Bayesian Additive Regression Trees Using Bayesian Model Averaging

Tech Report Number
636

 

Abstract

Bayesian Additive Regression Trees (BART) is a statistical sum of trees model. It can be considered a Bayesian version of machine learning tree ensemble methods where the individual trees are the base learners. However for datasets where the number of variables p is large (e.g. p > 5, 000) the algorithm can become prohibitively expensive, computationally. Another method which is popular for high dimensional data is random forests, a machine learning algorithm which grows trees using a greedy search for the best split points. However, as it is not a statistical model, it cannot produce probabilistic estimates or predictions. We propose an alternative algorithm for BART called BART-BMA, which uses Bayesian Model Averaging and a greedy search algorithm to produce a model which is much more efficient than BART for datasets with large p. BART-BMA incorporates elements of both BART and random forests to offer a model-based algorithm which can deal with highdimensional data. We have found that BART-BMA can be run in a reasonable time on a standard laptop for the “small n large p” scenario which is common in many areas of bioinformatics. We showcase this method using simulated data and data from two real proteomic experiments; one to distinguish between patients with cardiovascular disease and controls and another to classify agressive from non-agressive prostate cancer. We compare our results to their main competitors. Open source code written in R and Rcpp to run BART-BMA can be found at: https://github.com/BelindaHernandez/BART-BMA.git

Keywords: Bayesian Additive Regression Trees, Bayesian Model Averaging, Biomarker Selection, Random Forest, Small n large p.

 

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