MEDLANG: Medical Language Study Group

MEDLANG
Medical Language Study Group

A collaboration between
the Department of Computer Science and Enginneering, the Program in Linguistics, University of Minnesota
and the Mayo Clinic Biomedical Informatics Division.

Meetings

Guest Speakers

Karin Kipper Schuler, "Lexical Semantic Resources for Information Processing," May 1, 2006,
Jerry R. Hobbs, "Ontologies of Time, Space, and Events," February 13, 2006.
Donna Byron, "Building Reference Software 101," November 5, 2005.
Andrew Kehler, "Adventures in Statistical Pronoun Interpretation," May 5, 2005.
Ron Zacharski, "Finding relevant information: From statistical methods to advanced question answering," May 3, 2004.
Thomas C. Rindflesch, "Knowledge-Based Semantic Interpretation for Biomedical Text," April 2, 2004.

Projects

Coreference annotation project for the AAAI 2005 workshop on Knowledge Collection from Volunteer Contributors (KCVC05)
A collection of medical abstracts annotated for coreference and used in "Anaphora Resolution in Biomedical Literature" (Castaño, Zhang, & Pustejovsky, see bibliography) may be found at http://medstract.org/gold-standards.html. A more readable version of the abstracts (stripped of annotation) may be found here.

Bibliography

medlang.bib

Data

Sample Journal Article

People

Faculty and Fellows

Computer Science	Linguistics	Mayo Clinic
Daniel Boley Maria Gini William Schuler	Jeanette Gundel Hooi Ling Soh	Serguei Pakhomov, Mayo Clinic Guergana Savova, Mayo Clinic

Students

Graduate	Undergraduate
David McKoskey Tim Miller Shana Watters	Matthew Beckman Anya Polukeyeva

Readings

Papers Discussed

Thomas Rindflesch, Jayant Rajan, and Lawrence Hunter, "Extracting Molecular Binding Relationships from Biomedical Text", Proceedings of the ANLP-NAACL, pp. 188-195, 2000
Lynette Hirschman, Jong Park, Junichi Tsujii, and Limsoon Wong, "Accomplishments and Challenges in Literature Data Mining for Biology", Bioinformatics Review, Volume 18, Number 12, pp. 1-12, 2002
José Castaño, Jason Zhang, and James Pustejovsky, "Anaphora Resolution in Biomedical Literature", International Symposium on Reference Resolution, 2002
Gerard Salton and Christopher Buckley, "Term-weighting approaches in automatic text retrieval", Information Processing & Management, Volume 24, Number 5, pp. 513-523, 1988
Olivier Bodenrider, "The Unified Medical Language System (UMLS): integrating biomedical terminology", Nucleic Acids Research, Volume 32, pp. D267-D270, 2004
Other interesting work by Olivier Bodenrider on medical ontologies and terminology development.
UMLS Main Site
UMLS 2003AC System Documentation
Marilyn Walker, Aravind Joshi, and Ellen Prince, "Centering in Naturally Occuring Discourse: An Overview" (i.e. the introductory chapter) in Centering Theory and Discourse, Marilyn Walker, Aravind Joshi, and Ellen Prince (eds.), Clarendon Press, Oxford, 1998
André Grüning and Andrej A. Kibrik, "Referential Choice and Activation Factors: A Neural Network Approach" in Proceedings of the Discourse Anaphora and Anaphor Resolution Colloquium (DAARC), 2002.
Jerry Hobbs, "Resolving Pronoun References" in Lingua, Volume 44, pp. 311 - 338, 1978.
Wee Meng Soon, Daniel Chung Yong Lim and Hwee Tou Ng, "A Machine Learning Approach to Coreference Resolution of Noun Phrases" in Computational Linguistics, Volume 27, Number 4, December 2001
Niyu Ge, John Hale, and Eugene Charniak "A Statistical Approach to Anaphora Resolution" in Proceedings of the Sixth Workshop on Very Large Corpora, 1998

Additional Papers: COLING 2004

Michael Schiehlen, "Optimizing Algorithms for Pronoun Resolution" in Proceedings of the 20th International Conference on Computational Linguistics (COLING 2004)
Xiaofeng Yang, Jian Su, Guodong Zhou and Chew Lim Tan, "An NP-Cluster Based Approach to Coreference Resolution" in Proceedings of the 20th International Conference on Computational Linguistics (COLING 2004)
Guodong Zhou and Jian Su, "A High-Performance Coreference Resolution System using a Constraint-based Multi-Agent Strategy" in Proceedings of the 20th International Conference on Computational Linguistics (COLING 2004)
Ryohei Sasano, Daisuke Kawahara and Sadao Kurohashi, "Automatic Construction of Nominal Case Frames and its Application to Indirect Anaphora Resolution" in Proceedings of the 20th International Conference on Computational Linguistics (COLING 2004)
Costanza Navarretta, "Resolving Individual and Abstract Anaphora in Texts and Dialogues" in Proceedings of the 20th International Conference on Computational Linguistics (COLING 2004)
Kaja Borthen, "Predicative NPs and the Annotation of Reference Chains" in Proceedings of the 20th International Conference on Computational Linguistics (COLING 2004)
Roderick Son, Ricky Taira, and Hooshang Kangarloo, "Inter-document Coreference Resolution of Abnorman Findings in Radiology Documents" in Proceedings of MEDINFO 2004

Background

Michael W. Berry, Zlatko Drmac, and Elizabeth R. Jessup, "Matrices, Vector Spaces, and Information Retrieval", SIAM Review, Volume 42, Number 2, pp. 335-362,

Funding from the University of Minnesota Graduate School IRSCA program for "Exploratory Initiative in Interdisciplinary Research in Natural Language Processing, Text Understanding, and Information Extraction/Data Mining, within a Biomedical Domain" is gratefully acknowledged.