Fredrik Ronquist

Viktor Palmkvist, Fredrik Ronquist, David Broman

An important aspect of making inference based on a probabilistic program practical is efficiency; faster evaluation enables more work per unit of time, which can be translated into more precision. Inference via Markov chain Monte Carlo has a property that can be favorably exploited for efficiency: most proposed samples are computed as minor variations of previous samples, i.e., a clever implementation can skip computations pertaining to what is unchanged. This paper provides an approach for automatically translating a probabilistic program to a dynamic graph, reminiscent of functional reactive programming, that explicitly represents data dependencies, enabling proposals to only recompute the parts of the graph that depend on redrawn random variables. The graph-building interface follows familiar functional programming interfaces, which also connect to their expressiveness in terms of probabilistic programming: models using the applicative functor portion express Bayesian networks, while those using monads represent universal probabilistic programming languages.

Jan Kudlicka, Lawrence M. Murray, Fredrik Ronquist et al.

We consider probabilistic programming for birth-death models of evolution and introduce a new widely-applicable inference method that combines an extension of the alive particle filter (APF) with automatic Rao-Blackwellization via delayed sampling. Birth-death models of evolution are an important family of phylogenetic models of the diversification processes that lead to evolutionary trees. Probabilistic programming languages (PPLs) give phylogeneticists a new and exciting tool: their models can be implemented as probabilistic programs with just a basic knowledge of programming. The general inference methods in PPLs reduce the need for external experts, allow quick prototyping and testing, and accelerate the development and deployment of new models. We show how these birth-death models can be implemented as simple programs in existing PPLs, and demonstrate the usefulness of the proposed inference method for such models. For the popular BiSSE model the method yields an increase of the effective sample size and the conditional acceptance rate by a factor of 30 in comparison with a standard bootstrap particle filter. Although concentrating on phylogenetics, the extended APF is a general inference method that shows its strength in situations where particles are often assigned zero weight. In the case when the weights are always positive, the extra cost of using the APF rather than the bootstrap particle filter is negligible, making our method a suitable drop-in replacement for the bootstrap particle filter in probabilistic programming inference.