Bayesian gamma frailty models for survival data with semi-competing risks and treatment switching

Motivated from a colorectal cancer study, we propose a class of frailty semi-competing risks survival models to account for the dependence between disease progression time, survival time, and treatment switching. Properties of the proposed models are examined and an efficient Gibbs sampling algorithm using the collapsed Gibbs technique is developed. A Bayesian procedure for assessing the treatment effect is also proposed. The deviance information criterion (DIC) with an appropriate deviance function and Logarithm of the pseudomarginal likelihood (LPML) are constructed for model comparison. A simulation study is conducted to examine the empirical performance of DIC and LPML and as well as the posterior estimates. The proposed method is further applied to analyze data from a colorectal cancer study.     

A Class of Multidimensional Latent Class IRT Models for Ordinal Polytomous Item Responses

We propose a class of multidimensional Item Response Theory models for polytomously-scored items with ordinal response categories. This class extends an existing class of multidimensional models for dichotomously-scored items in which the latent abilities are represented by a random vector assumed to have a discrete distribution, with support points corresponding to different latent classes in the population. In the proposed approach, we allow for different parameterizations for the conditional distribution of the response variables given the latent traits, which depend on the type of link function and the constraints imposed on the item parameters. Moreover, we suggest a strategy for model selection that is based on a series of steps consisting of selecting specific features, such as the dimension of the model (number of latent traits), the number of latent classes, and the specific parameterization. In order to illustrate the proposed approach, we analyze a dataset from a study on anxiety and depression on a sample of oncological patients.     

Bayesian covariance estimation and inference in latent Gaussian process models

This paper describes inference methods for functional data under the assumption that the functional data of interest are smooth latent functions, characterized by a Gaussian process, which have been observed with noise over a finite set of time points. The methods we propose are completely specified in a Bayesian environment that allows for all inferences to be performed through a simple Gibbs sampler. Our main focus is in estimating and describing uncertainty in the covariance function. However, these models also encompass functional data estimation, functional regression where the predictors are latent functions, and an automatic approach to smoothing parameter selection. Furthermore, these models require minimal assumptions on the data structure as the time points for observations do not need to be equally spaced, the number and placement of observations are allowed to vary among functions, and special treatment is not required when the number of functional observations is less than the dimensionality of those observations. We illustrate the effectiveness of these models in estimating latent functional data, capturing variation in the functional covariance estimate, and in selecting appropriate smoothing parameters in both a simulation study and a regression analysis of medfly fertility data.     

Bayesian spatial prediction of skew and censored data via a hybrid algorithm

A correct detection of areas with excess of pollution relies first on accurate predictions of pollutant concentrations, a task that is usually complicated by skewed histograms and the presence of censored data. The unified skew-Gaussian (SUG) random field proposed by Zareifard and Jafari Khaledi [19] offers a more flexible class of sampling spatial models to account for skewness. In this paper, we adopt a Bayesian framework to perform prediction for the SUG model in the presence of censored data. Owing to the presence of many latent variables with strongly dependent components in the model, we encounter convergence issues when using Monte Carlo Markov Chain algorithms. To overcome this obstacle, we use a computationally efficient inverse Bayes formulas sampling procedure to obtain approximately independent samples from the posterior distribution of latent variables. Then they are applied to update parameters in a Gibbs sampler scheme. This hybrid algorithm provides effective samples, resulting in some computational advantages and precise predictions. The proposed approach is illustrated with a simulation study and applied to a spatial data set which contains right censored data.     

Efficient MCMC sampling in dynamic mixture models

We show how to improve the efficiency of Markov Chain Monte Carlo (MCMC) simulations in dynamic mixture models by block-sampling the discrete latent variables. Two algorithms are proposed: the first is a multi-move extension of the single-move Gibbs sampler devised by Gerlach, Carter and Kohn (in J. Am. Stat. Assoc. 95, 819–828, 2000); the second is an adaptive Metropolis-Hastings scheme that performs well even when the number of discrete states is large. Three empirical examples illustrate the gain in efficiency achieved. We also show that visual inspection of sample partial autocorrelations of the discrete latent variables helps anticipating whether blocking can be effective.     

A Bayesian multivariate partially linear single-index probit model for ordinal responses

Combining the multivariate probit models with the multivariate partially linear single-index models, we propose new semiparametric latent variable models for multivariate ordinal response data. Based on the reversible jump Markov chain Monte Carlo technique, we develop a fully Bayesian method with free-knot splines to analyse the proposed models. To address the problem that the ordinary Gibbs sampler usually converges slowly, we make use of the partial-collapse and parameter-expansion techniques in our algorithm. The proposed methodology are demonstrated by simulated and real data examples.     

Bayesian variable selection and estimation in maximum entropy quantile regression

Quantile regression has gained increasing popularity as it provides richer information than the regular mean regression, and variable selection plays an important role in the quantile regression model building process, as it improves the prediction accuracy by choosing an appropriate subset of regression predictors. Unlike the traditional quantile regression, we consider the quantile as an unknown parameter and estimate it jointly with other regression coefficients. In particular, we adopt the Bayesian adaptive Lasso for the maximum entropy quantile regression. A flat prior is chosen for the quantile parameter due to the lack of information on it. The proposed method not only addresses the problem about which quantile would be the most probable one among all the candidates, but also reflects the inner relationship of the data through the estimated quantile. We develop an efficient Gibbs sampler algorithm and show that the performance of our proposed method is superior than the Bayesian adaptive Lasso and Bayesian Lasso through simulation studies and a real data analysis.     

Nonparametric binary regression using a Gaussian process prior

The article describes a nonparametric Bayesian approach to estimating the regression function for binary response data measured with multiple covariates. A multiparameter Gaussian process, after some transformation, is used as a prior on the regression function. Such a prior does not require any assumptions like monotonicity or additivity of the covariate effects. However, additivity, if desired, may be imposed through the selection of appropriate parameters of the prior. By introducing some latent variables, the conditional distributions in the posterior may be shown to be conjugate, and thus an efficient Gibbs sampler to compute the posterior distribution may be developed. A hierarchical scheme to construct a prior around a parametric family is described. A robustification technique to protect the resulting Bayes estimator against miscoded observations is also designed. A detailed simulation study is conducted to investigate the performance of the proposed methods. We also analyze some real data using the methods developed in this article.     

Bayesian factor analysis for spatially correlated data: application to cancer incidence data in Scotland

A hierarchical Bayesian factor model for multivariate spatially correlated data is proposed. Multiple cancer incidence data in Scotland are jointly analyzed, looking for common components, able to detect etiological factors of diseases hidden behind the data. The proposed method searches factor scores incorporating a dependence within observations due to a geographical structure. The great flexibility of the Bayesian approach allows the inclusion of prior opinions about adjacent regions having highly correlated observable and latent variables. The proposed model is an extension of a model proposed by Rowe (2003a) and starts from the introduction of separable covariance matrix for the observations. A Gibbs sampling algorithm is implemented to sample from the posterior distributions.     

Latent class models for financial data analysis: some statistical developments

I exploit the potential of latent class models for proposing an innovative framework for financial data analysis. By stressing the latent nature of the most important financial variables, expected return and risk, I am able to introduce a new methodological dimension in the analysis of financial phenomena. In my proposal, (i) I provide innovative measures of expected return and risk, (ii) I suggest a financial data classification consistent with the latent risk-return profile, and (iii) I propose a set of statistical methods for detecting and testing the number of groups of the new data classification. The results lead to an improvement in both risk measurement theory and practice and, if compared to traditional methods, allow for new insights into the analysis of financial data. Finally, I illustrate the potentiality of my proposal by investigating the European stock market and detailing the steps for the appropriate choice of a financial portfolio.     

Trace Class Markov Chains for Bayesian Inference with Generalized Double Pareto Shrinkage Priors

Bayesian shrinkage methods have generated a lot of interest in recent years, especially in the context of high‐dimensional linear regression. In recent work, a Bayesian shrinkage approach using generalized double Pareto priors has been proposed. Several useful properties of this approach, including the derivation of a tractable three‐block Gibbs sampler to sample from the resulting posterior density, have been established. We show that the Markov operator corresponding to this three‐block Gibbs sampler is not Hilbert–Schmidt. We propose a simpler two‐block Gibbs sampler and show that the corresponding Markov operator is trace class (and hence Hilbert–Schmidt). Establishing the trace class property for the proposed two‐block Gibbs sampler has several useful consequences. Firstly, it implies that the corresponding Markov chain is geometrically ergodic, thereby implying the existence of a Markov chain central limit theorem, which in turn enables computation of asymptotic standard errors for Markov chain‐based estimates of posterior quantities. Secondly, because the proposed Gibbs sampler uses two blocks, standard recipes in the literature can be used to construct a sandwich Markov chain (by inserting an appropriate extra step) to gain further efficiency and to achieve faster convergence. The trace class property for the two‐block sampler implies that the corresponding sandwich Markov chain is also trace class and thereby geometrically ergodic. Finally, it also guarantees that all eigenvalues of the sandwich chain are dominated by the corresponding eigenvalues of the Gibbs sampling chain (with at least one strict domination). Our results demonstrate that a minor change in the structure of a Markov chain can lead to fundamental changes in its theoretical properties. We illustrate the improvement in efficiency resulting from our proposed Markov chains using simulated and real examples.     

Latent variable models with ordinal categorical covariates

We propose a general latent variable model for multivariate ordinal categorical variables, in which both the responses and the covariates are ordinal, to assess the effect of the covariates on the responses and to model the covariance structure of the response variables. A?fully Bayesian approach is employed to analyze the model. The Gibbs sampler is used to simulate the joint posterior distribution of the latent variables and the parameters, and the parameter expansion and reparameterization techniques are used to speed up the convergence procedure. The proposed model and method are demonstrated by simulation studies and a real data example.     

Latent single-index models for ordinal data

We propose a latent semi-parametric model for ordinal data in which the single-index model is used to evaluate the effects of the latent covariates on the latent response. We develop a Bayesian sampling-based method with free-knot splines to analyze the proposed model. As the index may vary from minus infinity to plus infinity, the traditional spline that is defined on a finite interval cannot be applied directly to approximate the unknown link function. We consider a modified version to address this problem by first transforming the index into the unit interval via a continuously cumulative distribution function and then constructing the spline bases on the unit interval. To obtain a rapidly convergent algorithm, we make use of the partial collapse and parameter expansion and reparameterization techniques, improve the movement step of Bayesian splines with free knots so that all the knots can be relocated each time instead of only one knot, and design a generalized Gibbs step. We check the performance of the proposed model and estimation method by a simulation study and apply them to analyze a real dataset.     

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.     

Hierarchical bayes quality measurement plan

Quality Measurement Plan (QMP) as developed by Hoadley (1981) is a statistical method for analyzing discrete quality audit data which consist of the expected number of defects given the standard quality. The QMP is based on an empirical Bayes (EB) model of the audit sampling process. Despite its wide publicity, Hoadley's method has often been described as heuristic. In this paper we offer an hierarchical Bayes (HB) alternative to Hoadley's EB model, and overcome much of the criticism against this model. Gibbs sampling is used to implement the HB model proposed in this paper. Also, the convergence of the Gibbs sampler is monitored via the algorithm of Gelman and Rubin (1992).     

Inference for low- and high-dimensional inhomogeneous Gibbs point processes

Gibbs point processes (GPPs) constitute a large and flexible class of spatial point processes with explicit dependence between the points. They can model attractive as well as repulsive point patterns. Feature selection procedures are an important topic in high-dimensional statistical modeling. In this paper, a composite likelihood (in particular pseudo-likelihood) approach regularized with convex and nonconvex penalty functions is proposed to handle statistical inference for possibly high-dimensional inhomogeneous GPPs. We particularly investigate the setting where the number of covariates diverges as the domain of observation increases. Under some conditions provided on the spatial GPP and on penalty functions, we show that the oracle property, consistency and asymptotic normality hold. Our results also cover the low-dimensional case which fills a large gap in the literature. Through simulation experiments, we validate our theoretical results and finally, an application to a tropical forestry dataset illustrates the use of the proposed approach.     

Simple Computation of Maximum Likelihood Estimates in Latent Class Model with Equality and Constant Constraints

A simple computational method for estimation of parameters via a type of EM algorithm is proposed in restricted latent class analysis, where equality and constant constraints are considered. These constraints create difficulty in estimation. In order to simply and stably estimate parameters in restricted latent class analysis, a simple computational method using only first-order differentials is proposed, where the step-halving method is adopted. A simulation study shows that in almost all cases the new method gives parameter sequences monotonously increasing the Q-function in the EM algorithm. Analysis of real data is provided.     

基于贝叶斯方法的比例数据分位数推断及其应用

为了尝试使用贝叶斯方法研究比例数据的分位数回归统计推断问题,首先基于Tobit模型给出了分位数回归建模方法,然后通过选取合适的先验分布得到了贝叶斯层次模型,进而给出了各参数的后验分布并用于Gibbs抽样。数值模拟分析验证了所提出的贝叶斯推断方法对于比例数据分析的有效性。最后,将贝叶斯方法应用于美国加州海洛因吸毒数据,在不同的分位数水平下揭示了吸毒频率的影响因素。     

Reparameterizing the generalized linear model to accelerate gibbs sampler convergence

Albert and Chib introduced a complete Bayesian method to analyze data arising from the generalized linear model in which they used the Gibbs sampling algorithm facilitated by latent variables. Recently, Cowles proposed an alternative algorithm to accelerate the convergence of the Albert-Chib algorithm. The novelty in this latter algorithm is achieved by using a Hastings algorithm to generate latent variables and bin boundary parameters jointly instead of individually from their respective full conditionals. In the same spirit, we reparameterize the cumulative-link generalized linear model to accelerate the convergence of Cowles’ algorithm even further. One important advantage of our method is that for the three-bin problem it does not require the Hastings algorithm. In addition, for problems with more than three bins, while the Hastings algorithm is required, we provide a proposal density based on the Dirichlet distribution which is more natural than the truncated normal density used in the competing algorithm. Also, using diagnostic procedures recommended in the literature for the Markov chain Monte Carlo algorithm (both single and multiple runs) we show that our algorithm is substantially better than the one recently obtained. Precisely, our algorithm provides faster convergence and smaller autocorrelations between the iterates. Using the probit link function, extensive results are obtained for the three-bin and the five-bin multinomial ordinal data problems.     

Mixture models, latent variables and partitioned importance sampling

Gibbs sampling has had great success in the analysis of mixture models. In particular, the “latent variable” formulation of the mixture model greatly reduces computational complexity. However, one failing of this approach is the possible existence of almost-absorbing states, called trapping states, as it may require an enormous number of iterations to escape from these states. Here we examine an alternative approach to estimation in mixture models, one based on a Rao–Blackwellization argument applied to a latent-variable-based estimator. From this derivation we construct an alternative Monte Carlo sampling scheme that avoids trapping states.