Steady-state Gibbs sampler estimation for lung cancer data

This paper is based on the application of a Bayesian model to a clinical trial study to determine a more effective treatment to lower mortality rates and consequently to increase survival times among patients with lung cancer. In this study, Qian et al. [13 J. Qian, D.K. Stangl, and S. George, A Weibull model for survival data: Using prediction to decide when to stop a clinical trial, in Bayesian Biostatistics, D. Berry and D. Stangl, eds., Marcel Dekker, New York, 1996, pp. 187–205. [Google Scholar]] strived to determine if a Weibull survival model can be used to decide whether to stop a clinical trial. The traditional Gibbs sampler was used to estimate the model parameters. This paper proposes to use the independent steady-state Gibbs sampling (ISSGS) approach, introduced by Dunbar et al. [3 M. Dunbar, H.M. Samawi, R. Vogel, and L. Yu, A more efficient Gibbs sampler estimation using steady state simulation: Application to public health studies, J. Stat. Simul. Comput. 10.1080/00949655.2013.770857.[Taylor &; Francis Online] , [Google Scholar]], to improve the original Gibbs sampler in multidimensional problems. It is demonstrated that ISSGS provides accuracy with unbiased estimation and improves the performance and convergence of the Gibbs sampler in this application.     

Steady-state ranked Gibbs sampler

Gibbs sampler as a computer-intensive algorithm is an important statistical tool both in application and in theoretical work. This algorithm, in many cases, is time-consuming; this paper extends the concept of using the steady-state ranked simulated sampling approach, utilized in Monte Carlo methods by Samawi [On the approximation of multiple integrals using steady state ranked simulated sampling, 2010, submitted for publication], to improve the well-known Gibbs sampling algorithm. It is demonstrated that this approach provides unbiased estimators, in the case of estimating the means and the distribution function, and substantially improves the performance of the Gibbs sampling algorithm and convergence, which results in a significant reduction in the costs and time required to attain a certain level of accuracy. Similar to Casella and George [Explaining the Gibbs sampler, Am. Statist. 46(3) (1992), pp. 167–174], we provide some analytical properties in simple cases and compare the performance of our method using the same illustrations.     

Random variate transformations in the Gibbs sampler: issues of efficiency and convergence

In the non-conjugate Gibbs sampler, the required sampling from the full conditional densities needs the adoption of black-box sampling methods. Recent suggestions include rejection sampling, adaptive rejection sampling, generalized ratio of uniforms, and the Griddy-Gibbs sampler. This paper describes a general idea based on variate transformations which can be tailored in all the above methods and increase the Gibbs sampler efficiency. Moreover, a simple technique to assess convergence is suggested and illustrative examples are presented.     

Bayesian estimation in the multidimensional three-parameter logistic model

The Gibbs sampler has a great potential to be an efficient and versatile estimation procedure in item response theory. In this article, based on a data augmentation scheme using the Gibbs sampler, we propose a Bayesian procedure to estimate the multidimensional three-parameter logistic model. With the introduction of the two latent variables, the full conditional distributions are tractable, and consequently the Gibbs sampling is easy to implement. Finally, the technique is illustrated by using simulated and real data, respectively.     

Optimal direction Gibbs sampler for truncated multivariate normal distributions

Generalized Gibbs samplers simulate from any direction, not necessarily limited to the coordinate directions of the parameters of the objective function. We study how to optimally choose such directions in a random scan Gibbs sampler setting. We consider that optimal directions will be those that minimize the Kullback–Leibler divergence of two Markov chain Monte Carlo steps. Two distributions over direction are proposed for the multivariate Normal objective function. The resulting algorithms are used to simulate from a truncated multivariate Normal distribution, and the performance of our algorithms is compared with the performance of two algorithms based on the Gibbs sampler.     

Behaviour of the Gibbs sampler when conditional distributions are potentially incompatible

The Gibbs sampler has been used extensively in the statistics literature. It relies on iteratively sampling from a set of compatible conditional distributions and the sampler is known to converge to a unique invariant joint distribution. However, the Gibbs sampler behaves rather differently when the conditional distributions are not compatible. Such applications have seen increasing use in areas such as multiple imputation. In this paper, we demonstrate that what a Gibbs sampler converges to is a function of the order of the sampling scheme. Besides providing the mathematical background of this behaviour, we also explain how that happens through a thorough analysis of the examples.     

Sampling the Dirichlet Mixture Model with Slices

We provide a new approach to the sampling of the well known mixture of Dirichlet process model. Recent attention has focused on retention of the random distribution function in the model, but sampling algorithms have then suffered from the countably infinite representation these distributions have. The key to the algorithm detailed in this article, which also keeps the random distribution functions, is the introduction of a latent variable which allows a finite number, which is known, of objects to be sampled within each iteration of a Gibbs sampler.     

Sequential importance sampling for nonparametric Bayes models: The next generation

There are two generations of Gibbs sampling methods for semiparametric models involving the Dirichlet process. The first generation suffered from a severe drawback: the locations of the clusters, or groups of parameters, could essentially become fixed, moving only rarely. Two strategies that have been proposed to create the second generation of Gibbs samplers are integration and appending a second stage to the Gibbs sampler wherein the cluster locations are moved. We show that these same strategies are easily implemented for the sequential importance sampler, and that the first strategy dramatically improves results. As in the case of Gibbs sampling, these strategies are applicable to a much wider class of models. They are shown to provide more uniform importance sampling weights and lead to additional Rao-Blackwellization of estimators.     

A Comparison of Methods for Analysing a Nested Frailty Model to Child Survival in Malawi

Demographic and Health Surveys collect child survival times that are clustered at the family and community levels. It is assumed that each cluster has a specific, unobservable, random frailty that induces an association in the survival times within the cluster. The Cox proportional hazards model, with family and community random frailties acting multiplicatively on the hazard rate, is presented. The estimation of the fixed effect and the association parameters of the modified model is then examined using the Gibbs sampler and the expectation–maximization (EM) algorithm. The methods are compared using child survival data collected in the 1992 Demographic and Health Survey of Malawi. The two methods lead to very similar estimates of fixed effect parameters. However, the estimates of random effect variances from the EM algorithm are smaller than those of the Gibbs sampler. Both estimation methods reveal considerable family variation in the survival of children, and very little variability over the communities.     

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.     

Simulating posterior Gibbs distributions: a comparison of the Swendsen-Wang and Gibbs sampler methods

We show in detail how the Swendsen-Wang algorithm, for simulating Potts models, may be used to simulate certain types of posterior Gibbs distribution, as a special case of Edwards and Sokal (1988), and we empirically compare the behaviour of the algorithm with that of the Gibbs sampler. Some marginal posterior mode and simulated annealing image restorations are also examined. Our results demonstrate the importance of the starting configuration. If this is inappropriate, the Swendsen-Wang method can suffer from critical slowing in moderately noise-free situations where the Gibbs sampler convergence is very fast, whereas the reverse is true when noise level is high.     

Parameter estimation for partially observed hypoelliptic diffusions

Summary.  Hypoelliptic diffusion processes can be used to model a variety of phenomena in applications ranging from molecular dynamics to audio signal analysis. We study parameter estimation for such processes in situations where we observe some components of the solution at discrete times. Since exact likelihoods for the transition densities are typically not known, approximations are used that are expected to work well in the limit of small intersample times Δ t and large total observation times N  Δ t . Hypoellipticity together with partial observation leads to ill conditioning requiring a judicious combination of approximate likelihoods for the various parameters to be estimated. We combine these in a deterministic scan Gibbs sampler alternating between missing data in the unobserved solution components, and parameters. Numerical experiments illustrate asymptotic consistency of the method when applied to simulated data. The paper concludes with an application of the Gibbs sampler to molecular dynamics data.     

Variable selection in quantile regression via Gibbs sampling

Due to computational challenges and non-availability of conjugate prior distributions, Bayesian variable selection in quantile regression models is often a difficult task. In this paper, we address these two issues for quantile regression models. In particular, we develop an informative stochastic search variable selection (ISSVS) for quantile regression models that introduces an informative prior distribution. We adopt prior structures which incorporate historical data into the current data by quantifying them with a suitable prior distribution on the model parameters. This allows ISSVS to search more efficiently in the model space and choose the more likely models. In addition, a Gibbs sampler is derived to facilitate the computation of the posterior probabilities. A major advantage of ISSVS is that it avoids instability in the posterior estimates for the Gibbs sampler as well as convergence problems that may arise from choosing vague priors. Finally, the proposed methods are illustrated with both simulation and real data.     

Sampling-based Inference of Time Deformation Models with Heavy Tail Distributions

This article focuses on simulation-based inference for the time-deformation models directed by a duration process. In order to better capture the heavy tail property of the time series of financial asset returns, the innovation of the observation equation is subsequently assumed to have a Student-t distribution. Suitable Markov chain Monte Carlo (MCMC) algorithms, which are hybrids of Gibbs and slice samplers, are proposed for estimation of the parameters of these models. In the algorithms, the parameters of the models can be sampled either directly from known distributions or through an efficient slice sampler. The states are simulated one at a time by using a Metropolis-Hastings method, where the proposal distributions are sampled through a slice sampler. Simulation studies conducted in this article suggest that our extended models and accompanying MCMC algorithms work well in terms of parameter estimation and volatility forecast.     

Analysis of the Gibbs sampler for a model related to James-Stein estimators

We analyse a hierarchical Bayes model which is related to the usual empirical Bayes formulation of James-Stein estimators. We consider running a Gibbs sampler on this model. Using previous results about convergence rates of Markov chains, we provide rigorous, numerical, reasonable bounds on the running time of the Gibbs sampler, for a suitable range of prior distributions. We apply these results to baseball data from Efron and Morris (1975). For a different range of prior distributions, we prove that the Gibbs sampler will fail to converge, and use this information to prove that in this case the associated posterior distribution is non-normalizable.     

A new strategy for speeding Markov chain Monte Carlo algorithms

Markov chain Monte Carlo (MCMC) methods have become popular as a basis for drawing inference from complex statistical models. Two common difficulties with MCMC algorithms are slow mixing and long run-times, which are frequently closely related. Mixing over the entire state space can often be aided by careful tuning of the chain's transition kernel. In order to preserve the algorithm's stationary distribution, however, care must be taken when updating a chain's transition kernel based on that same chain's history. In this paper we introduce a technique that allows the transition kernel of the Gibbs sampler to be updated at user specified intervals, while preserving the chain's stationary distribution. This technique seems to be beneficial both in increasing efficiency of the resulting estimates (via Rao-Blackwellization) and in reducing the run-time. A reinterpretation of the modified Gibbs sampling scheme introduced in terms of auxiliary samples allows its extension to the more general Metropolis-Hastings framework. The strategies we develop are particularly helpful when calculation of the full conditional (for a Gibbs algorithm) or of the proposal distribution (for a Metropolis-Hastings algorithm) is computationally expensive. Partial financial support from FAR 2002-3, University of Insubria is gratefully acknowledged.     

Accelerating Monte Carlo Markov chain convergence for cumulative-link generalized linear models

The ordinal probit, univariate or multivariate, is a generalized linear model (GLM) structure that arises frequently in such disparate areas of statistical applications as medicine and econometrics. Despite the straightforwardness of its implementation using the Gibbs sampler, the ordinal probit may present challenges in obtaining satisfactory convergence.We present a multivariate Hastings-within-Gibbs update step for generating latent data and bin boundary parameters jointly, instead of individually from their respective full conditionals. When the latent data are parameters of interest, this algorithm substantially improves Gibbs sampler convergence for large datasets. We also discuss Monte Carlo Markov chain (MCMC) implementation of cumulative logit (proportional odds) and cumulative complementary log-log (proportional hazards) models with latent data.     

An iterative Monte Carlo method for nonconjugate Bayesian analysis

The Gibbs sampler has been proposed as a general method for Bayesian calculation in Gelfand and Smith (1990). However, the predominance of experience to date resides in applications assuming conjugacy where implementation is reasonably straightforward. This paper describes a tailored approximate rejection method approach for implementation of the Gibbs sampler when nonconjugate structure is present. Several challenging applications are presented for illustration.     

Bayesian Analysis of an Unobserved-Component Time Series Model of GDP With Markov-Switching and Time-Varying Growths

We propose an unobserved-component time series model of gross domestic product that includes Markov switching as an unobserved component. In addition to a trend component, the model has two time-varying drift components. One drift represents the expected rate of growth during recession; the other drift represents the expected rate during expansion. Estimates indicate a substantial decline in the latter annual rate for the United States from 6.4% in 1950 to 3.6% by 1990. We have employed weak priors based on prewar data. The estimation makes use of the Gibbs sampler and the Metropolis algorithm.     

Gibbs sampling for Bayesian non-conjugate and hierarchical models by using auxiliary variables

We demonstrate the use of auxiliary (or latent) variables for sampling non-standard densities which arise in the context of the Bayesian analysis of non-conjugate and hierarchical models by using a Gibbs sampler. Their strategic use can result in a Gibbs sampler having easily sampled full conditionals. We propose such a procedure to simplify or speed up the Markov chain Monte Carlo algorithm. The strength of this approach lies in its generality and its ease of implementation. The aim of the paper, therefore, is to provide an alternative sampling algorithm to rejection-based methods and other sampling approaches such as the Metropolis–Hastings algorithm.