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.     

Efficient Regularization Parameter Selection Via Information Criteria

In a nonlinear regression model based on a regularization method, selection of appropriate regularization parameters is crucial. Information criteria such as generalized information criterion (GIC) and generalized Bayesian information criterion (GBIC) are useful for selecting the optimal regularization parameters. However, the optimal parameter is often determined by calculating information criterion for all candidate regularization parameters, and so the computational cost is high. One simple method by which to accomplish this is to regard GIC or GBIC as a function of the regularization parameters and to find a value minimizing GIC or GBIC. However, it is unclear how to solve the optimization problem. In the present article, we propose an efficient Newton–Raphson type iterative method for selecting optimal regularization parameters with respect to GIC or GBIC in a nonlinear regression model based on basis expansions. This method reduces the computational time remarkably compared to the grid search and can select more suitable regularization parameters. The effectiveness of the method is illustrated through real data examples.     

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.     

Maximum entropy sampling and optimal Bayesian experimental design

When Shannon entropy is used as a criterion in the optimal design of experiments, advantage can be taken of the classical identity representing the joint entropy of parameters and observations as the sum of the marginal entropy of the observations and the preposterior conditional entropy of the parameters. Following previous work in which this idea was used in spatial sampling, the method is applied to standard parameterized Bayesian optimal experimental design. Under suitable conditions, which include non-linear as well as linear regression models, it is shown in a few steps that maximizing the marginal entropy of the sample is equivalent to minimizing the preposterior entropy, the usual Bayesian criterion, thus avoiding the use of conditional distributions. It is shown using this marginal formulation that under normality assumptions every standard model which has a two-point prior distribution on the parameters gives an optimal design supported on a single point. Other results include a new asymptotic formula which applies as the error variance is large and bounds on support size.     

A clustering-based coordinate exchange algorithm for generating G-optimal experimental designs

In the optimal experimental design literature, the G-optimality is defined as minimizing the maximum prediction variance over the entire experimental design space. Although the G-optimality is a highly desirable property in many applications, there are few computer algorithms developed for constructing G-optimal designs. Some existing methods employ an exhaustive search over all candidate designs, which is time-consuming and inefficient. In this paper, a new algorithm for constructing G-optimal experimental designs is developed for both linear and generalized linear models. The new algorithm is made based on the clustering of candidate or evaluation points over the design space and it is a combination of point exchange algorithm and coordinate exchange algorithm. In addition, a robust design algorithm is proposed for generalized linear models with modification of an existing method. The proposed algorithm are compared with the methods proposed by Rodriguez et al. [Generating and assessing exact G-optimal designs. J. Qual. Technol. 2010;42(1):3–20] and Borkowski [Using a genetic algorithm to generate small exact response surface designs. J. Prob. Stat. Sci. 2003;1(1):65–88] for linear models and with the simulated annealing method and the genetic algorithm for generalized linear models through several examples in terms of the G-efficiency and computation time. The result shows that the proposed algorithm can obtain a design with higher G-efficiency in a much shorter time. Moreover, the computation time of the proposed algorithm only increases polynomially when the size of model increases.     

Thin plate regression splines

Summary. I discuss the production of low rank smoothers for d  ≥ 1 dimensional data, which can be fitted by regression or penalized regression methods. The smoothers are constructed by a simple transformation and truncation of the basis that arises from the solution of the thin plate spline smoothing problem and are optimal in the sense that the truncation is designed to result in the minimum possible perturbation of the thin plate spline smoothing problem given the dimension of the basis used to construct the smoother. By making use of Lanczos iteration the basis change and truncation are computationally efficient. The smoothers allow the use of approximate thin plate spline models with large data sets, avoid the problems that are associated with 'knot placement' that usually complicate modelling with regression splines or penalized regression splines, provide a sensible way of modelling interaction terms in generalized additive models, provide low rank approximations to generalized smoothing spline models, appropriate for use with large data sets, provide a means for incorporating smooth functions of more than one variable into non-linear models and improve the computational efficiency of penalized likelihood models incorporating thin plate splines. Given that the approach produces spline-like models with a sparse basis, it also provides a natural way of incorporating unpenalized spline-like terms in linear and generalized linear models, and these can be treated just like any other model terms from the point of view of model selection, inference and diagnostics.     

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.     

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

Summary.  Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models , where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.     

On the Choice of a Prior for Bayesian D-Optimal Designs for the Logistic Regression Model with a Single Predictor

The Bayesian design approach accounts for uncertainty of the parameter values on which optimal design depends, but Bayesian designs themselves depend on the choice of a prior distribution for the parameter values. This article investigates Bayesian D-optimal designs for two-parameter logistic models, using numerical search. We show three things: (1) a prior with large variance leads to a design that remains highly efficient under other priors, (2) uniform and normal priors lead to equally efficient designs, and (3) designs with four or five equidistant equally weighted design points are highly efficient relative to the Bayesian D-optimal designs.     

On Exact K-optimal Designs Minimizing the Condition Number

A new design criterion based on the condition number of an information matrix is proposed to construct optimal designs for linear models, and the resulting designs are called K-optimal designs. The relationship between exact and asymptotic K-optimal designs is derived. Since it is usually hard to find exact optimal designs analytically, we apply a simulated annealing algorithm to compute K-optimal design points on continuous design spaces. Specific issues are addressed to make the algorithm effective. Through exact designs, we can examine some properties of the K-optimal designs such as symmetry and the number of support points. Examples and results are given for polynomial regression models and linear models for fractional factorial experiments. In addition, K-optimal designs are compared with A-optimal and D-optimal designs for polynomial regression models, showing that K-optimal designs are quite similar to A-optimal designs.     

Bayesian optimal sequential design for nonparametric regression via inhomogeneous evolutionary MCMC

We develop a novel computational methodology for Bayesian optimal sequential design for nonparametric regression. This computational methodology, that we call inhomogeneous evolutionary Markov chain Monte Carlo, combines ideas of simulated annealing, genetic or evolutionary algorithms, and Markov chain Monte Carlo. Our framework allows optimality criteria with general utility functions and general classes of priors for the underlying regression function. We illustrate the usefulness of our novel methodology with applications to experimental design for nonparametric function estimation using Gaussian process priors and free-knot cubic splines priors.     

Bayesian and maximin optimal designs for heteroscedastic regression models

The authors consider the problem of constructing standardized maximin D‐optimal designs for weighted polynomial regression models. In particular they show that by following the approach to the construction of maximin designs introduced recently by Dette, Haines & Imhof (2003), such designs can be obtained as weak limits of the corresponding Bayesian _q‐optimal designs. They further demonstrate that the results are more broadly applicable to certain families of nonlinear models. The authors examine two specific weighted polynomial models in some detail and illustrate their results by means of a weighted quadratic regression model and the Bleasdale–Nelder model. They also present a capstone example involving a generalized exponential growth model.     

Posterior consistency of random effects models for binary data

In longitudinal studies or clustered designs, observations for each subject or cluster are dependent and exhibit intra-correlation. To account for this dependency, we consider Bayesian analysis for conditionally specified models, so-called generalized linear mixed model. In nonlinear mixed models, the maximum likelihood estimator of the regression coefficients is typically a function of the distribution of random effects, and so the misspecified choice of the distribution of random effects can cause bias in the estimator. To avoid the problem of the misspecification of the distribution of random effects, one can resort in nonparametric approaches. We give sufficient conditions for posterior consistency of the distribution of random effects as well as regression coefficients.     

An efficient Monte Carlo EM algorithm for Bayesian lasso

The lasso is a popular technique of simultaneous estimation and variable selection in many research areas. The marginal posterior mode of the regression coefficients is equivalent to estimates given by the non-Bayesian lasso when the regression coefficients have independent Laplace priors. Because of its flexibility of statistical inferences, the Bayesian approach is attracting a growing body of research in recent years. Current approaches are primarily to either do a fully Bayesian analysis using Markov chain Monte Carlo (MCMC) algorithm or use Monte Carlo expectation maximization (MCEM) methods with an MCMC algorithm in each E-step. However, MCMC-based Bayesian method has much computational burden and slow convergence. Tan et al. [An efficient MCEM algorithm for fitting generalized linear mixed models for correlated binary data. J Stat Comput Simul. 2007;77:929–943] proposed a non-iterative sampling approach, the inverse Bayes formula (IBF) sampler, for computing posteriors of a hierarchical model in the structure of MCEM. Motivated by their paper, we develop this IBF sampler in the structure of MCEM to give the marginal posterior mode of the regression coefficients for the Bayesian lasso, by adjusting the weights of importance sampling, when the full conditional distribution is not explicit. Simulation experiments show that the computational time is much reduced with our method based on the expectation maximization algorithm and our algorithms and our methods behave comparably with other Bayesian lasso methods not only in prediction accuracy but also in variable selection accuracy and even better especially when the sample size is relatively large.     

Constructing optimal designs for fitting pharmacokinetic models

We consider some computational issues that arise when searching for optimal designs for pharmacokinetic (PK) studies. Special factors that distinguish these are (i) repeated observations are taken from each subject and the observations are usually described by a nonlinear mixed model (NLMM), (ii) design criteria depend on the model fitting procedure, (iii) in addition to providing efficient parameter estimates, the design must also permit model checking, (iv) in practice there are several design constraints, (v) the design criteria are computationally expensive to evaluate and often numerical integration is needed and finally (vi) local optimisation procedures may fail to converge or get trapped at local optima.We review current optimal design algorithms and explore the possibility of using global optimisation procedures. We use these latter procedures to find some optimal designs.For multi-purpose designs we suggest two surrogate design criteria for model checking and illustrate their use.     

Optimal experimental design criterion for discriminating semiparametric models

This paper studies the optimal experimental design problem to discriminate two regression models. Recently, López-Fidalgo et al. [2007. An optimal experimental design criterion for discriminating between non-normal models. J. Roy. Statist. Soc. B 69, 231–242] extended the conventional T-optimality criterion by Atkinson and Fedorov [1975a. The designs of experiments for discriminating between two rival models. Biometrika 62, 57–70; 1975b. Optimal design: experiments for discriminating between several models. Biometrika 62, 289–303] to deal with non-normal parametric regression models, and proposed a new optimal experimental design criterion based on the Kullback–Leibler information divergence. In this paper, we extend their parametric optimality criterion to a semiparametric setup, where we only need to specify some moment conditions for the null or alternative regression model. Our criteria, called the semiparametric Kullback–Leibler optimality criteria, can be implemented by applying a convex duality result of partially finite convex programming. The proposed method is illustrated by a simple numerical example.     

Rational Regression Models with Continuous Chebyshev Design

In rational regression models, the G-optimal designs are very difficult to derive in general. Even when an G-optimal design can be found, it has, from the point of view of modern nonparametric regression, certain drawbacks because the optimal design crucially depends on the model. Hence, it can be used only when the model is given in advance. This leads to the problem of finding designs which would be nearly optimal for a broad class of rational regression models. In this article, we will show that the so-called continuous Chebyshev Design is a practical solution to this problem.     

A new characterization of Elfving's method for high dimensional computation

We give a new characterization of Elfving's (1952) method for computing c-optimal designs in k dimensions which gives explicit formulae for the k unknown optimal weights and k unknown signs in Elfving's characterization. This eliminates the need to search over these parameters to compute c-optimal designs, and thus reduces the computational burden from solving a family of optimization problems to solving a single optimization problem for the optimal finite support set. We give two illustrative examples: a high dimensional polynomial regression model and a logistic regression model, the latter showing that the method can be used for locally optimal designs in nonlinear models as well.     

Comparison between Bayesian approach and frequentist methods for estimating relative risk in randomized controlled trials: a simulation study

Relative risks (RRs) are often considered as preferred measures of association in randomized controlled trials especially when the binary outcome of interest is common. To directly estimate RRs, log-binomial regression has been recommended. Although log-binomial regression is a special case of generalized linear models, it does not respect the natural parameter constraints, and maximum likelihood estimation is often subject to numerical instability that leads to convergence problems. Alternative methods for solving log-binomial regression convergence problems have been proposed. A Bayesian approach also was introduced, but the comparison between this method and frequentist methods has not been fully explored. We compared five frequentist and one Bayesian methods for estimating RRs under a variety of scenario. Based on our simulation study, there is not a method that can perform well based on different statistical properties, but COPY 1000 and modified log-Poisson regression can be considered in practice.     

Fast Bayesian variable screenings for binary response regressions with small sample size

Screening procedures play an important role in data analysis, especially in high-throughput biological studies where the datasets consist of more covariates than independent subjects. In this article, a Bayesian screening procedure is introduced for the binary response models with logit and probit links. In contrast to many screening rules based on marginal information involving one or a few covariates, the proposed Bayesian procedure simultaneously models all covariates and uses closed-form screening statistics. Specifically, we use the posterior means of the regression coefficients as screening statistics; by imposing a generalized g-prior on the regression coefficients, we derive the analytical form of their posterior means and compute the screening statistics without Markov chain Monte Carlo implementation. We evaluate the utility of the proposed Bayesian screening method using simulations and real data analysis. When the sample size is small, the simulation results suggest improved performance with comparable computational cost.