Bayesian composite quantile regression for linear mixed-effects models

Longitudinal data are commonly modeled with the normal mixed-effects models. Most modeling methods are based on traditional mean regression, which results in non robust estimation when suffering extreme values or outliers. Median regression is also not a best choice to estimation especially for non normal errors. Compared to conventional modeling methods, composite quantile regression can provide robust estimation results even for non normal errors. In this paper, based on a so-called pseudo composite asymmetric Laplace distribution (PCALD), we develop a Bayesian treatment to composite quantile regression for mixed-effects models. Furthermore, with the location-scale mixture representation of the PCALD, we establish a Bayesian hierarchical model and achieve the posterior inference of all unknown parameters and latent variables using Markov Chain Monte Carlo (MCMC) method. Finally, this newly developed procedure is illustrated by some Monte Carlo simulations and a case analysis of HIV/AIDS clinical data set.     

Linear Bayesian Inference for Accelerated Weibull Model

In this paper, we present a Bayesian approach for inference from accelerated life tests when the underlying life model is Weibull. Our approach is based on the General Linear Models framework of West, Harrison and Migon (1985). We discuss inference for the model and show that computable results can be obtained using linear Bayesian methods. We illustrate the usefulness of our approach by applying it to some actual data from accelerated life tests. This revised version was published online in July 2006 with corrections to the Cover Date.     

Bayesian semiparametric inference for the accelerated failure-time model

Bayesian semiparametric inference is considered for a loglinear model. This model consists of a parametric component for the regression coefficients and a nonparametric component for the unknown error distribution. Bayesian analysis is studied for the case of a parametric prior on the regression coefficients and a mixture-of-Dirichlet-processes prior on the unknown error distribution. A Markov-chain Monte Carlo (MCMC) method is developed to compute the features of the posterior distribution. A model selection method for obtaining a more parsimonious set of predictors is studied. The method adds indicator variables to the regression equation. The set of indicator variables represents all the possible subsets to be considered. A MCMC method is developed to search stochastically for the best subset. These procedures are applied to two examples, one with censored data.     

Bivariate Constant-Stress Accelerated Degradation Model and Inference

To assess the reliability of highly reliable products that have two or more performance characteristics (PCs) in an accurate manner, relations between the PCs should be taken duly into account. If they are not independent, it would then become important to describe the dependence of the PCs. For many products, the constant-stress degradation test cannot provide sufficient data for reliability evaluation and for this reason, accelerated degradation test is usually performed. In this article, we assume that a product has two PCs and that the PCs are governed by a Wiener process with a time scale transformation, and the relationship between the PCs is described by the Frank copula function. The copula parameter is dependent on stress and assumed to be a function of stress level that can be described by a logistic function. Based on these assumptions, a bivariate constant-stress accelerated degradation model is proposed here. The direct likelihood estimation of parameters of such a model becomes analytically intractable, and so the Bayesian Markov chain Monte Carlo (MCMC) method is developed here for this model for obtaining the maximum likelihood estimates (MLEs) efficiently. For an illustration of the proposed model and the method of inference, a simulated example is presented along with the associated computational results.     

Multivariate Poisson regression with covariance structure

In recent years the applications of multivariate Poisson models have increased, mainly because of the gradual increase in computer performance. The multivariate Poisson model used in practice is based on a common covariance term for all the pairs of variables. This is rather restrictive and does not allow for modelling the covariance structure of the data in a flexible way. In this paper we propose inference for a multivariate Poisson model with larger structure, i.e. different covariance for each pair of variables. Maximum likelihood estimation, as well as Bayesian estimation methods are proposed. Both are based on a data augmentation scheme that reflects the multivariate reduction derivation of the joint probability function. In order to enlarge the applicability of the model we allow for covariates in the specification of both the mean and the covariance parameters. Extension to models with complete structure with many multi-way covariance terms is discussed. The method is demonstrated by analyzing a real life data set.     

Bayesian inference over ICA models: application to multibiometric score fusion with quality estimates

Bayesian networks are not well-formulated for continuous variables. The majority of recent works dealing with Bayesian inference are restricted only to special types of continuous variables such as the conditional linear Gaussian model for Gaussian variables. In this context, an exact Bayesian inference algorithm for clusters of continuous variables which may be approximated by independent component analysis models is proposed. The complexity in memory space is linear and the overfitting problem is attenuated, while the inference time is still exponential. Experiments for multibiometric score fusion with quality estimates are conducted, and it is observed that the performances are satisfactory compared to some known fusion techniques.     

Constant Stress Accelerated Life Test on a Multiple-Component Series System under Weibull Lifetime Distributions

We will discuss the reliability analysis of the constant stress accelerated life test on a series system connected with multiple components under independent Weibull lifetime distributions whose scale parameters are log-linear in the level of the stress variable. The system lifetimes are collected under Type I censoring but the components that cause the systems to fail may or may not be observed. The data are so called masked for the latter case. Maximum likelihood approach and the Bayesian method are considered when the data are masked. Statistical inference on the estimation of the underlying model parameters as well as the mean time to failure and the reliability function will be addressed. Simulation study for a three-component case shows that Bayesian analysis outperforms the maximum likelihood approach especially when the data are highly masked.     

A Bayesian Analysis for Accelerated Lifetime Tests Under an Exponential Power Law Model with Threshold Stress

In this paper, we present a Bayesian methodology for modelling accelerated lifetime tests under a stress response relationship with a threshold stress. Both Laplace and MCMC methods are considered. The methodology is described in detail for the case when an exponential distribution is assumed to express the behaviour of lifetimes, and a power law model with a threshold stress is assumed as the stress response relationship. We assume vague but proper priors for the parameters of interest. The methodology is illustrated by a accelerated failure test on an electrical insulation film.     

Monte Carlo Methods for Bayesian Inference on the Linear Hazard Rate Distribution

The Bayesian estimation and prediction problems for the linear hazard rate distribution under general progressively Type-II censored samples are considered in this article. The conventional Bayesian framework as well as the Markov Chain Monte Carlo (MCMC) method to generate the Bayesian conditional probabilities of interest are discussed. Sensitivity of the prior for the model is also examined. The flood data on Fox River, Wisconsin, from 1918 to 1950, are used to illustrate all the methods of inference discussed in this article.     

Bayesian analysis for step-stress accelerated life testing using weibull proportional hazard model

In this paper, we present a Bayesian analysis for the Weibull proportional hazard (PH) model used in step-stress accelerated life testings. The key mathematical and graphical difference between the Weibull cumulative exposure (CE) model and the PH model is illustrated. Compared with the CE model, the PH model provides more flexibility in fitting step-stress testing data and has the attractive mathematical properties of being desirable in the Bayesian framework. A Markov chain Monte Carlo algorithm with adaptive rejection sampling technique is used for posterior inference. We demonstrate the performance of this method on both simulated and real datasets.     

Bayesian Analysis of Masked Data in Step-stress Accelerated Life Testing

This article considers a k level step-stress accelerated life testing (ALT) on series system products, where independent Weibull-distributed lifetimes are assumed for the components. Due to cost considerations or environmental restrictions, causes of system failures are masked and type-I censored observations might occur in the collected data. Bayesian approach combined with auxiliary variables is developed for estimating the parameters of the model. Further, the reliability and hazard rate functions of the system and components are estimated at a specified time at use stress level. The proposed method is illustrated through a numerical example based on two priors and various masking probabilities.     

Hybrid Bayesian inference on HIV viral dynamic models

Modelling of HIV dynamics in AIDS research has greatly improved our understanding of the pathogenesis of HIV-1 infection and guided for the treatment of AIDS patients and evaluation of antiretroviral therapies. Some of the model parameters may have practical meanings with prior knowledge available, but others might not have prior knowledge. Incorporating priors can improve the statistical inference. Although there have been extensive Bayesian and frequentist estimation methods for the viral dynamic models, little work has been done on making simultaneous inference about the Bayesian and frequentist parameters. In this article, we propose a hybrid Bayesian inference approach for viral dynamic nonlinear mixed-effects models using the Bayesian frequentist hybrid theory developed in Yuan [Bayesian frequentist hybrid inference, Ann. Statist. 37 (2009), pp. 2458–2501]. Compared with frequentist inference in a real example and two simulation examples, the hybrid Bayesian approach is able to improve the inference accuracy without compromising the computational load.     

A rare event approach to high-dimensional approximate Bayesian computation

Approximate Bayesian computation (ABC) methods permit approximate inference for intractable likelihoods when it is possible to simulate from the model. However, they perform poorly for high-dimensional data and in practice must usually be used in conjunction with dimension reduction methods, resulting in a loss of accuracy which is hard to quantify or control. We propose a new ABC method for high-dimensional data based on rare event methods which we refer to as RE-ABC. This uses a latent variable representation of the model. For a given parameter value, we estimate the probability of the rare event that the latent variables correspond to data roughly consistent with the observations. This is performed using sequential Monte Carlo and slice sampling to systematically search the space of latent variables. In contrast, standard ABC can be viewed as using a more naive Monte Carlo estimate. We use our rare event probability estimator as a likelihood estimate within the pseudo-marginal Metropolis–Hastings algorithm for parameter inference. We provide asymptotics showing that RE-ABC has a lower computational cost for high-dimensional data than standard ABC methods. We also illustrate our approach empirically, on a Gaussian distribution and an application in infectious disease modelling.     

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.     

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.     

Variational Bayes with synthetic likelihood

Synthetic likelihood is an attractive approach to likelihood-free inference when an approximately Gaussian summary statistic for the data, informative for inference about the parameters, is available. The synthetic likelihood method derives an approximate likelihood function from a plug-in normal density estimate for the summary statistic, with plug-in mean and covariance matrix obtained by Monte Carlo simulation from the model. In this article, we develop alternatives to Markov chain Monte Carlo implementations of Bayesian synthetic likelihoods with reduced computational overheads. Our approach uses stochastic gradient variational inference methods for posterior approximation in the synthetic likelihood context, employing unbiased estimates of the log likelihood. We compare the new method with a related likelihood-free variational inference technique in the literature, while at the same time improving the implementation of that approach in a number of ways. These new algorithms are feasible to implement in situations which are challenging for conventional approximate Bayesian computation methods, in terms of the dimensionality of the parameter and summary statistic.     

Planning sequential constant-stress accelerated life tests with stepwise loaded auxiliary acceleration factor

This article presents a design approach for sequential constant-stress accelerated life tests (ALT) with an auxiliary acceleration factor (AAF). The use of an AAF, if it exists, is to further amplify the failure probability of highly reliability testing items at low stress levels while maintaining an acceptable degree of extrapolation for reliability inference. Based on a Bayesian design criterion, the optimal plan optimizes the sample allocation, stress combination, as well as the loading profile of the AAF. In particular, a step-stress loading profile based on an appropriate cumulative exposure (CE) model is chosen for the AAF such that the initial auxiliary stress will not be too harsh. A case study, providing the motivation and practical importance of our study, is presented to illustrate the proposed planning approach.     

Bayesian Additive Machine: classification with a semiparametric discriminant function

In this paper, we propose a new Bayesian inference approach for classification based on the traditional hinge loss used for classical support vector machines, which we call the Bayesian Additive Machine (BAM). Unlike existing approaches, the new model has a semiparametric discriminant function where some feature effects are nonlinear and others are linear. This separation of features is achieved automatically during model fitting without user pre-specification. Following the literature on sparse regression of high-dimensional models, we can also identify the irrelevant features. By introducing spike-and-slab priors using two sets of indicator variables, these multiple goals are achieved simultaneously and automatically, without any parameter tuning such as cross-validation. An efficient partially collapsed Markov chain Monte Carlo algorithm is developed for posterior exploration based on a data augmentation scheme for the hinge loss. Our simulations and three real data examples demonstrate that the new approach is a strong competitor to some approaches that were proposed recently for dealing with challenging classification examples with high dimensionality.     

On the estimation problem of periodic autoregressive time series: symmetric and asymmetric innovations

Periodic autoregressive (PAR) models with symmetric innovations are widely used on time series analysis, whereas its asymmetric counterpart inference remains a challenge, because of a number of problems related to the existing computational methods. In this paper, we use an interesting relationship between periodic autoregressive and vector autoregressive (VAR) models to study maximum likelihood and Bayesian approaches to the inference of a PAR model with normal and skew-normal innovations, where different kinds of estimation methods for the unknown parameters are examined. Several technical difficulties which are usually complicated to handle are reported. Results are compared with the existing classical solutions and the practical implementations of the proposed algorithms are illustrated via comprehensive simulation studies. The methods developed in the study are applied and illustrate a real-time series. The Bayes factor is also used to compare the multivariate normal model versus the multivariate skew-normal model.     

Perfect simulation for Reed-Frost epidemic models

The Reed-Frost epidemic model is a simple stochastic process with parameter q that describes the spread of an infectious disease among a closed population. Given data on the final outcome of an epidemic, it is possible to perform Bayesian inference for q using a simple Gibbs sampler algorithm. In this paper it is illustrated that by choosing latent variables appropriately, certain monotonicity properties hold which facilitate the use of a perfect simulation algorithm. The methods are applied to real data.