The Bayesian elastic net regression

A Bayesian elastic net approach is presented for variable selection and coefficient estimation in linear regression models. A simple Gibbs sampling algorithm was developed for posterior inference using a location-scale mixture representation of the Bayesian elastic net prior for the regression coefficients. The penalty parameters are chosen through an empirical method that maximizes the data marginal likelihood. Both simulated and real data examples show that the proposed method performs well in comparison to the other approaches.     

Bayesian Elastic Net Tobit Quantile Regression

In this article, the problem of parameter estimation and variable selection in the Tobit quantile regression model is considered. A Tobit quantile regression with the elastic net penalty from a Bayesian perspective is proposed. Independent gamma priors are put on the l₁ norm penalty parameters. A novel aspect of the Bayesian elastic net Tobit quantile regression is to treat the hyperparameters of the gamma priors as unknowns and let the data estimate them along with other parameters. A Bayesian Tobit quantile regression with the adaptive elastic net penalty is also proposed. The Gibbs sampling computational technique is adapted to simulate the parameters from the posterior distributions. The proposed methods are demonstrated by both simulated and real data examples.     

A note on the posterior inference for the Yule–Simon distribution

The Yule–Simon distribution has been out of the radar of the Bayesian community, so far. In this note, we propose an explicit Gibbs sampling scheme when a Gamma prior is chosen for the shape parameter. The performance of the algorithm is illustrated with simulation studies, including count data regression, and a real data application to text analysis. We compare our proposal to the frequentist counterparts showing better performance of our algorithm when a small sample size is considered.     

Bayesian Transformation Models for Multivariate Survival Data

In this paper, we propose a general class of Gamma frailty transformation models for multivariate survival data. The transformation class includes the commonly used proportional hazards and proportional odds models. The proposed class also includes a family of cure rate models. Under an improper prior for the parameters, we establish propriety of the posterior distribution. A novel Gibbs sampling algorithm is developed for sampling from the observed data posterior distribution. A simulation study is conducted to examine the properties of the proposed methodology. An application to a data set from a cord blood transplantation study is also reported.     

Gibbs sampling methods for Bayesian quantile regression

This paper considers quantile regression models using an asymmetric Laplace distribution from a Bayesian point of view. We develop a simple and efficient Gibbs sampling algorithm for fitting the quantile regression model based on a location-scale mixture representation of the asymmetric Laplace distribution. It is shown that the resulting Gibbs sampler can be accomplished by sampling from either normal or generalized inverse Gaussian distribution. We also discuss some possible extensions of our approach, including the incorporation of a scale parameter, the use of double exponential prior, and a Bayesian analysis of Tobit quantile regression. The proposed methods are illustrated by both simulated and real data.     

Exact sampling of the unobserved covariates in Bayesian spline models for measurement error problems

In truncated polynomial spline or B-spline models where the covariates are measured with error, a fully Bayesian approach to model fitting requires the covariates and model parameters to be sampled at every Markov chain Monte Carlo iteration. Sampling the unobserved covariates poses a major computational problem and usually Gibbs sampling is not possible. This forces the practitioner to use a Metropolis–Hastings step which might suffer from unacceptable performance due to poor mixing and might require careful tuning. In this article we show for the cases of truncated polynomial spline or B-spline models of degree equal to one, the complete conditional distribution of the covariates measured with error is available explicitly as a mixture of double-truncated normals, thereby enabling a Gibbs sampling scheme. We demonstrate via a simulation study that our technique performs favorably in terms of computational efficiency and statistical performance. Our results indicate up to 62 and 54 % increase in mean integrated squared error efficiency when compared to existing alternatives while using truncated polynomial splines and B-splines respectively. Furthermore, there is evidence that the gain in efficiency increases with the measurement error variance, indicating the proposed method is a particularly valuable tool for challenging applications that present high measurement error. We conclude with a demonstration on a nutritional epidemiology data set from the NIH-AARP study and by pointing out some possible extensions of the current work.     

Adaptive sampling for Bayesian geospatial models

Bayesian hierarchical modeling with Gaussian process random effects provides a popular approach for analyzing point-referenced spatial data. For large spatial data sets, however, generic posterior sampling is infeasible due to the extremely high computational burden in decomposing the spatial correlation matrix. In this paper, we propose an efficient algorithm—the adaptive griddy Gibbs (AGG) algorithm—to address the computational issues with large spatial data sets. The proposed algorithm dramatically reduces the computational complexity. We show theoretically that the proposed method can approximate the real posterior distribution accurately. The sufficient number of grid points for a required accuracy has also been derived. We compare the performance of AGG with that of the state-of-the-art methods in simulation studies. Finally, we apply AGG to spatially indexed data concerning building energy consumption.     

Bayesian multiple change-point estimation for exponential distribution with truncated and censored data

This paper considers the multiple change-point estimation for exponential distribution with truncated and censored data by Gibbs sampling. After all the missing data of interest is filled in by some sampling methods such as rejection sampling method, the complete-data likelihood function is obtained. The full conditional distributions of all parameters are discussed. The means of Gibbs samples are taken as Bayesian estimations of the parameters. The implementation steps of Gibbs sampling are introduced in detail. Finally random simulation test is developed, and the results show that Bayesian estimations are fairly accurate.     

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.     

On the grouped selection and model complexity of the adaptive elastic net

Lasso proved to be an extremely successful technique for simultaneous estimation and variable selection. However lasso has two major drawbacks. First, it does not enforce any grouping effect and secondly in some situation lasso solutions are inconsistent for variable selection. To overcome this inconsistency adaptive lasso is proposed where adaptive weights are used for penalizing different coefficients. Recently a doubly regularized technique namely elastic net is proposed which encourages grouping effect i.e. either selection or omission of the correlated variables together. However elastic net is also inconsistent. In this paper we study adaptive elastic net which does not have this drawback. In this article we specially focus on the grouped selection property of adaptive elastic net along with its model selection complexity. We also shed some light on the bias-variance tradeoff of different regularization methods including adaptive elastic net. An efficient algorithm was proposed in the line of LARS-EN, which is then illustrated with simulated as well as real life data examples.     

Bayesian semiparametric reproductive dispersion mixed models for non-normal longitudinal data: estimation and case influence analysis

Semiparametric reproductive dispersion mixed model (SPRDMM) is a natural extension of the reproductive dispersion model and the semiparametric mixed model. In this paper, we relax the normality assumption of random effects in SPRDMM and use a truncated and centred Dirichlet process prior to specify random effects, and present the Bayesian P-spline to approximate the smoothing unknown function. A hybrid algorithm combining the block Gibbs sampler and the Metropolis–Hastings algorithm is implemented to sample observations from the posterior distribution. Also, we develop Bayesian case deletion influence measure for SPRDMM based on the φ-divergence and present those computationally feasible formulas. Several simulation studies and a real example are presented to illustrate the proposed methodologies.     

INFERENCE IN DIRICHLET PROCESS MIXED GENERALIZED LINEAR MODELS BY USING MONTE CARLO EM

Generalized linear mixed models are widely used for describing overdispersed and correlated data. Such data arise frequently in studies involving clustered and hierarchical designs. A more flexible class of models has been developed here through the Dirichlet process mixture. An additional advantage of using such mixture models is that the observations can be grouped together on the basis of the overdispersion present in the data. This paper proposes a partial empirical Bayes method for estimating all the model parameters by adopting a version of the EM algorithm. An augmented model that helps to implement an efficient Gibbs sampling scheme, under the non‐conjugate Dirichlet process generalized linear model, generates observations from the conditional predictive distribution of unobserved random effects and provides an estimate of the average number of mixing components in the Dirichlet process mixture. A simulation study has been carried out to demonstrate the consistency of the proposed method. The approach is also applied to a study on outdoor bacteria concentration in the air and to data from 14 retrospective lung‐cancer studies.     

Bayesian inference for the randomly censored Weibull distribution

In this paper, we consider the Bayesian inference of the unknown parameters of the randomly censored Weibull distribution. A joint conjugate prior on the model parameters does not exist; we assume that the parameters have independent gamma priors. Since closed-form expressions for the Bayes estimators cannot be obtained, we use Lindley's approximation, importance sampling and Gibbs sampling techniques to obtain the approximate Bayes estimates and the corresponding credible intervals. A simulation study is performed to observe the behaviour of the proposed estimators. A real data analysis is presented for illustrative purposes.     

A Bayesian multiple comparison procedure for simply ordered treatment medians

This article considers a Bayesian hierarchical model for multiple comparisons in linear models where the population medians satisfy a simple order restriction. Representing the asymmetric Laplace distribution as a scale mixture of normals with an exponential mixing density and a continuous prior restricted to order constraints, a Gibbs sampling algorithm for parameter estimation and simultaneous comparison of treatment medians is proposed. Posterior probabilities of all possible hypotheses on the equality/inequality of treatment medians are estimated using Bayes factors that are computed via the Savage-Dickey density ratios. The performance of the proposed median-based model is investigated in the simulated and real datasets. The results show that the proposed method can outperform the commonly used method that is based on treatment means, when data are from nonnormal distributions.     

A semiparametric Bayesian approach to simplex regression model with heterogeneous dispersion

ABSTRACT

Simplex regression model is often employed to analyze continuous proportion data in many studies. In this paper, we extend the assumption of a constant dispersion parameter (homogeneity) to varying dispersion parameter (heterogeneity) in Simplex regression model, and present the B-spline to approximate the smoothing unknown function within the Bayesian framework. A hybrid algorithm combining the block Gibbs sampler and the Metropolis-Hastings algorithm is presented for sampling observations from the posterior distribution. The procedures for computing model comparison criteria such as conditional predictive ordinate statistic, deviance information criterion, and averaged mean squared error are presented. Also, we develop a computationally feasible Bayesian case-deletion influence measure based on the Kullback-Leibler divergence. Several simulation studies and a real example are employed to illustrate the proposed methodologies.     

Time truncated attribute control chart for the Weibull distribution using multiple dependent state sampling

In this article, an attribute control chart is proposed for time truncated tests using the Weibull distribution. The design of proposed control chart is presented using the multiple dependent state (MDS) sampling. The control chart coefficients are determined for various specified average run length. The efficiency of the proposed control chart is elaborated with the help of a simulation data and a real data. The proposed control chart perform better than the existing control chart in terms of average run length.     

Bayesian bridge-randomized penalized quantile regression estimation for linear regression model with AP(q) perturbation

Bridge penalized regression has many desirable statistical properties such as unbiasedness, sparseness as well as ‘oracle’. In Bayesian framework, bridge regularized penalty can be implemented based on generalized Gaussian distribution (GGD) prior. In this paper, we incorporate Bayesian bridge-randomized penalty and its adaptive version into the quantile regression (QR) models with autoregressive perturbations to conduct Bayesian penalization estimation. Employing the working likelihood of the asymmetric Laplace distribution (ALD) perturbations, the Bayesian joint hierarchical models are established. Based on the mixture representations of the ALD and generalized Gaussian distribution (GGD) priors of coefficients, the hybrid algorithms based on Gibbs sampler and Metropolis-Hasting sampler are provided to conduct fully Bayesian posterior estimation. Finally, the proposed Bayesian procedures are illustrated by some simulation examples and applied to a real data application of the electricity consumption.     

Bayesian elastic net single index quantile regression

Single index model conditional quantile regression is proposed in order to overcome the dimensionality problem in nonparametric quantile regression. In the proposed method, the Bayesian elastic net is suggested for single index quantile regression for estimation and variables selection. The Gaussian process prior is considered for unknown link function and a Gibbs sampler algorithm is adopted for posterior inference. The results of the simulation studies and numerical example indicate that our propose method, BENSIQReg, offers substantial improvements over two existing methods, SIQReg and BSIQReg. The BENSIQReg has consistently show a good convergent property, has the least value of median of mean absolute deviations and smallest standard deviations, compared to the other two methods.     

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 quantile regression for ordinal longitudinal data

Since the pioneering work by Koenker and Bassett [27], quantile regression models and its applications have become increasingly popular and important for research in many areas. In this paper, a random effects ordinal quantile regression model is proposed for analysis of longitudinal data with ordinal outcome of interest. An efficient Gibbs sampling algorithm was derived for fitting the model to the data based on a location-scale mixture representation of the skewed double-exponential distribution. The proposed approach is illustrated using simulated data and a real data example. This is the first work to discuss quantile regression for analysis of longitudinal data with ordinal outcome.