perms: Marginal likelihood estimation for binary Bayesian nonparametric models in Python and R

Binary responses arise in a multitude of statistical problems, including binary classification, bioassay, current status data problems and sensitivity estimation. There has been an interest in such problems in the Bayesian nonparametrics community since the early 1970s, but inference given binary data is intractable for a wide range of modern simulation-based models, even when employing MCMC methods. Recently, Christensen (2023) introduced a novel simulation technique based on counting permutations, which can estimate both posterior distributions and marginal likelihoods for any model from which a random sample can be generated. However, the accompanying implementation of this technique struggles when the sample size is too large (n > 250). Here we present perms, a new implementation of said technique which is substantially faster and able to handle larger data problems than the original implementation. It is available both as an R package and a Python library. The basic usage of perms is illustrated via two simple examples: a tractable toy problem and a bioassay problem. A more complex example involving changepoint analysis is also considered. We also cover the details of the implementation and illustrate the computational speed gain of perms via a simple simulation study.