Application of Breiman’s Random Forest to Modeling Structure-Activity Relationships of Pharmaceutical Molecules

  • Vladimir Svetnik
  • Andy Liaw
  • Christopher Tong
  • Ting Wang
Conference paper

DOI: 10.1007/978-3-540-25966-4_33

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3077)
Cite this paper as:
Svetnik V., Liaw A., Tong C., Wang T. (2004) Application of Breiman’s Random Forest to Modeling Structure-Activity Relationships of Pharmaceutical Molecules. In: Roli F., Kittler J., Windeatt T. (eds) Multiple Classifier Systems. MCS 2004. Lecture Notes in Computer Science, vol 3077. Springer, Berlin, Heidelberg

Abstract

Leo Breiman’s Random Forest ensemble learning procedure is applied to the problem of Quantitative Structure-Activity Relationship (QSAR) modeling for pharmaceutical molecules. This entails using a quantitative description of a compound’s molecular structure to predict that compound’s biological activity as measured in an in vitro assay. Without any parameter tuning, the performance of Random Forest with default settings on six publicly available data sets is already as good or better than that of three other prominent QSAR methods: Decision Tree, Partial Least Squares, and Support Vector Machine. In addition to reliable prediction accuracy, Random Forest provides variable importance measures which can be used in a variable reduction wrapper algorithm. Comparisons of various such wrappers and between Random Forest and Bagging are presented.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Vladimir Svetnik
    • 1
  • Andy Liaw
    • 1
  • Christopher Tong
    • 1
  • Ting Wang
    • 1
  1. 1.Biometrics Research RY33-300Merck & Co., Inc.RahwayUSA

Personalised recommendations