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.     

On the Value of derivative evaluations and random walk suppression in Markov Chain Monte Carlo algorithms

Two strategies that can potentially improve Markov Chain Monte Carlo algorithms are to use derivative evaluations of the target density, and to suppress random walk behaviour in the chain. The use of one or both of these strategies has been investigated in a few specific applications, but neither is used routinely. We undertake a broader evaluation of these techniques, with a view to assessing their utility for routine use. In addition to comparing different algorithms, we also compare two different ways in which the algorithms can be applied to a multivariate target distribution. Specifically, the univariate version of an algorithm can be applied repeatedly to one-dimensional conditional distributions, or the multivariate version can be applied directly to the target distribution.     

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.     

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.     

Spatial Modeling of Habitat Preferences of Biological Species using Markov Random Fields

Spatial modeling has gained interest in ecology during the past two decades, especially in the area of biodiversity, where reliable distribution maps are required. Several methods have been proposed to construct distribution maps, most of them acknowledging the presence of spatial interactions. In many cases, a key problem is the lack of true absence data. We present here a model suitable for use when true absence data are missing. The quality of the estimates obtained from the model is evaluated using ROC curve analysis as well as a quadratic cost function, computed from the false positive and false negative error rates. The model is also tested under random and clustered scattering of the presence records. We also present an application of the model to the construction of distribution maps of two endemic bird species in México.     

A random cluster algorithm for some continuous Markov random fields

Based on a random cluster representation, the Swendsen–Wang algorithm for the Ising and Potts distributions is extended to a class of continuous Markov random fields. The algorithm can be described briefly as follows. A given configuration is decomposed into clusters. Probabilities for flipping the values of the random variables in each cluster are calculated. According to these probabilities, values of all the random variables in each cluster will be either updated or kept unchanged and this is done independently across the clusters. A new configuration is then obtained. We will show through a simulation study that, like the Swendsen–Wang algorithm in the case of Ising and Potts distributions, the cluster algorithm here also outperforms the Gibbs sampler in beating the critical slowing down for some strongly correlated Markov random fields.     

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.     

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.     

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.     

Bayesian inference in hidden Markov models through the reversible jump Markov chain Monte Carlo method

Hidden Markov models form an extension of mixture models which provides a flexible class of models exhibiting dependence and a possibly large degree of variability. We show how reversible jump Markov chain Monte Carlo techniques can be used to estimate the parameters as well as the number of components of a hidden Markov model in a Bayesian framework. We employ a mixture of zero-mean normal distributions as our main example and apply this model to three sets of data from finance, meteorology and geomagnetism.     

Markov Chain Monte Carlo for Exact Inference for Diffusions

ABSTRACT. We develop exact Markov chain Monte Carlo methods for discretely sampled, directly and indirectly observed diffusions. The qualification ‘exact’ refers to the fact that the invariant and limiting distribution of the Markov chains is the posterior distribution of the parameters free of any discretization error. The class of processes to which our methods directly apply are those which can be simulated using the most general to date exact simulation algorithm. The article introduces various methods to boost the performance of the basic scheme, including reparametrizations and auxiliary Poisson sampling. We contrast both theoretically and empirically how this new approach compares to irreducible high frequency imputation, which is the state‐of‐the‐art alternative for the class of processes we consider, and we uncover intriguing connections. All methods discussed in the article are tested on typical examples.     

Fully Bayesian Binary Markov Random Field Models: Prior Specification and Posterior Simulation

We propose a flexible prior model for the parameters of binary Markov random fields (MRF), defined on rectangular lattices and with maximal cliques defined from a template maximal clique. The prior model allows higher‐order interactions to be included. We also define a reversible jump Markov chain Monte Carlo algorithm to sample from the associated posterior distribution. The number of possible parameters for a higher‐order MRF becomes high, even for small template maximal cliques. We define a flexible parametric form where the parameters have interpretation as potentials for clique configurations, and limit the effective number of parameters by assigning apriori discrete probabilities for events where groups of parameter values are equal. To cope with the computationally intractable normalising constant of MRFs, we adopt a previously defined approximation of binary MRFs. We demonstrate the flexibility of our prior formulation with simulated and real data examples.     

Approximate Bayesian Computation for Exponential Random Graph Models for Large Social Networks

We consider the issue of sampling from the posterior distribution of exponential random graph (ERG) models and other statistical models with intractable normalizing constants. Existing methods based on exact sampling are either infeasible or require very long computing time. We study a class of approximate Markov chain Monte Carlo (MCMC) sampling schemes that deal with this issue. We also develop a new Metropolis–Hastings kernel to sample sparse large networks from ERG models. We illustrate the proposed methods on several examples.     

Adaptive Gaussian Markov random fields with applications in human brain mapping

Summary.  Functional magnetic resonance imaging has become a standard technology in human brain mapping. Analyses of the massive spatiotemporal functional magnetic resonance imaging data sets often focus on parametric or non-parametric modelling of the temporal component, whereas spatial smoothing is based on Gaussian kernels or random fields. A weakness of Gaussian spatial smoothing is underestimation of activation peaks or blurring of high curvature transitions between activated and non-activated regions of the brain. To improve spatial adaptivity, we introduce a class of inhomogeneous Markov random fields with stochastic interaction weights in a space-varying coefficient model. For given weights, the random field is conditionally Gaussian, but marginally it is non-Gaussian. Fully Bayesian inference, including estimation of weights and variance parameters, can be carried out through efficient Markov chain Monte Carlo simulation. Although motivated by the analysis of functional magnetic resonance imaging data, the methodological development is general and can also be used for spatial smoothing and regression analysis of areal data on irregular lattices. An application to stylized artificial data and to real functional magnetic resonance imaging data from a visual stimulation experiment demonstrates the performance of our approach in comparison with Gaussian and robustified non-Gaussian Markov random-field models.     

Bounding convergence rates for Markov chains: An example of the use of computer algebra

Kolassa and Tanner (J. Am. Stat. Assoc. (1994) 89, 697–702) present the Gibbs-Skovgaard algorithm for approximate conditional inference. Kolassa (Ann Statist. (1999), 27, 129–142) gives conditions under which their Markov chain is known to converge. This paper calculates explicity bounds on convergence rates in terms calculable directly from chain transition operators. These results are useful in cases like those considered by Kolassa (1999).     

Statistical inference for discretely observed Markov jump processes

Summary.  Likelihood inference for discretely observed Markov jump processes with finite state space is investigated. The existence and uniqueness of the maximum likelihood estimator of the intensity matrix are investigated. This topic is closely related to the imbedding problem for Markov chains. It is demonstrated that the maximum likelihood estimator can be found either by the EM algorithm or by a Markov chain Monte Carlo procedure. When the maximum likelihood estimator does not exist, an estimator can be obtained by using a penalized likelihood function or by the Markov chain Monte Carlo procedure with a suitable prior. The methodology and its implementation are illustrated by examples and simulation studies.     

Random Bernstein Polynomials

Random Bernstein polynomials which are also probability distribution functions on the closed unit interval are studied. The probability law of a Bernstein polynomial so defined provides a novel prior on the space of distribution functions on [0, 1] which has full support and can easily select absolutely continuous distribution functions with a continuous and smooth derivative. In particular, the Bernstein polynomial which approximates a Dirichlet process is studied. This may be of interest in Bayesian non-parametric inference. In the second part of the paper, we study the posterior from a Bernstein–Dirichlet prior and suggest a hybrid Monte Carlo approximation of it. The proposed algorithm has some aspects of novelty since the problem under examination has a changing dimension parameter space.     

Bayesian texture segmentation of weed and crop images using reversible jump Markov chain Monte Carlo methods

Summary. A Bayesian method for segmenting weed and crop textures is described and implemented. The work forms part of a project to identify weeds and crops in images so that selective crop spraying can be carried out. An image is subdivided into blocks and each block is modelled as a single texture. The number of different textures in the image is assumed unknown. A hierarchical Bayesian procedure is used where the texture labels have a Potts model (colour Ising Markov random field) prior and the pixels within a block are distributed according to a Gaussian Markov random field, with the parameters dependent on the type of texture. We simulate from the posterior distribution by using a reversible jump Metropolis–Hastings algorithm, where the number of different texture components is allowed to vary. The methodology is applied to a simulated image and then we carry out texture segmentation on the weed and crop images that motivated the work.     

Bayesian Estimation for the Exponentiated Weibull Model via Markov Chain Monte Carlo Simulation

Bayesian estimation for the two unknown parameters and the reliability function of the exponentiated Weibull model are obtained based on generalized order statistics. Markov chain Monte Carlo (MCMC) methods are considered to compute the Bayes estimates of the target parameters. Our computations are based on the balanced loss function which contains the symmetric and asymmetric loss functions as special cases. The results have been specialized to the progressively Type-II censored data and upper record values. Comparisons are made between Bayesian and maximum likelihood estimators via Monte Carlo simulation.     

Bayesian Inference and Forecasting in Dynamic Neural Networks with Fully Markov Switching ARCH Noises

We deal with one-layer feed-forward neural network for the Bayesian analysis of nonlinear time series. Noises are modeled nonlinearly and nonnormally, by means of ARCH models whose parameters are all dependent on a hidden Markov chain. Parameter estimation is performed by sampling from the posterior distribution via Evolutionary Monte Carlo algorithm, in which two new crossover operators have been introduced. Unknown parameters of the model also include the missing values which can occur within the observed series, so, considering future values as missing, it is also possible to compute point and interval multi-step-ahead predictions.