title: Using kernel alignment to select features of molecular descriptors in a QSAR study.
abstract: Quantitative structure-activity relationships (QSARs) correlate biological activities of chemical compounds with their physicochemical descriptors. By modeling the observed relationship seen between molecular descriptors and their corresponding biological activities, we may predict the behavior of other molecules with similar descriptors. In QSAR studies, it has been shown that the quality of the prediction model strongly depends on the selected features within molecular descriptors. Thus, methods capable of automatic selection of relevant features are very desirable. In this paper, we present a new feature selection algorithm for a QSAR study based on kernel alignment which has been used as a measure of similarity between two kernel functions. In our algorithm, we deploy kernel alignment as an evaluation tool, using recursive feature elimination to compute a molecular descriptor containing the most important features needed for a classification application. Empirical results show that the algorithm works well for the computation of descriptors for various applications involving different QSAR data sets. The prediction accuracies are substantially increased and are comparable to those from earlier studies.
authors.affiliation: Toronto Health Economics and Technology Assessment Collaborative, Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada. wwl.wong@utoronto.ca..
authors.forename: William W L
authors.initials: WW
authors.lastname: Wong
authors.forename: Forbes J
authors.initials: FJ
authors.lastname: Burkowski
mesh_terms: D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1; D000806:Angiotensin-Converting Enzyme Inhibitors; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D007408:Intestinal Absorption; D008958:Models, Molecular; D004364:Pharmaceutical Preparations; D021281:Quantitative Structure-Activity Relationship; D060388:Support Vector Machine; D016171:Torsades de Pointes
chemical_list: D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1; D000806:Angiotensin-Converting Enzyme Inhibitors; D004364:Pharmaceutical Preparations