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Utilizing Various Natural Language Processing Techniques for Biomedical Interaction Extraction

  • Park, Kyung-Mi (Dept. of Computer Science and Engineering, Korea University) ;
  • Cho, Han-Cheol (Dept. of Computer Science and Engineering, Korea University) ;
  • Rim, Hae-Chang (Dept. of Computer Science and Engineering, Korea University)
  • Received : 2010.11.25
  • Accepted : 2011.04.12
  • Published : 2011.09.30

Abstract

The vast number of biomedical literature is an important source of biomedical interaction information discovery. However, it is complicated to obtain interaction information from them because most of them are not easily readable by machine. In this paper, we present a method for extracting biomedical interaction information assuming that the biomedical Named Entities (NEs) are already identified. The proposed method labels all possible pairs of given biomedical NEs as INTERACTION or NO-INTERACTION by using a Maximum Entropy (ME) classifier. The features used for the classifier are obtained by applying various NLP techniques such as POS tagging, base phrase recognition, parsing and predicate-argument recognition. Especially, specific verb predicates (activate, inhibit, diminish and etc.) and their biomedical NE arguments are very useful features for identifying interactive NE pairs. Based on this, we devised a twostep method: 1) an interaction verb extraction step to find biomedically salient verbs, and 2) an argument relation identification step to generate partial predicate-argument structures between extracted interaction verbs and their NE arguments. In the experiments, we analyzed how much each applied NLP technique improves the performance. The proposed method can be completely improved by more than 2% compared to the baseline method. The use of external contextual features, which are obtained from outside of NEs, is crucial for the performance improvement. We also compare the performance of the proposed method against the co-occurrence-based and the rule-based methods. The result demonstrates that the proposed method considerably improves the performance.

Keywords

Biomedical Interaction Extraction;Natural Language Processing;Interaction Verb Extraction;Argument Relation Identification

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