Hong  Yu, Ph.D. 

Assistant Professor 

Interests and Expertise
I am interested in building information systems for biologists and physicians that allow them to efficiently access information from heterogenous databases (e.g., literature, electronic medical records, images, Web, and other types of databases). I am interested in developing natural language processing, information retrieval and extraction, text-mining and question answering techniques.


Professional Service:
Co-chair: Pacific Symposium on Biocomputing 2007 New Frontiers in Biomedical Text Mining.

Review Panel: NIH Grant Review panel; R01, R21, R03, and SBIR research proposals.

Programming Committee Member Journals: Bioinformatics, Journal of Biomedical Informatics, IEEE Transactions Systems, Man and Cybernetics, Computational Intelligence

Programming Committee Member Conferences: AMIA. BioLINK SIG, AAAI, BioNLP

Recent Publications
2007:
Yu, H and Kaufman D. 2007. A cognitive evaluation of four online search engines for answering definitional questions posed by physicians. To appear in Pacific Symposium on Biocomputing New Frontiers in Biomedical Text Mining.


2006:
Lee M, Wang WQ and Yu H. 2006. Topic detection in biomedical text. BMC Bioinformatics, 7(1):140.

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.

Lee M, Cimino J, Osheroff J, Ely J, and Yu H. 2006. Beyond information retrieval-Medical question answering. To appear in Proceedings of American Medical Informatics Association (AMIA).

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 Assocation (AMIA).

Lee, M, Cimino J, Osheroff J, Ely J, and Yu H, 2006. Beyond information retrieval--medical question answering. To apear in Proceedings of American Medical Informatics Association (AMIA).

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).

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.

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).

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).

Yu, H, Kim W, Hatzivassiloglou V, and Wilbur J. 2006. Disambiguating biomedical abbreviations. To appear in ACM Transactions on Information Systems (TOIS) Vol (24), Issue No. 3.


2005:
Bethard S, Yu H, Thornton A, Hatzivassiloglou V, and Jurafsky D. Extracting opinion propositions and opinion holders using syntactic and lexical cues. Exploring Attitude and Affect in Text: Theories and Applications. Kluwer Academic Publisher.

Yu, H and Sable C. 2005. Being Erlang Shen: Identifying Answerable Questions. Paper in International Joint Conference of Artificial Intelligence (IJCAI'05) Workshop on Knowledge and Reasoning for Answering Questions.

Yu, H, Sable C and Zhu HR. 2005. Classifying medical questions based on an Evidence Taxonomy. In American Association for Artificial Intelligence (AAAI'05) Workshop on Question Answering in Restricted Domains.


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, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboue PA, Weng WB, Hatzivassiloglou V and Friedman C. 2004. GeneWays: A System for Extracting, Analyzing, Visualizing and Integrating Molecular Pathway Data. Journal of Biomedical Informatics 2004 Feb;37(1):43-53.

Yu, H, Kim W and Wilbur WJ. 2004. Using MEDLINE as a knowledge source for disambiguating abbreviations in biomedical full-text articles. In 17th IEEE Symposium on Computer-Based Medical Systems


2003:
Pradhan SS, Illouz G, Blair-Goldensohn SJ, Schlaikjer AH, Krugler V, Filatova E, Duboue PA, Yu H, Passonneau R, Bethard S, Hatzivassiloglou V, Ward W, Jurafsky D, McKeown KR and Martin JM. 2003. Building a foundation system for producing short answers to factual questions. In Proceedings of the Eleventh Text REtrieval Conference (TREC).

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

Yu, H and Agichtein E. 2003. Extracting Synonymous Gene and Protein Terms from Biological Literature. Bioinformatics Vol 19 (Suppl 1): i340-i349. Paper also appears in Proceedings of the 11th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2003).

Yu, H, Hatzivassiloglou V, Rzhetsky A and Wilbur WJ. 2003. Automatically Identifying Gene/Protein Terms in MEDLINE abstracts. Journal of Biomedical Informatics (JBI), Vol 35 (5-6): 322-330.


2002:
Yu, H, Hatzivassiloglou V, Friedman C and Wilbur WJ. 2002. Automatic Extraction of Gene and Protein Synonyms from the MEDLINE Abstracts and Journal Articles, In Proceeding of American Medical Informatics Association (AMIA) Symposium 2002.

Yu, H, Hripcsak G and Friedman C. 2002. Mapping Abbreviations to Full Forms in Biomedical Articles. Journal of American Medical Informatics Association (JAMIA) 9(3): 262-272.


Prior to 2002:
Yu, H, Friedman C, Rzhetsky A and Kra P. 1999. Representing Genomic Knowledge in the UMLS Semantic Network. Proc AMIA Symp 1999: 181-5. Nominated for Best Paper Award (one out of five), In Proceeding of American Medical Informatics Association (AMIA) Symposium 1999.

Yu, H and Hripcsak G. 2000. Hereditary Disease Discovery from a Clinical Data Warehouse. In Proceedings of American Medical Informatics Association (AMIA) Symposium 2001:1161.

Yu, H and Hripcsak G. 2000. A Large Scale, Cross-Disease Family Health History. In Proceedings of American Medical Informatics Association (AMIA) Symposium 2001: 1162.

Friedman C, Kra P, Yu H, Krauthammer M, and Rzhetsky A. 2001. GENIES: A Natural-Language Processing System for the Extraction of Molecular Pathways from Journal Articles. Bioinformatics 2001 Suppl 1:S74-82. Paper also appears in Proceedings of the 9th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2001).

Yu, H. 2001. Automatic Extraction from MEDLINE of Synonyms for Proteins and Genes. In Proceedings of American Medical Informatics Association (AMIA) Symposium 2001:1066.

Yu, H. 2001. Knowledge-Based Disambiguation of Abbreviations. In Proceedings of American Medical Informatics Association (AMIA) Symposium 2001:1067.

Speaker Topics 
Information Systems, Health Care
Health Informatics
Health Care Terminology
Digital Libraries