Alternative Markov Properties for Chain Graphs

Graphical Markov models use graphs to represent possible dependences among statistical variables. Lauritzen, Wermuth, and Frydenberg (LWF) introduced a Markov property for chain graphs (CG): graphs that can be used to represent both structural and associative dependences simultaneously and that include both undirected graphs (UG) and acyclic directed graphs (ADG) as special cases. Here an alternative Markov property (AMP) for CGs is introduced and shown to be the Markov property satisfied by a block-recursive linear system with multivariate normal errors. This model can be decomposed into a collection of conditional normal models, each of which combines the features of multivariate linear regression models and covariance selection models, facilitating the estimation of its parameters. In the general case, necessary and sufficient conditions are given for the equivalence of the LWF and AMP Markov properties of a CG, for the AMP Markov equivalence of two CGs, for the AMP Markov equivalence of a CG to some ADG or decomposable UG, and for other equivalences. For CGs, in some ways the AMP property is a more direct extension of the ADG Markov property than is the LWF property.     

Coordinate sampler: a non-reversible Gibbs-like MCMC sampler

We derive a novel non-reversible, continuous-time Markov chain Monte Carlo sampler, called Coordinate Sampler, based on a piecewise deterministic Markov process, which is a variant of the Zigzag sampler of Bierkens et al. (Ann Stat 47(3):1288–1320, 2019). In addition to providing a theoretical validation for this new simulation algorithm, we show that the Markov chain it induces exhibits geometrical ergodicity convergence, for distributions whose tails decay at least as fast as an exponential distribution and at most as fast as a Gaussian distribution. Several numerical examples highlight that our coordinate sampler is more efficient than the Zigzag sampler, in terms of effective sample size.     

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.     

Adaptive evolutionary Monte Carlo algorithm for optimization with applications to sensor placement problems

In this paper, we present an adaptive evolutionary Monte Carlo algorithm (AEMC), which combines a tree-based predictive model with an evolutionary Monte Carlo sampling procedure for the purpose of global optimization. Our development is motivated by sensor placement applications in engineering, which requires optimizing certain complicated “black-box” objective function. The proposed method is able to enhance the optimization efficiency and effectiveness as compared to a few alternative strategies. AEMC falls into the category of adaptive Markov chain Monte Carlo (MCMC) algorithms and is the first adaptive MCMC algorithm that simulates multiple Markov chains in parallel. A theorem about the ergodicity property of the AEMC algorithm is stated and proven. We demonstrate the advantages of the proposed method by applying it to a sensor placement problem in a manufacturing process, as well as to a standard Griewank test function.     

Learning a multivariate Gaussian mixture model with the reversible jump MCMC algorithm

This paper is a contribution to the methodology of fully Bayesian inference in a multivariate Gaussian mixture model using the reversible jump Markov chain Monte Carlo algorithm. To follow the constraints of preserving the first two moments before and after the split or combine moves, we concentrate on a simplified multivariate Gaussian mixture model, in which the covariance matrices of all components share a common eigenvector matrix. We then propose an approach to the construction of the reversible jump Markov chain Monte Carlo algorithm for this model. Experimental results on several data sets demonstrate the efficacy of our algorithm.     

A Unified Approach to the Characterization of Equivalence Classes of DAGs, Chain Graphs with no Flags and Chain Graphs

Abstract.  A Markov property associates a set of conditional independencies to a graph. Two alternative Markov properties are available for chain graphs (CGs), the Lauritzen–Wermuth–Frydenberg (LWF) and the Andersson–Madigan– Perlman (AMP) Markov properties, which are different in general but coincide for the subclass of CGs with no flags . Markov equivalence induces a partition of the class of CGs into equivalence classes and every equivalence class contains a, possibly empty, subclass of CGs with no flags itself containing a, possibly empty, subclass of directed acyclic graphs (DAGs). LWF-Markov equivalence classes of CGs can be naturally characterized by means of the so-called largest CGs , whereas a graphical characterization of equivalence classes of DAGs is provided by the essential graphs . In this paper, we show the existence of largest CGs with no flags that provide a natural characterization of equivalence classes of CGs of this kind, with respect to both the LWF- and the AMP-Markov properties. We propose a procedure for the construction of the largest CGs, the largest CGs with no flags and the essential graphs, thereby providing a unified approach to the problem. As by-products we obtain a characterization of graphs that are largest CGs with no flags and an alternative characterization of graphs which are largest CGs. Furthermore, a known characterization of the essential graphs is shown to be a special case of our more general framework. The three graphical characterizations have a common structure: they use two versions of a locally verifiable graphical rule. Moreover, in case of DAGs, an immediate comparison of three characterizing graphs is possible.     

Asymptotic equipartition property for second-order circular Markov chains indexed by a two-rooted Cayley tree

In this paper, we introduce a model of a second-order circular Markov chain indexed by a two-rooted Cayley tree and establish two strong law of large numbers and the asymptotic equipartition property (AEP) for circular second-order finite Markov chains indexed by this homogeneous tree. In the proof, we apply a limit property for a sequence of multi-variable functions of a non homogeneous Markov chain indexed by such tree. As a corollary, we obtain the strong law of large numbers and AEP about the second-order finite homogeneous Markov chain indexed by the two-rooted homogeneous tree.     

A hierarchical Bayesian regression model for the uncertain functional constraint using screened scale mixtures of Gaussian distributions

This paper considers a hierarchical Bayesian analysis of regression models using a class of Gaussian scale mixtures. This class provides a robust alternative to the common use of the Gaussian distribution as a prior distribution in particular for estimating the regression function subject to uncertainty about the constraint. For this purpose, we use a family of rectangular screened multivariate scale mixtures of Gaussian distribution as a prior for the regression function, which is flexible enough to reflect the degrees of uncertainty about the functional constraint. Specifically, we propose a hierarchical Bayesian regression model for the constrained regression function with uncertainty on the basis of three stages of a prior hierarchy with Gaussian scale mixtures, referred to as a hierarchical screened scale mixture of Gaussian regression models (HSMGRM). We describe distributional properties of HSMGRM and an efficient Markov chain Monte Carlo algorithm for posterior inference, and apply the proposed model to real applications with constrained regression models subject to uncertainty.     

Over-relaxation methods and coupled Markov chains for Monte Carlo simulation

This paper is concerned with improving the performance of certain Markov chain algorithms for Monte Carlo simulation. We propose a new algorithm for simulating from multivariate Gaussian densities. This algorithm combines ideas from coupled Markov chain methods and from an existing algorithm based only on over-relaxation. The rate of convergence of the proposed and existing algorithms can be measured in terms of the square of the spectral radius of certain matrices. We present examples in which the proposed algorithm converges faster than the existing algorithm and the Gibbs sampler. We also derive an expression for the asymptotic variance of any linear combination of the variables simulated by the proposed algorithm. We outline how the proposed algorithm can be extended to non-Gaussian densities.     

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.     

Adaptive multiple importance sampling for Gaussian processes

In applications of Gaussian processes (GPs) where quantification of uncertainty is a strict requirement, it is necessary to accurately characterize the posterior distribution over Gaussian process covariance parameters. This is normally done by means of standard Markov chain Monte Carlo (MCMC) algorithms, which require repeated expensive calculations involving the marginal likelihood. Motivated by the desire to avoid the inefficiencies of MCMC algorithms rejecting a considerable amount of expensive proposals, this paper develops an alternative inference framework based on adaptive multiple importance sampling (AMIS). In particular, this paper studies the application of AMIS for GPs in the case of a Gaussian likelihood, and proposes a novel pseudo-marginal-based AMIS algorithm for non-Gaussian likelihoods, where the marginal likelihood is unbiasedly estimated. The results suggest that the proposed framework outperforms MCMC-based inference of covariance parameters in a wide range of scenarios.     

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.     

Convergence Analysis of MCMC Algorithms for Bayesian Multivariate Linear Regression with Non‐Gaussian Errors

When Gaussian errors are inappropriate in a multivariate linear regression setting, it is often assumed that the errors are iid from a distribution that is a scale mixture of multivariate normals. Combining this robust regression model with a default prior on the unknown parameters results in a highly intractable posterior density. Fortunately, there is a simple data augmentation (DA) algorithm and a corresponding Haar PX‐DA algorithm that can be used to explore this posterior. This paper provides conditions (on the mixing density) for geometric ergodicity of the Markov chains underlying these Markov chain Monte Carlo algorithms. Letting d denote the dimension of the response, the main result shows that the DA and Haar PX‐DA Markov chains are geometrically ergodic whenever the mixing density is generalized inverse Gaussian, log‐normal, inverted Gamma (with shape parameter larger than d /2) or Fréchet (with shape parameter larger than d /2). The results also apply to certain subsets of the Gamma, F and Weibull families.     

Computing the conditional stationary distribution in Markov chains of level-dependent M/G/1-type

This paper considers the computation of the conditional stationary distribution in Markov chains of level-dependent M/G/1-type, given that the level is not greater than a predefined threshold. This problem has been studied recently and a computational algorithm is proposed under the assumption that matrices representing downward jumps are nonsingular. We first show that this assumption can be eliminated in a general setting of Markov chains of level-dependent G/G/1-type. Next we develop a computational algorithm for the conditional stationary distribution in Markov chains of level-dependent M/G/1-type, by modifying the above-mentioned algorithm slightly. In principle, our algorithm is applicable to any Markov chain of level-dependent M/G/1-type, if the Markov chain is irreducible and positive-recurrent. Furthermore, as an input to the algorithm, we can set an error bound for the computed conditional distribution, which is a notable feature of our algorithm. Some numerical examples are also provided.     

Bayesian model averaging in longitudinal regression models with AR(1) errors with application to a myopia data set

We propose a new iterative algorithm, called model walking algorithm, to the Bayesian model averaging method on the longitudinal regression models with AR(1) random errors within subjects. The Markov chain Monte Carlo method together with the model walking algorithm are employed. The proposed method is successfully applied to predict the progression rates on a myopia intervention trial in children.     

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.     

Large Bayesian VARs: A Flexible Kronecker Error Covariance Structure

ABSTRACT

We introduce a class of large Bayesian vector autoregressions (BVARs) that allows for non-Gaussian, heteroscedastic, and serially dependent innovations. To make estimation computationally tractable, we exploit a certain Kronecker structure of the likelihood implied by this class of models. We propose a unified approach for estimating these models using Markov chain Monte Carlo (MCMC) methods. In an application that involves 20 macroeconomic variables, we find that these BVARs with more flexible covariance structures outperform the standard variant with independent, homoscedastic Gaussian innovations in both in-sample model-fit and out-of-sample forecast performance.     

Non-reversible Metropolis-Hastings

The classical Metropolis-Hastings (MH) algorithm can be extended to generate non-reversible Markov chains. This is achieved by means of a modification of the acceptance probability, using the notion of vorticity matrix. The resulting Markov chain is non-reversible. Results from the literature on asymptotic variance, large deviations theory and mixing time are mentioned, and in the case of a large deviations result, adapted, to explain how non-reversible Markov chains have favorable properties in these respects. We provide an application of NRMH in a continuous setting by developing the necessary theory and applying, as first examples, the theory to Gaussian distributions in three and nine dimensions. The empirical autocorrelation and estimated asymptotic variance for NRMH applied to these examples show significant improvement compared to MH with identical stepsize.     

Stochastic volatility modelling in continuous time with general marginal distributions: Inference,prediction and model selection

We compare results for stochastic volatility models where the underlying volatility process having generalized inverse Gaussian (GIG) and tempered stable marginal laws. We use a continuous time stochastic volatility model where the volatility follows an Ornstein–Uhlenbeck stochastic differential equation driven by a Lévy process. A model for long-range dependence is also considered, its merit and practical relevance discussed. We find that the full GIG and a special case, the inverse gamma, marginal distributions accurately fit real data. Inference is carried out in a Bayesian framework, with computation using Markov chain Monte Carlo (MCMC). We develop an MCMC algorithm that can be used for a general marginal model.