Monte Carlo approximation of likelihood function in spatial GLMMs through an empirical Bayes method

In spatial generalized linear mixed models (SGLMMs), statistical inference encounters problems, since random effects in the model imply high-dimensional integrals to calculate the marginal likelihood function. In this article, we temporarily treat parameters as random variables and express the marginal likelihood function as a posterior expectation. Hence, the marginal likelihood function is approximated using the obtained samples from the posterior density of the latent variables and parameters given the data. However, in this setting, misspecification of prior distribution of correlation function parameter and problems associated with convergence of Markov chain Monte Carlo (MCMC) methods could have an unpleasant influence on the likelihood approximation. To avoid these challenges, we utilize an empirical Bayes approach to estimate prior hyperparameters. We also use a computationally efficient hybrid algorithm by combining inverse Bayes formula (IBF) and Gibbs sampler procedures. A simulation study is conducted to assess the performance of our method. Finally, we illustrate the method applying a dataset of standard penetration test of soil in an area in south of Iran.     

Bayesian inverse problems with heterogeneous variance

We consider inverse problems in Hilbert spaces under correlated Gaussian noise, and use a Bayesian approach to find their regularized solution. We focus on mildly ill-posed inverse problems with fractional noise, using a novel wavelet-based vaguelette–vaguelette approach. It allows us to apply sequence space methods without assuming that all operators are simultaneously diagonalizable. The results are proved for more general bases and covariance operators. Our primary aim is to study posterior contraction rate in such inverse problems over Sobolev classes and compare it to the derived minimax rate. Secondly, we study effect of plugging in a consistent estimator of variances in sequence space on the posterior contraction rate. This result is applied to the problem with error in forward operator. Thirdly, we show that empirical Bayes posterior distribution with a plugged-in maximum marginal likelihood estimator of the prior scale contracts at the optimal rate, adaptively, in the minimax sense.     

Analysis of Bivariate Survival Data using Shared Inverse Gaussian Frailty Model

In this article, we consider shared frailty model with inverse Gaussian distribution as frailty distribution and log-logistic distribution (LLD) as baseline distribution for bivariate survival times. We fit this model to three real-life bivariate survival data sets. The problem of analyzing and estimating parameters of shared inverse Gaussian frailty is the interest of this article and then compare the results with shared gamma frailty model under the same baseline for considered three data sets. Data are analyzed using Bayesian approach to the analysis of clustered survival data in which there is a dependence of failure time observations within the same group. The variance component estimation provides the estimated dispersion of the random effects. We carried out a test for frailty (or heterogeneity) using Bayes factor. Model comparison is made using information criteria and Bayes factor. We observed that the shared inverse Gaussian frailty model with LLD as baseline is the better fit for all three bivariate data sets.     

Gaussian Scale Mixture Models for Robust Linear Multivariate Regression with Missing Data

We present an algorithm for multivariate robust Bayesian linear regression with missing data. The iterative algorithm computes an approximative posterior for the model parameters based on the variational Bayes (VB) method. Compared to the EM algorithm, the VB method has the advantage that the variance for the model parameters is also computed directly by the algorithm. We consider three families of Gaussian scale mixture models for the measurements, which include as special cases the multivariate t distribution, the multivariate Laplace distribution, and the contaminated normal model. The observations can contain missing values, assuming that the missing data mechanism can be ignored. A Matlab/Octave implementation of the algorithm is presented and applied to solve three reference examples from the literature.     

Variational Bayes for Phase-Type Distribution

This article develops an algorithm for estimating parameters of general phase-type (PH) distribution based on Bayes estimation. The idea of Bayes estimation is to regard parameters as random variables, and the posterior distribution of parameters which is updated by the likelihood function provides estimators of parameters. One of the advantages of Bayes estimation is to evaluate uncertainty of estimators. In this article, we propose a fast algorithm for computing posterior distributions approximately, based on variational approximation. We formulate the optimal variational posterior distributions for PH distributions and develop the efficient computation algorithm for the optimal variational posterior distributions of discrete and continuous PH distributions.     

Bayesian parameter estimation via variational methods

We consider a logistic regression model with a Gaussian prior distribution over the parameters. We show that an accurate variational transformation can be used to obtain a closed form approximation to the posterior distribution of the parameters thereby yielding an approximate posterior predictive model. This approach is readily extended to binary graphical model with complete observations. For graphical models with incomplete observations we utilize an additional variational transformation and again obtain a closed form approximation to the posterior. Finally, we show that the dual of the regression problem gives a latent variable density model, the variational formulation of which leads to exactly solvable EM updates.     

Density-Tempered Marginalized Sequential Monte Carlo Samplers

We propose a density-tempered marginalized sequential Monte Carlo (SMC) sampler, a new class of samplers for full Bayesian inference of general state-space models. The dynamic states are approximately marginalized out using a particle filter, and the parameters are sampled via a sequential Monte Carlo sampler over a density-tempered bridge between the prior and the posterior. Our approach delivers exact draws from the joint posterior of the parameters and the latent states for any given number of state particles and is thus easily parallelizable in implementation. We also build into the proposed method a device that can automatically select a suitable number of state particles. Since the method incorporates sample information in a smooth fashion, it delivers good performance in the presence of outliers. We check the performance of the density-tempered SMC algorithm using simulated data based on a linear Gaussian state-space model with and without misspecification. We also apply it on real stock prices using a GARCH-type model with microstructure noise.     

Particle filters for mixture models with an unknown number of components

We consider the analysis of data under mixture models where the number of components in the mixture is unknown. We concentrate on mixture Dirichlet process models, and in particular we consider such models under conjugate priors. This conjugacy enables us to integrate out many of the parameters in the model, and to discretize the posterior distribution. Particle filters are particularly well suited to such discrete problems, and we propose the use of the particle filter of Fearnhead and Clifford for this problem. The performance of this particle filter, when analyzing both simulated and real data from a Gaussian mixture model, is uniformly better than the particle filter algorithm of Chen and Liu. In many situations it outperforms a Gibbs Sampler. We also show how models without the required amount of conjugacy can be efficiently analyzed by the same particle filter algorithm.     

Inferences on the coefficient of variation of an inverse gaussian distribution

The likelihood ratio test for a characteristic parameter of the inverse Gaussian distribution is derived. The parameter of interest characterizes the coefficient of variation, the skewness and the kurtosis of the distribution. The distribution of the test statistic is presented in a simplified form. Useful quanfiles of the distribution are given. Methods for constructing confidence bounds for the parameter, including Bayes highest posterior density intervals, are considered.     

Estimation and prediction for Chen distribution with bathtub shape under progressive censoring

We consider estimation of the unknown parameters of Chen distribution [Chen Z. A new two-parameter lifetime distribution with bathtub shape or increasing failure rate function. Statist Probab Lett. 2000;49:155–161] with bathtub shape using progressive-censored samples. We obtain maximum likelihood estimates by making use of an expectation–maximization algorithm. Different Bayes estimates are derived under squared error and balanced squared error loss functions. It is observed that the associated posterior distribution appears in an intractable form. So we have used an approximation method to compute these estimates. A Metropolis–Hasting algorithm is also proposed and some more approximate Bayes estimates are obtained. Asymptotic confidence interval is constructed using observed Fisher information matrix. Bootstrap intervals are proposed as well. Sample generated from MH algorithm are further used in the construction of HPD intervals. Finally, we have obtained prediction intervals and estimates for future observations in one- and two-sample situations. A numerical study is conducted to compare the performance of proposed methods using simulations. Finally, we analyse real data sets for illustration purposes.     

Particle filtering for partially observed Gaussian state space models

Summary. Solving Bayesian estimation problems where the posterior distribution evolves over time through the accumulation of data has many applications for dynamic models. A large number of algorithms based on particle filtering methods, also known as sequential Monte Carlo algorithms, have recently been proposed to solve these problems. We propose a special particle filtering method which uses random mixtures of normal distributions to represent the posterior distributions of partially observed Gaussian state space models. This algorithm is based on a marginalization idea for improving efficiency and can lead to substantial gains over standard algorithms. It differs from previous algorithms which were only applicable to conditionally linear Gaussian state space models. Computer simulations are carried out to evaluate the performance of the proposed algorithm for dynamic tobit and probit models.     

Objective Bayes Factors for Gaussian Directed Acyclic Graphical Models

Abstract. We propose an objective Bayesian method for the comparison of all Gaussian directed acyclic graphical models defined on a given set of variables. The method, which is based on the notion of fractional Bayes factor (BF), requires a single default (typically improper) prior on the space of unconstrained covariance matrices, together with a prior sample size hyper‐parameter, which can be set to its minimal value. We show that our approach produces genuine BFs. The implied prior on the concentration matrix of any complete graph is a data‐dependent Wishart distribution, and this in turn guarantees that Markov equivalent graphs are scored with the same marginal likelihood. We specialize our results to the smaller class of Gaussian decomposable undirected graphical models and show that in this case they coincide with those recently obtained using limiting versions of hyper‐inverse Wishart distributions as priors on the graph‐constrained covariance matrices.     

The mode oriented stochastic search (MOSS) algorithm for log-linear models with conjugate priors

We describe a novel stochastic search algorithm for rapidly identifying regions of high posterior probability in the space of decomposable, graphical and hierarchical log-linear models. Our approach is based on the Diaconis–Ylvisaker conjugate prior for log-linear parameters. We discuss the computation of Bayes factors through Laplace approximations and the Bayesian iterative proportional fitting algorithm for sampling model parameters. We use our model determination approach in a sparse eight-way contingency table.     

Estimation for an inverted exponentiated Rayleigh distribution under type II progressive censoring

In this paper, we consider estimation of unknown parameters of an inverted exponentiated Rayleigh distribution under type II progressive censored samples. Estimation of reliability and hazard functions is also considered. Maximum likelihood estimators are obtained using the Expectation–Maximization (EM) algorithm. Further, we obtain expected Fisher information matrix using the missing value principle. Bayes estimators are derived under squared error and linex loss functions. We have used Lindley, and Tiernery and Kadane methods to compute these estimates. In addition, Bayes estimators are computed using importance sampling scheme as well. Samples generated from this scheme are further utilized for constructing highest posterior density intervals for unknown parameters. For comparison purposes asymptotic intervals are also obtained. A numerical comparison is made between proposed estimators using simulations and observations are given. A real-life data set is analyzed for illustrative purposes.     

Statistical analysis for competing risks model from a Weibull distribution under progressively hybrid censoring

This paper considers the statistical analysis for competing risks model under the Type-I progressively hybrid censoring from a Weibull distribution. We derive the maximum likelihood estimates and the approximate maximum likelihood estimates of the unknown parameters. We then use the bootstrap method to construct the confidence intervals. Based on the non informative prior, a sampling algorithm using the acceptance–rejection sampling method is presented to obtain the Bayes estimates, and Monte Carlo method is employed to construct the highest posterior density credible intervals. The simulation results are provided to show the effectiveness of all the methods discussed here and one data set is analyzed.     

A non-iterative posterior sampling algorithm for linear quantile regression model

In this article, a non-iterative posterior sampling algorithm for linear quantile regression model based on the asymmetric Laplace distribution is proposed. The algorithm combines the inverse Bayes formulae, sampling/importance resampling, and the expectation maximization algorithm to obtain independently and identically distributed samples approximately from the observed posterior distribution, which eliminates the convergence problems in the iterative Gibbs sampling and overcomes the difficulty in evaluating the standard deviance in the EM algorithm. The numeric results in simulations and application to the classical Engel data show that the non-iterative sampling algorithm is more effective than the Gibbs sampling and EM algorithm.     

Approximate bayes estimation of reliability of two parameter inverse gaussian distribution

This paper extends the result of Padgett (1981) and gives a Bayes estimate of the reliability function of two-parameter inverse Gaussian distribution using Jeffreys' non-informative joint prior and a squared error loss fun ction . A numerical example is given. Based on a Monte Carlo simulation, Bayes estimator of reliability is compared with its maximum likelihood counterpart.     

Bayesian estimation and prediction with multiply Type-II censored samples of sequential order statistics from one- and two-parameter exponential distributions

Based on multiply Type-II censored samples of sequential order statistics, Bayesian estimators are derived for the parameters of one- and two-parameter exponential distributions. In the one-parameter set-up, the posterior density is obtained under the assumption that the prior distribution is given by an inverse Gamma distribution, and the Bayes estimator with respect to squared error loss is calculated. Its performance is illustrated by a numerical example and compared with two non-Bayesian estimators, namely the BLUE and the approximate maximum likelihood estimator (AMLE). Moreover, prediction of future failure times is considered. Minimum risk equivariant estimators and predictors are deduced from the given results. Finally, similar results are presented for the two-parameter situation.     

Poisson-mixed Inverse Gaussian Regression Model and Its Application

In this article, we have developed a Poisson-mixed inverse Gaussian (PMIG) distribution. The mixed inverse Gaussian distribution is a mixture of the inverse Gaussian distribution and its length-biased counterpart. A PMIG regression model is developed and the maximum likelihood estimation of the parameters is studied. A dataset dealing with the number of hospital stays among the elderly population is analyzed by using the PMIG and the PIG (Poisson-inverse Gaussian) regression models and it has been shown that the PMIG model fits the data better than the PIG model.     

Variational Bayes for estimating the parameters of a hidden Potts model

Hidden Markov random field models provide an appealing representation of images and other spatial problems. The drawback is that inference is not straightforward for these models as the normalisation constant for the likelihood is generally intractable except for very small observation sets. Variational methods are an emerging tool for Bayesian inference and they have already been successfully applied in other contexts. Focusing on the particular case of a hidden Potts model with Gaussian noise, we show how variational Bayesian methods can be applied to hidden Markov random field inference. To tackle the obstacle of the intractable normalising constant for the likelihood, we explore alternative estimation approaches for incorporation into the variational Bayes algorithm. We consider a pseudo-likelihood approach as well as the more recent reduced dependence approximation of the normalisation constant. To illustrate the effectiveness of these approaches we present empirical results from the analysis of simulated datasets. We also analyse a real dataset and compare results with those of previous analyses as well as those obtained from the recently developed auxiliary variable MCMC method and the recursive MCMC method. Our results show that the variational Bayesian analyses can be carried out much faster than the MCMC analyses and produce good estimates of model parameters. We also found that the reduced dependence approximation of the normalisation constant outperformed the pseudo-likelihood approximation in our analysis of real and synthetic datasets.