R*: A robust MCMC convergence diagnostic with uncertainty using decision tree classifiers
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Published version
Author(s)
Lambert, Benjamin
Vehtari, Aki
Type
Journal Article
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 predominant̂ 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 by product, we obtain uncertainty in R∗. The method is straight forward to implement and could be a complementary additional check on MCMC convergence for applied analyses.
Date Issued
2022-06-01
Date Acceptance
2020-11-17
Citation
Bayesian Analysis, 2022, 17 (2), pp.353-379
ISSN
1931-6690
Publisher
International Society for Bayesian Analysis (ISBA)
Start Page
353
End Page
379
Journal / Book Title
Bayesian Analysis
Volume
17
Issue
2
Copyright Statement
© 2022 International Society for Bayesian Analysis. This article is open access under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/)
License URL
Subjects
Statistics & Probability
0104 Statistics
Publication Status
Published