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Andrew Parnell
Stephen R Pennington
Adrianm Raftery
Belinda Hernández



cardiovascular disease trees regression bayesian additive model prostate cancer machine learning open source

Bayesian Additive Regression Trees using Bayesian model averaging (2017)

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 the algorithm can become inefficient and computationally expensive. 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, its default implementation does not produce probabilistic estimates or predictions. We propose an alternative fitting algorithm for BART called BART-BMA, which uses Bayesian model averaging and a greedy search algorithm to obtain a posterior distribution more efficiently 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 high-dimensional 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 aggressive from non-aggressive 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.
Collections Ireland -> Maynooth University -> Academic Unit = Faculty of Science and Engineering: Research Institutes: Hamilton Institute
Ireland -> Maynooth University -> Status = Published
Ireland -> Maynooth University -> Type = Monograph

Full list of authors on original publication

Andrew Parnell, Stephen R Pennington, Adrianm Raftery, Belinda Hernández

Experts in our system

Andrew Parnell
Maynooth University
Total Publications: 45
Stephen R Pennington
University College Dublin
Belinda Hernández
University College Dublin
Total Publications: 5