Particle MCMC Research Articles

Joint Tracking and Ground Plane Estimation

We propose a novel framework that jointly estimates the ground plane and a target's motion trajectory. This results in improvements for both. Estimating their joint posterior is based on Particle Markov Chain Monte Carlo (Particle MCMC). In Particle MCMC, the best target state is inferred by a particle filter and the best ground plane is obtained by MCMC. Compared with conventional sampling methods that iteratively infer the best target states and ground plane parameters, our method infers them jointly. This reduces sampling errors drastically. Experimental results demonstrate that our method outperforms several state-of-the-art tracking methods, while the ground plane accuracy is also improved.

The use of a single pseudo-sample in approximate Bayesian computation

We analyze the computational efficiency of approximate Bayesian computation (ABC), which approximates a likelihood function by drawing pseudo-samples from the associated model. For the rejection sampling version of ABC, it is known that multiple pseudo-samples cannot substantially increase (and can substantially decrease) the efficiency of the algorithm as compared to employing a high-variance estimate based on a single pseudo-sample. We show that this conclusion also holds for a Markov chain Monte Carlo version of ABC, implying that it is unnecessary to tune the number of pseudo-samples used in ABC-MCMC. This conclusion is in contrast to particle MCMC methods, for which increasing the number of particles can provide large gains in computational efficiency.

Augmentation schemes for particle MCMC

Particle MCMC involves using a particle filter within an MCMC algorithm. For inference of a model which involves an unobserved stochastic process, the standard implementation uses the particle filter to propose new values for the stochastic process, and MCMC moves to propose new values for the parameters. We show how particle MCMC can be generalised beyond this. Our key idea is to introduce new latent variables. We then use the MCMC moves to update the latent variables, and the particle filter to propose new values for the parameters and stochastic process given the latent variables. A generic way of defining these latent variables is to model them as pseudo-observations of the parameters or of the stochastic process. By choosing the amount of information these latent variables have about the parameters and the stochastic process we can often improve the mixing of the particle MCMC algorithm by trading off the Monte Carlo error of the particle filter and the mixing of the MCMC moves. We show that using pseudo-observations within particle MCMC can improve its efficiency in certain scenarios: dealing with initialisation problems of the particle filter; speeding up the mixing of particle Gibbs when there is strong dependence between the parameters and the stochastic process; and enabling further MCMC steps to be used within the particle filter.

Combining particle MCMC with Rao-Blackwellized Monte Carlo data association for parameter estimation in multiple target tracking

We consider state and parameter estimation in multiple target tracking problems with data association uncertainties and unknown number of targets. We show how the problem can be recast into a conditionally linear Gaussian state-space model with unknown parameters and present an algorithm for computationally efficient inference on the resulting model. The proposed algorithm is based on combining the Rao-Blackwellized Monte Carlo data association algorithm with particle Markov chain Monte Carlo algorithms to jointly estimate both parameters and data associations. Both particle marginal Metropolis–Hastings and particle Gibbs variants of particle MCMC are considered. We demonstrate the performance of the method both using simulated data and in a real-data case study of using multiple target tracking to estimate the brown bear population in Finland.

Bayesian inference for Markov jump processes with informative observations.

In this paper we consider the problem of parameter inference for Markov jump process (MJP) representations of stochastic kinetic models. Since transition probabilities are intractable for most processes of interest yet forward simulation is straightforward, Bayesian inference typically proceeds through computationally intensive methods such as (particle) MCMC. Such methods ostensibly require the ability to simulate trajectories from the conditioned jump process. When observations are highly informative, use of the forward simulator is likely to be inefficient and may even preclude an exact (simulation based) analysis. We therefore propose three methods for improving the efficiency of simulating conditioned jump processes. A conditioned hazard is derived based on an approximation to the jump process, and used to generate end-point conditioned trajectories for use inside an importance sampling algorithm. We also adapt a recently proposed sequential Monte Carlo scheme to our problem. Essentially, trajectories are reweighted at a set of intermediate time points, with more weight assigned to trajectories that are consistent with the next observation. We consider two implementations of this approach, based on two continuous approximations of the MJP. We compare these constructs for a simple tractable jump process before using them to perform inference for a Lotka-Volterra system. The best performing construct is used to infer the parameters governing a simple model of motility regulation in Bacillus subtilis.

On Blocks, Tempering and Particle MCMC for Systems Identification

The widespread use of particle methods for addressing the filtering and smoothing problems in state-space models has, in recent years, been complemented by the development of particle Markov Chain Monte Carlo (PMCMC) methods. PMCMC uses particle filters within offline systems-identification settings. We develop a modified particle filter, based around block sampling and tempering, intended to improve their exploration of the state space and the associated estimation of the marginal likelihood. The aim is to develop particle methods with improved robustness properties, particularly for parameter values which are not able to explain observed data well, for use within PMCMC algorithms. The proposed strategies do not require a substantial analytic understanding of the model structure, unlike most techniques for improving particle-filter performance.

Bayesian inference for hybrid discrete-continuous stochastic kinetic models

We consider the problem of efficiently performing simulation and inference for stochastic kinetic models. Whilst it is possible to work directly with the resulting Markov jump process (MJP), computational cost can be prohibitive for networks of realistic size and complexity. In this paper, we consider an inference scheme based on a novel hybrid simulator that classifies reactions as either ‘fast’ or ‘slow’ with fast reactions evolving as a continuous Markov process whilst the remaining slow reaction occurrences are modelled through a MJP with time-dependent hazards. A linear noise approximation (LNA) of fast reaction dynamics is employed and slow reaction events are captured by exploiting the ability to solve the stochastic differential equation driving the LNA. This simulation procedure is used as a proposal mechanism inside a particle MCMC scheme, thus allowing Bayesian inference for the model parameters. We apply the scheme to a simple application and compare the output with an existing hybrid approach and also a scheme for performing inference for the underlying discrete stochastic model.

Particle MCMC for Bayesian Microwave Control

We consider the problem of local radioelectric property estimation from global electromagnetic scattering measurements. This challenging ill-posed high dimensional inverse problem can be explored by intensive computations of a parallel Maxwell solver on a petaflopic supercomputer. Then, it is shown how Bayesian inference can be perfomed with a Particle Marginal Metropolis-Hastings (PMMH) approach, which includes a Rao-Blackwellised Sequential Monte Carlo algorithm with interacting Kalman filters. Material properties, including a multiple components "Debye relaxation"/"Lorenzian resonant" material model, are estimated; it is illustrated on synthetic data. Eventually, we propose different ways to deal with higher dimensional problems, from parallelization to the original introduction of efficient sequential data assimilation techniques, widely used in weather forecasting, oceanography, geophysics, etc.

Delayed acceptance particle MCMC for exact inference in stochastic kinetic models

Recently-proposed particle MCMC methods provide a flexible way of performing Bayesian inference for parameters governing stochastic kinetic models defined as Markov (jump) processes (MJPs). Each iteration of the scheme requires an estimate of the marginal likelihood calculated from the output of a sequential Monte Carlo scheme (also known as a particle filter). Consequently, the method can be extremely computationally intensive. We therefore aim to avoid most instances of the expensive likelihood calculation through use of a fast approximation. We consider two approximations: the chemical Langevin equation diffusion approximation (CLE) and the linear noise approximation (LNA). Either an estimate of the marginal likelihood under the CLE, or the tractable marginal likelihood under the LNA can be used to calculate a first step acceptance probability. Only if a proposal is accepted under the approximation do we then run a sequential Monte Carlo scheme to compute an estimate of the marginal likelihood under the true MJP and construct a second stage acceptance probability that permits exact (simulation based) inference for the MJP. We therefore avoid expensive calculations for proposals that are likely to be rejected. We illustrate the method by considering inference for parameters governing a Lotka-Volterra system, a model of gene expression and a simple epidemic process.

Posterior inference on parameters of stochastic differential equations via non-linear Gaussian filtering and adaptive MCMC

This article is concerned with Bayesian estimation of parameters in non-linear multivariate stochastic differential equation (SDE) models occurring, for example, in physics, engineering, and financial applications. In particular, we study the use of adaptive Markov chain Monte Carlo (AMCMC) based numerical integration methods with non-linear Kalman-type approximate Gaussian filters for parameter estimation in non-linear SDEs. We study the accuracy and computational efficiency of gradient-free sigma-point approximations (Gaussian quadratures) in the context of parameter estimation, and compare them with Taylor series and particle MCMC approximations. The results indicate that the sigma-point based Gaussian approximations lead to better approximations of the parameter posterior distribution than the Taylor series, and the accuracy of the approximations is comparable to that of the computationally significantly heavier particle MCMC approximations.

Marginal likelihood for Markov-switching and change-point GARCH models

GARCH volatility models with fixed parameters are too restrictive for long time series due to breaks in the volatility process. Flexible alternatives are Markov-switching GARCH and change-point GARCH models. They require estimation by MCMC methods due to the path dependence problem. An unsolved issue is the computation of their marginal likelihood, which is essential for determining the number of regimes or change-points. We solve the problem by using particle MCMC, a technique proposed by Andrieu et al. (2010). We examine the performance of this new method on simulated data, and we illustrate its use on several return series.

Marginal Likelihood for Markov-Switching and Change-Point GARCH Models

GARCH volatility models with fixed parameters are too restrictive for long time series due to breaks in the volatility process. Flexible alternatives are Markov-switching GARCH and change-point GARCH models. They require estimation by MCMC methods due to the path dependence problem. An unsolved issue is the computation of their marginal likelihood, which is essential for determining the number of regimes or change-points. We solve the problem by using particle MCMC, a technique proposed by Andrieu, Doucet, and Holenstein (2010). We examine the performance of this new method on simulated data, and we illustrate its use on several return series.

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

Phylodynamics - the field aiming to quantitatively integrate the ecological and evolutionary dynamics of rapidly evolving populations like those of RNA viruses – increasingly relies upon coalescent approaches to infer past population dynamics from reconstructed genealogies. As sequence data have become more abundant, these approaches are beginning to be used on populations undergoing rapid and rather complex dynamics. In such cases, the simple demographic models that current phylodynamic methods employ can be limiting. First, these models are not ideal for yielding biological insight into the processes that drive the dynamics of the populations of interest. Second, these models differ in form from mechanistic and often stochastic population dynamic models that are currently widely used when fitting models to time series data. As such, their use does not allow for both genealogical data and time series data to be considered in tandem when conducting inference. Here, we present a flexible statistical framework for phylodynamic inference that goes beyond these current limitations. The framework we present employs a recently developed method known as particle MCMC to fit stochastic, nonlinear mechanistic models for complex population dynamics to gene genealogies and time series data in a Bayesian framework. We demonstrate our approach using a nonlinear Susceptible-Infected-Recovered (SIR) model for the transmission dynamics of an infectious disease and show through simulations that it provides accurate estimates of past disease dynamics and key epidemiological parameters from genealogies with or without accompanying time series data.

The Ornstein–Uhlenbeck Dirichlet process and other time-varying processes for Bayesian nonparametric inference

This paper introduces a new class of time-varying, measure-valued stochastic processes for Bayesian nonparametric inference. The class of priors is constructed by normalising a stochastic process derived from non-Gaussian Ornstein–Uhlenbeck processes and generalises the class of normalised random measures with independent increments from static problems. Some properties of the normalised measure are investigated. A particle filter and MCMC schemes are described for inference. The methods are applied to an example in the modelling of financial data.