Unbiased and Consistent Nested Sampling via Sequential Monte Carlo

We introduce a new class of sequential Monte Carlo methods called Nested Sampling via Sequential Monte Carlo (NS-SMC), which reframes the Nested Sampling method of Skilling (2006) in terms of sequential Monte Carlo techniques. This new framework allows convergence results to be obtained in the setting when Markov chain Monte Carlo (MCMC) is used to produce new samples. An additional benefit is that marginal likelihood estimates are unbiased. In contrast to NS, the analysis of NS-SMC does not require the (unrealistic) assumption that the simulated samples be independent. As the original NS algorithm is a special case of NS-SMC, this provides insights as to why NS seems to produce accurate estimates despite a typical violation of its assumptions. For applications of NS-SMC, we give advice on tuning MCMC kernels in an automated manner via a preliminary pilot run, and present a new method for appropriately choosing the number of MCMC repeats at each iteration. Finally, a numerical study is conducted where the performance of NS-SMC and temperature-annealed SMC is compared on several challenging and realistic problems. MATLAB code for our experiments is made available at https://github.com/LeahPrice/SMC-NS .Comment: 45 pages, some minor typographical errors fixed since last versio

Orthogonal parallel MCMC methods for sampling and optimization

Monte Carlo (MC) methods are widely used for Bayesian inference and optimization in statistics, signal processing and machine learning. A well-known class of MC methods are Markov Chain Monte Carlo (MCMC) algorithms. In order to foster better exploration of the state space, specially in high-dimensional applications, several schemes employing multiple parallel MCMC chains have been recently introduced. In this work, we describe a novel parallel interacting MCMC scheme, called {\it orthogonal MCMC} (O-MCMC), where a set of "vertical" parallel MCMC chains share information using some "horizontal" MCMC techniques working on the entire population of current states. More specifically, the vertical chains are led by random-walk proposals, whereas the horizontal MCMC techniques employ independent proposals, thus allowing an efficient combination of global exploration and local approximation. The interaction is contained in these horizontal iterations. Within the analysis of different implementations of O-MCMC, novel schemes in order to reduce the overall computational cost of parallel multiple try Metropolis (MTM) chains are also presented. Furthermore, a modified version of O-MCMC for optimization is provided by considering parallel simulated annealing (SA) algorithms. Numerical results show the advantages of the proposed sampling scheme in terms of efficiency in the estimation, as well as robustness in terms of independence with respect to initial values and the choice of the parameters

Cost free hyper-parameter selection/averaging for Bayesian inverse problems with vanilla and Rao-Blackwellized SMC samplers

In Bayesian inverse problems, one aims at characterizing the posterior distribution of a set of unknowns, given indirect measurements. For non-linear/non-Gaussian problems, analytic solutions are seldom available: Sequential Monte Carlo samplers offer a powerful tool for approximating complex posteriors, by constructing an auxiliary sequence of densities that smoothly reaches the posterior. Often the posterior depends on a scalar hyper-parameter, for which limited prior information is available. In this work, we show that properly designed Sequential Monte Carlo (SMC) samplers naturally provide an approximation of the marginal likelihood associated with this hyper-parameter for free, i.e. at a negligible additional computational cost. The proposed method proceeds by constructing the auxiliary sequence of distributions in such a way that each of them can be interpreted as a posterior distribution corresponding to a different value of the hyper-parameter. This can be exploited to perform selection of the hyper-parameter in Empirical Bayes (EB) approaches, as well as averaging across values of the hyper-parameter according to some hyper-prior distribution in Fully Bayesian (FB) approaches. For FB approaches, the proposed method has the further benefit of allowing prior sensitivity analysis at a negligible computational cost. In addition, the proposed method exploits particles at all the (relevant) iterations, thus alleviating one of the known limitations of SMC samplers, i.e. the fact that all samples at intermediate iterations are typically discarded. We show numerical results for two distinct cases where the hyper-parameter affects only the likelihood: a toy example, where an SMC sampler is used to approximate the full posterior distribution; and a brain imaging example, where a Rao-Blackwellized SMC sampler is used to approximate the posterior distribution of a subset of parameters in a conditionally linear Gaussian model

Advances in Importance Sampling

Importance sampling (IS) is a Monte Carlo technique for the approximation of intractable distributions and integrals with respect to them. The origin of IS dates from the early 1950s. In the last decades, the rise of the Bayesian paradigm and the increase of the available computational resources have propelled the interest in this theoretically sound methodology. In this paper, we first describe the basic IS algorithm and then revisit the recent advances in this methodology. We pay particular attention to two sophisticated lines. First, we focus on multiple IS (MIS), the case where more than one proposal is available. Second, we describe adaptive IS (AIS), the generic methodology for adapting one or more proposals

Scalable Bayesian inference for stochastic epidemic processes

The research reported in this thesis is motivated by the goal of using mathematical models to better understand the within-herd disease dynamics of Bovine tuberculosis (BTB) in UK cattle. This led to the development of new Bayesian methods and tools, including an open-source software package for Bayesian data analysis. In particular, those applicable to Discrete-state-space Partially Observed Markov Processes (DPOMP models). These were applied to the problem of model and parameter inference for a sample of individual herds selected from UK BTB surveillance records. Those findings led to the alternative models and methods utilised in the penultimate chapter, where we present a large scale, system-of-herds model and report novel parameter estimates for BTB. The latter include those that relate to disease detection; regional background risk; and farmer behaviour (specifically, the trading of live cattle). The work goes beyond previous, similar published research in three ways: it incorporates individual herd records, not just aggregated data; it includes formal methods of model assessment; that work is (partially) extended to systems comprising up to thousands of herds

On extended state-space constructions for monte carlo methods

This thesis develops computationally efficient methodology in two areas. Firstly, we consider a particularly challenging class of discretely observed continuous-time point-process models. For these, we analyse and improve an existing filtering algorithm based on sequential Monte Carlo (smc) methods. To estimate the static parameters in such models, we devise novel particle Gibbs samplers. One of these exploits a sophisticated non-entred parametrisation whose benefits in a Markov chain Monte Carlo (mcmc) context have previously been limited by the lack of blockwise updates for the latent point process. We apply this algorithm to a Lévy-driven stochastic volatility model. Secondly, we devise novel Monte Carlo methods – based around pseudo-marginal and conditional smc approaches – for performing optimisation in latent-variable models and more generally. To ease the explanation of the wide range of techniques employed in this work, we describe a generic importance-sampling framework which admits virtually all Monte Carlo methods, including smc and mcmc methods, as special cases. Indeed, hierarchical combinations of different Monte Carlo schemes such as smc within mcmc or smc within smc can be justified as repeated applications of this framework