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Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency

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  • Behrouz Bokharaeian
  • Alberto Diaz
  • Hamidreza Chitsaz

Abstract

Motivation: Supervised biomedical relation extraction plays an important role in biomedical natural language processing, endeavoring to obtain the relations between biomedical entities. Drug-drug interactions, which are investigated in the present paper, are notably among the critical biomedical relations. Thus far many methods have been developed with the aim of extracting DDI relations. However, unfortunately there has been a scarcity of comprehensive studies on the effects of negation, complex sentences, clause dependency, and neutral candidates in the course of DDI extraction from biomedical articles. Results: Our study proposes clause dependency features and a number of features for identifying neutral candidates as well as negation cues and scopes. Furthermore, our experiments indicate that the proposed features significantly improve the performance of the relation extraction task combined with other kernel methods. We characterize the contribution of each category of features and finally conclude that neutral candidate features have the most prominent role among all of the three categories.

Suggested Citation

  • Behrouz Bokharaeian & Alberto Diaz & Hamidreza Chitsaz, 2016. "Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency," PLOS ONE, Public Library of Science, vol. 11(10), pages 1-20, October.
    • Handle: RePEc:plo:pone00:0163480
    DOI: 10.1371/journal.pone.0163480
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    References listed on IDEAS

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    1. Domonkos Tikk & Philippe Thomas & Peter Palaga & Jörg Hakenberg & Ulf Leser, 2010. "A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature," PLOS Computational Biology, Public Library of Science, vol. 6(7), pages 1-19, July.
    2. Linna He & Zhihao Yang & Zhehuan Zhao & Hongfei Lin & Yanpeng Li, 2013. "Extracting Drug-Drug Interaction from the Biomedical Literature Using a Stacked Generalization-Based Approach," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-12, June.
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