title: Integrating semantic information into multiple kernels for protein-protein interaction extraction from biomedical literatures.
abstract: Protein-Protein Interaction (PPI) extraction is an important task in the biomedical information extraction. Presently, many machine learning methods for PPI extraction have achieved promising results. However, the performance is still not satisfactory. One reason is that the semantic resources were basically ignored. In this paper, we propose a multiple-kernel learning-based approach to extract PPIs, combining the feature-based kernel, tree kernel and semantic kernel. Particularly, we extend the shortest path-enclosed tree kernel (SPT) by a dynamic extended strategy to retrieve the richer syntactic information. Our semantic kernel calculates the protein-protein pair similarity and the context similarity based on two semantic resources: WordNet and Medical Subject Heading (MeSH). We evaluate our method with Support Vector Machine (SVM) and achieve an F-score of 69.40% and an AUC of 92.00%, which show that our method outperforms most of the state-of-the-art systems by integrating semantic information.
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, China.
authors.forename: Lishuang
authors.initials: L
authors.lastname: Li
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, China.
authors.forename: Panpan
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, China.
authors.forename: Tianfu
authors.initials: T
authors.lastname: Zheng
authors.affiliation: Department of Pathology, Dalian Medical University, Dalian, China.
authors.forename: Hongying
authors.initials: H
authors.lastname: Zhang
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, China.
authors.forename: Zhenchao
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: School of Computer Science and Technology, Dalian University of Technology, Dalian, China.
authors.forename: Degen
authors.initials: D
authors.lastname: Huang
mesh_terms: D000465:Algorithms; D035843:Biomedical Research; D046650:Medical Subject Headings; D009323:Natural Language Processing; D025941:Protein Interaction Mapping; D011642:Publications; D012660:Semantics