Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models

Zheng Shao, Yuya Hirayama, Yoshihiro Yamanishi, Hiroto Saigo

研究成果: Contribution to journalArticle査読

3 被引用数 (Scopus)

抄録

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.

本文言語英語
ページ(範囲)2519-2527
ページ数9
ジャーナルJournal of Chemical Information and Modeling
55
12
DOI
出版ステータス出版済み - 12 28 2015

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

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