arXiv subjects

Gareth Roberts

Publications and source records attributed to Gareth Roberts.

26 records · Page 2Linked to original sources

arXiv2012

Enhancing Bayesian risk prediction for epidemics using contact tracing

Contact tracing data collected from disease outbreaks has received relatively little attention in the epidemic modelling literature because it is thought to be unreliable: infection sources might be wrongly attributed, or data might be missing due to resource contraints in the questionnaire exercise. Nevertheless, these data might provide a rich source of information on disease transmission rate. This paper presents novel methodology for combining contact tracing data with rate-based contact network data to improve posterior precision, and therefore predictive accuracy. We present an advancement in Bayesian inference for epidemics that assimilates these data, and is robust to partial contact tracing. Using a simulation study based on the British poultry industry, we show how the presence of contact tracing data improves posterior predictive accuracy, and can directly inform a more effective control strategy.

stat.ME↗

arXiv2009

Optimal scaling of the random walk Metropolis on elliptically symmetric unimodal targets

Scaling of proposals for Metropolis algorithms is an important practical problem in MCMC implementation. Criteria for scaling based on empirical acceptance rates of algorithms have been found to work consistently well across a broad range of problems. Essentially, proposal jump sizes are increased when acceptance rates are high and decreased when rates are low. In recent years, considerable theoretical support has been given for rules of this type which work on the basis that acceptance rates around 0.234 should be preferred. This has been based on asymptotic results that approximate high dimensional algorithm trajectories by diffusions. In this paper, we develop a novel approach to understanding 0.234 which avoids the need for diffusion limits. We derive explicit formulae for algorithm efficiency and acceptance rates as functions of the scaling parameter. We apply these to the family of elliptically symmetric target densities, where further illuminating explicit results are possible. Under suitable conditions, we verify the 0.234 rule for a new class of target densities. Moreover, we can characterise cases where 0.234 fails to hold, either because the target density is too diffuse in a sense we make precise, or because the eccentricity of the target density is too severe, again in a sense we make precise. We provide numerical verifications of our results.

stat.CO↗

arXiv2009

Optimal scalings for local Metropolis--Hastings chains on nonproduct targets in high dimensions

We investigate local MCMC algorithms, namely the random-walk Metropolis and the Langevin algorithms, and identify the optimal choice of the local step-size as a function of the dimension $n$ of the state space, asymptotically as $n\to\infty$. We consider target distributions defined as a change of measure from a product law. Such structures arise, for instance, in inverse problems or Bayesian contexts when a product prior is combined with the likelihood. We state analytical results on the asymptotic behavior of the algorithms under general conditions on the change of measure. Our theory is motivated by applications on conditioned diffusion processes and inverse problems related to the 2D Navier--Stokes equation.

math.PR↗

arXiv2009

Monte Carlo maximum likelihood estimation for discretely observed diffusion processes

This paper introduces a Monte Carlo method for maximum likelihood inference in the context of discretely observed diffusion processes. The method gives unbiased and a.s.\@ continuous estimators of the likelihood function for a family of diffusion models and its performance in numerical examples is computationally efficient. It uses a recently developed technique for the exact simulation of diffusions, and involves no discretization error. We show that, under regularity conditions, the Monte Carlo MLE converges a.s. to the true MLE. For datasize $n\to\infty$, we show that the number of Monte Carlo iterations should be tuned as $\mathcal{O}(n^{1/2})$ and we demonstrate the consistency properties of the Monte Carlo MLE as an estimator of the true parameter value.

math.ST↗

arXiv2007

Retrospective Markov chain Monte Carlo methods for Dirichlet process hierarchical model

Inference for Dirichlet process hierarchical models is typically performed using Markov chain Monte Carlo methods, which can be roughly categorised into marginal and conditional methods. The former integrate out analytically the infinite-dimensional component of the hierarchical model and sample from the marginal distribution of the remaining variables using the Gibbs sampler. Conditional methods impute the Dirichlet process and update it as a component of the Gibbs sampler. Since this requires imputation of an infinite-dimensional process, implementation of the conditional method has relied on finite approximations. In this paper we show how to avoid such approximations by designing two novel Markov chain Monte Carlo algorithms which sample from the exact posterior distribution of quantities of interest. The approximations are avoided by the new technique of retrospective sampling. We also show how the algorithms can obtain samples from functionals of the Dirichlet process. The marginal and the conditional methods are compared and a careful simulation study is included, which involves a non-conjugate model, different datasets and prior specifications.

stat.ME↗

arXiv2007

Stability of the Gibbs Sampler for Bayesian Hierarchical Models

We characterise the convergence of the Gibbs sampler which samples from the joint posterior distribution of parameters and missing data in hierarchical linear models with arbitrary symmetric error distributions. We show that the convergence can be uniform, geometric or sub-geometric depending on the relative tail behaviour of the error distributions, and on the parametrisation chosen. Our theory is applied to characterise the convergence of the Gibbs sampler on latent Gaussian process models. We indicate how the theoretical framework we introduce will be useful in analyzing more complex models.

stat.ME↗

arXiv2007

Particle Filters for Partially Observed Diffusions

In this paper we introduce a novel particle filter scheme for a class of partially-observed multivariate diffusions. %continuous-time dynamic models where the %signal is given by a multivariate diffusion process. We consider a variety of observation schemes, including diffusion observed with error, observation of a subset of the components of the multivariate diffusion and arrival times of a Poisson process whose intensity is a known function of the diffusion (Cox process). Unlike currently available methods, our particle filters do not require approximations of the transition and/or the observation density using time-discretisations. Instead, they build on recent methodology for the exact simulation of the diffusion process and the unbiased estimation of the transition density as described in \cite{besk:papa:robe:fear:2006}. %In particular, w We introduce the Generalised Poisson Estimator, which generalises the Poisson Estimator of \cite{besk:papa:robe:fear:2006}. %Thus, our filters avoid the systematic biases caused by %time-discretisations and they have significant computational %advantages over alternative continuous-time filters. These %advantages are supported theoretically by a A central limit theorem is given for our particle filter scheme.

stat.ME↗

arXiv2006

Optimal scaling for partially updating MCMC algorithms

In this paper we shall consider optimal scaling problems for high-dimensional Metropolis--Hastings algorithms where updates can be chosen to be lower dimensional than the target density itself. We find that the optimal scaling rule for the Metropolis algorithm, which tunes the overall algorithm acceptance rate to be 0.234, holds for the so-called Metropolis-within-Gibbs algorithm as well. Furthermore, the optimal efficiency obtainable is independent of the dimensionality of the update rule. This has important implications for the MCMC practitioner since high-dimensional updates are generally computationally more demanding, so that lower-dimensional updates are therefore to be preferred. Similar results with rather different conclusions are given for so-called Langevin updates. In this case, it is found that high-dimensional updates are frequently most efficient, even taking into account computing costs.

math.PR↗