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Simple algorithms for complex relation extraction with applications to biomedical IE

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Published:25 June 2005Publication History

ABSTRACT

A complex relation is any n-ary relation in which some of the arguments may be be unspecified. We present here a simple two-stage method for extracting complex relations between named entities in text. The first stage creates a graph from pairs of entities that are likely to be related, and the second stage scores maximal cliques in that graph as potential complex relation instances. We evaluate the new method against a standard baseline for extracting genomic variation relations from biomedical text.

References

  1. A. L. Berger, S. A. Della Pietra, and V. J. Della Pietra. 1996. A maximum entropy approach to natural language processing. Computational Linguistics, 22(1). Google ScholarGoogle ScholarDigital LibraryDigital Library
  2. D. M. Bikel, R. Schwartz, and R. M. Weischedel. 1999. An algorithm that learns what's in a name. Machine Learning Journal Special Issue on Natural Language Learning, 34(1/3):221--231. Google ScholarGoogle ScholarDigital LibraryDigital Library
  3. C. Bron and J. Kerbosch. 1973. Algorithm 457: finding all cliques of an undirected graph. Communications of the ACM, 16(9):575--577. Google ScholarGoogle ScholarDigital LibraryDigital Library
  4. N. Collier, C. Nobata, and J. Tsujii. 2000. Extracting the names of genes and gene products with a hidden Markov model. In Proc. COLING. Google ScholarGoogle ScholarDigital LibraryDigital Library
  5. D. Gildea and D. Jurafsky. 2002. Automatic labeling of semantic roles. Computational Linguistics. Google ScholarGoogle ScholarDigital LibraryDigital Library
  6. Taku Kudo and Yuji Matsumoto. 2001. Chunking with support vector machines. In Proc. NAACL. Google ScholarGoogle ScholarDigital LibraryDigital Library
  7. J. Lafferty, A. McCallum, and F. Pereira. 2001. Conditional random fields: Probabilistic models for segmenting and labeling sequence data. In Proc. ICML. Google ScholarGoogle ScholarDigital LibraryDigital Library
  8. A. McCallum and B. Wellner. 2003. Toward conditional models of identity uncertainty with application to proper noun coreference. In IJCAI Workshop on Information Integration on the Web.Google ScholarGoogle Scholar
  9. A. McCallum, D. Freitag, and F. Pereira. 2000. Maximum entropy Markov models for information extraction and segmentation. In Proc. ICML. Google ScholarGoogle ScholarDigital LibraryDigital Library
  10. A. K. McCallum. 2002. MALLET: A machine learning for language toolkit.Google ScholarGoogle Scholar
  11. D. M. McDonald, H. Chen, H. Su, and B. B. Marshall. 2004a. Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser. Bioinformatics, 20(18):3370--78. Google ScholarGoogle ScholarDigital LibraryDigital Library
  12. R. T. McDonald, R. S. Winters, M. Mandel, Y. Jin, P. S. White, and F. Pereira. 2004b. An entity tagger for recognizing acquired genomic variations in cancer literature. Bioinformatics, 20(17):3249--3251. Google ScholarGoogle ScholarDigital LibraryDigital Library
  13. S. Miller, H. Fox, L. A. Ramshaw, and R. M. Weischedel. 2000. A novel use of statistical parsing to extract information from text. In Proc. NAACL. Google ScholarGoogle ScholarDigital LibraryDigital Library
  14. V. Punyakanok, D. Roth, W. Yih, and D. Zimak. 2004. Learning via inference over structurally constrained output. In Workshop on Learning Structured with Output, NIPS.Google ScholarGoogle Scholar
  15. Barbara Rosario and Marti A. Hearst. 2004. Classifying semantic relations in bioscience texts. In ACL. Google ScholarGoogle ScholarDigital LibraryDigital Library
  16. D. Roth and W. Yih. 2004. A linear programming formulation for global inference in natural language tasks. In Proc. CoNLL.Google ScholarGoogle Scholar
  17. D. Zelenko, C. Aone, and A. Richardella. 2003. Kernel methods for relation extraction. JMLR. Google ScholarGoogle ScholarDigital LibraryDigital Library
  1. Simple algorithms for complex relation extraction with applications to biomedical IE

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      • Published in

        cover image DL Hosted proceedings
        ACL '05: Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics
        June 2005
        657 pages
        • General Chair:
        • Kevin Knight

        Publisher

        Association for Computational Linguistics

        United States

        Publication History

        • Published: 25 June 2005

        Qualifiers

        • Article

        Acceptance Rates

        ACL '05 Paper Acceptance Rate77of423submissions,18%Overall Acceptance Rate85of443submissions,19%

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