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Richard G. Everitt

Publications and source records attributed to Richard G. Everitt.

17 recordsLinked to original sources
arXiv2026

Prequential posteriors

Data assimilation is a fundamental task in updating forecasting models upon observing new data, with applications ranging from weather prediction to online reinforcement learning. Deep generative forecasting models (DGFMs) have shown excellent performance in these areas, but assimilating data into such models is challenging due to their intractable likelihood functions. This limitation restricts the use of standard Bayesian data assimilation methodologies for DGFMs. To overcome this, we introduce prequential posteriors, based upon a predictive-sequential (prequential) loss function; an approach naturally suited for temporally dependent data which is the focus of forecasting tasks. Since the true data-generating process often lies outside the assumed model class, we adopt an alternative notion of consistency and prove that, under mild conditions, both the prequential loss minimizer and the prequential posterior concentrate around parameters with optimal predictive performance. For scalable inference, we employ easily parallelizable wastefree sequential Monte Carlo (SMC) samplers with preconditioned gradient-based kernels, enabling efficient exploration of high-dimensional parameter spaces such as those in DGFMs. We validate our method on both a synthetic multi-dimensional time series and a real-world meteorological dataset; highlighting its practical utility for data assimilation for complex dynamical systems.

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arXiv2026

Exploring Pareto smoothing in sequential Monte Carlo

A popular technique for reducing the variance of importance sampling (IS) estimators is to modify the weights of some importance points. One approach is to truncate the largest weights, which reduces variance but can introduce substantial bias. Pareto smoothed importance sampling (PSIS), by contrast, reduces the variance of the weights by fitting a generalised Pareto distribution to the upper tail of the weight distribution and replacing the weights in this tail with the corresponding expected quantiles from the fitted distribution. PSIS can therefore also reduce variance, but typically with less bias, and has been used successfully in IS-based approximations for Bayesian cross-validation. This paper explores the use of PSIS steps within sequential Monte Carlo (SMC) samplers, with a particular focus on approximate Bayesian computation (ABC)-SMC algorithms, where we aim to use Pareto smoothing to reduce the use of Markov chain Monte Carlo (MCMC) moves, each of which requires simulation from a model that is often computationally expensive. Our empirical investigation suggests that there are only minimal benefits to using Pareto smoothing in SMC, since the variance reduction through using a sequence of targets dominates the impact of the weight adjustment.

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arXiv2025

Inference for Diffusion Processes via Controlled Sequential Monte Carlo and Splitting Schemes

We introduce an inferential framework for a wide class of semi-linear stochastic differential equations (SDEs). Recent work has shown that numerical splitting schemes can preserve critical properties of such types of SDEs, give rise to explicit pseudolikelihoods, and hence allow for parameter inference for fully observed processes. Here, under several discrete time observation regimes (particularly, partially and fully observed with and without noise), we represent the implied pseudolikelihood as the normalising constant of a Feynman--Kac flow, allowing its efficient estimation via controlled sequential Monte Carlo and adapt likelihood-based methods to exploit this pseudolikelihood for inference. The strategy developed herein allows us to obtain good inferential results across a range of problems. Using diffusion bridges, we are able to computationally reduce bias coming from time-discretisation without recourse to more complex numerical schemes which typically require considerable application-specific efforts. Simulations illustrate that our method provides an excellent trade-off between computational efficiency and accuracy, under hypoellipticity, for both point and posterior estimation. Application to a neuroscience example shows the good performance of the method in challenging settings.

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arXiv2025

Generalized Bayesian deep reinforcement learning

Bayesian reinforcement learning (BRL) is a method that merges principles from Bayesian statistics and reinforcement learning to make optimal decisions in uncertain environments. As a model-based RL method, it has two key components: (1) inferring the posterior distribution of the model for the data-generating process (DGP) and (2) policy learning using the learned posterior. We propose to model the dynamics of the unknown environment through deep generative models, assuming Markov dependence. In the absence of likelihood functions for these models, we train them by learning a generalized predictive-sequential (or prequential) scoring rule (SR) posterior. We used sequential Monte Carlo (SMC) samplers to draw samples from this generalized Bayesian posterior distribution. In conjunction, to achieve scalability in the high-dimensional parameter space of the neural networks, we use the gradient-based Markov kernels within SMC. To justify the use of the prequential scoring rule posterior, we prove a Bernstein-von Mises-type theorem. For policy learning, we propose expected Thompson sampling (ETS) to learn the optimal policy by maximising the expected value function with respect to the posterior distribution. This improves upon traditional Thompson sampling (TS) and its extensions, which utilize only one sample drawn from the posterior distribution. This improvement is studied both theoretically and using simulation studies, assuming a discrete action space. Finally, we successfully extended our setup for a challenging problem with a continuous action space without theoretical guarantees.

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arXiv2025

Bayesian Inference of Reproduction Number from Epidemiological and Genetic Data Using Particle MCMC

Inference of the reproduction number through time is of vital importance during an epidemic outbreak. Typically, epidemiologists tackle this using observed prevalence or incidence data. However, prevalence and incidence data alone is often noisy or partial. Models can also have identifiability issues with determining whether a large amount of a small epidemic or a small amount of a large epidemic has been observed. Sequencing data however is becoming more abundant, so approaches which can incorporate genetic data are an active area of research. We propose using particle MCMC methods to infer the time-varying reproduction number from a combination of prevalence data reported at a set of discrete times and a dated phylogeny reconstructed from sequences. We validate our approach on simulated epidemics with a variety of scenarios. We then apply the method to real data sets of HIV-1 in North Carolina, USA and tuberculosis in Buenos Aires, Argentina. The models and algorithms are implemented in an open source R package called EpiSky which is available at https://github.com/alicia-gill/EpiSky.

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arXiv2025

Improved MCMC with active subspaces

Constantine et al. (2016) introduced a Metropolis-Hastings (MH) approach that target the active subspace of a posterior distribution: a linearly projected subspace that is informed by the likelihood. Schuster et al. (2017) refined this approach to introduce a pseudo-marginal Metropolis-Hastings, integrating out inactive variables through estimating a marginal likelihood at every MH iteration. In this paper we show empirically that the effectiveness of these approaches is limited in the case where the linearity assumption is violated, and suggest a particle marginal Metropolis-Hastings algorithm as an alternative for this situation. Finally, the high computational cost of these approaches leads us to consider alternative approaches to using active subspaces in MCMC that avoid the need to estimate a marginal likelihood: we introduce Metropolis-within-Gibbs and Metropolis-within-particle Gibbs methods that provide a more computationally efficient use of the active subspace.

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arXiv2024

Sequential Monte Carlo with active subspaces

Monte Carlo methods, such as Markov chain Monte Carlo (MCMC), remain the most regularly-used approach for implementing Bayesian inference. However, the computational cost of these approaches usually scales worse than linearly with the dimension of the parameter space, limiting their use for models with a large number of parameters. However, it is not uncommon for models to have identifiability problems. In this case, the likelihood is not informative about some subspaces of the parameter space, and hence the model effectively has a dimension that is lower than the number of parameters. Constantine et al. (2016) and Schuster et al. (2017) introduced the concept of directly using a Metropolis-Hastings (MH) MCMC on the subspaces of the parameter space that are informed by the likelihood as a means to reduce the dimension of the parameter space that needs to be explored. The same paper introduces an approach for identifying such a subspace in the case where it is a linear transformation of the parameter space: this subspace is known as the active subspace. This paper introduces sequential Monte Carlo (SMC) methods that make use of an active subspace. As well as an SMC counterpart to MH approach of Schuster et al. (2017), we introduce an approach to learn the active subspace adaptively, and an SMC$^{2}$ approach that is more robust to the linearity assumptions made when using active subspaces.

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arXiv2022

Rare event ABC-SMC$^{2}$

Approximate Bayesian computation (ABC) is a well-established family of Monte Carlo methods for performing approximate Bayesian inference in the case where an ``implicit'' model is used for the data: when the data model can be simulated, but the likelihood cannot easily be pointwise evaluated. A fundamental property of standard ABC approaches is that the number of Monte Carlo points required to achieve a given accuracy scales exponentially with the dimension of the data. Prangle et al. (2018) proposes a Markov chain Monte Carlo (MCMC) method that uses a rare event sequential Monte Carlo (SMC) approach to estimating the ABC likelihood that avoids this exponential scaling, and thus allows ABC to be used on higher dimensional data. This paper builds on the work of Prangle et al. (2018) by using the rare event SMC approach within an SMC algorithm, instead of within an MCMC algorithm. The new method has a similar structure to SMC$^{2}$ (Chopin et al., 2013), and requires less tuning than the MCMC approach. We demonstrate the new approach, compared to existing ABC-SMC methods, on a toy example and on a duplication-divergence random graph model used for modelling protein interaction networks.

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arXiv2021

Stratified sampling and bootstrapping for approximate Bayesian computation

Approximate Bayesian computation (ABC) is computationally intensive for complex model simulators. To exploit expensive simulations, data-resampling via bootstrapping can be employed to obtain many artificial datasets at little cost. However, when using this approach within ABC, the posterior variance is inflated, thus resulting in biased posterior inference. Here we use stratified Monte Carlo to considerably reduce the bias induced by data resampling. We also show empirically that it is possible to obtain reliable inference using a larger than usual ABC threshold. Finally, we show that with stratified Monte Carlo we obtain a less variable ABC likelihood. Ultimately we show how our approach improves the computational efficiency of the ABC samplers. We construct several ABC samplers employing our methodology, such as rejection and importance ABC samplers, and ABC-MCMC samplers. We consider simulation studies for static (Gaussian, g-and-k distribution, Ising model, astronomical model) and dynamic models (Lotka-Volterra). We compare against state-of-art sequential Monte Carlo ABC samplers, synthetic likelihoods, and likelihood-free Bayesian optimization. For a computationally expensive Lotka-Volterra case study, we found that our strategy leads to a more than 10-fold computational saving, compared to a sampler that does not use our novel approach.

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arXiv2020

Delayed acceptance ABC-SMC

Approximate Bayesian computation (ABC) is now an established technique for statistical inference used in cases where the likelihood function is computationally expensive or not available. It relies on the use of a~model that is specified in the form of a~simulator, and approximates the likelihood at a~parameter value $θ$ by simulating auxiliary data sets $x$ and evaluating the distance of $x$ from the true data $y$. However, ABC is not computationally feasible in cases where using the simulator for each $θ$ is very expensive. This paper investigates this situation in cases where a~cheap, but approximate, simulator is available. The approach is to employ delayed acceptance Markov chain Monte Carlo (MCMC) within an ABC sequential Monte Carlo (SMC) sampler in order to, in a~first stage of the kernel, use the cheap simulator to rule out parts of the parameter space that are not worth exploring, so that the ``true'' simulator is only run (in the second stage of the kernel) where there is a~reasonable chance of accepting proposed values of $θ$. We show that this approach can be used quite automatically, with few tuning parameters. Applications to stochastic differential equation models and latent doubly intractable distributions are presented.

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arXiv2018

Bootstrapped synthetic likelihood

Approximate Bayesian computation (ABC) and synthetic likelihood (SL) techniques have enabled the use of Bayesian inference for models that may be simulated, but for which the likelihood cannot be evaluated pointwise at values of an unknown parameter $θ$. The main idea in ABC and SL is to, for different values of $θ$ (usually chosen using a Monte Carlo algorithm), build estimates of the likelihood based on simulations from the model conditional on $θ$. The quality of these estimates determines the efficiency of an ABC/SL algorithm. In standard ABC/SL, the only means to improve an estimated likelihood at $θ$ is to simulate more times from the model conditional on $θ$, which is infeasible in cases where the simulator is computationally expensive. In this paper we describe how to use bootstrapping as a means for improving SL estimates whilst using fewer simulations from the model, and also investigate its use in ABC. Further, we investigate the use of the bag of little bootstraps as a means for applying this approach to large datasets, yielding Monte Carlo algorithms that accurately approximate posterior distributions whilst only simulating subsamples of the full data. Examples of the approach applied to i.i.d., temporal and spatial data are given.

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arXiv2017

Fast approximate Bayesian inference for stable differential equation models

Inference for mechanistic models is challenging because of nonlinear interactions between model parameters and a lack of identifiability. Here we focus on a specific class of mechanistic models, which we term stable differential equations. The dynamics in these models are approximately linear around a stable fixed point of the system. We exploit this property to develop fast approximate methods for posterior inference. We illustrate our approach using simulated data on a mechanistic neuroscience model with EEG data. More generally, stable differential equation models and the corresponding inference methods are useful for analysis of stationary time-series data. Compared to the existing state-of-the art, our methods are several orders of magnitude faster, and are particularly suited to analysis of long time-series (>10,000 time-points) and models of moderate dimension (10-50 state variables and 10-50 parameters.)

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arXiv2017

Marginal sequential Monte Carlo for doubly intractable models

Bayesian inference for models that have an intractable partition function is known as a doubly intractable problem, where standard Monte Carlo methods are not applicable. The past decade has seen the development of auxiliary variable Monte Carlo techniques (Møller et al., 2006; Murray et al., 2006) for tackling this problem; these approaches being members of the more general class of pseudo-marginal, or exact-approximate, Monte Carlo algorithms (Andrieu and Roberts, 2009), which make use of unbiased estimates of intractable posteriors. Everitt et al. (2017) investigated the use of exact-approximate importance sampling (IS) and sequential Monte Carlo (SMC) in doubly intractable problems, but focussed only on SMC algorithms that used data-point tempering. This paper describes SMC samplers that may use alternative sequences of distributions, and describes ways in which likelihood estimates may be improved adaptively as the algorithm progresses, building on ideas from Moores et al. (2015). This approach is compared with a number of alternative algorithms for doubly intractable problems, including approximate Bayesian computation (ABC), which we show is closely related to the method of Møller et al. (2006).

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arXiv2017

A rare event approach to high dimensional Approximate Bayesian computation

Approximate Bayesian computation (ABC) methods permit approximate inference for intractable likelihoods when it is possible to simulate from the model. However they perform poorly for high dimensional data, and in practice must usually be used in conjunction with dimension reduction methods, resulting in a loss of accuracy which is hard to quantify or control. We propose a new ABC method for high dimensional data based on rare event methods which we refer to as RE-ABC. This uses a latent variable representation of the model. For a given parameter value, we estimate the probability of the rare event that the latent variables correspond to data roughly consistent with the observations. This is performed using sequential Monte Carlo and slice sampling to systematically search the space of latent variables. In contrast standard ABC can be viewed as using a more naive Monte Carlo estimate. We use our rare event probability estimator as a likelihood estimate within the pseudo-marginal Metropolis-Hastings algorithm for parameter inference. We provide asymptotics showing that RE-ABC has a lower computational cost for high dimensional data than standard ABC methods. We also illustrate our approach empirically, on a Gaussian distribution and an application in infectious disease modelling.

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arXiv2016

Bayesian model comparison with un-normalised likelihoods

Models for which the likelihood function can be evaluated only up to a parameter-dependent unknown normalising constant, such as Markov random field models, are used widely in computer science, statistical physics, spatial statistics, and network analysis. However, Bayesian analysis of these models using standard Monte Carlo methods is not possible due to the intractability of their likelihood functions. Several methods that permit exact, or close to exact, simulation from the posterior distribution have recently been developed. However, estimating the evidence and Bayes' factors (BFs) for these models remains challenging in general. This paper describes new random weight importance sampling and sequential Monte Carlo methods for estimating BFs that use simulation to circumvent the evaluation of the intractable likelihood, and compares them to existing methods. In some cases we observe an advantage in the use of biased weight estimates. An initial investigation into the theoretical and empirical properties of this class of methods is presented. Some support for the use of biased estimates is presented, but we advocate caution in the use of such estimates.

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arXiv2012

Bayesian Parameter Estimation for Latent Markov Random Fields and Social Networks

Undirected graphical models are widely used in statistics, physics and machine vision. However Bayesian parameter estimation for undirected models is extremely challenging, since evaluation of the posterior typically involves the calculation of an intractable normalising constant. This problem has received much attention, but very little of this has focussed on the important practical case where the data consists of noisy or incomplete observations of the underlying hidden structure. This paper specifically addresses this problem, comparing two alternative methodologies. In the first of these approaches particle Markov chain Monte Carlo (Andrieu et al., 2010) is used to efficiently explore the parameter space, combined with the exchange algorithm (Murray et al., 2006) for avoiding the calculation of the intractable normalising constant (a proof showing that this combination targets the correct distribution in found in a supplementary appendix online). This approach is compared with approximate Bayesian computation (Pritchard et al., 1999). Applications to estimating the parameters of Ising models and exponential random graphs from noisy data are presented. Each algorithm used in the paper targets an approximation to the true posterior due to the use of MCMC to simulate from the latent graphical model, in lieu of being able to do this exactly in general. The supplementary appendix also describes the nature of the resulting approximation.

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