R*: A Robust MCMC Convergence Diagnostic with Uncertainty Using Decision Tree Classifiers

Abstract

Markov chain Monte Carlo (MCMC) has transformed Bayesian model inference over the past three decades: mainly because of this, Bayesian inference is now a workhorse of applied scientists. Under general conditions, MCMC sampling converges asymptotically to the posterior distribution, but this provides no guarantees about its performance in finite time. The predominant method for monitoring convergence is to run multiple chains and monitor individual chains’ characteristics and compare these to the population as a whole: if within-chain and between-chain summaries are comparable, then this is taken to indicate that the chains have converged to a common stationary distribution. Here, we introduce a new method for diagnosing convergence based on how well a machine learning classifier model can successfully discriminate the individual chains. We call this convergence measure R*. In contrast to the predominant R, R* is a single statistic across all parameters that indicates lack of mixing, although individual variables’ importance for this metric can also be determined. Additionally, R* is not based on any single characteristic of the sampling distribution; instead it uses all the information in the chain, including that given by the joint sampling distribution, which is currently largely overlooked by existing approaches. We recommend calculating R* using two different machine learning classifiers — gradient-boosted regression trees and random forests — which each work well in models of different dimensions. Because each of these methods outputs a classification probability, as a byproduct, we obtain uncertainty in R ∗. The method is straightforward to implement and could be a complementary additional check on MCMC convergence for applied analyses.