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Probabilistic programming is an approach to reasoning under uncertainty by encoding inference problems as programs. In order to solve these inference problems, probabilistic programming languages (PPLs) employ different inference algorithms, such as sequential Monte Carlo (SMC), Markov chain Monte Carlo (MCMC), or variational methods. Existing research on such algorithms mainly concerns their implementation and efficiency, rather than the correctness of the algorithms themselves when applied in the context of expressive PPLs. To remedy this, we give a correctness proof for SMC methods in the context of an expressive PPL calculus, representative of popular PPLs such as WebPPL, Anglican, and Birch. Previous work have studied correctness of MCMC using an operational semantics, and correctness of SMC and MCMC in a denotational setting without term recursion. However, for SMC inference-one of the most commonly used algorithms in PPLs as of today-no formal correctness proof exists in an operational setting. In particular, an open question is if the resample locations in a probabilistic program affects the correctness of SMC. We solve this fundamental problem, and make four novel contributions: (i) we extend an untyped PPL lambda calculus and operational semantics to include explicit resample terms, expressing synchronization points in SMC inference; (ii) we prove, for the first time, that subject to mild restrictions, any placement of the explicit resample terms is valid for a generic form of SMC inference; (iii) as a result of (ii), our calculus benefits from classic results from the SMC literature: a law of large numbers and an unbiased estimate of the model evidence; and (iv) we formalize the bootstrap particle filter for the calculus and discuss how our results can be further extended to other SMC algorithms.

We define a general notion of transition system where states and action labels can be from arbitrary nominal sets, actions may bind names, and state predicates from an arbitrary logic define properties of states. A Hennessy-Milner logic for these systems is introduced, and proved adequate and expressively complete for bisimulation equivalence. A main technical novelty is the use of finitely supported infinite conjunctions. We show how to treat different bisimulation variants such as early, late, open and weak in a systematic way, explore the folklore theorem that state predicates can be replaced by actions, and make substantial comparisons with related work. The main definitions and theorems have been formalised in Nominal Isabelle.

Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here, we show that universal probabilistic programming languages (PPLs) solve the expressivity problem, while still supporting automated generation of efficient inference algorithms. To prove the latter point, we develop automated generation of sequential Monte Carlo (SMC) algorithms for PPL descriptions of arbitrary biological diversification (birth-death) models. SMC is a new inference strategy for these problems, supporting both parameter inference and efficient estimation of Bayes factors that are used in model testing. We take advantage of this in automatically generating SMC algorithms for several recent diversification models that have been difficult or impossible to tackle previously. Finally, applying these algorithms to 40 bird phylogenies, we show that models with slowing diversification, constant turnover and many small shifts generally explain the data best. Our work opens up several related problem domains to PPL approaches, and shows that few hurdles remain before these techniques can be effectively applied to the full range of phylogenetic models.

The probability density function of a probability distribution is a fundamental concept in probability theory and a key ingredient in various widely used machine learning methods. However, the necessary framework for compiling probabilistic functional programs to density functions has only recently been developed. In this work, we present a density compiler for a probabilistic language with failure and both discrete and continuous distributions, and provide a proof of its soundness. The compiler greatly reduces the development effort of domain experts, which we demonstrate by solving inference problems from various scientific applications, such as modelling the global carbon cycle, using a standard Markov chain Monte Carlo framework.

Applied process calculi include advanced programming constructs such as type systems, communication with pattern matching, encryption primitives, concurrent constraints, nondeterminism, process creation, and dynamic connection topologies. Several such formalisms, e.g. the applied pi calculus, are extensions of the the pi-calculus; a growing number is geared towards particular applications or computational paradigms.

Our goal is a unified framework to represent different process calculi and notions of computation. To this end, we extend our previous work on psi-calculi with novel abstract patterns and pattern matching, and add sorts to the data term language, giving sufficient criteria for subject reduction to hold. Our framework can directly represent several existing process calculi; the resulting transition systems are isomorphic to the originals up to strong bisimulation. We also demonstrate different notions of computation on data terms, including cryptographic primitives and a lambda-calculus with erratic choice. Finally, we prove standard congruence and structural properties of bisimulation; the proof has been machine-checked using Nominal Isabelle in the case of a single name sort.

Psi-calculi is a parametric framework for extensions of the pi-calculus, with arbitrary data structures and logical assertions for facts about data. In this paper we add primitives for broadcast communication in order to model wireless protocols. The additions preserve the purity of the psi-calculi semantics, and we formally prove the standard congruence and structural properties of bisimilarity. We demonstrate the expressive power of broadcast psi-calculi by modelling the wireless ad-hoc routing protocol LUNAR and verifying a basic reachability property.