title: Ensemble methods for classification in cheminformatics.
abstract: We describe the application of ensemble methods to binary classification problems on two pharmaceutical compound data sets. Several variants of single and ensembles models of k-nearest neighbors classifiers, support vector machines (SVMs), and single ridge regression models are compared. All methods exhibit robust classification even when more features are given than observations. On two data sets dealing with specific properties of drug-like substances (cytochrome P450 inhibition and "Frequent Hitters", i.e., unspecific protein inhibition), we achieve classification rates above 90%. We are able to reduce the cross-validated misclassification rate for the Frequent Hitters problem by a factor of 2 compared to previous results obtained for the same data set with different modeling techniques.
authors.affiliation: Computational Biology & Applied Algorithmics Group, Max-Planck-Institut für Informatik, Stuhlsatzenhauseg 85, 66123 Saarbrücken, Germany, and Roche Pharma Research, Basel, Switzerland. cmerk@mpi-sb.mpg.de
authors.forename: Christian
authors.initials: C
authors.lastname: Merkwirth
authors.forename: Harald
authors.initials: H
authors.lastname: Mauser
authors.forename: Tanja
authors.initials: T
authors.lastname: Schulz-Gasch
authors.forename: Olivier
authors.initials: O
authors.lastname: Roche
authors.forename: Martin
authors.initials: M
authors.lastname: Stahl
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer