Choosing Prior Hyperparameters: With Applications to Time-Varying Parameter Models

Time-varying parameter models with stochastic volatility are widely used to study macroeconomic and financial data. These models are almost exclusively estimated using Bayesian methods. A common practice is to focus on prior distributions that themselves depend on relatively few hyperparameters such as the scaling factor for the prior covariance matrix of the residuals governing time variation in the parameters. The choice of these hyperparameters is crucial because their influence is sizeable for standard sample sizes. In this article, we treat the hyperparameters as part of a hierarchical model and propose a fast, tractable, easy-to-implement, and fully Bayesian approach to estimate those hyperparameters jointly with all other parameters in the model. We show via Monte Carlo simulations that, in this class of models, our approach can drastically improve on using fixed hyperparameters previously proposed in the literature. Supplementary materials for this article are available online.     

Bayesian inference for sinh-normal/independent nonlinear regression models

Sinh-normal/independent distributions are a class of symmetric heavy-tailed distributions that include the sinh-normal distribution as a special case, which has been used extensively in Birnbaum–Saunders regression models. Here, we explore the use of Markov Chain Monte Carlo methods to develop a Bayesian analysis in nonlinear regression models when Sinh-normal/independent distributions are assumed for the random errors term, and it provides a robust alternative to the sinh-normal nonlinear regression model. Bayesian mechanisms for parameter estimation, residual analysis and influence diagnostics are then developed, which extend the results of Farias and Lemonte [Bayesian inference for the Birnbaum-Saunders nonlinear regression model, Stat. Methods Appl. 20 (2011), pp. 423-438] who used the Sinh-normal/independent distributions with known scale parameter. Some special cases, based on the sinh-Student-t (sinh-St), sinh-slash (sinh-SL) and sinh-contaminated normal (sinh-CN) distributions are discussed in detail. Two real datasets are finally analyzed to illustrate the developed procedures.     

Bayesian D-optimal design for logistic regression model with exponential distribution for random intercept

ABSTRACT

Nowadays, generalized linear models have many applications. Some of these models which have more applications in the real world are the models with random effects; that is, some of the unknown parameters are considered random variables. In this article, this situation is considered in logistic regression models with a random intercept having exponential distribution. The aim is to obtain the Bayesian D-optimal design; thus, the method is to maximize the Bayesian D-optimal criterion. For the model was considered here, this criterion is a function of the quasi-information matrix that depends on the unknown parameters of the model. In the Bayesian D-optimal criterion, the expectation is acquired in respect of the prior distributions that are considered for the unknown parameters. Thus, it will only be a function of experimental settings (support points) and their weights. The prior distribution of the fixed parameters is considered uniform and normal. The Bayesian D-optimal design is finally calculated numerically by R3.1.1 software.     

Optimal acceptance sampling policy considering Bayesian risks

In this paper, we propose a sampling policy considering Bayesian risks. Various definitions of producer's risk and consumer's risk have been made. Bayesian risks for both producer and consumer are proven to give better information to decision-makers than classical definitions of the risks. So considering the Bayesian risk constraints, we seek to find optimal acceptance sampling policy by minimizing total cost, including the cost of rejecting the batch, the cost of inspection, and the cost of defective items detected during the operation. Proper distributions to construct the objective function of the model are specified. In order to demonstrate the application of the proposed model, we illustrate a numerical example. Furthermore, the results of the sensitivity analysis show that lot size, the cost of inspection, and the cost of one defective item are key factors in sampling policies. The acceptable quality level, the lot tolerance proportion defective, and Bayesian risks also affect the sampling policy, but variations of acceptable quality level and producer Bayesian risks, for values more than a specified value, cause no changes in sampling policy.     

Model weights for model choice and averaging

A method is suggested to estimate posterior model probabilities and model averaged parameters via MCMC sampling under a Bayesian approach. The estimates use pooled output for J models (J>1) whereby all models are updated at each iteration. Posterior probabilities are based on averages of continuous weights obtained for each model at each iteration, while samples of averaged parameters are obtained from iteration specific averages that are based on these weights. Parallel sampling of models assists in deriving posterior densities for parameter contrasts between models and in assessing hypotheses regarding model averaged parameters. Four worked examples illustrate application of the approach, two involving fixed effect regression, and two involving random effects.     

A Bayesian piecewise exponential phase II design for monitoring a time-to-event endpoint

A robust Bayesian design is presented for a single-arm phase II trial with an early stopping rule to monitor a time to event endpoint. The assumed model is a piecewise exponential distribution with non-informative gamma priors on the hazard parameters in subintervals of a fixed follow up interval. As an additional comparator, we also define and evaluate a version of the design based on an assumed Weibull distribution. Except for the assumed models, the piecewise exponential and Weibull model based designs are identical to an established design that assumes an exponential event time distribution with an inverse gamma prior on the mean event time. The three designs are compared by simulation under several log-logistic and Weibull distributions having different shape parameters, and for different monitoring schedules. The simulations show that, compared to the exponential inverse gamma model based design, the piecewise exponential design has substantially better performance, with much higher probabilities of correctly stopping the trial early, and shorter and less variable trial duration, when the assumed median event time is unacceptably low. Compared to the Weibull model based design, the piecewise exponential design does a much better job of maintaining small incorrect stopping probabilities in cases where the true median survival time is desirably large.     

The posterior distribution of the fixed and random effects in a mixed-effects linear model

The subject of this paper is Bayesian inference about the fixed and random effects of a mixed-effects linear statistical model with two variance components. It is assumed that a priori the fixed effects have a noninformative distribution and that the reciprocals of the variance components are distributed independently (of each other and of the fixed effects) as gamma random variables. It is shown that techniques similar to those employed in a ridge analysis of a response surface can be used to construct a one-dimensional curve that contains all of the stationary points of the posterior density of the random effects. The “ridge analysis” (of the posterior density) can be useful (from a computational standpoint) in finding the number and the locations of the stationary points and can be very informative about various features of the posterior density. Depending on what is revealed by the ridge analysis, a multivariate normal or multivariate-t distribution that is centered at a posterior mode may provide a satisfactory approximation to the posterior distribution of the random effects (which is of the poly-t form).     

Bayesian analysis of censored linear regression models with scale mixtures of normal distributions

As is the case of many studies, the data collected are limited and an exact value is recorded only if it falls within an interval range. Hence, the responses can be either left, interval or right censored. Linear (and nonlinear) regression models are routinely used to analyze these types of data and are based on normality assumptions for the errors terms. However, those analyzes might not provide robust inference when the normality assumptions are questionable. In this article, we develop a Bayesian framework for censored linear regression models by replacing the Gaussian assumptions for the random errors with scale mixtures of normal (SMN) distributions. The SMN is an attractive class of symmetric heavy-tailed densities that includes the normal, Student-t, Pearson type VII, slash and the contaminated normal distributions, as special cases. Using a Bayesian paradigm, an efficient Markov chain Monte Carlo algorithm is introduced to carry out posterior inference. A new hierarchical prior distribution is suggested for the degrees of freedom parameter in the Student-t distribution. The likelihood function is utilized to compute not only some Bayesian model selection measures but also to develop Bayesian case-deletion influence diagnostics based on the q-divergence measure. The proposed Bayesian methods are implemented in the R package BayesCR. The newly developed procedures are illustrated with applications using real and simulated data.     

Investigating the sensitivity of Gaussian processes to the choice of their correlation function and prior specifications

A Gaussian process (GP) can be thought of as an infinite collection of random variables with the property that any subset, say of dimension n, of these variables have a multivariate normal distribution of dimension n, mean vector β and covariance matrix Σ [O'Hagan, A., 1994, Kendall's Advanced Theory of Statistics, Vol. 2B, Bayesian Inference (John Wiley & Sons, Inc.)]. The elements of the covariance matrix are routinely specified through the multiplication of a common variance by a correlation function. It is important to use a correlation function that provides a valid covariance matrix (positive definite). Further, it is well known that the smoothness of a GP is directly related to the specification of its correlation function. Also, from a Bayesian point of view, a prior distribution must be assigned to the unknowns of the model. Therefore, when using a GP to model a phenomenon, the researcher faces two challenges: the need of specifying a correlation function and a prior distribution for its parameters. In the literature there are many classes of correlation functions which provide a valid covariance structure. Also, there are many suggestions of prior distributions to be used for the parameters involved in these functions. We aim to investigate how sensitive the GPs are to the (sometimes arbitrary) choices of their correlation functions. For this, we have simulated 25 sets of data each of size 64 over the square [0, 5]×[0, 5] with a specific correlation function and fixed values of the GP's parameters. We then fit different correlation structures to these data, with different prior specifications and check the performance of the adjusted models using different model comparison criteria.     

带线性约束的多元线性回归模型参数估计

本文首先构造线性约束条件下的多元线性回归模型的样本似然函数,利用Lagrange法证明其合理性。其次,从似然函数的角度讨论线性约束条件对模型参数的影响,对由传统理论得出的参数估计作出贝叶斯与经验贝叶斯的改进。做贝叶斯改进时,将矩阵正态-Wishart分布作为模型参数和精度阵的联合共轭先验分布,结合构造的似然函数得出参数的后验分布,计算出参数的贝叶斯估计;做经验贝叶斯改进时,将样本分组,从方差的角度讨论由子样得出的参数估计对总样本的参数估计的影响,计算出经验贝叶斯估计。最后,利用Matlab软件生成的随机矩阵做模拟。结果表明,这两种改进后的参数估计均较由传统理论得出的参数估计更精确,拟合结果的误差比更小,可信度更高,在大数据的情况下,这种计算方法的速度更快。     

The Bayesian D-optimal design for simple beta regression model in two cases (both known and unknown nuisance parameter)

According to investigated topic in the context of optimal designs, various methods can be used to obtain optimal design, of which Bayesian method is one. In this paper, considering the model and the features of the information matrix, this method (Bayesian optimality criterion) has been used for obtaining optimal designs which due to the variation range of the model parameters, prior distributions such as Uniform, Normal and Exponential have been used and the results analysed.     

Bayesian Accelerated Life Testing under Competing Weibull Causes of Failure

Consider a J-component series system which is put on Accelerated Life Test (ALT) involving K stress variables. First, a general formulation of ALT is provided for log-location-scale family of distributions. A general stress translation function of location parameter of the component log-lifetime distribution is proposed which can accommodate standard ones like Arrhenius, power-rule, log-linear model, etc., as special cases. Later, the component lives are assumed to be independent Weibull random variables with a common shape parameter. A full Bayesian methodology is then developed by letting only the scale parameters of the Weibull component lives depend on the stress variables through the general stress translation function. Priors on all the parameters, namely the stress coefficients and the Weibull shape parameter, are assumed to be log-concave and independent of each other. This assumption is to facilitate Gibbs sampling from the joint posterior. The samples thus generated from the joint posterior is then used to obtain the Bayesian point and interval estimates of the system reliability at usage condition.     

Hierarchical Generalized Linear Models and Frailty Models with Bayesian Nonparametric Mixing

This paper proposes Bayesian nonparametric mixing for some well-known and popular models. The distribution of the observations is assumed to contain an unknown mixed effects term which includes a fixed effects term, a function of the observed covariates, and an additive or multiplicative random effects term. Typically these random effects are assumed to be independent of the observed covariates and independent and identically distributed from a distribution from some known parametric family. This assumption may be suspect if either there is interaction between observed covariates and unobserved covariates or the fixed effects predictor of observed covariates is misspecified. Another cause for concern might be simply that the covariates affect more than just the location of the mixed effects distribution. As a consequence the distribution of the random effects could be highly irregular in modality and skewness leaving parametric families unable to model the distribution adequately. This paper therefore proposes a Bayesian nonparametric prior for the random effects to capture possible deviances in modality and skewness and to explore the observed covariates' effect on the distribution of the mixed effects.     

Mixed-effects Models with Skewed Distributions for Time-varying Decay Rate in HIV Dynamics

After initiation of treatment, HIV viral load has multiphasic changes, which indicates that the viral decay rate is a time-varying process. Mixed-effects models with different time-varying decay rate functions have been proposed in literature. However, there are two unresolved critical issues: (i) it is not clear which model is more appropriate for practical use, and (ii) the model random errors are commonly assumed to follow a normal distribution, which may be unrealistic and can obscure important features of within- and among-subject variations. Because asymmetry of HIV viral load data is still noticeable even after transformation, it is important to use a more general distribution family that enables the unrealistic normal assumption to be relaxed. We developed skew-elliptical (SE) Bayesian mixed-effects models by considering the model random errors to have an SE distribution. We compared the performance among five SE models that have different time-varying decay rate functions. For each model, we also contrasted the performance under different model random error assumptions such as normal, Student-t, skew-normal, or skew-t distribution. Two AIDS clinical trial datasets were used to illustrate the proposed models and methods. The results indicate that the model with a time-varying viral decay rate that has two exponential components is preferred. Among the four distribution assumptions, the skew-t and skew-normal models provided better fitting to the data than normal or Student-t model, suggesting that it is important to assume a model with a skewed distribution in order to achieve reasonable results when the data exhibit skewness.     

Bayesian Inference in Generalized Error and Generalized Student-t Regression Models

This study takes up inference in linear models with generalized error and generalized t distributions. For the generalized error distribution, two computational algorithms are proposed. The first is based on indirect Bayesian inference using an approximating finite scale mixture of normal distributions. The second is based on Gibbs sampling. The Gibbs sampler involves only drawing random numbers from standard distributions. This is important because previously the impression has been that an exact analysis of the generalized error regression model using Gibbs sampling is not possible. Next, we describe computational Bayesian inference for linear models with generalized t disturbances based on Gibbs sampling, and exploiting the fact that the model is a mixture of generalized error distributions with inverse generalized gamma distributions for the scale parameter. The linear model with this specification has also been thought not to be amenable to exact Bayesian analysis. All computational methods are applied to actual data involving the exchange rates of the British pound, the French franc, and the German mark relative to the U.S. dollar.     

Bayesian analysis of longitudinal ordered data with flexible random effects using McMC: application to diabetic macular Edema data

In the analysis of correlated ordered data, mixed-effect models are frequently used to control the subject heterogeneity effects. A common assumption in fitting these models is the normality of random effects. In many cases, this is unrealistic, making the estimation results unreliable. This paper considers several flexible models for random effects and investigates their properties in the model fitting. We adopt a proportional odds logistic regression model and incorporate the skewed version of the normal, Student's t and slash distributions for the effects. Stochastic representations for various flexible distributions are proposed afterwards based on the mixing strategy approach. This reduces the computational burden being performed by the McMC technique. Furthermore, this paper addresses the identifiability restrictions and suggests a procedure to handle this issue. We analyze a real data set taken from an ophthalmic clinical trial. Model selection is performed by suitable Bayesian model selection criteria.     

On a redundant repairable system with switching failure: Bayesian approach

System characteristics of a redundant repairable system are studied from a Bayesian viewpoint with different types of priors assumed for the unknown parameters. The system consists of two primary units, one standby unit, and one repair facility which is activated when switching to standby fails. Times to failure and times to repair of the operating units are assumed to follow exponential distributions. When time to failure and time to repair have uncertain parameters, a Bayesian approach is adopted to evaluate system characteristics. Monte Carlo simulation is used to derive the posterior distribution for the mean time to system failure and steady-state availability. Some numerical experiments are performed to illustrate the results derived in this paper.     

The repair alert models with fixed and random effects

This article extends a random preventive maintenance scheme, called repair alert model, when there exist environmental variables that effect on system lifetimes. It can be used for implementing age-dependent maintenance policies on engineering devices. In other words, consider a device that works for a job and is subject to failure at a random time X, and the maintenance crew can avoid the failure by a possible replacement at some random time Z. The new model is flexible to including covariates with both fixed and random effects. The problem of estimating parameters is also investigated in details. Here, the observations are in the form of random signs censoring data (RSCD) with covariates. Therefore, this article generalizes derived statistical inferences on the basis of RSCD albeit without covariates in past literature. To do this, it is assumed that the system lifetime distribution belongs to the log-location-scale family of distributions. A real dataset is also analyzed on basis of the results obtained.     

Bayesian Analysis for a Redundant Repairable System with Imperfect Coverage

System characteristics of a redundant repairable system with two primary units and one standby are studied from a Bayesian viewpoint with different types of priors assumed for unknown parameters, in which the coverage factor is the same for an operating unit failure as that for a standby unit failure. Times to failure and times to repair of the operating and standby units are assumed to follow exponential distributions. When times to failure and times to repair with uncertain parameters, a Bayesian approach is adopted to evaluate system characteristics. Monte Carlo simulation is used to derive the posterior distribution for the mean time to system failure and the steady-state availability. Some numerical experiments are performed to illustrate the results derived in this paper.     

Bayesian analysis of hierarchical linear mixed modeling using the multivariate t distribution

This article presents a fully Bayesian approach to modeling incomplete longitudinal data using the t linear mixed model with AR(p) dependence. Markov chain Monte Carlo (MCMC) techniques are implemented for computing posterior distributions of parameters. To facilitate the computation, two types of auxiliary indicator matrices are incorporated into the model. Meanwhile, the constraints on the parameter space arising from the stationarity conditions for the autoregressive parameters are handled by a reparametrization scheme. Bayesian predictive inferences for the future vector are also investigated. An application is illustrated through a real example from a multiple sclerosis clinical trial.