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Issue No.04 - July-Aug. (2012 vol.9)
pp: 1190-1202
Yanpeng Li , Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
ABSTRACT
Extracting protein-protein interaction (PPI) from biomedical literature is an important task in biomedical text mining (BioTM). In this paper, we propose a hash subgraph pairwise (HSP) kernel-based approach for this task. The key to the novel kernel is to use the hierarchical hash labels to express the structural information of subgraphs in a linear time. We apply the graph kernel to compute dependency graphs representing the sentence structure for protein-protein interaction extraction task, which can efficiently make use of full graph structural information, and particularly capture the contiguous topological and label information ignored before. We evaluate the proposed approach on five publicly available PPI corpora. The experimental results show that our approach significantly outperforms all-path kernel approach on all five corpora and achieves state-of-the-art performance.
INDEX TERMS
proteins, data mining, graph theory, medical information systems, PPI corpora, hash subgraph pairwise kernel, protein-protein interaction extraction, biomedical literature, biomedical text mining, graph kernel, dependency graphs, sentence structure, Kernel, Syntactics, Proteins, Protein engineering, Feature extraction, Bioinformatics, Arrays, graph kernel., Biomedical text mining, hash, interaction extraction
CITATION
Yanpeng Li, "Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no. 4, pp. 1190-1202, July-Aug. 2012, doi:10.1109/TCBB.2012.50
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