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.     

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.     

Bayesian adjustment for unidirectional misclassification in ordinal covariates

In this paper, we study the identification of Bayesian regression models, when an ordinal covariate is subject to unidirectional misclassification. Xia and Gustafson [Bayesian regression models adjusting for unidirectional covariate misclassification. Can J Stat. 2016;44(2):198–218] obtained model identifiability for non-binary regression models, when there is a binary covariate subject to unidirectional misclassification. In the current paper, we establish the moment identifiability of regression models for misclassified ordinal covariates with more than two categories, based on forms of observable moments. Computational studies are conducted that confirm the theoretical results. We apply the method to two datasets, one from the Medical Expenditure Panel Survey (MEPS), and the other from Translational Research Investigating Underlying Disparities in Acute Myocardial infarction Patients Health Status (TRIUMPH).     

Hierarchical Bayesian meta-analysis models for cross-platform microarray studies

The development of new technologies to measure gene expression has been calling for statistical methods to integrate findings across multiple-platform studies. A common goal of microarray analysis is to identify genes with differential expression between two conditions, such as treatment versus control. Here, we introduce a hierarchical Bayesian meta-analysis model to pool gene expression studies from different microarray platforms: spotted DNA arrays and short oligonucleotide arrays. The studies have different array design layouts, each with multiple sources of data replication, including repeated experiments, slides and probes. Our model produces the gene-specific posterior probability of differential expression, which is the basis for inference. In simulations combining two and five independent studies, our meta-analysis model outperformed separate analyses for three commonly used comparison measures; it also showed improved receiver operating characteristic curves. When combining spotted DNA and CombiMatrix short oligonucleotide array studies of Geobacter sulfurreducens, our meta-analysis model discovered more genes for fixed thresholds of posterior probability of differential expression and Bayesian false discovery than individual study analyses. We also examine an alternative model and compare models using the deviance information criterion.     

A Robust Conflict Measure of Inconsistencies in Bayesian Hierarchical Models

Abstract.  O'Hagan ( Highly Structured Stochastic Systems , Oxford University Press, Oxford, 2003) introduces some tools for criticism of Bayesian hierarchical models that can be applied at each node of the model, with a view to diagnosing problems of model fit at any point in the model structure. His method relies on computing the posterior median of a conflict index, typically through Markov chain Monte Carlo simulations. We investigate a Gaussian model of one-way analysis of variance, and show that O'Hagan's approach gives unreliable false warning probabilities. We extend and refine the method, especially avoiding double use of data by a data-splitting approach, accompanied by theoretical justifications from a non-trivial special case. Through extensive numerical experiments we show that our method detects model mis-specification about as well as the method of O'Hagan, while retaining the desired false warning probability for data generated from the assumed model. This also holds for Student's- t and uniform distribution versions of the model.     

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.     

Bayesian inversion of geoelectrical resistivity data

Summary. Enormous quantities of geoelectrical data are produced daily and often used for large scale reservoir modelling. To interpret these data requires reliable and efficient inversion methods which adequately incorporate prior information and use realistically complex modelling structures. We use models based on random coloured polygonal graphs as a powerful and flexible modelling framework for the layered composition of the Earth and we contrast our approach with earlier methods based on smooth Gaussian fields. We demonstrate how the reconstruction algorithm may be efficiently implemented through the use of multigrid Metropolis–coupled Markov chain Monte Carlo methods and illustrate the method on a set of field data.     

Flexible Bayesian Modelling for Survival Data

The analysis of failure time data often involves two strong assumptions. The proportional hazards assumption postulates that hazard rates corresponding to different levels of explanatory variables are proportional. The additive effects assumption specifies that the effect associated with a particular explanatory variable does not depend on the levels of other explanatory variables. A hierarchical Bayes model is presented, under which both assumptions are relaxed. In particular, time-dependent covariate effects are explicitly modelled, and the additivity of effects is relaxed through the use of a modified neural network structure. The hierarchical nature of the model is useful in that it parsimoniously penalizes violations of the two assumptions, with the strength of the penalty being determined by the data.     

Bayesian Bandwidth Estimation in Nonparametric Time-Varying Coefficient Models

Bandwidth plays an important role in determining the performance of nonparametric estimators, such as the local constant estimator. In this article, we propose a Bayesian approach to bandwidth estimation for local constant estimators of time-varying coefficients in time series models. We establish a large sample theory for the proposed bandwidth estimator and Bayesian estimators of the unknown parameters involved in the error density. A Monte Carlo simulation study shows that (i) the proposed Bayesian estimators for bandwidth and parameters in the error density have satisfactory finite sample performance; and (ii) our proposed Bayesian approach achieves better performance in estimating the bandwidths than the normal reference rule and cross-validation. Moreover, we apply our proposed Bayesian bandwidth estimation method for the time-varying coefficient models that explain Okun’s law and the relationship between consumption growth and income growth in the U.S. For each model, we also provide calibrated parametric forms of the time-varying coefficients. Supplementary materials for this article are available online.     

Bayesian Estimators for Small Area Models when Auxiliary Information is Measured with Error

Small area estimators in linear models are typically expressed as a convex combination of direct estimators and synthetic estimators from a suitable model. When auxiliary information used in the model is measured with error, a new estimator, accounting for the measurement error in the covariates, has been proposed in the literature. Recently, for area‐level model, Ybarra & Lohr (Biometrika, 95, 2008, 919) suggested a suitable modification to the estimates of small area means based on Fay & Herriot (J. Am. Stat. Assoc., 74, 1979, 269) model where some of the covariates are measured with error. They used a frequentist approach based on the method of moments. Adopting a Bayesian approach, we propose to rewrite the measurement error model as a hierarchical model; we use improper non‐informative priors on the model parameters and show, under a mild condition, that the joint posterior distribution is proper and the marginal posterior distributions of the model parameters have finite variances. We conduct a simulation study exploring different scenarios. The Bayesian predictors we propose show smaller empirical mean squared errors than the frequentist predictors of Ybarra & Lohr (Biometrika, 95, 2008, 919), and they seem also to be more stable in terms of variability and bias. We apply the proposed methodology to two real examples.     

Bayesian inference for semiparametric regression using a Fourier representation

This paper presents the Bayesian analysis of a semiparametric regression model that consists of parametric and nonparametric components. The nonparametric component is represented with a Fourier series where the Fourier coefficients are assumed a priori to have zero means and to decay to 0 in probability at either algebraic or geometric rates. The rate of decay controls the smoothness of the response function. The posterior analysis automatically selects the amount of smoothing that is coherent with the model and data. Posterior probabilities of the parametric and semiparametric models provide a method for testing the parametric model against a non-specific alternative. The Bayes estimator's mean integrated squared error compares favourably with the theoretically optimal estimator for kernel regression.     

A Bayesian prediction using the skew Gaussian distribution

A model based on the skew Gaussian distribution is presented to handle skewed spatial data. It extends the results of popular Gaussian process models. Markov chain Monte Carlo techniques are used to generate samples from the posterior distributions of the parameters. Finally, this model is applied in the spatial prediction of weekly rainfall. Cross-validation shows that the predictive performance of our model compares favorably with several kriging variants.     

Bayesian tests for unit root and multiple breaks

A Bayesian approach is considered for identifying sources of nonstationarity for models with a unit root and breaks. Different types of multiple breaks are allowed through crash models, changing growth models, and mixed models. All possible nonstationary models are represented by combinations of zero or nonzero parameters associated with time trends, dummy for breaks, or previous levels, for which Bayesian posterior probabilities are computed. Multiple tests based on Markov chain Monte Carlo procedures are implemented. The proposed method is applied to a real data set, the Korean GDP data set, showing a strong evidence for two breaks rather than the usual unit root or one break.     

Equilibrium dynamics of ice streams: a Bayesian statistical analysis

Studies of the behaviors of glaciers, ice sheets, and ice streams rely heavily on both observations and physical models. Data acquired via remote sensing provide critical information on geometry and movement of ice over large sections of Antarctica and Greenland. However, uncertainties are present in both the observations and the models. Hence, there is a need for combining these information sources in a fashion that incorporates uncertainty and quantifies its impact on conclusions. We present a hierarchical Bayesian approach to modeling ice-stream velocities incorporating physical models and observations regarding velocity, ice thickness, and surface elevation from the North East Ice Stream in Greenland. The Bayesian model leads to interesting issues in model assessment and computation.     

Extensions of a Conflict Measure of Inconsistencies in Bayesian Hierarchical Models

Abstract.  In a recent paper we extended and refined some tools introduced by O'Hagan for criticism of Bayesian hierarchical models. Especially, avoiding double use of data by a data-splitting approach was a main concern. Such tools can be applied at each node of the model, with a view to diagnosing problems of model fit at any point in the model structure. As O'Hagan, we investigated a Gaussian model of one-way analysis of variance. Through extensive Markov chain Monte Carlo simulations it was shown that our method detects model misspecification about as well as the one of O'Hagan, when this is properly calibrated, while retaining the desired false warning probability for data generated from the assumed model. In the present paper, we suggest some new measures of conflict based on tail probabilities of the so-called integrated posterior distributions introduced in our recent paper. These new measures are equivalent to the measure applied in the latter paper in simple Gaussian models, but seem more appropriately adjusted to deviations from normality and to conflicts not concerning location parameters. A general linear normal model with known covariance matrices is considered in detail.     

Bayesian inference for generalized extreme value distributions via Hamiltonian Monte Carlo

In this article, we propose to evaluate and compare Markov chain Monte Carlo (MCMC) methods to estimate the parameters in a generalized extreme value model. We employed the Bayesian approach using traditional Metropolis-Hastings methods, Hamiltonian Monte Carlo (HMC), and Riemann manifold HMC (RMHMC) methods to obtain the approximations to the posterior marginal distributions of interest. Applications to real datasets and simulation studies provide evidence that the extra analytical work involved in Hamiltonian Monte Carlo algorithms is compensated by a more efficient exploration of the parameter space.     

Caries on Permanent Teeth: A Non-parametric Bayesian Analysis

Most earlier epidemiological investigations of dental caries have been based on cross-sectional data. Subject-specific information of dental caries in the past, and the duration of exposure of each tooth to the oral environment, are obviously important factors also influencing the presence of dental caries in the future. This has led us to consider multivariate survival models in which the information about the tooth eruption and failure times are combined to assess caries risk. A non-parametric Bayesian intensity model is presented, reflecting, on the one hand, the within subject and between subject sources of variability, and a corresponding split of variability when considering the 28 permanent teeth. We analyse a data set consisting of the dental history of 240 boys, where the observations are based on predetermined dental examinations taking place approximately once every year. Markov chain Monte Carlo integration techniques are applied in the numerical work.     

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.