An Interaction Pattern Kernel Approach for Protein-Protein Interaction Extraction from Biomedical Literature

  • Yung-Chun Chang
  • Yu-Chen Su
  • Nai-Wen Chang
  • Wen-Lian Hsu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8916)

Abstract

Discovering the interactions between proteins mentioned in biomedical literature is one of the core topics of text mining in the life sciences. In this paper, we propose an interaction pattern generation approach to capture frequent PPI patterns in text. We also present an interaction pattern tree kernel method that integrates the PPI pattern with convolution tree kernel to extract protein-protein interactions. Empirical evaluations on LLL, IEPA, and HPRD50 corpora demonstrate that our method is effective and outperforms several well-known PPI extraction methods.

Keywords

Text Mining Protein-Protein Interaction Interaction Pattern Generation Interaction Pattern Tree Kernel 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Yung-Chun Chang
    • 1
    • 2
  • Yu-Chen Su
    • 2
  • Nai-Wen Chang
    • 1
    • 3
  • Wen-Lian Hsu
    • 1
  1. 1.Institute of Information ScienceAcademia SimicaTaipei CityTaiwan (R.O.C)
  2. 2.Department of Information ManagementNational Taiwan UniversityTaipei CityTaiwan (R.O.C)
  3. 3.Graduate Institute of Biomedical Electronics and BioinformaticsTaipei CityTaiwan (R.O.C)

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