Non parametric Bayesian analysis of the two-sample problem with censoring

Testing for differences between two groups is a fundamental problem in statistics, and due to developments in Bayesian non parametrics and semiparametrics there has been renewed interest in approaches to this problem. Here we describe a new approach to developing such tests and introduce a class of such tests that take advantage of developments in Bayesian non parametric computing. This class of tests uses the connection between the Dirichlet process (DP) prior and the Wilcoxon rank sum test but extends this idea to the DP mixture prior. Here tests are developed that have appropriate frequentist sampling procedures for large samples but have the potential to outperform the usual frequentist tests. Extensions to interval and right censoring are considered and an application to a high-dimensional data set obtained from an RNA-Seq investigation demonstrates the practical utility of the method.     

Bayesian nonparametric survival analysis for grouped data

A Bayesian nonparametric estimate of the survival distribution is derived under a particular sampling scheme for grouped data that includes the possibility of censoring. The estimate uses the prior information to smooth the data, giving an estimate which is continuous. As special cases survival estimates for life tables are obtained and the estimate of Susarla and Van Ryzin (1976) is derived. As the weight of the prior information tends to zero, the Bayesian estimate reduces to a continuous version of the nonparametric maximum-likelihood estimate. An empirical Bayes modification of the procedure is illustrated on a data set from Cutler and Ederer (1958).     

Incomplete categorical data analysis: a bayesian perspective

In this paper the Bayesian analysis of incomplete categorical data under informative general censoring proposed by Paulino and Pereira (1995) is revisited. That analysis is based on Dirichlet priors and can be applied to any missing data pattern. However, the known properties of the posterior distributions are scarce and therefore severe limitations to the posterior computations remain. Here is shown how a Monte Carlo simulation approach based on an alternative parameterisation can be used to overcome the former computational difficulties. The proposed simulation approach makes available the approximate estimation of general parametric functions and can be implemented in a very straightforward way.     

Bayesian Semiparametric Regression for Median Residual Life

Abstract.  With survival data there is often interest not only in the survival time distribution but also in the residual survival time distribution. In fact, regression models to explain residual survival time might be desired. Building upon recent work of Kottas & Gelfand [ J. Amer. Statist. Assoc. 96 (2001) 1458], we formulate a semiparametric median residual life regression model induced by a semiparametric accelerated failure time regression model. We utilize a Bayesian approach which allows full and exact inference. Classical work essentially ignores covariates and is either based upon parametric assumptions or is limited to asymptotic inference in non-parametric settings. No regression modelling of median residual life appears to exist. The Bayesian modelling is developed through Dirichlet process mixing. The models are fitted using Gibbs sampling. Residual life inference is implemented extending the approach of Gelfand & Kottas [ J. Comput. Graph. Statist. 11 (2002) 289]. Finally, we present a fairly detailed analysis of a set of survival times with moderate censoring for patients with small cell lung cancer.     

A Bayesian nonparametric estimator based on left censored data

Summary This paper introduces a Bayesian nonparametric estimator for an unknown distribution function based on left censored observations. Hjort (1990)/Lo (1993) introduced Bayesian nonparametric estimators derived from beta/beta-neutral processes which allow for right censoring. These processes are taken as priors from the class ofneutral to the right processes (Doksum, 1974). The Kaplan-Meier nonparametric product limit estimator can be obtained from these Bayesian nonparametric estimators in the limiting case of a vague prior. The present paper introduces what can be seen as the correspondingleft beta/beta-neutral process prior which allow for left censoring. The Bayesian nonparametyric estimator is obtained as in the corresponding product limit estimator based on left censored data.     

Optimal Bayesian variable sampling plans for exponential distributions based on modified type-II hybrid censored samples

For the conventional type-II hybrid censoring scheme (HCS) in Childs et al., a Bayesian variable sampling plan among the class of the maximum likelihood estimators was derived by Lin et al. under the loss function, which does not include the cost of experimental time. Instead of taking the conventional type-II hybrid censoring scheme, a persuasive argument leads to taking the modified type-II hybrid censoring scheme (MHCS) if the cost of experimental time is included in the loss function. In this article, we apply the decision-theoretic approach for the concerned acceptance sampling. With the type-II MHCS, based on a sufficient statistics, the optimal Bayesian sampling plan is derived under a general loss function. Furthermore, for the conjugate prior distribution, the closed-form formula of the Bayes decision rule can be obtained under the quadratic decision loss. Numerical study is given to demonstrate the performance of the proposed Bayesian sampling plan.     

On progressively censored inverted exponentiated Rayleigh distribution

In this paper, we discuss a progressively censored inverted exponentiated Rayleigh distribution. Estimation of unknown parameters is considered under progressive censoring using maximum likelihood and Bayesian approaches. Bayes estimators of unknown parameters are derived with respect to different symmetric and asymmetric loss functions using gamma prior distributions. An importance sampling procedure is taken into consideration for deriving these estimates. Further highest posterior density intervals for unknown parameters are constructed and for comparison purposes bootstrap intervals are also obtained. Prediction of future observations is studied in one- and two-sample situations from classical and Bayesian viewpoint. We further establish optimum censoring schemes using Bayesian approach. Finally, we conduct a simulation study to compare the performance of proposed methods and analyse two real data sets for illustration purposes.     

A note on the finite-dimensional Dirichlet prior

As an approximation to the Dirichlet process which involves the infinite-dimensional distribution, finite-dimensional Dirichlet prior is a widely appreciated method to model the underlying distribution in non parametric Bayesian analysis. In this short note, we present some key characteristics of finite-dimensional Dirichlet process and exploit some important sampling properties which are very useful in Bayesian non parametric/semiparametric analysis.     

Flexible clustering via hidden hierarchical Dirichlet priors

The Bayesian approach to inference stands out for naturally allowing borrowing information across heterogeneous populations, with different samples possibly sharing the same distribution. A popular Bayesian nonparametric model for clustering probability distributions is the nested Dirichlet process, which however has the drawback of grouping distributions in a single cluster when ties are observed across samples. With the goal of achieving a flexible and effective clustering method for both samples and observations, we investigate a nonparametric prior that arises as the composition of two different discrete random structures and derive a closed-form expression for the induced distribution of the random partition, the fundamental tool regulating the clustering behavior of the model. On the one hand, this allows to gain a deeper insight into the theoretical properties of the model and, on the other hand, it yields an MCMC algorithm for evaluating Bayesian inferences of interest. Moreover, we single out limitations of this algorithm when working with more than two populations and, consequently, devise an alternative more efficient sampling scheme, which as a by-product, allows testing homogeneity between different populations. Finally, we perform a comparison with the nested Dirichlet process and provide illustrative examples of both synthetic and real data.     

An Empirical Comparison of Multiple Imputation Methods for Categorical Data

Multiple imputation is a common approach for dealing with missing values in statistical databases. The imputer fills in missing values with draws from predictive models estimated from the observed data, resulting in multiple, completed versions of the database. Researchers have developed a variety of default routines to implement multiple imputation; however, there has been limited research comparing the performance of these methods, particularly for categorical data. We use simulation studies to compare repeated sampling properties of three default multiple imputation methods for categorical data, including chained equations using generalized linear models, chained equations using classification and regression trees, and a fully Bayesian joint distribution based on Dirichlet process mixture models. We base the simulations on categorical data from the American Community Survey. In the circumstances of this study, the results suggest that default chained equations approaches based on generalized linear models are dominated by the default regression tree and Bayesian mixture model approaches. They also suggest competing advantages for the regression tree and Bayesian mixture model approaches, making both reasonable default engines for multiple imputation of categorical data. Supplementary material for this article is available online.     

Bayesian estimation and prediction for the inverse weibull distribution under general progressive censoring

Abstract

This paper deals with Bayesian estimation and prediction for the inverse Weibull distribution with shape parameter α and scale parameter λ under general progressive censoring. We prove that the posterior conditional density functions of α and λ are both log-concave based on the assumption that λ has a gamma prior distribution and α follows a prior distribution with log-concave density. Then, we present the Gibbs sampling strategy to estimate under squared-error loss any function of the unknown parameter vector (α, λ) and find credible intervals, as well as to obtain prediction intervals for future order statistics. Monte Carlo simulations are given to compare the performance of Bayesian estimators derived via Gibbs sampling with the corresponding maximum likelihood estimators, and a real data analysis is discussed in order to illustrate the proposed procedure. Finally, we extend the developed methodology to other two-parameter distributions, including the Weibull, Burr type XII, and flexible Weibull distributions, and also to general progressive hybrid censoring.     

Bayesian Analysis of Different Hybrid and Progressive Life Tests

Type-I and Type-II censoring schemes are the widely used censoring schemes available for life testing experiments. A mixture of Type-I and Type-II censoring schemes is known as a hybrid censoring scheme. Different hybrid censoring schemes have been introduced in recent years. In the last few years, a progressive censoring scheme has also received considerable attention. In this article, we mainly consider the Bayesian inference of the unknown parameters of two-parameter exponential distribution under different hybrid and progressive censoring schemes. It is observed that in general the Bayes estimate and the associated credible interval of any function of the unknown parameters, cannot be obtained in explicit form. We propose to use the Monte Carlo sampling procedure to compute the Bayes estimate and also to construct the associated credible interval. Monte Carlo Simulation experiments have been performed to see the effectiveness of the proposed method in case of Type-I hybrid censored samples. The performances are quite satisfactory. One data analysis has been performed for illustrative purposes.     

A non-iterative Bayesian sampling algorithm for censored Student-t linear regression models

ABSTRACT

In this paper, we consider an effective Bayesian inference for censored Student-t linear regression model, which is a robust alternative to the usual censored Normal linear regression model. Based on the mixture representation of the Student-t distribution, we propose a non-iterative Bayesian sampling procedure to obtain independently and identically distributed samples approximately from the observed posterior distributions, which is different from the iterative Markov Chain Monte Carlo algorithm. We conduct model selection and influential analysis using the posterior samples to choose the best fitted model and to detect latent outliers. We illustrate the performance of the procedure through simulation studies, and finally, we apply the procedure to two real data sets, one is the insulation life data with right censoring and the other is the wage rates data with left censoring, and we get some interesting results.     

Efficient Bayesian sampling plans for exponential distributions with random censoring

This paper considers Bayesian sampling plans for exponential distribution with random censoring. The efficient Bayesian sampling plan for a general loss function is derived. This sampling plan possesses the property that it may make decisions prior to the end of the life test experiment, and its decision function is the same as the Bayes decision function which makes decisions based on data collected at the end of the life test experiment. Compared with the optimal Bayesian sampling plan of Chen et al. (2004), the efficient Bayesian sampling plan has the smaller Bayes risk due to the less duration time of life test experiment. Computations of the efficient Bayes risks for the conjugate prior are given. Numerical comparisons between the proposed efficient Bayesian sampling plan and the optimal Bayesian sampling plan of Chen et al. (2004) under two special decision losses, including the quadratic decision loss, are provided. Numerical results also demonstrate that the performance of the proposed efficient sampling plan is superior to that of the optimal sampling plan by Chen et al. (2004).     

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.     

A bayesian alternative to the analysis of matched categorical responces

This study investigates the Bayesian appeoach to the analysis of parired responess when the responses are categorical. Using resampling and analytical procedures, inferences for homogeneity and agreement are develped. The posterior analysis is based on the Dirichlet distribution from which repeated samples can be geneated with a random number generator. Resampling and analytical techniques are employed to make Bayesian inferences, and when it is not appropriate to use analytical procedures, resampling techniques are easily implemented. Bayesian methodoloogy is illustrated with several examples and the results show that they are exacr-small sample procedures that can easily solve inference problems for matched designs.     

On semiparametric pivotal bayesian inference for quantiles

In semiparametric inference we distinguish between the parameter of interest which may be a location parameter, and a nuisance parameter that determines the remaining shape of the sampling distribution. As was pointed out by Diaconis and Freedman the main problem in semiparametric Bayesian inference is to obtain a consistent posterior distribution for the parameter of interest. The present paper considers a semiparametric Bayesian method based on a pivotal likelihood function. It is shown that when the parameter of interest is the median, this method produces a consistent posterior distribution and is easily implemented, Numerical comparisons with classical methods and with Bayesian methods based on a Dirichlet prior are provided. It is also shown that in the case of symmetric intervals, the classical confidence coefficients have a Bayesian interpretation as the limiting posterior probability of the interval based on the Dirichlet prior with a parameter that converges to zero.     

Bayesian estimation methods for categorical data with misclassifications

This article considers Bayesian estimation methods for categorical data with misclassifications. To adjust for misclassification, double sampling schemes are utilized. Observations are represented in a contingency table categorized by error-free categorical variables and error-prone categorical variables. Posterior means of probabilities in cells are considered as estimates. In some cases, the posterior means can be calculated exactly. However,in some cases, the exact calculation may be too difficult to perform, but we can easily use the expectation-maximiza-tion(EM) algorithm to obtain approximate posterior means.     

Efficient Bayesian sampling plans for exponential distributions with type-I-censored samples

The aim of this paper is to introduce an efficient Bayesian sampling procedure for exponential distribution with type-I censoring. An online inspection method is suggested to reach a Bayes decision prior the termination time of life test. Bayesian sampling plans (BSPs) with quadratic loss function are established to illustrate the use of the proposed method. Some BSPs are tabulated, and the performance of the proposed BSPs is compared with two existing competitive methods. Numerical results indicate that a significant reduction in the experimental time over the conventional BSP can be achieved when the online inspection method is applied.     

Posterior Analysis for Normalized Random Measures with Independent Increments

Abstract.  One of the main research areas in Bayesian Nonparametrics is the proposal and study of priors which generalize the Dirichlet process. In this paper, we provide a comprehensive Bayesian non-parametric analysis of random probabilities which are obtained by normalizing random measures with independent increments (NRMI). Special cases of these priors have already shown to be useful for statistical applications such as mixture models and species sampling problems. However, in order to fully exploit these priors, the derivation of the posterior distribution of NRMIs is crucial: here we achieve this goal and, indeed, provide explicit and tractable expressions suitable for practical implementation. The posterior distribution of an NRMI turns out to be a mixture with respect to the distribution of a specific latent variable. The analysis is completed by the derivation of the corresponding predictive distributions and by a thorough investigation of the marginal structure. These results allow to derive a generalized Blackwell–MacQueen sampling scheme, which is then adapted to cover also mixture models driven by general NRMIs.