Event extraction as dependency parsing for BioNLP 2011

David McClosky, Mihai Surdeanu, Christopher D. Manning

Research output: Chapter in Book/Report/Conference proceedingConference contribution

38 Scopus citations

Abstract

We describe the Stanford entry to the BioNLP 2011 shared task on biomolecular event extraction (Kim et al., 2011a). Our framework is based on the observation that event structures bear a close relation to dependency graphs. We show that if biomolecular events are cast as these pseudosyntactic structures, standard parsing tools (maximum-spanning tree parsers and parse rerankers) can be applied to perform event extraction with minimum domain-specific tuning. The vast majority of our domain-specific knowledge comes from the conversion to and from dependency graphs. Our system performed competitively, obtaining 3rd place in the Infectious Diseases track (50.6% f-score), 5th place in Epigenetics and Post-translational Modifications (31.2%), and 7th place in Genia (50.0%). Additionally, this system was part of the combined system in Riedel et al. (2011) to produce the highest scoring system in three out of the four event extraction tasks.

Original languageEnglish (US)
Title of host publicationProceedings of BioNLP Shared Task 2011 Workshop at the 49th Annual Meeting of the Association for Computational Linguistics
Subtitle of host publicationHuman Language Technologies, ACL HLT 2011
EditorsJun'ichi Tsujii, Jin-Dong Kim, Sampo Pyysalo
PublisherAssociation for Computational Linguistics (ACL)
Pages41-45
Number of pages5
ISBN (Electronic)9781937284091
StatePublished - 2011
EventBioNLP Shared Task 2011 Workshop at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL HLT 2011 - Portland, United States
Duration: Jun 24 2011 → …

Publication series

NameProceedings of BioNLP Shared Task 2011 Workshop at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL HLT 2011

Conference

ConferenceBioNLP Shared Task 2011 Workshop at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL HLT 2011
Country/TerritoryUnited States
CityPortland
Period6/24/11 → …

ASJC Scopus subject areas

  • Language and Linguistics
  • Computer Science Applications
  • Information Systems
  • Software
  • Biomedical Engineering
  • Health Informatics

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