Bayesian and fiducial inference for the inverse gaussian distribution via Gibbs sampler

This paper presents a kernel estimation of the distribution of the scale parameter of the inverse Gaussian distribution under type II censoring together with the distribution of the remaining time. Estimation is carried out via the Gibbs sampling algorithm combined with a missing data approach. Estimates and confidence intervals for the parameters of interest are also presented.     

Inference for nonconjugate Bayesian Models using the Gibbs sampler

A Bayesian approach to modeling a rich class of nonconjugate problems is presented. An adaptive Monte Carlo integration technique known as the Gibbs sampler is proposed as a mechanism for implementing a conceptually and computationally simple solution in such a framework. The result is a general strategy for obtaining marginal posterior densities under changing specification of the model error densities and related prior densities. We illustrate the approach in a nonlinear regression setting, comparing the merits of three candidate error distributions.     

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.     

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.     

Slow convergence of the Gibbs sampler

We consider the Gibbs sampler as a tool for generating an absolutely continuous probability measure ≥ on R^d. When an appropriate irreducibility condition is satisfied, the Gibbs Markov chain (X_n;n ≥ 0) converges in total variation to its target distribution ≥. Sufficient conditions for geometric convergence have been given by various authors. Here we illustrate, by means of simple examples, how slow the convergence can be. In particular, we show that given a sequence of positive numbers decreasing to zero, say (b_n;n ≥ 1), one can construct an absolutely continuous probability measure ≥ on R^d which is such that the total variation distance between ≥ and the distribution of X_n, converges to 0 at a rate slower than that of the sequence (b_n;n ≥ 1). This can even be done in such a way that ≥ is the uniform distribution over a bounded connected open subset of R^d. Our results extend to hit-and-run samplers with direction distributions having supports with symmetric gaps.     

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.     

Survival analysis for the inverse Gaussian distribution with the Gibbs sampler

This paper describes a comprehensive survival analysis for the inverse Gaussian distribution employing Bayesian and Fiducial approaches. It focuses on making inferences on the inverse Gaussian (IG) parameters μ and λ and the average remaining time of censored units. A flexible Gibbs sampling approach applicable in the presence of censoring is discussed and illustrations with Type II, progressive Type II, and random rightly censored observations are included. The analyses are performed using both simulated IG data and empirical data examples. Further, the bootstrap comparisons are made between the Bayesian and Fiducial estimates. It is concluded that the shape parameter ( ϕ=λ/μ) of the inverse Gaussian distribution has the most impact on the two analyses, Bayesian vs. Fiducial, and so does the size of censoring in data to a lesser extent. Overall, both these approaches are effective in estimating IG parameters and the average remaining lifetime. The suggested Gibbs sampler allowed a great deal of flexibility in implementation for all types of censoring considered.     

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.     

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.     

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.     

Assessing convergence diagnostic tests for Bayesian Cox regression

The Markov chain Monte Carlo (MCMC) method generates samples from the posterior distribution and uses these samples to approximate expectations of quantities of interest. For the process, researchers have to decide whether the Markov chain has reached the desired posterior distribution. Using convergence diagnostic tests are very important to decide whether the Markov chain has reached the target distribution. Our interest in this study was to compare the performances of convergence diagnostic tests for all parameters of Bayesian Cox regression model with different number of iterations by using a simulation and a real lung cancer dataset.     

Simulation-based designs for accelerated life tests

In this paper we present a Bayesian decision theoretic approach to the design of accelerated life tests (ALT). We discuss computational issues regarding the evaluation of expectation and optimization steps in the solution of the decision problem. We illustrate how Monte Carlo methods can be used in preposterior analysis to find optimal designs and how the required computational effort can be avoided by using curve-fitting techniques. In so doing, we adopt the recent Monte-Carlo-based approaches of Muller and Parmigiani (1995. J. Amer. Statist. Assoc. 90, 503–510) and Muller (2000. Bayesian Statistics 6, forthcoming) to develop optimal Bayesian designs. These approaches facilitate the preposterior analysis by replacing it with a sequence of scatter plot smoothing/regression techniques and optimization of the corresponding fitted surfaces. We present our development by considering single and multiple-point fixed, as well as, sequential design problems when the underlying life model is exponential, and illustrate the implementation of our approach with some examples.     

A test for diagnostic utility

A criterion of usefulness for a diagnostic test is suggested. Based on sensitivity and specificity data, Bayesian and likelihood-ratio procedures to examine whether the criterion is satisfied are presented.     

Correlation-adjusted estimation of sensitivity and specificity of two diagnostic tests

Summary. Models for multiple-test screening data generally require the assumption that the tests are independent conditional on disease state. This assumption may be unreasonable, especially when the biological basis of the tests is the same. We propose a model that allows for correlation between two diagnostic test results. Since models that incorporate test correlation involve more parameters than can be estimated with the available data, posterior inferences will depend more heavily on prior distributions, even with large sample sizes. If we have reasonably accurate information about one of the two screening tests (perhaps the standard currently used test) or the prevalences of the populations tested, accurate inferences about all the parameters, including the test correlation, are possible. We present a model for evaluating dependent diagnostic tests and analyse real and simulated data sets. Our analysis shows that, when the tests are correlated, a model that assumes conditional independence can perform very poorly. We recommend that, if the tests are only moderately accurate and measure the same biological responses, researchers use the dependence model for their analyses.     

Gibbs sampling method for the Bayesian adaptive elastic net

This article considers the adaptive elastic net estimator for regularized mean regression from a Bayesian perspective. Representing the Laplace distribution as a mixture of Bartlett–Fejer kernels with a Gamma mixing density, a Gibbs sampling algorithm for the adaptive elastic net is developed. By introducing slice variables, it is shown that the mixture representation provides a Gibbs sampler that can be accomplished by sampling from either truncated normal or truncated Gamma distribution. The proposed method is illustrated using several simulation studies and analyzing a real dataset. Both simulation studies and real data analysis indicate that the proposed approach performs well.     

Bayesian estimates of predictive value and related parameters of a diagnostic test

Bayesian analysis of predictive values and related parameters of a diagnostic test are derived. In one case, the estimates are conditional on values of the prevalence of the disease; in the second case, the corresponding unconditional estimates are presented. Small-sample point estimates, posterior moments, and credibility intervals for all related parameters are obtained. Numerical methods of solution are also discussed.     

On convergence of the EM algorithmand the Gibbs sampler

In this article we investigate the relationship between the EM algorithm and the Gibbs sampler. We show that the approximate rate of convergence of the Gibbs sampler by Gaussian approximation is equal to that of the corresponding EM-type algorithm. This helps in implementing either of the algorithms as improvement strategies for one algorithm can be directly transported to the other. In particular, by running the EM algorithm we know approximately how many iterations are needed for convergence of the Gibbs sampler. We also obtain a result that under certain conditions, the EM algorithm used for finding the maximum likelihood estimates can be slower to converge than the corresponding Gibbs sampler for Bayesian inference. We illustrate our results in a number of realistic examples all based on the generalized linear mixed models.     

Comparison of the accuracy of multiple binary tests in the presence of partial disease verification

In the presence of partial disease verification, the comparison of the accuracy of binary diagnostic tests cannot be carried out through the paired comparison of the diagnostic tests applying McNemar's test, since for a subsample of patients the disease status is unknown. In this study, we have deduced the maximum likelihood estimators for the sensitivities and specificities of multiple binary diagnostic tests and we have studied various joint hypothesis tests based on the chi-square distribution to compare simultaneously the accuracy of these binary diagnostic tests when for some patients in the sample the disease status is unknown. Simulation experiments were carried out to study the type I error and the power of each hypothesis test deduced. The results obtained were applied to the diagnosis of coronary stenosis.     

Comparing diagnostic tests: test of hypothesis for likelihood ratios

Likelihood ratios (LRs) are used to characterize the efficiency of diagnostic tests. In this paper, we use the classical weighted least squares (CWLS) test procedure, which was originally used for testing the homogeneity of relative risks, for comparing the LRs of two or more binary diagnostic tests. We compare the performance of this method with the relative diagnostic likelihood ratio (rDLR) method and the diagnostic likelihood ratio regression (DLRReg) approach in terms of size and power, and we observe that the performances of CWLS and rDLR are the same when used to compare two diagnostic tests, while DLRReg method has higher type I error rates and powers. We also examine the performances of the CWLS and DLRReg methods for comparing three diagnostic tests in various sample size and prevalence combinations. On the basis of Monte Carlo simulations, we conclude that all of the tests are generally conservative and have low power, especially in settings of small sample size and low prevalence.