A computationally fast variable importance test for random forests for high-dimensional data

  • Silke Janitza
  • Ender Celik
  • Anne-Laure Boulesteix
Regular Article

DOI: 10.1007/s11634-016-0270-x

Cite this article as:
Janitza, S., Celik, E. & Boulesteix, AL. Adv Data Anal Classif (2016). doi:10.1007/s11634-016-0270-x


Random forests are a commonly used tool for classification and for ranking candidate predictors based on the so-called variable importance measures. These measures attribute scores to the variables reflecting their importance. A drawback of variable importance measures is that there is no natural cutoff that can be used to discriminate between important and non-important variables. Several approaches, for example approaches based on hypothesis testing, were developed for addressing this problem. The existing testing approaches require the repeated computation of random forests. While for low-dimensional settings those approaches might be computationally tractable, for high-dimensional settings typically including thousands of candidate predictors, computing time is enormous. In this article a computationally fast heuristic variable importance test is proposed that is appropriate for high-dimensional data where many variables do not carry any information. The testing approach is based on a modified version of the permutation variable importance, which is inspired by cross-validation procedures. The new approach is tested and compared to the approach of Altmann and colleagues using simulation studies, which are based on real data from high-dimensional binary classification settings. The new approach controls the type I error and has at least comparable power at a substantially smaller computation time in the studies. Thus, it might be used as a computationally fast alternative to existing procedures for high-dimensional data settings where many variables do not carry any information. The new approach is implemented in the R package vita.


Gene selection Feature selection Random forests Variable importance Variable selection Variable importance test 

Mathematics Subject Classification

62F07 65C60 62-07 

Supplementary material

11634_2016_270_MOESM1_ESM.pdf (671 kb)
Supplementary material 1 (pdf 671 KB)

Funding information

Funder NameGrant NumberFunding Note
Deutsche Forschungsgemeinschaft
  • BO3139/2-2
  • BO3139/6-1

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Medical Informatics, Biometry and EpidemiologyUniversity of MunichMunichGermany

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