title: Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models.
abstract: Graph data are becoming increasingly common in machine learning and data mining, and its application field pervades to bioinformatics and cheminformatics. Accordingly, as a method to extract patterns from graph data, graph mining recently has been studied and developed rapidly. Since the number of patterns in graph data is huge, a central issue is how to efficiently collect informative patterns suitable for subsequent tasks such as classification or regression. In this paper, we consider mining discriminative subgraphs from graph data with multiple labels. The resulting task has important applications in cheminformatics, such as finding common functional groups that trigger multiple drug side effects, or identifying ligand functional groups that hit multiple targets. In computational experiments, we first verify the effectiveness of the proposed approach in synthetic data, then we apply it to drug adverse effect prediction problem. In the latter dataset, we compared the proposed method with L1-norm logistic regression in combination with the PubChem/Open Babel fingerprint, in that the proposed method showed superior performance with a much smaller number of subgraph patterns. Software is available from https://github.com/axot/GLP.
authors.affiliation: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology , Iizuka, Fukuoka 820-8502, Japan.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Shao
authors.affiliation: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology , Iizuka, Fukuoka 820-8502, Japan.
authors.forename: Yuya
authors.initials: Y
authors.lastname: Hirayama
authors.affiliation: Division of System Cohort, Multi-Scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University , 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.|Institute for Advanced Study, Kyushu University , 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Yamanishi
authors.affiliation: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology , Iizuka, Fukuoka 820-8502, Japan.
authors.forename: Hiroto
authors.initials: H
authors.lastname: Saigo
mesh_terms: D000465:Algorithms; D057225:Data Mining / Q000379:methods* / Q000592:standards; D055808:Drug Discovery; D008962:Models, Theoretical; D015394:Molecular Structure; D021281:Quantitative Structure-Activity Relationship; D012044:Regression Analysis