Computability, inference and modeling in probabilistic programming

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 135-144).We investigate the class of computable probability distributions and explore the fundamental limitations of using this class to describe and compute conditional distributions. In addition to proving the existence of noncomputable conditional distributions, and thus ruling out the possibility of generic probabilistic inference algorithms (even inefficient ones), we highlight some positive results showing that posterior inference is possible in the presence of additional structure like exchangeability and noise, both of which are common in Bayesian hierarchical modeling. This theoretical work bears on the development of probabilistic programming languages (which enable the specification of complex probabilistic models) and their implementations (which can be used to perform Bayesian reasoning). The probabilistic programming approach is particularly well suited for defining infinite-dimensional, recursively-defined stochastic processes of the sort used in nonparametric Bayesian statistics. We present a new construction of the Mondrian process as a partition-valued Markov process in continuous time, which can be viewed as placing a distribution on an infinite kd-tree data structure.by Daniel M. Roy.Ph.D

Disintegration and Bayesian Inversion via String Diagrams

The notions of disintegration and Bayesian inversion are fundamental in conditional probability theory. They produce channels, as conditional probabilities, from a joint state, or from an already given channel (in opposite direction). These notions exist in the literature, in concrete situations, but are presented here in abstract graphical formulations. The resulting abstract descriptions are used for proving basic results in conditional probability theory. The existence of disintegration and Bayesian inversion is discussed for discrete probability, and also for measure-theoretic probability --- via standard Borel spaces and via likelihoods. Finally, the usefulness of disintegration and Bayesian inversion is illustrated in several examples.Comment: Accepted for publication in Mathematical Structures in Computer Scienc

Effects and Effect Handlers for Programmable Inference

Inference algorithms for probabilistic programming are complex imperative programs with many moving parts. Efficient inference often requires customising an algorithm to a particular probabilistic model or problem, sometimes called inference programming. Most inference frameworks are implemented in languages that lack a disciplined approach to side effects, which can result in monolithic implementations where the structure of the algorithms is obscured and inference programming is hard. Functional programming with typed effects offers a more structured and modular foundation for programmable inference, with monad transformers being the primary structuring mechanism explored to date. This paper presents an alternative approach to programmable inference, based on algebraic effects, building on recent work that used algebraic effects to represent probabilistic models. Using effect signatures to specify the key operations of the algorithms, and effect handlers to modularly interpret those operations for specific variants, we develop three abstract algorithms, or inference patterns, representing three important classes of inference: Metropolis-Hastings, particle filtering, and guided optimisation. We show how our approach reveals the algorithms' high-level structure, and makes it easy to tailor and recombine their parts into new variants. We implement the three inference patterns as a Haskell library, and discuss the pros and cons of algebraic effects vis-a-vis monad transformers as a structuring mechanism for modular imperative algorithm design. It should be possible to reimplement our library in any typed functional language able to emulate effects and effect handlers

Functional Programming for Modular Bayesian Inference

We present an architectural design of a library for Bayesian modelling and inference in modern functional programming languages. The novel aspect of our approach are modular implementations of existing state-of- the-art inference algorithms. Our design relies on three inherently functional features: higher-order functions, inductive data-types, and support for either type-classes or an expressive module system. We provide a perfor- mant Haskell implementation of this architecture, demonstrating that high-level and modular probabilistic programming can be added as a library in sufficiently expressive languages. We review the core abstractions in this architecture: inference representations, inference transformations, and inference representation transformers. We then implement concrete instances of these abstractions, counterparts to particle filters and Metropolis-Hastings samplers, which form the basic building blocks of our library. By composing these building blocks we obtain state-of-the-art inference algorithms: Resample-Move Sequential Monte Carlo, Particle Marginal Metropolis-Hastings, and Sequential Monte Carlo Squared. We evaluate our implementation against existing probabilistic programming systems and find it is already com- petitively performant, although we conjecture that existing functional programming optimisation techniques could reduce the overhead associated with the abstractions we use. We show that our modular design enables deterministic testing of inherently stochastic Monte Carlo algorithms. Finally, we demonstrate using OCaml that an expressive module system can also implement our design