A class of fast exact Bayesian filters in dynamical models with jumps

In this paper, we focus on the statistical filtering problem in dynamical models with jumps. When a particular application relies on physical properties which are modeled by linear and Gaussian probability density functions with jumps, an usualmethod consists in approximating the optimal Bayesian estimate (in the sense of the Minimum Mean Square Error (MMSE)) in a linear and Gaussian Jump Markov State Space System (JMSS). Practical solutions include algorithms based on numerical approximations or based on Sequential Monte Carlo (SMC) methods. In this paper, we propose a class of alternative methods which consists in building statistical models which share the same physical properties of interest but in which the computation of the optimal MMSE estimate can be done at a computational cost which is linear in the number of observations.Comment: 21 pages, 7 figure

Latent Gaussian Count Time Series Modeling

This paper develops theory and methods for the copula modeling of stationary count time series. The techniques use a latent Gaussian process and a distributional transformation to construct stationary series with very flexible correlation features that can have any pre-specified marginal distribution, including the classical Poisson, generalized Poisson, negative binomial, and binomial count structures. A Gaussian pseudo-likelihood estimation paradigm, based only on the mean and autocovariance function of the count series, is developed via some new Hermite expansions. Particle filtering methods are studied to approximate the true likelihood of the count series. Here, connections to hidden Markov models and other copula likelihood approximations are made. The efficacy of the approach is demonstrated and the methods are used to analyze a count series containing the annual number of no-hitter baseball games pitched in major league baseball since 1893

Sequential Bayesian inference for implicit hidden Markov models and current limitations

Hidden Markov models can describe time series arising in various fields of science, by treating the data as noisy measurements of an arbitrarily complex Markov process. Sequential Monte Carlo (SMC) methods have become standard tools to estimate the hidden Markov process given the observations and a fixed parameter value. We review some of the recent developments allowing the inclusion of parameter uncertainty as well as model uncertainty. The shortcomings of the currently available methodology are emphasised from an algorithmic complexity perspective. The statistical objects of interest for time series analysis are illustrated on a toy "Lotka-Volterra" model used in population ecology. Some open challenges are discussed regarding the scalability of the reviewed methodology to longer time series, higher-dimensional state spaces and more flexible models.Comment: Review article written for ESAIM: proceedings and surveys. 25 pages, 10 figure

Statistical Inference for Partially Observed Markov Processes via the R Package pomp

Partially observed Markov process (POMP) models, also known as hidden Markov models or state space models, are ubiquitous tools for time series analysis. The R package pomp provides a very flexible framework for Monte Carlo statistical investigations using nonlinear, non-Gaussian POMP models. A range of modern statistical methods for POMP models have been implemented in this framework including sequential Monte Carlo, iterated filtering, particle Markov chain Monte Carlo, approximate Bayesian computation, maximum synthetic likelihood estimation, nonlinear forecasting, and trajectory matching. In this paper, we demonstrate the application of these methodologies using some simple toy problems. We also illustrate the specification of more complex POMP models, using a nonlinear epidemiological model with a discrete population, seasonality, and extra-demographic stochasticity. We discuss the specification of user-defined models and the development of additional methods within the programming environment provided by pomp.Comment: In press at the Journal of Statistical Software. A version of this paper is provided at the pomp package website: http://kingaa.github.io/pom

Multilevel ensemble Kalman filtering for spatio-temporal processes

We design and analyse the performance of a multilevel ensemble Kalman filter method (MLEnKF) for filtering settings where the underlying state-space model is an infinite-dimensional spatio-temporal process. We consider underlying models that needs to be simulated by numerical methods, with discretization in both space and time. The multilevel Monte Carlo (MLMC) sampling strategy, achieving variance reduction through pairwise coupling of ensemble particles on neighboring resolutions, is used in the sample-moment step of MLEnKF to produce an efficient hierarchical filtering method for spatio-temporal models. Under sufficient regularity, MLEnKF is proven to be more efficient for weak approximations than EnKF, asymptotically in the large-ensemble and fine-numerical-resolution limit. Numerical examples support our theoretical findings.Comment: Version 1: 39 pages, 4 figures.arXiv admin note: substantial text overlap with arXiv:1608.08558 . Version 2 (this version): 52 pages, 6 figures. Revision primarily of the introduction and the numerical examples sectio