Markov chain Monte Carlo exact tests for incomplete two-way contingency tables

We consider testing the quasi-independence hypothesis for two-way contingency tables which contain some structural zero cells. For sparse contingency tables where the large sample approximation is not adequate, the Markov chain Monte Carlo exact tests are powerful tools. To construct a connected chain over the two-way contingency tables with fixed sufficient statistics and an arbitrary configuration of structural zero cells, an algebraic algorithm proposed by Diaconis and Sturmfels [Diaconis, P. and Sturmfels, B. (1998). The Annals of statistics, 26, pp. 363–397.] can be used. However, their algorithm does not seem to be a satisfactory answer, because the Markov basis produced by the algorithm often contains many redundant elements and is hard to interpret. We derive an explicit characterization of a minimal Markov basis, prove its uniqueness, and present an algorithm for obtaining the unique minimal basis. A computational example and the discussion on further basis reduction for the case of positive sufficient statistics are also given.     

Conditional entropy,entropy density,and strong law of large numbers for generalized controlled tree-indexed Markov chains

In this paper, we first introduces a tree model without degree boundedness restriction namely generalized controlled tree T, which is an extension of some known tree models, such as homogeneous tree model, uniformly bounded degree tree model, controlled tree model, etc. Then some limit properties including strong law of large numbers for generalized controlled tree-indexed non homogeneous Markov chain are obtained. Finally, we establish some entropy density properties, monotonicity of conditional entropy, and entropy properties for generalized controlled tree-indexed Markov chains.     

Minimal Markov Basis for Tests of Main Effect Models for 2p-1 Fractional Factorial Designs of Resolution p

We consider conditional exact tests of factor effects in design of experiments for discrete response variables. Similarly to the analysis of contingency tables, Markov chain Monte Carlo methods can be used to perform exact tests, especially when large-sample approximations of the null distributions are poor and the enumeration of the conditional sample space is infeasible. In order to construct a connected Markov chain over the appropriate sample space, one approach is to compute a Markov basis. Theoretically, a Markov basis can be characterized as a generator of a well-specified toric ideal in a polynomial ring and is computed by computational algebraic software. However, the computation of a Markov basis sometimes becomes infeasible, even for problems of moderate sizes. In the present article, we obtain the closed-form expression of minimal Markov bases for the main effect models of 2^{p ? 1} fractional factorial designs of resolution p.     

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.     

Minimal Basis for a Connected Markov Chain over 3 × 3 ×K Contingency Tables with Fixed Two-Dimensional Marginals

This paper considers a connected Markov chain for sampling 3 × 3 ×K contingency tables having fixed two‐dimensional marginal totals. Such sampling arises in performing various tests of the hypothesis of no three‐factor interactions. A Markov chain algorithm is a valuable tool for evaluating P‐values, especially for sparse datasets where large‐sample theory does not work well. To construct a connected Markov chain over high‐dimensional contingency tables with fixed marginals, algebraic algorithms have been proposed. These algorithms involve computations in polynomial rings using Gröbner bases. However, algorithms based on Gröbner bases do not incorporate symmetry among variables and are very time‐consuming when the contingency tables are large. We construct a minimal basis for a connected Markov chain over 3 × 3 ×K contingency tables. The minimal basis is unique. Some numerical examples illustrate the practicality of our algorithms.     

Estimation of the Entropy Rate of a Countable Markov Chain

We consider here ergodic homogeneous Markov chains with countable state spaces. The entropy rate of the chain is an explicit function of its transition and stationary distributions. We construct estimators for this entropy rate and for the entropy of the stationary distribution of the chain, in the parametric and nonparametric cases. We study estimation from one sample with long length and from many independent samples with given length. In the parametric case, the estimators are deduced by plug-in from the maximum likelihood estimator of the parameter. In the nonparametric case, the estimators are deduced by plug-in from the empirical estimators of the transition and stationary distributions. They are proven to have good asymptotic properties.     

A latent Markov model for detecting patterns of criminal activity

Summary.  The paper investigates the problem of determining patterns of criminal behaviour from official criminal histories, concentrating on the variety and type of offending convictions. The analysis is carried out on the basis of a multivariate latent Markov model which allows for discrete covariates affecting the initial and the transition probabilities of the latent process. We also show some simplifications which reduce the number of parameters substantially; we include a Rasch-like parameterization of the conditional distribution of the response variables given the latent process and a constraint of partial homogeneity of the latent Markov chain. For the maximum likelihood estimation of the model we outline an EM algorithm based on recursions known in the hidden Markov literature, which make the estimation feasible also when the number of time occasions is large. Through this model, we analyse the conviction histories of a cohort of offenders who were born in England and Wales in 1953. The final model identifies five latent classes and specifies common transition probabilities for males and females between 5-year age periods, but with different initial probabilities.     

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 stationarity test on Markov chain models based on marginal distribution

A stationarity test on Markov chain models is proposed in this paper. Most of the previous test procedures for the Markov chain models have been done based on the conditional probabilities of a transition matrix. The likelihood ratio and Pearson type chi-square tests have been used for testing stationarity and order of Markov chains. This paper uses the efficient score test, an extension of the test developed by Tsiatis (1980) [18], for testing the stationarity of Markov chain models based on the marginal distribution as obtained by Azzalini (1994) [2]. For testing the suitability of the proposed method, a numerical example of real life data and simulation studies for comparison with an alternative test procedure are given.     

Markov Chain Markov Field dynamics: Models and statistics

This study deals with time dynamics of Markov fields defined on a finite set of sites with state space <$>E<$>, focussing on Markov Chain Markov Field (MCMF) evolution. Such a model is characterized by two families of potentials: the instantaneous interaction potentials, and the time delay potentials. Four models are specified: auto-exponential dynamics (<$>E = {\of R}^+<$>), auto-normal dynamics (<$>E = {\of R}<$>), auto-Poissonian dynamics (<$>E = {\of N}<$>) and auto-logistic dynamics ( E qualitative and finite). Sufficient conditions ensuring ergodicity and strong law of large numbers are given by using a Lyapunov criterion of stability, and the conditional pseudo-likelihood statistics are summarized. We discuss the identification procedure of the two Markovian graphs and look for validation tests using martingale central limit theorems. An application to meteorological data illustrates such a modelling.     

A New Markov Binomial Distribution

In this article, we introduce a two-state homogeneous Markov chain and define a geometric distribution related to this Markov chain. We define also the negative binomial distribution similar to the classical case and call it NB related to interrupted Markov chain. The new binomial distribution is related to the interrupted Markov chain. Some characterization properties of the geometric distributions are given. Recursion formulas and probability mass functions for the NB distribution and the new binomial distribution are derived.     

Hypothesis testing for Markov chain Monte Carlo

Testing between hypotheses, when independent sampling is possible, is a well developed subject. In this paper, we propose hypothesis tests that are applicable when the samples are obtained using Markov chain Monte Carlo. These tests are useful when one is interested in deciding whether the expected value of a certain quantity is above or below a given threshold. We show non-asymptotic error bounds and bounds on the expected number of samples for three types of tests, a fixed sample size test, a sequential test with indifference region, and a sequential test without indifference region. Our tests can lead to significant savings in sample size. We illustrate our results on an example of Bayesian parameter inference involving an ODE model of a biochemical pathway.     

Markov chain Monte Carlo tests for designed experiments

We consider conditional exact tests of factor effects in designed experiments for discrete response variables. Similarly to the analysis of contingency tables, a Markov chain Monte Carlo method can be used for performing exact tests, when large-sample approximations are poor and the enumeration of the conditional sample space is infeasible. For designed experiments with a single observation for each run, we formulate log-linear or logistic models and consider a connected Markov chain over an appropriate sample space. In particular, we investigate fractional factorial designs with 2^p-q$2^{p-q}$ runs, noting correspondences to the models for 2^p-q$2^{p-q}$ contingency tables.     

Strong law of large numbers for generalized sample relative entropy of non homogeneous Markov chains

In this paper, we study the strong law of large numbers for the generalized sample relative entropy of non homogeneous Markov chains taking values from a finite state space. First, we introduce the definitions of generalized sample relative entropy and generalized sample relative entropy rate. Then, using a strong limit theorem for the delayed sums of the functions of two variables and a strong law of large numbers for non homogeneous Markov chains, we obtain the strong law of large numbers for the generalized sample relative entropy of non homogeneous Markov chains. As corollaries, we obtain some important results.     

Algebraic Markov Bases and MCMC for Two-Way Contingency Tables

ABSTRACT.  The Diaconis–Sturmfels algorithm is a method for sampling from conditional distributions, based on the algebraic theory of toric ideals. This algorithm is applied to categorical data analysis through the notion of Markov basis. An application of this algorithm is a non-parametric Monte Carlo approach to the goodness of fit tests for contingency tables. In this paper, we characterize or compute the Markov bases for some log-linear models for two-way contingency tables using techniques from Computational Commutative Algebra, namely Gröbner bases. This applies to a large set of cases including independence, quasi-independence, symmetry, quasi-symmetry. Three examples of quasi-symmetry and quasi-independence from Fingleton ( Models of category counts , Cambridge University Press, Cambridge, 1984) and Agresti ( An Introduction to categorical data analysis , Wiley, New York, 1996) illustrate the practical applicability and the relevance of this algebraic methodology.     

A New Model for Multivariate Markov Chains

We propose a new model for multivariate Markov chains of order one or higher on the basis of the mixture transition distribution (MTD) model. We call it the MTD‐Probit. The proposed model presents two attractive features: it is completely free of constraints, thereby facilitating the estimation procedure, and it is more precise at estimating the transition probabilities of a multivariate or higher‐order Markov chain than the standard MTD model.     

Adaptive estimators for parameters of the autoregression function of a Markov chain

Suppose we observe an ergodic Markov chain on the real line, with a parametric model for the autoregression function, i.e. the conditional mean of the transition distribution. If one specifies, in addition, a parametric model for the conditional variance, one can define a simple estimator for the parameter, the maximum quasi-likelihood estimator. It is robust against misspecification of the conditional variance, but not efficient. We construct an estimator which is adaptive in the sense that it is efficient if the conditional variance is misspecified, and asymptotically as good as the maximum quasi-likelihood estimator if the conditional variance is correctly specified. The adaptive estimator is a weighted nonlinear least-squares estimator, with weights given by predictors for the conditional variance.     

Quantitative convergence assessment for Markov chain Monte Carlo via cusums

Yu (1995) provides a novel convergence diagnostic for Markov chain Monte Carlo (MCMC) which provides a qualitative measure of mixing for Markov chains via a cusum path plot for univariate parameters of interest. The method is based upon the output of a single replication of an MCMC sampler and is therefore widely applicable and simple to use. One criticism of the method is that it is subjective in its interpretation, since it is based upon a graphical comparison of two cusum path plots. In this paper, we develop a quantitative measure of smoothness which we can associate with any given cusum path, and show how we can use this measure to obtain a quantitative measure of mixing. In particular, we derive the large sample distribution of this smoothness measure, so that objective inference is possible. In addition, we show how this quantitative measure may also be used to provide an estimate of the burn-in length for any given sampler. We discuss the utility of this quantitative approach, and highlight a problem which may occur if the chain is able to remain in any one state for some period of time. We provide a more general implementation of the method to overcome the problem in such cases.     

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.     

Regeneration-based bootstrap for Markov chains

We consider a bootstrap method for Markov chains where the original chain is broken into a (random) number of cycles based on an atom (regeneration point) and the bootstrap scheme resamples from these cycles. We investigate the asymptotic accuracy of this method for the case of a sum (or a sample mean) related to the Markov chain. Under some standard moment conditions, the method is shown to be at least as good as the normal approximation, and better (second-order accurate) in the case of nonlattice summands. We give three examples to illustrate the applicability of our results.