In machine learning, ensemble methods combine the predictions of multiple base learners to construct more accurate aggregate predictions. Established supervised learning algorithms inject randomness into the construction of the individual base learners in an effort to promote diversity within the resulting ensembles. An undesirable side effect of this approach is that it generally also reduces the accuracy of the base learners. In this paper, we introduce a method that is simple to implement yet general and effective in improving ensemble diversity with only modest impact on the accuracy of the individual base learners. By randomly rotating the feature space prior to inducing the base learners, we achieve favorable aggregate predictions on standard data sets compared to state of the art ensemble methods, most notably for tree-based ensembles, which are particularly sensitive to rotation.

MOTIVATION: Many standard statistical techniques are effective on data that are normally distributed with constant variance. Microarray data typically violate these assumptions since they come from non-Gaussian distributions with a non-trivial mean-variance relationship. Several methods have been proposed that transform microarray data to stabilize variance and draw its distribution towards the Gaussian. Some methods, such as log or generalized log, rely on an underlying model for the data. Others, such as the spread-versus-level plot, do not. We propose an alternative data-driven multiscale approach, called the Data-Driven Haar-Fisz for microarrays (DDHFm) with replicates. DDHFm has the advantage of being 'distribution-free' in the sense that no parametric model for the underlying microarray data is required to be specified or estimated; hence, DDHFm can be applied very generally, not just to microarray data. RESULTS: DDHFm achieves very good variance stabilization of microarray data with replicates and produces transformed intensities that are approximately normally distributed. Simulation studies show that it performs better than other existing methods. Application of DDHFm to real one-color cDNA data validates these results. AVAILABILITY: The R package of the Data-Driven Haar-Fisz transform (DDHFm) for microarrays is available in Bioconductor and CRAN.