Non-parametric Bayesian Estimation of a Spatial Poisson Intensity

A method introduced by Arjas & Gasbarra (1994) and later modified by Arjas & Heikkinen (1997) for the non-parametric Bayesian estimation of an intensity on the real line is generalized to cover spatial processes. The method is based on a model approximation where the approximating intensities have the structure of a piecewise constant function. Random step functions on the plane are generated using Voronoi tessellations of random point patterns. Smoothing between nearby intensity values is applied by means of a Markov random field prior in the spirit of Bayesian image analysis. The performance of the method is illustrated in examples with both real and simulated data.     

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 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.     

Bayesian analysis of mortality data

Congdon argued that the use of parametric modelling of mortality data is necessary in many practical demographical problems. In this paper, we focus on a form of model introduced by Heligman and Pollard in 1980, and we adopt a Bayesian analysis, using Markov chain Monte Carlo simulation, to produce the posterior summaries required. This opens the way to richer, more flexible inference summaries and avoids the numerical problems that are encountered with classical methods. Particular methodologies to cope with incomplete life-tables and a derivation of joint lifetimes, median times to death and related quantities of interest are also presented.     

Bayesian semi-parametric analysis of Poisson change-point regression models: application to policy-making in Cali,Colombia

A Poisson regression model with an offset assumes a constant baseline rate after accounting for measured covariates, which may lead to biased estimates of coefficients in an inhomogeneous Poisson process. To correctly estimate the effect of time-dependent covariates, we propose a Poisson change-point regression model with an offset that allows a time-varying baseline rate. When the non-constant pattern of a log baseline rate is modeled with a non-parametric step function, the resulting semi-parametric model involves a model component of varying dimensions and thus requires a sophisticated varying-dimensional inference to obtain the correct estimates of model parameters of a fixed dimension. To fit the proposed varying-dimensional model, we devise a state-of-the-art Markov chain Monte Carlo-type algorithm based on partial collapse. The proposed model and methods are used to investigate the association between the daily homicide rates in Cali, Colombia, and the policies that restrict the hours during which the legal sale of alcoholic beverages is permitted. While simultaneously identifying the latent changes in the baseline homicide rate which correspond to the incidence of sociopolitical events, we explore the effect of policies governing the sale of alcohol on homicide rates and seek a policy that balances the economic and cultural dependencies on alcohol sales to the health of the public.     

Bayesian discrete latent spatial modeling of crack initiation in orthopaedic hip replacement bone cement

In this paper, we propose a spatial model for the initiation of cracks in the bone cement of hip replacement specimens. The failure of hip replacements can be attributed mainly to damage accumulation, consisting of crack initiation and growth, occurring in the cement mantle that interlocks the hip prosthesis and the femur bone. Since crack initiation is an important factor in determining the lifetime of a replacement, the understanding of the reasons for crack initiation is vital in attempting to prolong the life of the hip replacement. The data consist of crack location coordinates from five laboratory experimental models, together with stress measurements. It is known that stress plays a major role in the initiation of cracks, and it is also known that other unmeasurable factors such as air bubbles (pores) in the cement mantle are also influential. We propose an identity-link spatial Poisson regression model for the counts of cracks in discrete regions of the cement, incorporating both the measured (stress), and through a latent process, any unmeasured factors (possibly pores) that may be influential. All analysis is carried out in a Bayesian framework, allowing for the inclusion of prior information obtained from engineers, and parameter estimation for the model is done via Markov chain Monte Carlo techniques.     

Bayesian inference in hidden Markov models through the reversible jump Markov chain Monte Carlo method

Hidden Markov models form an extension of mixture models which provides a flexible class of models exhibiting dependence and a possibly large degree of variability. We show how reversible jump Markov chain Monte Carlo techniques can be used to estimate the parameters as well as the number of components of a hidden Markov model in a Bayesian framework. We employ a mixture of zero-mean normal distributions as our main example and apply this model to three sets of data from finance, meteorology and geomagnetism.     

Parallelizing MCMC for Bayesian spatiotemporal geostatistical models

When MCMC methods for Bayesian spatiotemporal modeling are applied to large geostatistical problems, challenges arise as a consequence of memory requirements, computing costs, and convergence monitoring. This article describes the parallelization of a reparametrized and marginalized posterior sampling (RAMPS) algorithm, which is carefully designed to generate posterior samples efficiently. The algorithm is implemented using the Parallel Linear Algebra Package (PLAPACK). The scalability of the algorithm is investigated via simulation experiments that are implemented using a cluster with 25 processors. The usefulness of the method is illustrated with an application to sulfur dioxide concentration data from the Air Quality System database of the U.S. Environmental Protection Agency.     

Bayesian analysis of two overdispersed poisson regression models

Shookri and Consul (1989) and Scollnik (1995) have previously considered the Bayesian analysis of an overdispersed generalized Poisson model. Scollnik (1995) also considered the Bayesian analysis of an ordinary Poisson and over-dispersed generalized Poisson mixture model. In this paper, we discuss the Bayesian analysis of these models when they are utilised in a regression context. Markov chain Monte Carlo methods are utilised, and an illustrative analysis is provided.     

Efficient Bayesian Multivariate Surface Regression

Methods for choosing a fixed set of knot locations in additive spline models are fairly well established in the statistical literature. The curse of dimensionality makes it nontrivial to extend these methods to nonadditive surface models, especially when there are more than a couple of covariates. We propose a multivariate Gaussian surface regression model that combines both additive splines and interactive splines, and a highly efficient Markov chain Monte Carlo algorithm that updates all the knot locations jointly. We use shrinkage prior to avoid overfitting with different estimated shrinkage factors for the additive and surface part of the model, and also different shrinkage parameters for the different response variables. Simulated data and an application to firm leverage data show that the approach is computationally efficient, and that allowing for freely estimated knot locations can offer a substantial improvement in out‐of‐sample predictive performance.     

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.     

Bayesian analysis of directed graphs data with applications to social networks

Summary.  A fully Bayesian analysis of directed graphs, with particular emphasis on applica- tions in social networks, is explored. The model is capable of incorporating the effects of covariates, within and between block ties and multiple responses. Inference is straightforward by using software that is based on Markov chain Monte Carlo methods. Examples are provided which highlight the variety of data sets that can be entertained and the ease with which they can be analysed.     

Bayesian expectile regression with asymmetric normal distribution

In this paper, we adopt the Bayesian approach to expectile regression employing a likelihood function that is based on an asymmetric normal distribution. We demonstrate that improper uniform priors for the unknown model parameters yield a proper joint posterior. Three simulated data sets were generated to evaluate the proposed method which show that Bayesian expectile regression performs well and has different characteristics comparing with Bayesian quantile regression. We also apply this approach into two real data analysis.     

On the performance of the Bayesian composite likelihood estimation of max-stable processes

The max-stable process is a natural approach for modelling extrenal dependence in spatial data. However, the estimation is difficult due to the intractability of the full likelihoods. One approach that can be used to estimate the posterior distribution of the parameters of the max-stable process is to employ composite likelihoods in the Markov chain Monte Carlo (MCMC) samplers, possibly with adjustment of the credible intervals. In this paper, we investigate the performance of the composite likelihood-based MCMC samplers under various settings of the Gaussian extreme value process and the Brown–Resnick process. Based on our findings, some suggestions are made to facilitate the application of this estimator in real data.     

Bayesian inference for non-Gaussian Ornstein–Uhlenbeck stochastic volatility processes

Summary.  We develop Markov chain Monte Carlo methodology for Bayesian inference for non-Gaussian Ornstein–Uhlenbeck stochastic volatility processes. The approach introduced involves expressing the unobserved stochastic volatility process in terms of a suitable marked Poisson process. We introduce two specific classes of Metropolis–Hastings algorithms which correspond to different ways of jointly parameterizing the marked point process and the model parameters. The performance of the methods is investigated for different types of simulated data. The approach is extended to consider the case where the volatility process is expressed as a superposition of Ornstein–Uhlenbeck processes. We apply our methodology to the US dollar–Deutschmark exchange rate.     

A simple method for finding a legal configuration in complex Bayesian networks

This paper deals with an important problem with large and complex Bayesian networks. Exact inference in these networks is simply not feasible owing to the huge storage requirements of exact methods. Markov chain Monte Carlo methods, however, are able to deal with these large networks but to do this they require an initial legal configuration to set off the sampler. So far nondeterministic methods such as forward sampling have often been used for this, even though the forward sampler may take an eternity to come up with a legal configuration. In this paper a novel algorithm will be presented that allows a legal configuration in a general Bayesian network to be found in polynomial time in almost all cases. The algorithm will not be proved deterministic but empirical results will demonstrate that this holds in most cases. Also, the algorithm will be justified by its simplicity and ease of implementation.     

A geometric approach to transdimensional markov chain monte carlo

The authors present theoretical results that show how one can simulate a mixture distribution whose components live in subspaces of different dimension by reformulating the problem in such a way that observations may be drawn from an auxiliary continuous distribution on the largest subspace and then transformed in an appropriate fashion. Motivated by the importance of enlarging the set of available Markov chain Monte Carlo (MCMC) techniques, the authors show how their results can be fruitfully employed in problems such as model selection (or averaging) of nested models, or regeneration of Markov chains for evaluating standard deviations of estimated expectations derived from MCMC simulations.     

Bayesian estimation for percolation models of disease spread in plant populations

Statistical methods are formulated for fitting and testing percolation-based, spatio-temporal models that are generally applicable to biological or physical processes that evolve in spatially distributed populations. The approach is developed and illustrated in the context of the spread of Rhizoctonia solani, a fungal pathogen, in radish but is readily generalized to other scenarios. The particular model considered represents processes of primary and secondary infection between nearest-neighbour hosts in a lattice, and time-varying susceptibility of the hosts. Bayesian methods for fitting the model to observations of disease spread through space and time in replicate populations are developed. These use Markov chain Monte Carlo methods to overcome the problems associated with partial observation of the process. We also consider how model testing can be achieved by embedding classical methods within the Bayesian analysis. In particular we show how a residual process, with known sampling distribution, can be defined. Model fit is then examined by generating samples from the posterior distribution of the residual process, to which a classical test for consistency with the known distribution is applied, enabling the posterior distribution of the P-value of the test used to be estimated. For the Rhizoctonia-radish system the methods confirm the findings of earlier non-spatial analyses regarding the dynamics of disease transmission and yield new evidence of environmental heterogeneity in the replicate experiments.     

Bayesian analysis of spatial data using different variance and neighbourhood structures

In disease mapping, the overall goal is to study the incidence or mortality risk caused by a specific disease in a number of geographical regions. It is common to assume that the response variable follows a Poisson distribution, whose average rate can be explained by a group of covariates and a random effect. For this random effect, it is considered conditional autoregressive (CAR) models, which carry information about the neighbourhood relationship between the regions. The focus of this paper was to explore and compare some CAR models proposed in the literature. An application with epidemiological data was conducted to model the risk of death due to Crohn's Disease and Ulcerative Colitis in the State of São Paulo – Brazil. Finally, a simulation study was done to strengthen the results and assess the performance of the models in the presence of various levels of spatial dependence.     

Bayes and MCMC for Undergraduates

Students of statistics should be taught the ideas and methods that are widely used in practice and that will help them understand the world of statistics. Today, this means teaching them about Bayesian methods. In this article, I present ideas on teaching an undergraduate Bayesian course that uses Markov chain Monte Carlo and that can be a second course or, for strong students, a first course in statistics.