Walk-Weighted Subsequence Kernels for Protein-Protein interaction extraction

Seonho Kim, Juntae Yoon, Jihoon Yang, Seog Park
2010 BMC Bioinformatics  
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. Results: 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
more » ... ying 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. Conclusions: 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. Authors' contributions SHK and JTY carried out PPI studies and suggested overall idea of this manuscript, and the system design. They performed the experiments and analyzed the results. JHY and SP participated in the system design and helped to draft the manuscript. All authors read and approved the final manuscript.
doi:10.1186/1471-2105-11-107 pmid:20184736 pmcid:PMC2844389 fatcat:uw65kplfjbewpg2goy35cqbalu