Protein-Protein interactions classification from text via local learning with class priors

  • Authors:
  • Yulan He;Chenghua Lin

  • Affiliations:
  • School of Engineering, Computing and Mathematics, University of Exeter, Exeter;School of Engineering, Computing and Mathematics, University of Exeter, Exeter

  • Venue:
  • NLDB'09 Proceedings of the 14th international conference on Applications of Natural Language to Information Systems
  • Year:
  • 2009

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Abstract

Text classification is essential for narrowing down the number of documents relevant to a particular topic for further pursual, especially when searching through large biomedical databases. Protein-protein interactions are an example of such a topic with databases being devoted specifically to them. This paper proposed a semi-supervised learning algorithm via local learning with class priors (LL-CP) for biomedical text classification where unlabeled data points are classified in a vector space based on their proximity to labeled nodes. The algorithm has been evaluated on a corpus of biomedical documents to identify abstracts containing information about protein-protein interactions with promising results. Experimental results show that LL-CP outperforms the traditional semi-supervised learning algorithms such as SVM and it also performs better than local learning without incorporating class priors.