Variable importance and model selection by decorrelation

Abstract

Variable selection is a difficult problem that is particularly challenging in the analysis of high-dimensional genomic data. Here, we introduce the CAR score, a novel and highly effective criterion for variable ranking in linear regression based on Mahalanobis-decorrelation of the explanatory variables. The CAR score provides a canonical ordering that encourages grouping of correlated predictors and down-weights antagonistic variables. It decomposes the proportion of variance explained and it is an intermediate between marginal correlation and the standardized regression coefficient. As a population quantity, any preferred inference scheme can be applied for its estimation. Using simulations we demonstrate that variable selection by CAR scores is very effective and yields prediction errors and true and false positive rates that compare favorably with modern regression techniques such as elastic net and boosting. We illustrate our approach by analyzing data concerned with diabetes progression and with the effect of aging on gene expression in the human brain. The R package "care" implementing CAR score regression is available from CRAN.