Contemporary QSAR classifiers compared.
We present a comparative assessment of several state-of-the-art machine learning tools for mining drug data, including support vector machines (SVMs) and the ensemble decision tree methods boosting, bagging, and random forest, using eight data sets and two sets of descriptors. We demonstrate, by rigorous multiple comparison statistical tests, that these techniques can provide consistent improvements in predictive performance over single decision trees. However, within these methods, there is no clearly best-performing algorithm. This motivates a more in-depth investigation into the properties of random forests. We identify a set of parameters for the random forest that provide optimal performance across all the studied data sets. Additionally, the tree ensemble structure of the forest may provide an interpretable model, a considerable advantage over SVMs. We test this possibility and compare it with standard decision tree models.
Bruce
Craig L
CL
School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
Melville
James L
JL
Pickett
Stephen D
SD
Hirst
Jonathan D
JD
D000465:Algorithms; D001185:Artificial Intelligence; D002965:Classification; D015233:Models, Statistical; D021281:Quantitative Structure-Activity Relationship