Searcharxiv⌕ Search

arXiv subjects

Mark Girolami

Publications and source records attributed to Mark Girolami.

At least 91 records · Page 5Linked to original sources

Hamiltonian Monte Carlo on Symmetric and Homogeneous Spaces via Symplectic Reduction

The Hamiltonian Monte Carlo method generates samples by introducing a mechanical system that explores the target density. For distributions on manifolds it is not always simple to perform the mechanics as a result of the lack of global coordinates, the constraints of the manifold, and the requirement to compute the geodesic flow. In this paper we explain how to construct the Hamiltonian system on naturally reductive homogeneous spaces using symplectic reduction, which lifts the HMC scheme to a matrix Lie group with global coordinates and constant metric. This provides a general framework that is applicable to many manifolds that arise in applications, such as hyperspheres, hyperbolic spaces, symmetric positive-definite matrices, Grassmannian, and Stiefel manifolds.

stat.CO↗

Bayesian Probabilistic Numerical Methods in Time-Dependent State Estimation for Industrial Hydrocyclone Equipment

The use of high-power industrial equipment, such as large-scale mixing equipment or a hydrocyclone for separation of particles in liquid suspension, demands careful monitoring to ensure correct operation. The fundamental task of state-estimation for the liquid suspension can be posed as a time-evolving inverse problem and solved with Bayesian statistical methods. In this paper, we extend Bayesian methods to incorporate statistical models for the error that is incurred in the numerical solution of the physical governing equations. This enables full uncertainty quantification within a principled computation-precision trade-off, in contrast to the over-confident inferences that are obtained when all sources of numerical error are ignored. The method is cast within a sequential Monte Carlo framework and an optimised implementation is provided in Python.

stat.AP↗

A Bayesian Conjugate Gradient Method

A fundamental task in numerical computation is the solution of large linear systems. The conjugate gradient method is an iterative method which offers rapid convergence to the solution, particularly when an effective preconditioner is employed. However, for more challenging systems a substantial error can be present even after many iterations have been performed. The estimates obtained in this case are of little value unless further information can be provided about the numerical error. In this paper we propose a novel statistical model for this numerical error set in a Bayesian framework. Our approach is a strict generalisation of the conjugate gradient method, which is recovered as the posterior mean for a particular choice of prior. The estimates obtained are analysed with Krylov subspace methods and a contraction result for the posterior is presented. The method is then analysed in a simulation study as well as being applied to a challenging problem in medical imaging.

stat.ME↗

Efficiency and robustness in Monte Carlo sampling of 3-D geophysical inversions with Obsidian v0.1.2: Setting up for success

The rigorous quantification of uncertainty in geophysical inversions is a challenging problem. Inversions are often ill-posed and the likelihood surface may be multi-modal; properties of any single mode become inadequate uncertainty measures, and sampling methods become inefficient for irregular posteriors or high-dimensional parameter spaces. We explore the influences of different choices made by the practitioner on the efficiency and accuracy of Bayesian geophysical inversion methods that rely on Markov chain Monte Carlo sampling to assess uncertainty, using a multi-sensor inversion of the three-dimensional structure and composition of a region in the Cooper Basin of South Australia as a case study. The inversion is performed using an updated version of the Obsidian distributed inversion software. We find that the posterior for this inversion has complex local covariance structure, hindering the efficiency of adaptive sampling methods that adjust the proposal based on the chain history. Within the context of a parallel-tempered Markov chain Monte Carlo scheme for exploring high-dimensional multi-modal posteriors, a preconditioned Crank-Nicholson proposal outperforms more conventional forms of random walk. Aspects of the problem setup, such as priors on petrophysics or on 3-D geological structure, affect the shape and separation of posterior modes, influencing sampling performance as well as the inversion results. Use of uninformative priors on sensor noise can improve inversion results by enabling optimal weighting among multiple sensors even if noise levels are uncertain. Efficiency could be further increased by using posterior gradient information within proposals, which Obsidian does not currently support, but which could be emulated using posterior surrogates.

stat.AP↗

Rejoinder for "Probabilistic Integration: A Role in Statistical Computation?"

This article is the rejoinder for the paper "Probabilistic Integration: A Role in Statistical Computation?" to appear in Statistical Science with discussion. We would first like to thank the reviewers and many of our colleagues who helped shape this paper, the editor for selecting our paper for discussion, and of course all of the discussants for their thoughtful, insightful and constructive comments. In this rejoinder, we respond to some of the points raised by the discussants and comment further on the fundamental questions underlying the paper: (i) Should Bayesian ideas be used in numerical analysis?, and (ii) If so, what role should such approaches have in statistical computation?

stat.CO↗

Posterior Integration on a Riemannian Manifold

The geodesic Markov chain Monte Carlo method and its variants enable computation of integrals with respect to a posterior supported on a manifold. However, for regular integrals, the convergence rate of the ergodic average will be sub-optimal. To fill this gap, this paper extends the efficient posterior integration method of Oates et al. (2017) to the case of a Riemannian manifold. In contrast to the original Euclidean case, no non-trivial boundary conditions are needed for a closed manifold. The method is assessed through simulation and deployed to compute posterior integrals for an Australian Mesozoic paleomagnetic pole model, whose parameters are constrained to lie on the manifold $M = \mathbb{S}^2 \times \mathbb{R}_+$.

stat.ME↗

Bayesian Quadrature for Multiple Related Integrals

Bayesian probabilistic numerical methods are a set of tools providing posterior distributions on the output of numerical methods. The use of these methods is usually motivated by the fact that they can represent our uncertainty due to incomplete/finite information about the continuous mathematical problem being approximated. In this paper, we demonstrate that this paradigm can provide additional advantages, such as the possibility of transferring information between several numerical methods. This allows users to represent uncertainty in a more faithful manner and, as a by-product, provide increased numerical efficiency. We propose the first such numerical method by extending the well-known Bayesian quadrature algorithm to the case where we are interested in computing the integral of several related functions. We then prove convergence rates for the method in the well-specified and misspecified cases, and demonstrate its efficiency in the context of multi-fidelity models for complex engineering systems and a problem of global illumination in computer graphics.

stat.CO↗

Convergence Rates for a Class of Estimators Based on Stein's Method

Gradient information on the sampling distribution can be used to reduce the variance of Monte Carlo estimators via Stein's method. An important application is that of estimating an expectation of a test function along the sample path of a Markov chain, where gradient information enables convergence rate improvement at the cost of a linear system which must be solved. The contribution of this paper is to establish theoretical bounds on convergence rates for a class of estimators based on Stein's method. Our analysis accounts for (i) the degree of smoothness of the sampling distribution and test function, (ii) the dimension of the state space, and (iii) the case of non-independent samples arising from a Markov chain. These results provide insight into the rapid convergence of gradient-based estimators observed for low-dimensional problems, as well as clarifying a curse-of-dimension that appears inherent to such methods.

math.ST↗

Probabilistic Models for Integration Error in the Assessment of Functional Cardiac Models

This paper studies the numerical computation of integrals, representing estimates or predictions, over the output $f(x)$ of a computational model with respect to a distribution $p(\mathrm{d}x)$ over uncertain inputs $x$ to the model. For the functional cardiac models that motivate this work, neither $f$ nor $p$ possess a closed-form expression and evaluation of either requires $\approx$ 100 CPU hours, precluding standard numerical integration methods. Our proposal is to treat integration as an estimation problem, with a joint model for both the a priori unknown function $f$ and the a priori unknown distribution $p$. The result is a posterior distribution over the integral that explicitly accounts for dual sources of numerical approximation error due to a severely limited computational budget. This construction is applied to account, in a statistically principled manner, for the impact of numerical errors that (at present) are confounding factors in functional cardiac model assessment.

stat.ME↗

Probabilistic Integration: A Role in Statistical Computation?

A research frontier has emerged in scientific computation, wherein numerical error is regarded as a source of epistemic uncertainty that can be modelled. This raises several statistical challenges, including the design of statistical methods that enable the coherent propagation of probabilities through a (possibly deterministic) computational work-flow. This paper examines the case for probabilistic numerical methods in routine statistical computation. Our focus is on numerical integration, where a probabilistic integrator is equipped with a full distribution over its output that reflects the presence of an unknown numerical error. Our main technical contribution is to establish, for the first time, rates of posterior contraction for these methods. These show that probabilistic integrators can in principle enjoy the "best of both worlds", leveraging the sampling efficiency of Monte Carlo methods whilst providing a principled route to assess the impact of numerical error on scientific conclusions. Several substantial applications are provided for illustration and critical evaluation, including examples from statistical modelling, computer graphics and a computer model for an oil reservoir.

stat.ML↗

A determinant-free method to simulate the parameters of large Gaussian fields

We propose a determinant-free approach for simulation-based Bayesian inference in high-dimensional Gaussian models. We introduce auxiliary variables with covariance equal to the inverse covariance of the model. The joint probability of the auxiliary model can be computed without evaluating determinants, which are often hard to compute in high dimensions. We develop a Markov chain Monte Carlo sampling scheme for the auxiliary model that requires no more than the application of inverse-matrix-square-roots and the solution of linear systems. These operations can be performed at large scales with rational approximations. We provide an empirical study on both synthetic and real-world data for sparse Gaussian processes and for large-scale Gaussian Markov random fields.

stat.CO↗

Probabilistic Numerical Methods for Partial Differential Equations and Bayesian Inverse Problems

This paper develops a probabilistic numerical method for solution of partial differential equations (PDEs) and studies application of that method to PDE-constrained inverse problems. This approach enables the solution of challenging inverse problems whilst accounting, in a statistically principled way, for the impact of discretisation error due to numerical solution of the PDE. In particular, the approach confers robustness to failure of the numerical PDE solver, with statistical inferences driven to be more conservative in the presence of substantial discretisation error. Going further, the problem of choosing a PDE solver is cast as a problem in the Bayesian design of experiments, where the aim is to minimise the impact of solver error on statistical inferences; here the challenge of non-linear PDEs is also considered. The method is applied to parameter inference problems in which discretisation error in non-negligible and must be accounted for in order to reach conclusions that are statistically valid.

stat.ME↗

Bayesian Probabilistic Numerical Methods

The emergent field of probabilistic numerics has thus far lacked clear statistical principals. This paper establishes Bayesian probabilistic numerical methods as those which can be cast as solutions to certain inverse problems within the Bayesian framework. This allows us to establish general conditions under which Bayesian probabilistic numerical methods are well-defined, encompassing both non-linear and non-Gaussian models. For general computation, a numerical approximation scheme is proposed and its asymptotic convergence established. The theoretical development is then extended to pipelines of computation, wherein probabilistic numerical methods are composed to solve more challenging numerical tasks. The contribution highlights an important research frontier at the interface of numerical analysis and uncertainty quantification, with a challenging industrial application presented.

stat.ME↗

On the Sampling Problem for Kernel Quadrature

The standard Kernel Quadrature method for numerical integration with random point sets (also called Bayesian Monte Carlo) is known to converge in root mean square error at a rate determined by the ratio $s/d$, where $s$ and $d$ encode the smoothness and dimension of the integrand. However, an empirical investigation reveals that the rate constant $C$ is highly sensitive to the distribution of the random points. In contrast to standard Monte Carlo integration, for which optimal importance sampling is well-understood, the sampling distribution that minimises $C$ for Kernel Quadrature does not admit a closed form. This paper argues that the practical choice of sampling distribution is an important open problem. One solution is considered; a novel automatic approach based on adaptive tempering and sequential Monte Carlo. Empirical results demonstrate a dramatic reduction in integration error of up to 4 orders of magnitude can be achieved with the proposed method.

stat.ML↗

Geometry and Dynamics for Markov Chain Monte Carlo

Markov Chain Monte Carlo methods have revolutionised mathematical computation and enabled statistical inference within many previously intractable models. In this context, Hamiltonian dynamics have been proposed as an efficient way of building chains which can explore probability densities efficiently. The method emerges from physics and geometry and these links have been extensively studied by a series of authors through the last thirty years. However, there is currently a gap between the intuitions and knowledge of users of the methodology and our deep understanding of these theoretical foundations. The aim of this review is to provide a comprehensive introduction to the geometric tools used in Hamiltonian Monte Carlo at a level accessible to statisticians, machine learners and other users of the methodology with only a basic understanding of Monte Carlo methods. This will be complemented with some discussion of the most recent advances in the field which we believe will become increasingly relevant to applied scientists.

stat.CO↗

Probabilistic Numerical Methods for PDE-constrained Bayesian Inverse Problems

This paper develops meshless methods for probabilistically describing discretisation error in the numerical solution of partial differential equations. This construction enables the solution of Bayesian inverse problems while accounting for the impact of the discretisation of the forward problem. In particular, this drives statistical inferences to be more conservative in the presence of significant solver error. Theoretical results are presented describing rates of convergence for the posteriors in both the forward and inverse problems. This method is tested on a challenging inverse problem with a nonlinear forward model.

stat.ME↗

Geometric MCMC for Infinite-Dimensional Inverse Problems

Bayesian inverse problems often involve sampling posterior distributions on infinite-dimensional function spaces. Traditional Markov chain Monte Carlo (MCMC) algorithms are characterized by deteriorating mixing times upon mesh-refinement, when the finite-dimensional approximations become more accurate. Such methods are typically forced to reduce step-sizes as the discretization gets finer, and thus are expensive as a function of dimension. Recently, a new class of MCMC methods with mesh-independent convergence times has emerged. However, few of them take into account the geometry of the posterior informed by the data. At the same time, recently developed geometric MCMC algorithms have been found to be powerful in exploring complicated distributions that deviate significantly from elliptic Gaussian laws, but are in general computationally intractable for models defined in infinite dimensions. In this work, we combine geometric methods on a finite-dimensional subspace with mesh-independent infinite-dimensional approaches. Our objective is to speed up MCMC mixing times, without significantly increasing the computational cost per step (for instance, in comparison with the vanilla preconditioned Crank-Nicolson (pCN) method). This is achieved by using ideas from geometric MCMC to probe the complex structure of an intrinsic finite-dimensional subspace where most data information concentrates, while retaining robust mixing times as the dimension grows by using pCN-like methods in the complementary subspace. The resulting algorithms are demonstrated in the context of three challenging inverse problems arising in subsurface flow, heat conduction and incompressible flow control. The algorithms exhibit up to two orders of magnitude improvement in sampling efficiency when compared with the pCN method.

stat.CO↗

Hyperpriors for Matérn fields with applications in Bayesian inversion

We introduce non-stationary Matérn field priors with stochastic partial differential equations, and construct correlation length-scaling with hyperpriors. We model both the hyperprior and the Matérn prior as continuous-parameter random fields. As hypermodels, we use Cauchy and Gaussian random fields, which we map suitably to a desired correlation length-scaling range. For computations, we discretise the models with finite difference methods. We consider the convergence of the discretised prior and posterior to the discretisation limit. We apply the developed methodology to certain interpolation and numerical differentiation problems, and show numerically that we can make Bayesian inversion which promotes competing constraints of smoothness and edge-preservation. For computing the conditional mean estimator of the posterior distribution, we use a combination of Gibbs and Metropolis-within-Gibbs sampling algorithms.

math.ST↗