Latent Gaussian modeling and INLA: A review with focus on space-time applications

Bayesian hierarchical models with latent Gaussian layers have proven very flexible in capturing complex stochastic behavior and hierarchical structures in high-dimensional spatial and spatio-temporal data. Whereas simulation-based Bayesian inference through Markov Chain Monte Carlo may be hampered by slow convergence and numerical instabilities, the inferential framework of Integrated Nested Laplace Approximation (INLA) is capable to provide accurate and relatively fast analytical approximations to posterior quantities of interest. It heavily relies on the use of Gauss-Markov dependence structures to avoid the numerical bottleneck of high-dimensional nonsparse matrix computations. With a view towards space-time applications, we here review the principal theoretical concepts, model classes and inference tools within the INLA framework. Important elements to construct space-time models are certain spatial Mat\'ern-like Gauss-Markov random fields, obtained as approximate solutions to a stochastic partial differential equation. Efficient implementation of statistical inference tools for a large variety of models is available through the INLA package of the R software. To showcase the practical use of R-INLA and to illustrate its principal commands and syntax, a comprehensive simulation experiment is presented using simulated non Gaussian space-time count data with a first-order autoregressive dependence structure in time

Hidden Gibbs random fields model selection using Block Likelihood Information Criterion

Performing model selection between Gibbs random fields is a very challenging task. Indeed, due to the Markovian dependence structure, the normalizing constant of the fields cannot be computed using standard analytical or numerical methods. Furthermore, such unobserved fields cannot be integrated out and the likelihood evaluztion is a doubly intractable problem. This forms a central issue to pick the model that best fits an observed data. We introduce a new approximate version of the Bayesian Information Criterion. We partition the lattice into continuous rectangular blocks and we approximate the probability measure of the hidden Gibbs field by the product of some Gibbs distributions over the blocks. On that basis, we estimate the likelihood and derive the Block Likelihood Information Criterion (BLIC) that answers model choice questions such as the selection of the dependency structure or the number of latent states. We study the performances of BLIC for those questions. In addition, we present a comparison with ABC algorithms to point out that the novel criterion offers a better trade-off between time efficiency and reliable results

The rational SPDE approach for Gaussian random fields with general smoothness

A popular approach for modeling and inference in spatial statistics is to represent Gaussian random fields as solutions to stochastic partial differential equations (SPDEs) of the form $L^{\beta}u = \mathcal{W}$, where $\mathcal{W}$ is Gaussian white noise, $L$ is a second-order differential operator, and $\beta>0$ is a parameter that determines the smoothness of $u$. However, this approach has been limited to the case $2\beta\in\mathbb{N}$, which excludes several important models and makes it necessary to keep $\beta$ fixed during inference. We propose a new method, the rational SPDE approach, which in spatial dimension $d\in\mathbb{N}$ is applicable for any $\beta>d/4$, and thus remedies the mentioned limitation. The presented scheme combines a finite element discretization with a rational approximation of the function $x^{-\beta}$ to approximate $u$. For the resulting approximation, an explicit rate of convergence to $u$ in mean-square sense is derived. Furthermore, we show that our method has the same computational benefits as in the restricted case $2\beta\in\mathbb{N}$. Several numerical experiments and a statistical application are used to illustrate the accuracy of the method, and to show that it facilitates likelihood-based inference for all model parameters including $\beta$.Comment: 28 pages, 4 figure

Spatial models generated by nested stochastic partial differential equations, with an application to global ozone mapping

A new class of stochastic field models is constructed using nested stochastic partial differential equations (SPDEs). The model class is computationally efficient, applicable to data on general smooth manifolds, and includes both the Gaussian Mat\'{e}rn fields and a wide family of fields with oscillating covariance functions. Nonstationary covariance models are obtained by spatially varying the parameters in the SPDEs, and the model parameters are estimated using direct numerical optimization, which is more efficient than standard Markov Chain Monte Carlo procedures. The model class is used to estimate daily ozone maps using a large data set of spatially irregular global total column ozone data.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS383 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Multilevel Markov Chain Monte Carlo Method for High-Contrast Single-Phase Flow Problems

In this paper we propose a general framework for the uncertainty quantification of quantities of interest for high-contrast single-phase flow problems. It is based on the generalized multiscale finite element method (GMsFEM) and multilevel Monte Carlo (MLMC) methods. The former provides a hierarchy of approximations of different resolution, whereas the latter gives an efficient way to estimate quantities of interest using samples on different levels. The number of basis functions in the online GMsFEM stage can be varied to determine the solution resolution and the computational cost, and to efficiently generate samples at different levels. In particular, it is cheap to generate samples on coarse grids but with low resolution, and it is expensive to generate samples on fine grids with high accuracy. By suitably choosing the number of samples at different levels, one can leverage the expensive computation in larger fine-grid spaces toward smaller coarse-grid spaces, while retaining the accuracy of the final Monte Carlo estimate. Further, we describe a multilevel Markov chain Monte Carlo method, which sequentially screens the proposal with different levels of approximations and reduces the number of evaluations required on fine grids, while combining the samples at different levels to arrive at an accurate estimate. The framework seamlessly integrates the multiscale features of the GMsFEM with the multilevel feature of the MLMC methods following the work in \cite{ketelson2013}, and our numerical experiments illustrate its efficiency and accuracy in comparison with standard Monte Carlo estimates.Comment: 29 pages, 6 figure