Fitting Gaussian Markov Random Fields to Gaussian Fields

This paper discusses the following task often encountered in building Bayesian spatial models: construct a homogeneous Gaussian Markov random field (GMRF) on a lattice with correlation properties either as present in some observed data, or consistent with prior knowledge. The Markov property is essential in designing computationally efficient Markov chain Monte Carlo algorithms to analyse such models. We argue that we can restate both tasks as that of fitting a GMRF to a prescribed stationary Gaussian field on a lattice when both local and global properties are important. We demonstrate that using the KullbackLeibler discrepancy often fails for this task, giving severely undesirable behaviour of the correlation function for lags outside the neighbourhood. We propose a new criterion that resolves this difficulty, and demonstrate that GMRFs with small neighbourhoods can approximate Gaussian fields surprisingly well even with long correlation lengths. Finally, we discuss implications of our findings for likelihood based inference for general Markov random fields when global properties are also important.     

Functional and dynamic magnetic resonance imaging using vector adaptive weights smoothing

We consider the problem of statistical inference for functional and dynamic magnetic resonance imaging (MRI). A new approach is proposed which extends the adaptive weights smoothing procedure of Polzehl and Spokoiny that was originally designed for image denoising. We demonstrate how the adaptive weights smoothing method can be applied to time series of images, which typically occur in functional and dynamic MRI. It is shown how signal detection in functional MRI and the analysis of dynamic MRI can benefit from spatially adaptive smoothing. The performance of the procedure is illustrated by using real and simulated data.     

Lévy‐based Modelling in Brain Imaging

Abstract. A substantive problem in neuroscience is the lack of valid statistical methods for non‐Gaussian random fields. In the present study, we develop a flexible, yet tractable model for a random field based on kernel smoothing of a so‐called Lévy basis. The resulting field may be Gaussian, but there are many other possibilities, including random fields based on Gamma, inverse Gaussian and normal inverse Gaussian (NIG) Lévy bases. It is easy to estimate the parameters of the model and accordingly to assess by simulation the quantiles of test statistics commonly used in neuroscience. We give a concrete example of magnetic resonance imaging scans that are non‐Gaussian. For these data, simulations under the fitted models show that traditional methods based on Gaussian random field theory may leave small, but significant changes in signal level undetected, while these changes are detectable under a non‐Gaussian Lévy model.     

Approximating hidden Gaussian Markov random fields

Summary.  Gaussian Markov random-field (GMRF) models are frequently used in a wide variety of applications. In most cases parts of the GMRF are observed through mutually independent data; hence the full conditional of the GMRF, a hidden GMRF (HGMRF), is of interest. We are concerned with the case where the likelihood is non-Gaussian, leading to non-Gaussian HGMRF models. Several researchers have constructed block sampling Markov chain Monte Carlo schemes based on approximations of the HGMRF by a GMRF, using a second-order expansion of the log-density at or near the mode. This is possible as the GMRF approximation can be sampled exactly with a known normalizing constant. The Markov property of the GMRF approximation yields computational efficiency.The main contribution in the paper is to go beyond the GMRF approximation and to construct a class of non-Gaussian approximations which adapt automatically to the particular HGMRF that is under study. The accuracy can be tuned by intuitive parameters to nearly any precision. These non-Gaussian approximations share the same computational complexity as those which are based on GMRFs and can be sampled exactly with computable normalizing constants. We apply our approximations in spatial disease mapping and model-based geostatistical models with different likelihoods, obtain procedures for block updating and construct Metropolized independence samplers.     

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

Summary.  Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models , where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.     

Propriety of posteriors in structured additive regression models: Theory and empirical evidence

Structured additive regression comprises many semiparametric regression models such as generalized additive (mixed) models, geoadditive models, and hazard regression models within a unified framework. In a Bayesian formulation, non-parametric functions, spatial effects and further model components are specified in terms of multivariate Gaussian priors for high-dimensional vectors of regression coefficients. For several model terms, such as penalized splines or Markov random fields, these Gaussian prior distributions involve rank-deficient precision matrices, yielding partially improper priors. Moreover, hyperpriors for the variances (corresponding to inverse smoothing parameters) may also be specified as improper, e.g. corresponding to Jeffreys prior or a flat prior for the standard deviation. Hence, propriety of the joint posterior is a crucial issue for full Bayesian inference in particular if based on Markov chain Monte Carlo simulations. We establish theoretical results providing sufficient (and sometimes necessary) conditions for propriety and provide empirical evidence through several accompanying simulation studies.     

On Block Updating in Markov Random Field Models for Disease Mapping

Gaussian Markov random field (GMRF) models are commonly used to model spatial correlation in disease mapping applications. For Bayesian inference by MCMC, so far mainly single-site updating algorithms have been considered. However, convergence and mixing properties of such algorithms can be extremely poor due to strong dependencies of parameters in the posterior distribution. In this paper, we propose various block sampling algorithms in order to improve the MCMC performance. The methodology is rather general, allows for non-standard full conditionals, and can be applied in a modular fashion in a large number of different scenarios. For illustration we consider three different applications: two formulations for spatial modelling of a single disease (with and without additional unstructured parameters respectively), and one formulation for the joint analysis of two diseases. The results indicate that the largest benefits are obtained if parameters and the corresponding hyperparameter are updated jointly in one large block. Implementation of such block algorithms is relatively easy using methods for fast sampling of Gaussian Markov random fields ( Rue, 2001 ). By comparison, Monte Carlo estimates based on single-site updating can be rather misleading, even for very long runs. Our results may have wider relevance for efficient MCMC simulation in hierarchical models with Markov random field components.     

Maximum likelihood from spatial random effects models via the stochastic approximation expectation maximization algorithm

We introduce a class of spatial random effects models that have Markov random fields (MRF) as latent processes. Calculating the maximum likelihood estimates of unknown parameters in SREs is extremely difficult, because the normalizing factors of MRFs and additional integrations from unobserved random effects are computationally prohibitive. We propose a stochastic approximation expectation-maximization (SAEM) algorithm to maximize the likelihood functions of spatial random effects models. The SAEM algorithm integrates recent improvements in stochastic approximation algorithms; it also includes components of the Newton-Raphson algorithm and the expectation-maximization (EM) gradient algorithm. The convergence of the SAEM algorithm is guaranteed under some mild conditions. We apply the SAEM algorithm to three examples that are representative of real-world applications: a state space model, a noisy Ising model, and segmenting magnetic resonance images (MRI) of the human brain. The SAEM algorithm gives satisfactory results in finding the maximum likelihood estimate of spatial random effects models in each of these instances.     

Gaussian Markov random field spatial models in GAMLSS

This paper describes the modelling and fitting of Gaussian Markov random field spatial components within a Generalized AdditiveModel for Location, Scale and Shape (GAMLSS) model. This allows modelling of any or all the parameters of the distribution for the response variable using explanatory variables and spatial effects. The response variable distribution is allowed to be a non-exponential family distribution. A new package developed in R to achieve this is presented. We use Gaussian Markov random fields to model the spatial effect in Munich rent data and explore some features and characteristics of the data. The potential of using spatial analysis within GAMLSS is discussed. We argue that the flexibility of parametric distributions, ability to model all the parameters of the distribution and diagnostic tools of GAMLSS provide an ideal environment for modelling spatial features of data.     

A Mixed Model Approach for Geoadditive Hazard Regression

Abstract.  Mixed model based approaches for semiparametric regression have gained much interest in recent years, both in theory and application. They provide a unified and modular framework for penalized likelihood and closely related empirical Bayes inference. In this article, we develop mixed model methodology for a broad class of Cox-type hazard regression models where the usual linear predictor is generalized to a geoadditive predictor incorporating non-parametric terms for the (log-)baseline hazard rate, time-varying coefficients and non-linear effects of continuous covariates, a spatial component, and additional cluster-specific frailties. Non-linear and time-varying effects are modelled through penalized splines, while spatial components are treated as correlated random effects following either a Markov random field or a stationary Gaussian random field prior. Generalizing existing mixed model methodology, inference is derived using penalized likelihood for regression coefficients and (approximate) marginal likelihood for smoothing parameters. In a simulation we study the performance of the proposed method, in particular comparing it with its fully Bayesian counterpart using Markov chain Monte Carlo methodology, and complement the results by some asymptotic considerations. As an application, we analyse leukaemia survival data from northwest England.     

Estimation in Truncated GLG Model for Ordered Categorical Spatial Data Using the SAEM Algorithm

In this article, we utilize a scale mixture of Gaussian random field as a tool for modeling spatial ordered categorical data with non-Gaussian latent variables. In fact, we assume a categorical random field is created by truncating a Gaussian Log-Gaussian latent variable model to accommodate heavy tails. Since the traditional likelihood approach for the considered model involves high-dimensional integrations which are computationally intensive, the maximum likelihood estimates are obtained using a stochastic approximation expectation–maximization algorithm. For this purpose, Markov chain Monte Carlo methods are employed to draw from the posterior distribution of latent variables. A numerical example illustrates the methodology.     

Spatial Matérn Fields Driven by Non‐Gaussian Noise

The article studies non‐Gaussian extensions of a recently discovered link between certain Gaussian random fields, expressed as solutions to stochastic partial differential equations (SPDEs), and Gaussian Markov random fields. The focus is on non‐Gaussian random fields with Matérn covariance functions, and in particular, we show how the SPDE formulation of a Laplace moving‐average model can be used to obtain an efficient simulation method as well as an accurate parameter estimation technique for the model. This should be seen as a demonstration of how these techniques can be used, and generalizations to more general SPDEs are readily available.     

Fast sampling of Gaussian Markov random fields

This paper demonstrates how Gaussian Markov random fields (conditional autoregressions) can be sampled quickly by using numerical techniques for sparse matrices. The algorithm is general and efficient, and expands easily to various forms for conditional simulation and evaluation of normalization constants. We demonstrate its use by constructing efficient block updates in Markov chain Monte Carlo algorithms for disease mapping.     

A Stochastic Geometry Model for Functional Magnetic Resonance Images

In functional magnetic resonance imaging, spatial activation patterns are commonly estimated using a non-parametric smoothing approach. Significant peaks or clusters in the smoothed image are subsequently identified by testing the null hypothesis of lack of activation in every volume element of the scans. A weakness of this approach is the lack of a model for the activation pattern; this makes it difficult to determine the variance of estimates, to test specific neuroscientific hypotheses or to incorporate prior information about the brain area under study in the analysis. These issues may be addressed by formulating explicit spatial models for the activation and using simulation methods for inference. We present one such approach, based on a marked point process prior. Informally, one may think of the points as centres of activation, and the marks as parameters describing the shape and area of the surrounding cluster. We present an MCMC algorithm for making inference in the model and compare the approach with a traditional non-parametric method, using both simulated and visual stimulation data. Finally we discuss extensions of the model and the inferential framework to account for non-stationary responses and spatio-temporal correlation.     

Construction of non-Gaussian random fields with any given correlation structure

A positive definite function can be thought of as the covariance function of a Gaussian random field, according to the celebrated Kolmogorov existence theorem. A question of great theoretical and practical interest is: how could one construct a non-Gaussian random field with the given positive definite function as its covariance function? In this paper we demonstrate a novel and simple method for constructing many such non-Gaussian random fields, with the corresponding finite-dimensional distributions identified. Also, we show how to construct a non-Gaussian random field with a given negative definite function as its variogram.     

A latent Gaussian Markov random-field model for spatiotemporal rainfall disaggregation

Summary. Rainfall data are often collected at coarser spatial scales than required for input into hydrology and agricultural models. We therefore describe a spatiotemporal model which allows multiple imputation of rainfall at fine spatial resolutions, with a realistic dependence structure in both space and time and with the total rainfall at the coarse scale consistent with that observed. The method involves the transformation of the fine scale rainfall to a thresholded Gaussian process which we model as a Gaussian Markov random field. Gibbs sampling is then used to generate realizations of rainfall efficiently at the fine scale. Results compare favourably with previous, less elegant methods.     

Markov Random Fields with Higher-order Interactions

Discrete-state Markov random fields on regular arrays have played a significant role in spatial statistics and image analysis. For example, they are used to represent objects against background in computer vision and pixel-based classification of a region into different crop types in remote sensing. Convenience has generally favoured formulations that involve only pairwise interactions. Such models are in themselves unrealistic and, although they often perform surprisingly well in tasks such as the restoration of degraded images, they are unsatisfactory for many other purposes. In this paper, we consider particular forms of Markov random fields that involve higher-order interactions and therefore are better able to represent the large-scale properties of typical spatial scenes. Interpretations of the parameters are given and realizations from a variety of models are produced via Markov chain Monte Carlo. Potential applications are illustrated in two examples. The first concerns Bayesian image analysis and confirms that pairwise-interaction priors may perform very poorly for image functionals such as number of objects, even when restoration apparently works well. The second example describes a model for a geological dataset and obtains maximum-likelihood parameter estimates using Markov chain Monte Carlo. Despite the complexity of the formulation, realizations of the estimated model suggest that the representation is quite realistic.     

Adaptive weights smoothing with applications to image restoration

We propose a new method of nonparametric estimation which is based on locally constant smoothing with an adaptive choice of weights for every pair of data points. Some theoretical properties of the procedure are investigated. Then we demonstrate the performance of the method on some simulated univariate and bivariate examples and compare it with other nonparametric methods. Finally we discuss applications of this procedure to magnetic resonance and satellite imaging.     

Hierarchical Bayesian Approach to a Multi-Site Hidden Markov Model

Multivariate data with a sequential or temporal structure occur in various fields of study. The hidden Markov model (HMM) provides an attractive framework for modeling long-term persistence in areas of pattern recognition through the extension of independent and identically distributed mixture models. Unlike in typical mixture models, the heterogeneity of data is represented by hidden Markov states. This article extends the HMM to a multi-site or multivariate case by taking a hierarchical Bayesian approach. This extension has many advantages over a single-site HMM. For example, it can provide more information for identifying the structure of the HMM than a single-site analysis. We evaluate the proposed approach by exploiting a spatial correlation that depends on the distance between sites.