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 semiparametric accelerated failure time model for arbitrarily censored data with covariates subject to measurement error

A flexible Bayesian semiparametric accelerated failure time (AFT) model is proposed for analyzing arbitrarily censored survival data with covariates subject to measurement error. Specifically, the baseline error distribution in the AFT model is nonparametrically modeled as a Dirichlet process mixture of normals. Classical measurement error models are imposed for covariates subject to measurement error. An efficient and easy-to-implement Gibbs sampler, based on the stick-breaking formulation of the Dirichlet process combined with the techniques of retrospective and slice sampling, is developed for the posterior calculation. An extensive simulation study is conducted to illustrate the advantages of our approach.     

Topics on Dynamic Panel Data Models with Random Effects Using Semi-Parametric Bayesian Approach

A common assumption in fitting panel data models is normality of stochastic subject effects. This can be extremely restrictive, making vague most potential features of true distributions. The objective of this article is to propose a modeling strategy, from a semi-parametric Bayesian perspective, to specify a flexible distribution for the random effects in dynamic panel data models. This is addressed here by assuming the Dirichlet process mixture model to introduce Dirichlet process prior for the random-effects distribution. We address the role of initial conditions in dynamic processes, emphasizing on joint modeling of start-up and subsequent responses. We adopt Gibbs sampling techniques to approximate posterior estimates. These important topics are illustrated by a simulation study and also by testing hypothetical models in two empirical contexts drawn from economic studies. We use modified versions of information criteria to compare the fitted models.     

Bayesian nonparametric survival analysis using mixture of Burr XII distributions

ABSTRACT

Recently, the Bayesian nonparametric approaches in survival studies attract much more attentions. Because of multimodality in survival data, the mixture models are very common. We introduce a Bayesian nonparametric mixture model with Burr distribution (Burr type XII) as the kernel. Since the Burr distribution shares good properties of common distributions on survival analysis, it has more flexibility than other distributions. By applying this model to simulated and real failure time datasets, we show the preference of this model and compare it with Dirichlet process mixture models with different kernels. The Markov chain Monte Carlo (MCMC) simulation methods to calculate the posterior distribution are used.     

A comparison of nonparametric priors in hierarchical mixture modelling for AFT regression

We will pursue a Bayesian nonparametric approach in the hierarchical mixture modelling of lifetime data in two situations: density estimation, when the distribution is a mixture of parametric densities with a nonparametric mixing measure, and accelerated failure time (AFT) regression modelling, when the same type of mixture is used for the distribution of the error term. The Dirichlet process is a popular choice for the mixing measure, yielding a Dirichlet process mixture model for the error; as an alternative, we also allow the mixing measure to be equal to a normalized inverse-Gaussian prior, built from normalized inverse-Gaussian finite dimensional distributions, as recently proposed in the literature. Markov chain Monte Carlo techniques will be used to estimate the predictive distribution of the survival time, along with the posterior distribution of the regression parameters. A comparison between the two models will be carried out on the grounds of their predictive power and their ability to identify the number of components in a given mixture density.     

Bayesian semiparametric modeling and inference with mixtures of?symmetric distributions

We propose a semiparametric modeling approach for mixtures of symmetric distributions. The mixture model is built from a common symmetric density with different components arising through different location parameters. This structure ensures identifiability for mixture components, which is a key feature of the model as it allows applications to settings where primary interest is inference for the subpopulations comprising the mixture. We focus on the two-component mixture setting and develop a Bayesian model using parametric priors for the location parameters and for the mixture proportion, and a nonparametric prior probability model, based on Dirichlet process mixtures, for the random symmetric density. We present an approach to inference using Markov chain Monte Carlo posterior simulation. The performance of the model is studied with a simulation experiment and through analysis of a rainfall precipitation data set as well as with data on eruptions of the Old Faithful geyser.     

Bayesian semiparametric modeling for stochastic precedence,with applications in epidemiology and survival analysis

We propose a prior probability model for two distributions that are ordered according to a stochastic precedence constraint, a weaker restriction than the more commonly utilized stochastic order constraint. The modeling approach is based on structured Dirichlet process mixtures of normal distributions. Full inference for functionals of the stochastic precedence constrained mixture distributions is obtained through a Markov chain Monte Carlo posterior simulation method. A motivating application involves study of the discriminatory ability of continuous diagnostic tests in epidemiologic research. Here, stochastic precedence provides a natural restriction for the distributions of test scores corresponding to the non-infected and infected groups. Inference under the model is illustrated with data from a diagnostic test for Johne’s disease in dairy cattle. We also apply the methodology to the comparison of survival distributions associated with two distinct conditions, and illustrate with analysis of data on survival time after bone marrow transplantation for treatment of leukemia.     

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.     

Bayesian non-parametric modeling for integro-difference equations

Integro-difference equations (IDEs) provide a flexible framework for dynamic modeling of spatio-temporal data. The choice of kernel in an IDE model relates directly to the underlying physical process modeled, and it can affect model fit and predictive accuracy. We introduce Bayesian non-parametric methods to the IDE literature as a means to allow flexibility in modeling the kernel. We propose a mixture of normal distributions for the IDE kernel, built from a spatial Dirichlet process for the mixing distribution, which can model kernels with shapes that change with location. This allows the IDE model to capture non-stationarity with respect to location and to reflect a changing physical process across the domain. We address computational concerns for inference that leverage the use of Hermite polynomials as a basis for the representation of the process and the IDE kernel, and incorporate Hamiltonian Markov chain Monte Carlo steps in the posterior simulation method. An example with synthetic data demonstrates that the model can successfully capture location-dependent dynamics. Moreover, using a data set of ozone pressure, we show that the spatial Dirichlet process mixture model outperforms several alternative models for the IDE kernel, including the state of the art in the IDE literature, that is, a Gaussian kernel with location-dependent parameters.     

On the Posterior Consistency of Mixtures of Dirichlet Process Priors with Censored Data

Mixtures of Dirichlet process priors offer a reasonable compromise between purely parametric and purely non‐parametric models, and are popularly used in survival analysis and for testing problems with non‐parametric alternatives. In this paper, we study large sample properties of the posterior distribution with a mixture of Dirichlet process priors. We show that the posterior distribution of the survival function is consistent with right censored data.     

Bayesian mixture modeling for spatial Poisson process intensities,with applications to extreme value analysis

We propose a method for the analysis of a spatial point pattern, which is assumed to arise as a set of observations from a spatial nonhomogeneous Poisson process. The spatial point pattern is observed in a bounded region, which, for most applications, is taken to be a rectangle in the space where the process is defined. The method is based on modeling a density function, defined on this bounded region, that is directly related with the intensity function of the Poisson process. We develop a flexible nonparametric mixture model for this density using a bivariate Beta distribution for the mixture kernel and a Dirichlet process prior for the mixing distribution. Using posterior simulation methods, we obtain full inference for the intensity function and any other functional of the process that might be of interest. We discuss applications to problems where inference for clustering in the spatial point pattern is of interest. Moreover, we consider applications of the methodology to extreme value analysis problems. We illustrate the modeling approach with three previously published data sets. Two of the data sets are from forestry and consist of locations of trees. The third data set consists of extremes from the Dow Jones index over a period of 1303 days.     

Nonparametric hierarchical Bayes analysis of binomial data via Bernstein polynomial priors

For binomial data analysis, many methods based on empirical Bayes interpretations have been developed, in which a variance‐stabilizing transformation and a normality assumption are usually required. To achieve the greatest model flexibility, we conduct nonparametric Bayesian inference for binomial data and employ a special nonparametric Bayesian prior—the Bernstein–Dirichlet process (BDP)—in the hierarchical Bayes model for the data. The BDP is a special Dirichlet process (DP) mixture based on beta distributions, and the posterior distribution resulting from it has a smooth density defined on [0, 1]. We examine two Markov chain Monte Carlo procedures for simulating from the resulting posterior distribution, and compare their convergence rates and computational efficiency. In contrast to existing results for posterior consistency based on direct observations, the posterior consistency of the BDP, given indirect binomial data, is established. We study shrinkage effects and the robustness of the BDP‐based posterior estimators in comparison with several other empirical and hierarchical Bayes estimators, and we illustrate through examples that the BDP‐based nonparametric Bayesian estimate is more robust to the sample variation and tends to have a smaller estimation error than those based on the DP prior. In certain settings, the new estimator can also beat Stein's estimator, Efron and Morris's limited‐translation estimator, and many other existing empirical Bayes estimators. The Canadian Journal of Statistics 40: 328–344; 2012 © 2012 Statistical Society of Canada     

Bayesian analysis of mixture modelling using the multivariate t distribution

A finite mixture model using the multivariate t distribution has been shown as a robust extension of normal mixtures. In this paper, we present a Bayesian approach for inference about parameters of t-mixture models. The specifications of prior distributions are weakly informative to avoid causing nonintegrable posterior distributions. We present two efficient EM-type algorithms for computing the joint posterior mode with the observed data and an incomplete future vector as the sample. Markov chain Monte Carlo sampling schemes are also developed to obtain the target posterior distribution of parameters. The advantages of Bayesian approach over the maximum likelihood method are demonstrated via a set of real data.     

Bayesian Nonparametric Instrumental Variables Regression Based on Penalized Splines and Dirichlet Process Mixtures

We propose a Bayesian nonparametric instrumental variable approach under additive separability that allows us to correct for endogeneity bias in regression models where the covariate effects enter with unknown functional form. Bias correction relies on a simultaneous equations specification with flexible modeling of the joint error distribution implemented via a Dirichlet process mixture prior. Both the structural and instrumental variable equation are specified in terms of additive predictors comprising penalized splines for nonlinear effects of continuous covariates. Inference is fully Bayesian, employing efficient Markov chain Monte Carlo simulation techniques. The resulting posterior samples do not only provide us with point estimates, but allow us to construct simultaneous credible bands for the nonparametric effects, including data-driven smoothing parameter selection. In addition, improved robustness properties are achieved due to the flexible error distribution specification. Both these features are challenging in the classical framework, making the Bayesian one advantageous. In simulations, we investigate small sample properties and an investigation of the effect of class size on student performance in Israel provides an illustration of the proposed approach which is implemented in an R package bayesIV. Supplementary materials for this article are available online.     

Nonparametric Bayesian Analysis of Competing Risks Problem with Masked Data

Bayesian analysis of system failure data under a competing-failure framework is considered when the failure causes have not been exactly identified but narrowed down to a subset of all potential failure causes. The usual assumption of independence of failure causes is relaxed. We obtain the posterior distribution of the joint survival function, assuming a Dirichlet process prior, and derive the limiting posterior distribution. We show that the posterior estimate of the reliability of the series system of interest in practice is consistent. A numerical example shows that our approach is feasible.     

Multiple Imputation of Missing or Faulty Values Under Linear Constraints

Many statistical agencies, survey organizations, and research centers collect data that suffer from item nonresponse and erroneous or inconsistent values. These data may be required to satisfy linear constraints, for example, bounds on individual variables and inequalities for ratios or sums of variables. Often these constraints are designed to identify faulty values, which then are blanked and imputed. The data also may exhibit complex distributional features, including nonlinear relationships and highly nonnormal distributions. We present a fully Bayesian, joint model for modeling or imputing data with missing/blanked values under linear constraints that (i) automatically incorporates the constraints in inferences and imputations, and (ii) uses a flexible Dirichlet process mixture of multivariate normal distributions to reflect complex distributional features. Our strategy for estimation is to augment the observed data with draws from a hypothetical population in which the constraints are not present, thereby taking advantage of computationally expedient methods for fitting mixture models. Missing/blanked items are sampled from their posterior distribution using the Hit-and-Run sampler, which guarantees that all imputations satisfy the constraints. We illustrate the approach using manufacturing data from Colombia, examining the potential to preserve joint distributions and a regression from the plant productivity literature. Supplementary materials for this article are available online.     

The Bernstein–von Mises theorem in semiparametric competing risks models

Semiparametric Bayesian models are nowadays a popular tool in event history analysis. An important area of research concerns the investigation of frequentist properties of posterior inference. In this paper, we propose novel semiparametric Bayesian models for the analysis of competing risks data and investigate the Bernstein–von Mises theorem for differentiable functionals of model parameters. The model is specified by expressing the cause-specific hazard as the product of the conditional probability of a failure type and the overall hazard rate. We take the conditional probability as a smooth function of time and leave the cumulative overall hazard unspecified. A prior distribution is defined on the joint parameter space, which includes a beta process prior for the cumulative overall hazard. We first develop the large-sample properties of maximum likelihood estimators by giving simple sufficient conditions for them to hold. Then, we show that, under the chosen priors, the posterior distribution for any differentiable functional of interest is asymptotically equivalent to the sampling distribution derived from maximum likelihood estimation. A simulation study is provided to illustrate the coverage properties of credible intervals on cumulative incidence functions.     

Bayesian Semiparametric Modelling in Quantile Regression

Abstract. We propose a Bayesian semiparametric methodology for quantile regression modelling. In particular, working with parametric quantile regression functions, we develop Dirichlet process mixture models for the error distribution in an additive quantile regression formulation. The proposed non‐parametric prior probability models allow the shape of the error density to adapt to the data and thus provide more reliable predictive inference than models based on parametric error distributions. We consider extensions to quantile regression for data sets that include censored observations. Moreover, we employ dependent Dirichlet processes to develop quantile regression models that allow the error distribution to change non‐parametrically with the covariates. Posterior inference is implemented using Markov chain Monte Carlo methods. We assess and compare the performance of our models using both simulated and real data sets.     

Bayesian quantile regression for single-index models

Using an asymmetric Laplace distribution, which provides a mechanism for Bayesian inference of quantile regression models, we develop a fully Bayesian approach to fitting single-index models in conditional quantile regression. In this work, we use a Gaussian process prior for the unknown nonparametric link function and a Laplace distribution on the index vector, with the latter motivated by the recent popularity of the Bayesian lasso idea. We design a Markov chain Monte Carlo algorithm for posterior inference. Careful consideration of the singularity of the kernel matrix, and tractability of some of the full conditional distributions leads to a partially collapsed approach where the nonparametric link function is integrated out in some of the sampling steps. Our simulations demonstrate the superior performance of the Bayesian method versus the frequentist approach. The method is further illustrated by an application to the hurricane data.     

A Bayesian nonparametric Markovian model for non-stationary time series

Stationary time series models built from parametric distributions are, in general, limited in scope due to the assumptions imposed on the residual distribution and autoregression relationship. We present a modeling approach for univariate time series data, which makes no assumptions of stationarity, and can accommodate complex dynamics and capture non-standard distributions. The model for the transition density arises from the conditional distribution implied by a Bayesian nonparametric mixture of bivariate normals. This results in a flexible autoregressive form for the conditional transition density, defining a time-homogeneous, non-stationary Markovian model for real-valued data indexed in discrete time. To obtain a computationally tractable algorithm for posterior inference, we utilize a square-root-free Cholesky decomposition of the mixture kernel covariance matrix. Results from simulated data suggest that the model is able to recover challenging transition densities and non-linear dynamic relationships. We also illustrate the model on time intervals between eruptions of the Old Faithful geyser. Extensions to accommodate higher order structure and to develop a state-space model are also discussed.