Bayesian Additive Regression Trees (BART) is a popular Bayesian non-parametric regression algorithm. The posterior is a distribution over sums of decision trees, and predictions are made by averaging approximate samples from the posterior. The combination of strong predictive performance and the ability to provide uncertainty measures has led BART to be commonly used in the social sciences, biostatistics, and causal inference. BART uses Markov Chain Monte Carlo (MCMC) to obtain approximate posterior samples over a parameterized space of sums of trees, but it has often been observed that the chains are slow to mix. In this paper, we provide the first lower bound on the mixing time for a simplified version of BART in which we reduce the sum to a single tree and use a subset of the possible moves for the MCMC proposal distribution. Our lower bound for the mixing time grows exponentially with the number of data points. Inspired by this new connection between the mixing time and the number of data points, we perform rigorous simulations on BART. We show qualitatively that BART's mixing time increases with the number of data points. The slow mixing time of the simplified BART suggests a large variation between different runs of the simplified BART algorithm and a similar large variation is known for BART in the literature. This large variation could result in a lack of stability in the models, predictions, and posterior intervals obtained from the BART MCMC samples. Our lower bound and simulations suggest increasing the number of chains with the number of data points.
Tree-based models such as decision trees and random forests (RF) are a cornerstone of modern machine-learning practice. To mitigate overfitting, trees are typically regularized by a variety of techniques that modify their structure (e.g. pruning). We introduce Hierarchical Shrinkage (HS), a post-hoc algorithm that does not modify the tree structure, and instead regularizes the tree by shrinking the prediction over each node towards the sample means of its ancestors. The amount of shrinkage is controlled by a single regularization parameter and the number of data points in each ancestor. Since HS is a post-hoc method, it is extremely fast, compatible with any tree growing algorithm, and can be used synergistically with other regularization techniques. Extensive experiments over a wide variety of real-world datasets show that HS substantially increases the predictive performance of decision trees, even when used in conjunction with other regularization techniques. Moreover, we find that applying HS to each tree in an RF often improves accuracy, as well as its interpretability by simplifying and stabilizing its decision boundaries and SHAP values. We further explain the success of HS in improving prediction performance by showing its equivalence to ridge regression on a (supervised) basis constructed of decision stumps associated with the internal nodes of a tree. All code and models are released in a full-fledged package available on Github (github.com/csinva/imodels)