title: SHOPIN: Semantic Homogeneity Optimization in Protein Interaction Networks.
abstract: Protein interaction networks (PINs) are argued to be the richest source of hidden knowledge of the intrinsic physical and/or functional meanings of the involved proteins. We propose a novel method for computational protein function prediction based on semantic homogeneity optimization in PIN (SHOPIN). The SHOPIN method creates graph representations of the PIN augmented by inclusion of the semantics of the proteins and their interacting contexts. Network wide semantic relationships, modeled using random walks, are used to map the augmented PIN graphs in a new semantic metric space. The method produces a hierarchical partitioning of the PIN optimal in terms of semantic homogeneity by iterative optimization of the ratio of between clusters dissimilarities and within clusters similarities in the new semantic metric space. Function prediction is done using cluster wide-hierarchy high function enrichment. Results validate the rationale of the SHOPIN method placing it right next to state-of-the-art approaches performance wise.
authors.affiliation: Faculty of Computer Science and Engineering, University Ss. Cyril and Methodius, Skopje, Macedonia.
authors.forename: Kire
authors.initials: K
authors.lastname: Trivodaliev
authors.affiliation: Faculty of Computer Science and Engineering, University Ss. Cyril and Methodius, Skopje, Macedonia.
authors.forename: Slobodan
authors.initials: S
authors.lastname: Kalajdziski
authors.affiliation: Faculty of Computer Science and Engineering, University Ss. Cyril and Methodius, Skopje, Macedonia.
authors.forename: Ilinka
authors.initials: I
authors.lastname: Ivanoska
authors.affiliation: Faculty of Computer Science and Engineering, University Ss. Cyril and Methodius, Skopje, Macedonia.
authors.forename: Biljana Risteska
authors.initials: BR
authors.lastname: Stojkoska
authors.affiliation: Faculty of Computer Science and Engineering, University Ss. Cyril and Methodius, Skopje, Macedonia; Macedonian Academy of Sciences and Arts, Skopje, Macedonia; BioCircuits Institute, University of California, San Diego, California, USA. Electronic address: lkocarev@manu.edu.mk.
authors.forename: Ljupco
authors.initials: L
authors.lastname: Kocarev
mesh_terms: D019295:Computational Biology; D008962:Models, Theoretical; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins
keywords: Clustering; Protein interaction networks; Semantic homogeneity; Semantic similarity