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Open Access Highly Accessed Open Badges Research article

Walk-weighted subsequence kernels for protein-protein interaction extraction

Seonho Kim1, Juntae Yoon2, Jihoon Yang1 and Seog Park1

Author Affiliations

1 Department of Computer Science, Sogang University, Seoul, Korea

2 Daumsoft Inc, Se-Ah Venture Tower, Seoul, Korea

BMC Bioinformatics 2010, 11:107  doi:10.1186/1471-2105-11-107

Published: 25 February 2010



The construction of interaction networks between proteins is central to understanding the underlying biological processes. However, since many useful relations are excluded in databases and remain hidden in raw text, a study on automatic interaction extraction from text is important in bioinformatics field.


Here, we suggest two kinds of kernel methods for genic interaction extraction, considering the structural aspects of sentences. First, we improve our prior dependency kernel by modifying the kernel function so that it can involve various substructures in terms of (1) e-walks, (2) partial match, (3) non-contiguous paths, and (4) different significance of substructures. Second, we propose the walk-weighted subsequence kernel to parameterize non-contiguous syntactic structures as well as semantic roles and lexical features, which makes learning structural aspects from a small amount of training data effective. Furthermore, we distinguish the significances of parameters such as syntactic locality, semantic roles, and lexical features by varying their weights.


We addressed the genic interaction problem with various dependency kernels and suggested various structural kernel scenarios based on the directed shortest dependency path connecting two entities. Consequently, we obtained promising results over genic interaction data sets with the walk-weighted subsequence kernel. The results are compared using automatically parsed third party protein-protein interaction (PPI) data as well as perfectly syntactic labeled PPI data.