Workflow Techniques for the Robust Use of Bayes Factors

Inferences about hypotheses are ubiquitous in the cognitive sciences. Bayes factors provide one general way to compare different hypotheses by their compatibility with the observed data. Those quantifications can then also be used to choose between hypotheses. While Bayes factors provide an immediate approach to hypothesis testing, they are highly sensitive to details of the data/model assumptions. Moreover it’s not clear how straightforwardly this approach can be implemented in practice, and in particular how sensitive it is to the details of the computational implementation. Here, we investigate these questions for Bayes factor analyses in the cognitive sciences. We explain the statistics underlying Bayes factors as a tool for Bayesian inferences and discuss that utility functions are needed for principled decisions on hypotheses. Next, we study how Bayes factors misbehave under different conditions. This includes a study of errors in the estimation of Bayes factors. Importantly, it is unknown whether Bayes factor estimates based on bridge sampling are unbiased for complex analyses. We are the first to use simulation-based calibration as a tool to test the accuracy of Bayes factor estimates. Moreover, we study how stable Bayes factors are against different MCMC draws. We moreover study how Bayes factors depend on variation in the data. We also look at variability of decisions based on Bayes factors and how to optimize decisions using a utility function. We outline a Bayes factor workflow that researchers can use to study whether Bayes factors are robust for their individual analysis, and we illustrate this workflow using an example from the cognitive sciences. We hope that this study will provide a workflow to test the strengths and limitations of Bayes factors as a way to quantify evidence in support of scientific hypotheses. Reproducible code is available from this https URL.   

Also see this interesting  twitter thread on this paper by Michael Betancourt:

I believe this paper was initiated towards the end of drafting the Bayesian workflow in cognitive science paper with Daniel and @ShravanVasishth when I mentioned that many of the workflow ideas could be generalized to Bayes factor implementations with a little bit of work.

— \mathfrak{Michael "Shapes Dude" Betancourt} (@betanalpha) March 17, 2021