Biomedical Relationship Extraction from literature based on bio-semantic token subsequences
by Jayasimha R. Katukuri, Ying Xie, Vijay V. Raghavan
International Journal of Functional Informatics and Personalised Medicine (IJFIPM), Vol. 3, No. 1, 2010

Abstract: Relationship Extraction (RE) from biomedical literature is an important and challenging problem in both text mining and bioinformatics. Although various approaches have been proposed to extract protein–protein interaction types, their accuracy rates leave a large room for further exploring. In this paper, two supervised learning algorithms based on newly defined ''bio-semantic token subsequence'' are proposed for multi-class biomedical relationship classification. The first approach calculates a ''bio-semantic token subsequence kernel'', whereas the second one explicitly extracts weighted features from bio-semantic token subsequences. The two proposed approaches outperform several alternatives reported in literature on multi-class protein–protein interaction classification.

Online publication date: Fri, 14-May-2010

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