Text Mining that CFP question answering, summarization, mining full-text, coreference resolution, user-driven systems, and evaluation.

PhD Students: Shashank Agarwal, Minsuk Lee, Kourosh Ravvaz, Yi Hong

Postdocs: offer made

Publications

2007

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

Yu, H and Kaufman D. 2007. A cognitive evaluation of four online search engines for answering definitional questions posed by physicians. Pacific Symposium on Biocomputing.pdf

Yu, H Kim W, Hatzivassiloglou V, and Wilbur WJ. Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. J Biomed Inform. 2007 Apr;40(2):150-9.abstract

Zweigenbaum, P, Demner-Fushman D, Yu H, Cohen KB. 2007. New frontiers in biomedical text mining. Pacific Symposium on Biocomputing (PSB) 12:205-208. pdf

Tulipano PK, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Chen LF, Yu H, Lussier, YA, Friedman C. 2007. Natural Language Processing and Visualization in the Molecular Imaging Domain. Journal of Biomedical Informatics (JBI). 40: 270-281.

2006

Yu, H and Lee M. 2006. Accessing Bioscience Images from Abstract Sentences. Bioinformatics. Vol 22 No. 14, pages e547-e556. Paper also appears in Proceedings of the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006). pdf

Yu, H , Kim W, Hatzivassiloglou V, and Wilbur J. 2006. Disambiguating biomedical abbreviations. ACM Transactions on Information Systems (TOIS) Vol (24), Issue No. 3. page 380-404 pdf

Yu, H and Lee M. 2006. BioEx: A Novel User-Interface that Accesses Images from Abstract Sentences. Paper in HLT-NAACL 2006.

Yu, H and Wei Y. 2006. The semantics of a definiendum constrains both the lexical semantics and the lexicosyntactic patterns in the definiens. Paper in HLT-NAACL 2006 Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis (BioNLP'06). pdf

Yu, H, Kim W, Hatzivassiloglou V, and Wilbur J. 2006. Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. To appear in Journal of Biomedical Informatics.

Rafkind, B, Lee M, Chang SF, and Yu H. 2006. Exploring text and image features to classify images in bioscience literature. Paper in HLT-NAACL 2006 Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis (BioNLP'06).pdf

Lee M, Cimino J, Zhu HR, Sable C, Shanker V, Ely J, and Yu H. 2006. Beyond information retrieval-Medical question answering. To appear in Proceedings of American Medical Informatics Association (AMIA).pdf

Lee M, Wang WQ, Yu H. Exploring supervised and unsupervised methods to detect topics in Biomedical text. BMC Bioinformatics. pdf

Yu, H. 2006. Towards answering biological questions with experimental evidence: Automatically identifying text that summarize image content in full-text articles. To appear in Proceedings of American Medical Informatics Association (AMIA).pdf

Tulipano PK, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Chen LF, Yu H, Lussier, YA, Friedman C. Natural Language Processing and Visualization in the Molecular Imaging Domain. To appear in Journal of Biomedical Informatics.

2005

Yu, H., Carl Sable. 2005. Being Erlang Shen: Identifying answerable questions. IJCAI-KRAQ.

Yu, H, Carl Sable, and Hai Ran Zhu. 2005. Classifying medical questions based on an evidence taxonomy. AAAI Workshop on Question Answering in Restricted Domains.

Zhu HR, Yu H. 2005. A Comparative Study for Automatic Zone Identification in MEDLINE. In BioLINK SIG: Linking Literature, Information and Knowledge for Biology. Poster.

Sable C, Lee M, Zhu HR, Yu H. 2005. Question Analysis for Biomedical Question Answering. In American Medical Informatics Association fall symposium 2005 Abstract.

Andrey Rzhetsky, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboue, Wubin Weng, John W. Wilbur, Vasileios Hatzivassiloglou, and Carol Friedman. Chapter 14: GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data. Databasing the Brain: From Data to Knowledge (Neuroinformatics). Steven H. Koslow (Editor), Shankar Subramaniam (Editor). Wiley Publisher, 2005.

Steven Bethard, Hong Yu, Ashley Thornton, Vasileios Hatzivassiloglou, and Dan Jurafsky. Extracting opinion propositions and opinion holders using syntactic and lexical cues. Computing Attitude and Affect in Text: Theories and Applications. James G. Shanahan, Yan Qu, Janyce Wiebe (Eds.) Springer, Dordrecht, The Netherlands, 2005.

2004

Bethard, S., Yu H, Thornton A, Hatzivassiloglou V and Jurafsky D. 2004. Semantic analysis of propositional opinions. In AAAI 2004 Spring Symposium on Exploring Attitude and Affect in Text: Theories and Applications.

Rzhetsky, A., I. Iossifov, T. Koike, M.Krauthammer, P. Kra, M. Morris, H. Yu, P.A. Duboue, W. Weng, V. Hatzivassiloglou and C. Friedman. GeneWays: A System for extracting, analyzing, visualizing and integrating molecular pathway data. Journal of Biomedical Informatics (JBI).

2003

Yu,H, V. Hatzivassiloglou, A. Rzhetsky and W.J. Wilbur. 2003. Automatically Identifying Gene/Protein Terms in MEDLINE Abstracts. Journal of Biomedical Informatics.

Yu,H and V. Hatzivassiloglou. 2003. Towards Answering Opinion Questons: Separating Facts from Opinions and Identifying the Polarity of Opinion Sentences, In Proceedings of the 2003 Conference on Empirical Methods in Natural Language Processing (EMNLP 2003).

Yu,H and E. Agichtein. Extracting Synonymous Gene and Protein Terms from Biological Literature, Journal of Bioinformatics Vol 19(Suppl):i340-i349 (ISMB).

2002

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

Yu,H., Hatzivassiloglou V, Friedman C, Wilbur WJ. 2002. Automatic Extraction of Gene and Protein Synonyms from MEDLINE and Journal Articles, Proc AMIA Symp 2002.

Theses

PhD thesis: Synonym and homonym resolution of gene and protein names.

Pradhan, S.S., Illouz G, Blair-Goldensohn SJ, Schlaikjer AH, Krugler V, Filatova E, Duboue PA, Yu H, Passonneau BJ, Bethard S,
Hatzivassiloglou V, Ward W, Jurafsky D, McKeown KR, Martin JH.  Building a foundation system for producing short answers to factual
questions. TREC.

2001

Friedman C, Kra P, Yu H., Krauthammer M, Rzhetsky A. 2001. GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles. Journal of Bioinformatics (ISMB). 2001 Suppl 1:S74-82.

Yu, H. 2001. Automatic extraction from MEDLINE of synonyms for proteins and genes. Proc AMIA Symp 2001.

Yu, H. 2001. Knowledge-based disambiguation of abbreviations.  Proc AMIA Symp 2001.

2000

Yu, H., Hripcsak G. 2000. Hereditary disease discovery from a clinical data warehouse. Proc AMIA Symp 2000.

Yu, H., Hripcsak G. 2000. A large scale, cross-disease family health history. Proc AMIA Symp 2000.

1999

Yu,H., Friedman C, Rzhetsky A, Kra P. 1999. Representing genomic knowledge in the UMLS semantic network. Proc AMIA Symp 1999:181-5. Nominated for Best Paper Award, AMIA annual symposium, 1999.