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Open Access Highly Accessed Methodology article

An AUC-based permutation variable importance measure for random forests

Silke Janitza1*, Carolin Strobl2 and Anne-Laure Boulesteix1

Author Affiliations

1 Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Marchioninistr. 15, D-81377, Munich, Germany

2 Department of Psychology, University of Zurich, Binzm├╝hlestr. 14, Zurich, CH-8050, Switzerland

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BMC Bioinformatics 2013, 14:119  doi:10.1186/1471-2105-14-119

Published: 5 April 2013

Abstract

Background

The random forest (RF) method is a commonly used tool for classification with high dimensional data as well as for ranking candidate predictors based on the so-called random forest variable importance measures (VIMs). However the classification performance of RF is known to be suboptimal in case of strongly unbalanced data, i.e. data where response class sizes differ considerably. Suggestions were made to obtain better classification performance based either on sampling procedures or on cost sensitivity analyses. However to our knowledge the performance of the VIMs has not yet been examined in the case of unbalanced response classes. In this paper we explore the performance of the permutation VIM for unbalanced data settings and introduce an alternative permutation VIM based on the area under the curve (AUC) that is expected to be more robust towards class imbalance.

Results

We investigated the performance of the standard permutation VIM and of our novel AUC-based permutation VIM for different class imbalance levels using simulated data and real data. The results suggest that the new AUC-based permutation VIM outperforms the standard permutation VIM for unbalanced data settings while both permutation VIMs have equal performance for balanced data settings.

Conclusions

The standard permutation VIM loses its ability to discriminate between associated predictors and predictors not associated with the response for increasing class imbalance. It is outperformed by our new AUC-based permutation VIM for unbalanced data settings, while the performance of both VIMs is very similar in the case of balanced classes. The new AUC-based VIM is implemented in the R package party for the unbiased RF variant based on conditional inference trees. The codes implementing our study are available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html. webcite

Keywords:
Random forest; Conditional inference trees; Variable importance measure; Feature selection; Unbalanced data; Class imbalance; Area under the curve.