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.     

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

In this article, a non-iterative sampling algorithm is developed to obtain an independently and identically distributed samples approximately from the posterior distribution of parameters in Laplace linear regression model. By combining the inverse Bayes formulae, sampling/importance resampling, and expectation maximum algorithm, the algorithm eliminates the diagnosis of convergence in the iterative Gibbs sampling and the samples generated from it can be used for inferences immediately. Simulations are conducted to illustrate the robustness and effectiveness of the algorithm. Finally, real data are studied to show the usefulness of the proposed methodology.     

Bayesian Transformation Models for Multivariate Survival Data

In this paper, we propose a general class of Gamma frailty transformation models for multivariate survival data. The transformation class includes the commonly used proportional hazards and proportional odds models. The proposed class also includes a family of cure rate models. Under an improper prior for the parameters, we establish propriety of the posterior distribution. A novel Gibbs sampling algorithm is developed for sampling from the observed data posterior distribution. A simulation study is conducted to examine the properties of the proposed methodology. An application to a data set from a cord blood transplantation study is also reported.     

Bayesian quantile regression for longitudinal data models

In this paper, we discuss a fully Bayesian quantile inference using Markov Chain Monte Carlo (MCMC) method for longitudinal data models with random effects. Under the assumption of error term subject to asymmetric Laplace distribution, we establish a hierarchical Bayesian model and obtain the posterior distribution of unknown parameters at τ-th level. We overcome the current computational limitations using two approaches. One is the general MCMC technique with Metropolis–Hastings algorithm and another is the Gibbs sampling from the full conditional distribution. These two methods outperform the traditional frequentist methods under a wide array of simulated data models and are flexible enough to easily accommodate changes in the number of random effects and in their assumed distribution. We apply the Gibbs sampling method to analyse a mouse growth data and some different conclusions from those in the literatures are obtained.     

A Bayesian analysis of clustered discrete and continuous outcomes

Many study designs yield a variety of outcomes from each subject clustered within an experimental unit. When these outcomes are of mixed data types, it is challenging to jointly model the effects of covariates on the responses using traditional methods. In this paper, we develop a Bayesian approach for a joint regression model of the different outcome variables and show that the fully conditional posterior distributions obtained under the model assumptions allow for estimation of posterior distributions using Gibbs sampling algorithm.     

The Bayesian elastic net regression

A Bayesian elastic net approach is presented for variable selection and coefficient estimation in linear regression models. A simple Gibbs sampling algorithm was developed for posterior inference using a location-scale mixture representation of the Bayesian elastic net prior for the regression coefficients. The penalty parameters are chosen through an empirical method that maximizes the data marginal likelihood. Both simulated and real data examples show that the proposed method performs well in comparison to the other approaches.     

Bayesian gamma frailty models for survival data with semi-competing risks and treatment switching

Motivated from a colorectal cancer study, we propose a class of frailty semi-competing risks survival models to account for the dependence between disease progression time, survival time, and treatment switching. Properties of the proposed models are examined and an efficient Gibbs sampling algorithm using the collapsed Gibbs technique is developed. A Bayesian procedure for assessing the treatment effect is also proposed. The deviance information criterion (DIC) with an appropriate deviance function and Logarithm of the pseudomarginal likelihood (LPML) are constructed for model comparison. A simulation study is conducted to examine the empirical performance of DIC and LPML and as well as the posterior estimates. The proposed method is further applied to analyze data from a colorectal cancer study.     

Adaptive sampling for Bayesian geospatial models

Bayesian hierarchical modeling with Gaussian process random effects provides a popular approach for analyzing point-referenced spatial data. For large spatial data sets, however, generic posterior sampling is infeasible due to the extremely high computational burden in decomposing the spatial correlation matrix. In this paper, we propose an efficient algorithm—the adaptive griddy Gibbs (AGG) algorithm—to address the computational issues with large spatial data sets. The proposed algorithm dramatically reduces the computational complexity. We show theoretically that the proposed method can approximate the real posterior distribution accurately. The sufficient number of grid points for a required accuracy has also been derived. We compare the performance of AGG with that of the state-of-the-art methods in simulation studies. Finally, we apply AGG to spatially indexed data concerning building energy consumption.     

Nonparametric Bayesian inference for multivariate density functions using Feller priors

Multivariate density estimation plays an important role in investigating the mechanism of high-dimensional data. This article describes a nonparametric Bayesian approach to the estimation of multivariate densities. A general procedure is proposed for constructing Feller priors for multivariate densities and their theoretical properties as nonparametric priors are established. A blocked Gibbs sampling algorithm is devised to sample from the posterior of the multivariate density. A simulation study is conducted to evaluate the performance of the procedure.     

A bayesian approach to dynamic tobit models

This paper develops a posterior simulation method for a dynamic Tobit model. The major obstacle rooted in such a problem lies in high dimensional integrals, induced by dependence among censored observations, in the likelihood function. The primary contribution of this study is to develop a practical and efficient sampling scheme for the conditional posterior distributions of the censored (i.e., unobserved) data, so that the Gibbs sampler with the data augmentation algorithm is successfully applied. The substantial differences between this approach and some existing methods are highlighted. The proposed simulation method is investigated by means of a Monte Carlo study and applied to a regression model of Japanese exports of passenger cars to the U.S. subject to a non-tariff trade barrier.     

A bayesian approach to dynamic tobit models

This paper develops a posterior simulation method for a dynamic Tobit model. The major obstacle rooted in such a problem lies in high dimensional integrals, induced by dependence among censored observations, in the likelihood function. The primary contribution of this study is to develop a practical and efficient sampling scheme for the conditional posterior distributions of the censored (i.e., unobserved) data, so that the Gibbs sampler with the data augmentation algorithm is successfully applied. The substantial differences between this approach and some existing methods are highlighted. The proposed simulation method is investigated by means of a Monte Carlo study and applied to a regression model of Japanese exports of passenger cars to the U.S. subject to a non-tariff trade barrier.     

Bayesian analysis of outlier problems using the Gibbs sampler

We consider the Bayesian analysis of outlier models. We show that the Gibbs sampler brings considerable conceptual and computational simplicity to the problem of calculating posterior marginals. Although other techniques for finding posterior marginals are available, the Gibbs sampling approach is notable for its ease of implementation. Allowing the probability of an outlier to be unknown introduces an extra parameter into the model but this turns out to involve only minor modification to the algorithm. We illustrate these ideas using a contaminated Gaussian distribution, at-distribution, a contaminated binomial model and logistic regression.     

Efficient Posterior Simulation for Cointegrated Models with Priors on the Cointegration Space

A message coming out of the recent Bayesian literature on cointegration is that it is important to elicit a prior on the space spanned by the cointegrating vectors (as opposed to a particular identified choice for these vectors). In previous work, such priors have been found to greatly complicate computation. In this article, we develop algorithms to carry out efficient posterior simulation in cointegration models. In particular, we develop a collapsed Gibbs sampling algorithm which can be used with just-identifed models and demonstrate that it has very large computational advantages relative to existing approaches. For over-identifed models, we develop a parameter-augmented Gibbs sampling algorithm and demonstrate that it also has attractive computational properties.     

A MCMC algorithm to fit a general exchangeable model

Consider the exchangeable Bayesian hierarchical model where observations y_i are independently distributed from sampling densities with unknown means, the means µi, are a random sample from a distribution g, and the parameters of g are assigned a known distribution h. A simple algorithm is presented for summarizing the posterior distribution based on Gibbs sampling and the Metropolis algorithm. The software program Matlab is used to implement the algorithm and provide a graphical output analysis. An binomial example is used to illustrate the flexibility of modeling possible using this algorithm. Methods of model checking and extensions to hierarchical regression modeling are discussed.     

Stochastic matching pursuit for Bayesian variable selection

This article proposes a stochastic version of the matching pursuit algorithm for Bayesian variable selection in linear regression. In the Bayesian formulation, the prior distribution of each regression coefficient is assumed to be a mixture of a point mass at 0 and a normal distribution with zero mean and a large variance. The proposed stochastic matching pursuit algorithm is designed for sampling from the posterior distribution of the coefficients for the purpose of variable selection. The proposed algorithm can be considered a modification of the componentwise Gibbs sampler. In the componentwise Gibbs sampler, the variables are visited by a random or a systematic scan. In the stochastic matching pursuit algorithm, the variables that better align with the current residual vector are given higher probabilities of being visited. The proposed algorithm combines the efficiency of the matching pursuit algorithm and the Bayesian formulation with well defined prior distributions on coefficients. Several simulated examples of small n and large p are used to illustrate the algorithm. These examples show that the algorithm is efficient for screening and selecting variables.     

Bayesian factor analysis for spatially correlated data: application to cancer incidence data in Scotland

A hierarchical Bayesian factor model for multivariate spatially correlated data is proposed. Multiple cancer incidence data in Scotland are jointly analyzed, looking for common components, able to detect etiological factors of diseases hidden behind the data. The proposed method searches factor scores incorporating a dependence within observations due to a geographical structure. The great flexibility of the Bayesian approach allows the inclusion of prior opinions about adjacent regions having highly correlated observable and latent variables. The proposed model is an extension of a model proposed by Rowe (2003a) and starts from the introduction of separable covariance matrix for the observations. A Gibbs sampling algorithm is implemented to sample from the posterior distributions.     

Conjugate analysis of multivariate normal data with incomplete observations

The authors discuss prior distributions that are conjugate to the multivariate normal likelihood when some of the observations are incomplete. They present a general class of priors for incorporating information about unidentified parameters in the covariance matrix. They analyze the special case of monotone patterns of missing data, providing an explicit recursive form for the posterior distribution resulting from a conjugate prior distribution. They develop an importance sampling and a Gibbs sampling approach to sample from a general posterior distribution and compare the two methods.     

Semiparametric Bayesian accelerated failure time model with interval-censored data

Many existing approaches to analysing interval-censored data lack flexibility or efficiency. In this paper, we propose an efficient, easy to implement approach on accelerated failure time model with a logarithm transformation of the failure time and flexible specifications on the error distribution. We use exact inference for the Dirichlet process without approximation in imputation. Our algorithm can be implemented with simple Gibbs sampling which produces exact posterior distributions on the features of interest. Simulation and real data analysis demonstrate the advantage of our method compared to some other methods.     

Bayesian spatial prediction of skew and censored data via a hybrid algorithm

A correct detection of areas with excess of pollution relies first on accurate predictions of pollutant concentrations, a task that is usually complicated by skewed histograms and the presence of censored data. The unified skew-Gaussian (SUG) random field proposed by Zareifard and Jafari Khaledi [19] offers a more flexible class of sampling spatial models to account for skewness. In this paper, we adopt a Bayesian framework to perform prediction for the SUG model in the presence of censored data. Owing to the presence of many latent variables with strongly dependent components in the model, we encounter convergence issues when using Monte Carlo Markov Chain algorithms. To overcome this obstacle, we use a computationally efficient inverse Bayes formulas sampling procedure to obtain approximately independent samples from the posterior distribution of latent variables. Then they are applied to update parameters in a Gibbs sampler scheme. This hybrid algorithm provides effective samples, resulting in some computational advantages and precise predictions. The proposed approach is illustrated with a simulation study and applied to a spatial data set which contains right censored data.     

Bayesian spectral analysis models for quantile regression with Dirichlet process mixtures

This paper presents a Bayesian analysis of partially linear additive models for quantile regression. We develop a semiparametric Bayesian approach to quantile regression models using a spectral representation of the nonparametric regression functions and the Dirichlet process (DP) mixture for error distribution. We also consider Bayesian variable selection procedures for both parametric and nonparametric components in a partially linear additive model structure based on the Bayesian shrinkage priors via a stochastic search algorithm. Based on the proposed Bayesian semiparametric additive quantile regression model referred to as BSAQ, the Bayesian inference is considered for estimation and model selection. For the posterior computation, we design a simple and efficient Gibbs sampler based on a location-scale mixture of exponential and normal distributions for an asymmetric Laplace distribution, which facilitates the commonly used collapsed Gibbs sampling algorithms for the DP mixture models. Additionally, we discuss the asymptotic property of the sempiparametric quantile regression model in terms of consistency of posterior distribution. Simulation studies and real data application examples illustrate the proposed method and compare it with Bayesian quantile regression methods in the literature.