Model combination for event extraction in BioNLP 2011

Sebastian Riedel, David McClosky, Mihai Surdeanu, Andrew McCallum, Christopher D. Manning

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

54 Scopus citations

Abstract

We describe the FAUST entry to the BioNLP 2011 shared task on biomolecular event extraction. The FAUST system explores several stacking models for combination using as base models the UMass dual decomposition (Riedel and McCallum, 2011) and Stanford event parsing (McClosky et al., 2011b) approaches. We show that using stacking is a straightforward way to improving performance for event extraction and find that it is most effective when using a small set of stacking features and the base models use slightly different representations of the input data. The FAUST system obtained 1st place in three out of four tasks: 1st place in Genia Task 1 (56.0% f-score) and Task 2 (53.9%), 2nd place in the Epigenetics and Post-translational Modifications track (35.0%), and 1st place in the Infectious Diseases track (55.6%).

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)
Pages51-55
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

Fingerprint

Dive into the research topics of 'Model combination for event extraction in BioNLP 2011'. Together they form a unique fingerprint.

Cite this