Hierarchical modeling with gaussian processes

We formulate a hierarchical version of the Gaussian Process model. In particular, we assume there to be data on several units randomly drawn from the same population. For each unit, several responses are available that arise from a Gaussian Process model. The parameters characterizing the Gaussian Process model for the units are modeled to arise from normal or gamma distributions. Results for two simulations are given that compare the performance of the hierarchical and non-hierarchical models.     

Gaussian Process Models for Non Parametric Functional Regression with Functional Responses

Nonparametric functional model with functional responses has been proposed within the functional reproducing kernel Hilbert spaces (fRKHS) framework. Motivated by its superior performance and also its limitations, we propose a Gaussian process model whose posterior mode coincide with the fRKHS estimator. The Bayesian approach has several advantages compared to its predecessor. We also use the predictive process models adapted from the spatial statistics literature to overcome the computational limitations. Modifications of predictive process models are nevertheless critical in our context to obtain valid inferences. The numerical results presented demonstrate the effectiveness of the modifications.     

Hierarchical Bayesian modeling of marked non-homogeneous Poisson processes with finite mixtures and inclusion of covariate information

We investigate marked non-homogeneous Poisson processes using finite mixtures of bivariate normal components to model the spatial intensity function. We employ a Bayesian hierarchical framework for estimation of the parameters in the model, and propose an approach for including covariate information in this context. The methodology is exemplified through an application involving modeling of and inference for tornado occurrences.     

Probability density estimation via an infinite Gaussian mixture model: application to statistical process monitoring

Summary.  The primary goal of multivariate statistical process performance monitoring is to identify deviations from normal operation within a manufacturing process. The basis of the monitoring schemes is historical data that have been collected when the process is running under normal operating conditions. These data are then used to establish confidence bounds to detect the onset of process deviations. In contrast with the traditional approaches that are based on the Gaussian assumption, this paper proposes the application of the infinite Gaussian mixture model (GMM) for the calculation of the confidence bounds, thereby relaxing the previous restrictive assumption. The infinite GMM is a special case of Dirichlet process mixtures and is introduced as the limit of the finite GMM, i.e. when the number of mixtures tends to ∞. On the basis of the estimation of the probability density function, via the infinite GMM, the confidence bounds are calculated by using the bootstrap algorithm. The methodology proposed is demonstrated through its application to a simulated continuous chemical process, and a batch semiconductor manufacturing process.     

Bayesian Tobit quantile regression with single-index models

Based on the Bayesian framework of utilizing a Gaussian prior for the univariate nonparametric link function and an asymmetric Laplace distribution (ALD) for the residuals, we develop a Bayesian treatment for the Tobit quantile single-index regression model (TQSIM). With the location-scale mixture representation of the ALD, the posterior inferences of the latent variables and other parameters are achieved via the Markov Chain Monte Carlo computation method. TQSIM broadens the scope of applicability of the Tobit models by accommodating nonlinearity in the data. The proposed method is illustrated by two simulation examples and a labour supply dataset.     

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.     

Fitting Gaussian Markov Random Fields to Gaussian Fields

This paper discusses the following task often encountered in building Bayesian spatial models: construct a homogeneous Gaussian Markov random field (GMRF) on a lattice with correlation properties either as present in some observed data, or consistent with prior knowledge. The Markov property is essential in designing computationally efficient Markov chain Monte Carlo algorithms to analyse such models. We argue that we can restate both tasks as that of fitting a GMRF to a prescribed stationary Gaussian field on a lattice when both local and global properties are important. We demonstrate that using the KullbackLeibler discrepancy often fails for this task, giving severely undesirable behaviour of the correlation function for lags outside the neighbourhood. We propose a new criterion that resolves this difficulty, and demonstrate that GMRFs with small neighbourhoods can approximate Gaussian fields surprisingly well even with long correlation lengths. Finally, we discuss implications of our findings for likelihood based inference for general Markov random fields when global properties are also important.     

Adaptive multiple importance sampling for Gaussian processes

In applications of Gaussian processes (GPs) where quantification of uncertainty is a strict requirement, it is necessary to accurately characterize the posterior distribution over Gaussian process covariance parameters. This is normally done by means of standard Markov chain Monte Carlo (MCMC) algorithms, which require repeated expensive calculations involving the marginal likelihood. Motivated by the desire to avoid the inefficiencies of MCMC algorithms rejecting a considerable amount of expensive proposals, this paper develops an alternative inference framework based on adaptive multiple importance sampling (AMIS). In particular, this paper studies the application of AMIS for GPs in the case of a Gaussian likelihood, and proposes a novel pseudo-marginal-based AMIS algorithm for non-Gaussian likelihoods, where the marginal likelihood is unbiasedly estimated. The results suggest that the proposed framework outperforms MCMC-based inference of covariance parameters in a wide range of scenarios.     

Hierarchical priors for Bayesian CART shrinkage

The Bayesian CART (classification and regression tree) approach proposed by Chipman, George and McCulloch (1998) entails putting a prior distribution on the set of all CART models and then using stochastic search to select a model. The main thrust of this paper is to propose a new class of hierarchical priors which enhance the potential of this Bayesian approach. These priors indicate a preference for smooth local mean structure, resulting in tree models which shrink predictions from adjacent terminal node towards each other. Past methods for tree shrinkage have searched for trees without shrinking, and applied shrinkage to the identified tree only after the search. By using hierarchical priors in the stochastic search, the proposed method searches for shrunk trees that fit well and improves the tree through shrinkage of predictions.     

Approximating hidden Gaussian Markov random fields

Summary.  Gaussian Markov random-field (GMRF) models are frequently used in a wide variety of applications. In most cases parts of the GMRF are observed through mutually independent data; hence the full conditional of the GMRF, a hidden GMRF (HGMRF), is of interest. We are concerned with the case where the likelihood is non-Gaussian, leading to non-Gaussian HGMRF models. Several researchers have constructed block sampling Markov chain Monte Carlo schemes based on approximations of the HGMRF by a GMRF, using a second-order expansion of the log-density at or near the mode. This is possible as the GMRF approximation can be sampled exactly with a known normalizing constant. The Markov property of the GMRF approximation yields computational efficiency.The main contribution in the paper is to go beyond the GMRF approximation and to construct a class of non-Gaussian approximations which adapt automatically to the particular HGMRF that is under study. The accuracy can be tuned by intuitive parameters to nearly any precision. These non-Gaussian approximations share the same computational complexity as those which are based on GMRFs and can be sampled exactly with computable normalizing constants. We apply our approximations in spatial disease mapping and model-based geostatistical models with different likelihoods, obtain procedures for block updating and construct Metropolized independence samplers.     

Nonparametric survival regression using the beta-Stacy process

A novel class of hierarchical nonparametric Bayesian survival regression models for time-to-event data with uninformative right censoring is introduced. The survival curve is modeled as a random function whose prior distribution is defined using the beta-Stacy (BS) process. The prior mean of each survival probability and its prior variance are linked to a standard parametric survival regression model. This nonparametric survival regression can thus be anchored to any reference parametric form, such as a proportional hazards or an accelerated failure time model, allowing substantial departures of the predictive survival probabilities when the reference model is not supported by the data. Also, under this formulation the predictive survival probabilities will be close to the empirical survival distribution near the mode of the reference model and they will be shrunken towards its probability density in the tails of the empirical distribution.     

On population-based simulation for static inference

In this paper we present a review of population-based simulation for static inference problems. Such methods can be described as generating a collection of random variables {X _n } _n=1,…,N in parallel in order to simulate from some target density π (or potentially sequence of target densities). Population-based simulation is important as many challenging sampling problems in applied statistics cannot be dealt with successfully by conventional Markov chain Monte Carlo (MCMC) methods. We summarize population-based MCMC (Geyer, Computing Science and Statistics: The 23rd Symposium on the Interface, pp. 156–163, 1991; Liang and Wong, J. Am. Stat. Assoc. 96, 653–666, 2001) and sequential Monte Carlo samplers (SMC) (Del Moral, Doucet and Jasra, J. Roy. Stat. Soc. Ser. B 68, 411–436, 2006a), providing a comparison of the approaches. We give numerical examples from Bayesian mixture modelling (Richardson and Green, J. Roy. Stat. Soc. Ser. B 59, 731–792, 1997).     

A hierarchical Bayesian regression model for the uncertain functional constraint using screened scale mixtures of Gaussian distributions

This paper considers a hierarchical Bayesian analysis of regression models using a class of Gaussian scale mixtures. This class provides a robust alternative to the common use of the Gaussian distribution as a prior distribution in particular for estimating the regression function subject to uncertainty about the constraint. For this purpose, we use a family of rectangular screened multivariate scale mixtures of Gaussian distribution as a prior for the regression function, which is flexible enough to reflect the degrees of uncertainty about the functional constraint. Specifically, we propose a hierarchical Bayesian regression model for the constrained regression function with uncertainty on the basis of three stages of a prior hierarchy with Gaussian scale mixtures, referred to as a hierarchical screened scale mixture of Gaussian regression models (HSMGRM). We describe distributional properties of HSMGRM and an efficient Markov chain Monte Carlo algorithm for posterior inference, and apply the proposed model to real applications with constrained regression models subject to uncertainty.     

Bayesian outlier analysis in binary regression

We propose alternative approaches to analyze residuals in binary regression models based on random effect components. Our preferred model does not depend upon any tuning parameter, being completely automatic. Although the focus is mainly on accommodation of outliers, the proposed methodology is also able to detect them. Our approach consists of evaluating the posterior distribution of random effects included in the linear predictor. The evaluation of the posterior distributions of interest involves cumbersome integration, which is easily dealt with through stochastic simulation methods. We also discuss different specifications of prior distributions for the random effects. The potential of these strategies is compared in a real data set. The main finding is that the inclusion of extra variability accommodates the outliers, improving the adjustment of the model substantially, besides correctly indicating the possible outliers.     

Curve prediction and clustering with mixtures of Gaussian process functional regression models

Shi, Wang, Murray-Smith and Titterington (Biometrics 63:714–723, 2007) proposed a Gaussian process functional regression (GPFR) model to model functional response curves with a set of functional covariates. Two main problems are addressed by their method: modelling nonlinear and nonparametric regression relationship and modelling covariance structure and mean structure simultaneously. The method gives very good results for curve fitting and prediction but side-steps the problem of heterogeneity. In this paper we present a new method for modelling functional data with ‘spatially’ indexed data, i.e., the heterogeneity is dependent on factors such as region and individual patient’s information. For data collected from different sources, we assume that the data corresponding to each curve (or batch) follows a Gaussian process functional regression model as a lower-level model, and introduce an allocation model for the latent indicator variables as a higher-level model. This higher-level model is dependent on the information related to each batch. This method takes advantage of both GPFR and mixture models and therefore improves the accuracy of predictions. The mixture model has also been used for curve clustering, but focusing on the problem of clustering functional relationships between response curve and covariates, i.e. the clustering is based on the surface shape of the functional response against the set of functional covariates. The model is examined on simulated data and real data.     

Bayesian model-averaged regularization for Gaussian graphical models

The graphical lasso has now become a useful tool to estimate high-dimensional Gaussian graphical models, but its practical applications suffer from the problem of choosing regularization parameters in a data-dependent way. In this article, we propose a model-averaged method for estimating sparse inverse covariance matrices for Gaussian graphical models. We consider the graphical lasso regularization path as the model space for Bayesian model averaging and use Markov chain Monte Carlo techniques for the regularization path point selection. Numerical performance of our method is investigated using both simulated and real datasets, in comparison with some state-of-art model selection procedures.     

A variable selection approach to monotonic regression with Bernstein polynomials

One of the standard problems in statistics consists of determining the relationship between a response variable and a single predictor variable through a regression function. Background scientific knowledge is often available that suggests that the regression function should have a certain shape (e.g. monotonically increasing or concave) but not necessarily a specific parametric form. Bernstein polynomials have been used to impose certain shape restrictions on regression functions. The Bernstein polynomials are known to provide a smooth estimate over equidistant knots. Bernstein polynomials are used in this paper due to their ease of implementation, continuous differentiability, and theoretical properties. In this work, we demonstrate a connection between the monotonic regression problem and the variable selection problem in the linear model. We develop a Bayesian procedure for fitting the monotonic regression model by adapting currently available variable selection procedures. We demonstrate the effectiveness of our method through simulations and the analysis of real data.     

Hierarchical random effect models for coastal erosion of cliffs in the Holderness coast

Prediction of possible cliff erosion at some future date is fundamental to coastal planning and shoreline management, for example to avoid development in vulnerable areas. Historically, to predict cliff recession rates deterministic methods were used. More recently, recession predictions have been expressed in probabilistic terms. However, to date, only simplistic models have been developed. We consider the cliff erosion along the Holderness Coast. Since 1951 a monitoring program has been started in 118 stations along the coast, providing an invaluable, but often missing, source of information. We build hierarchical random effect models, taking account of the known dynamics of the process and including the missing information.     

Smooth estimates of normal mixtures

Posterior distributions for mixture models often have multiple modes, particularly near the boundaries of the parameter space where the component variances are small. This multimodality results in predictive densities that are extremely rough. The authors propose an adjustment of the standard normal‐inverse‐gamma prior structure that directly controls the ratio of the largest component variance to the smallest component variance. The prior adjustment smooths out modes near the boundary of the parameter space, producing more reasonable estimates of the predictive density.