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

Inference for Differential Equation Models using Relaxation via Dynamical Systems

Statistical regression models whose mean functions are represented by ordinary differential equations (ODEs) can be used to describe phenomenons dynamical in nature, which are abundant in areas such as biology, climatology and genetics. The estimation of parameters of ODE based models is essential for understanding its dynamics, but the lack of an analytical solution of the ODE makes the parameter estimation challenging. The aim of this paper is to propose a general and fast framework of statistical inference for ODE based models by relaxation of the underlying ODE system. Relaxation is achieved by a properly chosen numerical procedure, such as the Runge-Kutta, and by introducing additive Gaussian noises with small variances. Consequently, filtering methods can be applied to obtain the posterior distribution of the parameters in the Bayesian framework. The main advantage of the proposed method is computation speed. In a simulation study, the proposed method was at least 14 times faster than the other methods. Theoretical results which guarantee the convergence of the posterior of the approximated dynamical system to the posterior of true model are presented. Explicit expressions are given that relate the order and the mesh size of the Runge-Kutta procedure to the rate of convergence of the approximated posterior as a function of sample size

Structure Learning in Coupled Dynamical Systems and Dynamic Causal Modelling

Identifying a coupled dynamical system out of many plausible candidates, each of which could serve as the underlying generator of some observed measurements, is a profoundly ill posed problem that commonly arises when modelling real world phenomena. In this review, we detail a set of statistical procedures for inferring the structure of nonlinear coupled dynamical systems (structure learning), which has proved useful in neuroscience research. A key focus here is the comparison of competing models of (ie, hypotheses about) network architectures and implicit coupling functions in terms of their Bayesian model evidence. These methods are collectively referred to as dynamical casual modelling (DCM). We focus on a relatively new approach that is proving remarkably useful; namely, Bayesian model reduction (BMR), which enables rapid evaluation and comparison of models that differ in their network architecture. We illustrate the usefulness of these techniques through modelling neurovascular coupling (cellular pathways linking neuronal and vascular systems), whose function is an active focus of research in neurobiology and the imaging of coupled neuronal systems