Biomedical event extraction from abstracts and full papers using search-based structured prediction

Authors:
Andreas Vlachos;Mark Craven
Affiliations:
University of Wisconsin-Madison;University of Wisconsin-Madison
Venue:
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Year:
2011

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Abstract

In this paper we describe our approach to the BioNLP 2011 shared task on biomedical event extraction from abstracts and full papers. We employ a joint inference system developed using the search-based structured prediction framework and show that it improves on a pipeline using the same features and it is better able to handle the domain shift from abstracts to full papers. In addition, we report on experiments using a simple domain adaptation method.