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Mark Girolami

Publications and source records attributed to Mark Girolami.

At least 109 records · Page 6Linked to original sources
arXiv2016

Control functionals for Monte Carlo integration

A non-parametric extension of control variates is presented. These leverage gradient information on the sampling density to achieve substantial variance reduction. It is not required that the sampling density be normalised. The novel contribution of this work is based on two important insights; (i) a trade-off between random sampling and deterministic approximation and (ii) a new gradient-based function space derived from Stein's identity. Unlike classical control variates, our estimators achieve super-root-$n$ convergence, often requiring orders of magnitude fewer simulations to achieve a fixed level of precision. Theoretical and empirical results are presented, the latter focusing on integration problems arising in hierarchical models and models based on non-linear ordinary differential equations.

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arXiv2016

Control Functionals for Quasi-Monte Carlo Integration

Quasi-Monte Carlo (QMC) methods are being adopted in statistical applications due to the increasingly challenging nature of numerical integrals that are now routinely encountered. For integrands with $d$-dimensions and derivatives of order $α$, an optimal QMC rule converges at a best-possible rate $O(N^{-α/d})$. However, in applications the value of $α$ can be unknown and/or a rate-optimal QMC rule can be unavailable. Standard practice is to employ $α_L$-optimal QMC where the lower bound $α_L \leq α$ is known, but in general this does not exploit the full power of QMC. One solution is to trade-off numerical integration with functional approximation. This strategy is explored herein and shown to be well-suited to modern statistical computation. A challenging application to robotic arm data demonstrates a substantial variance reduction in predictions for mechanical torques.

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arXiv2016

Unbiased local solutions of partial differential equations via the Feynman-Kac Identities

The Feynman-Kac formulae (FKF) express local solutions of partial differential equations (PDEs) as expectations with respect to some complementary stochastic differential equation (SDE). Repeatedly sampling paths from the complementary SDE enables the construction of Monte Carlo estimates of local solutions, which are more naturally suited to statistical inference than the numerical approximations obtained via finite difference and finite element methods. Until recently, simulating from the complementary SDE would have required the use of a discrete-time approximation, leading to biased estimates. In this paper we utilize recent developments in two areas to demonstrate that it is now possible to obtain unbiased solutions for a wide range of PDE models via the FKF. The first is the development of algorithms that simulate diffusion paths exactly (without discretization error), and so make it possible to obtain Monte Carlo estimates of the FKF directly. The second is the development of debiasing methods for SDEs, enabling the construction of unbiased estimates from a sequence of biased estimates.

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arXiv2015

On Russian Roulette Estimates for Bayesian Inference with Doubly-Intractable Likelihoods

A large number of statistical models are "doubly-intractable": the likelihood normalising term, which is a function of the model parameters, is intractable, as well as the marginal likelihood (model evidence). This means that standard inference techniques to sample from the posterior, such as Markov chain Monte Carlo (MCMC), cannot be used. Examples include, but are not confined to, massive Gaussian Markov random fields, autologistic models and Exponential random graph models. A number of approximate schemes based on MCMC techniques, Approximate Bayesian computation (ABC) or analytic approximations to the posterior have been suggested, and these are reviewed here. Exact MCMC schemes, which can be applied to a subset of doubly-intractable distributions, have also been developed and are described in this paper. As yet, no general method exists which can be applied to all classes of models with doubly-intractable posteriors. In addition, taking inspiration from the Physics literature, we study an alternative method based on representing the intractable likelihood as an infinite series. Unbiased estimates of the likelihood can then be obtained by finite time stochastic truncation of the series via Russian Roulette sampling, although the estimates are not necessarily positive. Results from the Quantum Chromodynamics literature are exploited to allow the use of possibly negative estimates in a pseudo-marginal MCMC scheme such that expectations with respect to the posterior distribution are preserved. The methodology is reviewed on well-known examples such as the parameters in Ising models, the posterior for Fisher-Bingham distributions on the $d$-Sphere and a large-scale Gaussian Markov Random Field model describing the Ozone Column data. This leads to a critical assessment of the strengths and weaknesses of the methodology with pointers to ongoing research.

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arXiv2015

Frank-Wolfe Bayesian Quadrature: Probabilistic Integration with Theoretical Guarantees

There is renewed interest in formulating integration as an inference problem, motivated by obtaining a full distribution over numerical error that can be propagated through subsequent computation. Current methods, such as Bayesian Quadrature, demonstrate impressive empirical performance but lack theoretical analysis. An important challenge is to reconcile these probabilistic integrators with rigorous convergence guarantees. In this paper, we present the first probabilistic integrator that admits such theoretical treatment, called Frank-Wolfe Bayesian Quadrature (FWBQ). Under FWBQ, convergence to the true value of the integral is shown to be exponential and posterior contraction rates are proven to be superexponential. In simulations, FWBQ is competitive with state-of-the-art methods and out-performs alternatives based on Frank-Wolfe optimisation. Our approach is applied to successfully quantify numerical error in the solution to a challenging model choice problem in cellular biology.

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arXiv2015

Emulation of Higher-Order Tensors in Manifold Monte Carlo Methods for Bayesian Inverse Problems

The Bayesian approach to Inverse Problems relies predominantly on Markov Chain Monte Carlo methods for posterior inference. The typical nonlinear concentration of posterior measure observed in many such Inverse Problems presents severe challenges to existing simulation based inference methods. Motivated by these challenges the exploitation of local geometric information in the form of covariant gradients, metric tensors, Levi-Civita connections, and local geodesic flows, have been introduced to more effectively locally explore the configuration space of the posterior measure. However, obtaining such geometric quantities usually requires extensive computational effort and despite their effectiveness affect the applicability of these geometrically-based Monte Carlo methods. In this paper we explore one way to address this issue by the construction of an emulator of the model from which all geometric objects can be obtained in a much more computationally feasible manner. The main concept is to approximate the geometric quantities using a Gaussian Process emulator which is conditioned on a carefully chosen design set of configuration points, which also determines the quality of the emulator. To this end we propose the use of statistical experiment design methods to refine a potentially arbitrarily initialized design online without destroying the convergence of the resulting Markov chain to the desired invariant measure. The practical examples considered in this paper provide a demonstration of the significant improvement possible in terms of computational loading suggesting this is a promising avenue of further development.

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arXiv2015

Probability Measures for Numerical Solutions of Differential Equations

In this paper, we present a formal quantification of epistemic uncertainty induced by numerical solutions of ordinary and partial differential equation models. Numerical solutions of differential equations contain inherent uncertainties due to the finite dimensional approximation of an unknown and implicitly defined function. When statistically analysing models based on differential equations describing physical, or other naturally occurring, phenomena, it is therefore important to explicitly account for the uncertainty introduced by the numerical method. This enables objective determination of its importance relative to other uncertainties, such as those caused by data contaminated with noise or model error induced by missing physical or inadequate descriptors. To this end we show that a wide variety of existing solvers can be randomised, inducing a probability measure over the solutions of such differential equations. These measures exhibit contraction to a Dirac measure around the true unknown solution, where the rates of convergence are consistent with the underlying deterministic numerical method. Ordinary differential equations and elliptic partial differential equations are used to illustrate the approach to quantifying uncertainty in both the statistical analysis of the forward and inverse problems.

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arXiv2015

Probabilistic Numerics and Uncertainty in Computations

We deliver a call to arms for probabilistic numerical methods: algorithms for numerical tasks, including linear algebra, integration, optimization and solving differential equations, that return uncertainties in their calculations. Such uncertainties, arising from the loss of precision induced by numerical calculation with limited time or hardware, are important for much contemporary science and industry. Within applications such as climate science and astrophysics, the need to make decisions on the basis of computations with large and complex data has led to a renewed focus on the management of numerical uncertainty. We describe how several seminal classic numerical methods can be interpreted naturally as probabilistic inference. We then show that the probabilistic view suggests new algorithms that can flexibly be adapted to suit application specifics, while delivering improved empirical performance. We provide concrete illustrations of the benefits of probabilistic numeric algorithms on real scientific problems from astrometry and astronomical imaging, while highlighting open problems with these new algorithms. Finally, we describe how probabilistic numerical methods provide a coherent framework for identifying the uncertainty in calculations performed with a combination of numerical algorithms (e.g. both numerical optimisers and differential equation solvers), potentially allowing the diagnosis (and control) of error sources in computations.

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arXiv2015

Unbiased Bayes for Big Data: Paths of Partial Posteriors

A key quantity of interest in Bayesian inference are expectations of functions with respect to a posterior distribution. Markov Chain Monte Carlo is a fundamental tool to consistently compute these expectations via averaging samples drawn from an approximate posterior. However, its feasibility is being challenged in the era of so called Big Data as all data needs to be processed in every iteration. Realising that such simulation is an unnecessarily hard problem if the goal is estimation, we construct a computationally scalable methodology that allows unbiased estimation of the required expectations -- without explicit simulation from the full posterior. The scheme's variance is finite by construction and straightforward to control, leading to algorithms that are provably unbiased and naturally arrive at a desired error tolerance. This is achieved at an average computational complexity that is sub-linear in the size of the dataset and its free parameters are easy to tune. We demonstrate the utility and generality of the methodology on a range of common statistical models applied to large-scale benchmark and real-world datasets.

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arXiv2015

Optimizing The Integrator Step Size for Hamiltonian Monte Carlo

Hamiltonian Monte Carlo can provide powerful inference in complex statistical problems, but ultimately its performance is sensitive to various tuning parameters. In this paper we use the underlying geometry of Hamiltonian Monte Carlo to construct a universal optimization criteria for tuning the step size of the symplectic integrator crucial to any implementation of the algorithm as well as diagnostics to monitor for any signs of invalidity. An immediate outcome of this result is that the suggested target average acceptance probability of 0.651 can be relaxed to $0.6 \lesssim a \lesssim 0.9$ with larger values more robust in practice.

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arXiv2014

The Geometric Foundations of Hamiltonian Monte Carlo

Although Hamiltonian Monte Carlo has proven an empirical success, the lack of a rigorous theoretical understanding of the algorithm has in many ways impeded both principled developments of the method and use of the algorithm in practice. In this paper we develop the formal foundations of the algorithm through the construction of measures on smooth manifolds, and demonstrate how the theory naturally identifies efficient implementations and motivates promising generalizations.

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arXiv2014

Solving Large-Scale PDE-constrained Bayesian Inverse Problems with Riemann Manifold Hamiltonian Monte Carlo

We consider the Riemann manifold Hamiltonian Monte Carlo (RMHMC) method for solving statistical inverse problems governed by partial differential equations (PDEs). The power of the RMHMC method is that it exploits the geometric structure induced by the PDE constraints of the underlying inverse problem. Consequently, each RMHMC posterior sample is almost independent from the others providing statistically efficient Markov chain simulation. We reduce the cost of forming the Fisher information matrix by using a low rank approximation via a randomized singular value decomposition technique. This is efficient since a small number of Hessian-vector products are required. The Hessian-vector product in turn requires only two extra PDE solves using the adjoint technique. The results suggest RMHMC as a highly efficient simulation scheme for sampling from PDE induced posterior measures.

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arXiv2014

The Controlled Thermodynamic Integral for Bayesian Model Comparison

Bayesian model comparison relies upon the model evidence, yet for many models of interest the model evidence is unavailable in closed form and must be approximated. Many of the estimators for evidence that have been proposed in the Monte Carlo literature suffer from high variability. This paper considers the reduction of variance that can be achieved by exploiting control variates in this setting. Our methodology is based on thermodynamic integration and applies whenever the gradient of both the log-likelihood and the log-prior with respect to the parameters can be efficiently evaluated. Results obtained on regression models and popular benchmark datasets demonstrate a significant and sometimes dramatic reduction in estimator variance and provide insight into the wider applicability of control variates to Bayesian model comparison.

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arXiv2014

Information-geometric Markov Chain Monte Carlo methods using Diffusions

Recent work incorporating geometric ideas in Markov chain Monte Carlo is reviewed in order to highlight these advances and their possible application in a range of domains beyond Statistics. A full exposition of Markov chains and their use in Monte Carlo simulation for Statistical inference and molecular dynamics is provided, with particular emphasis on methods based on Langevin diffusions. After this geometric concepts in Markov chain Monte Carlo are introduced. A full derivation of the Langevin diffusion on a Riemannian manifold is given, together with a discussion of appropriate Riemannian metric choice for different problems. A survey of applications is provided, and some open questions are discussed.

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arXiv2014

Pseudo-Marginal Bayesian Inference for Gaussian Processes

The main challenges that arise when adopting Gaussian Process priors in probabilistic modeling are how to carry out exact Bayesian inference and how to account for uncertainty on model parameters when making model-based predictions on out-of-sample data. Using probit regression as an illustrative working example, this paper presents a general and effective methodology based on the pseudo-marginal approach to Markov chain Monte Carlo that efficiently addresses both of these issues. The results presented in this paper show improvements over existing sampling methods to simulate from the posterior distribution over the parameters defining the covariance function of the Gaussian Process prior. This is particularly important as it offers a powerful tool to carry out full Bayesian inference of Gaussian Process based hierarchic statistical models in general. The results also demonstrate that Monte Carlo based integration of all model parameters is actually feasible in this class of models providing a superior quantification of uncertainty in predictions. Extensive comparisons with respect to state-of-the-art probabilistic classifiers confirm this assertion.

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arXiv2014

Probabilistic Model Checking of DTMC Models of User Activity Patterns

Software developers cannot always anticipate how users will actually use their software as it may vary from user to user, and even from use to use for an individual user. In order to address questions raised by system developers and evaluators about software usage, we define new probabilistic models that characterise user behaviour, based on activity patterns inferred from actual logged user traces. We encode these new models in a probabilistic model checker and use probabilistic temporal logics to gain insight into software usage. We motivate and illustrate our approach by application to the logged user traces of an iOS app.

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arXiv2013

Hamiltonian Monte Carlo for Hierarchical Models

Hierarchical modeling provides a framework for modeling the complex interactions typical of problems in applied statistics. By capturing these relationships, however, hierarchical models also introduce distinctive pathologies that quickly limit the efficiency of most common methods of in- ference. In this paper we explore the use of Hamiltonian Monte Carlo for hierarchical models and demonstrate how the algorithm can overcome those pathologies in practical applications.

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