VARIATIONAL BAYESIAN ANALYSIS FOR HIDDEN MARKOV MODELS

The variational approach to Bayesian inference enables simultaneous estimation of model parameters and model complexity. An interesting feature of this approach is that it also leads to an automatic choice of model complexity. Empirical results from the analysis of hidden Markov models with Gaussian observation densities illustrate this. If the variational algorithm is initialized with a large number of hidden states, redundant states are eliminated as the method converges to a solution, thereby leading to a selection of the number of hidden states. In addition, through the use of a variational approximation, the deviance information criterion for Bayesian model selection can be extended to the hidden Markov model framework. Calculation of the deviance information criterion provides a further tool for model selection, which can be used in conjunction with the variational approach.     

BAYESIAN ANALYSIS OF A FRACTIONAL COINTEGRATION MODEL

The concept of fractional cointegration, whereby deviations from an equilibrium relationship follow a fractionally integrated process, has attracted some attention of late. The extended concept allows cointegration to be associated with mean reversion in the error, rather than requiring the more stringent condition of stationarity. This paper presents a Bayesian method for conducting inference about fractional cointegration. The method is based on an approximation of the exact likelihood, with a Jeffreys prior being used to offset identification problems. Numerical results are produced via a combination of Markov chain Monte Carlo algorithms. The procedure is applied to several purchasing power parity relations, with substantial evidence found in favor of parity reversion.     

BAYESIAN ANALYSIS OF THE ADDITIVE MIXED MODEL FOR RANDOMIZED BLOCK DESIGNS

This paper deals with the Bayesian analysis of the additive mixed model experiments. Consider b randomly chosen subjects who respond once to each of t treatments. The subjects are treated as random effects and the treatment effects are fixed. Suppose that some prior information is available, thus motivating a Bayesian analysis. The Bayesian computation, however, can be difficult in this situation, especially when a large number of treatments is involved. Three computational methods are suggested to perform the analysis. The exact posterior density of any parameter of interest can be simulated based on random realizations taken from a restricted multivariate t distribution. The density can also be simulated using Markov chain Monte Carlo methods. The simulated density is accurate when a large number of random realizations is taken. However, it may take substantial amount of computer time when many treatments are involved. An alternative Laplacian approximation is discussed. The Laplacian method produces smooth and very accurate approximates to posterior densities, and takes only seconds of computer time. An example of a pipeline cracks experiment is used to illustrate the Bayesian approaches and the computational methods.     

BAYESIAN ANALYSIS FOR THE SUPERPOSITION OF TWO DEPENDENT NONHOMOGENEOUS POISSON PROCESSES

ABSTRACT

A Bayesian analysis for the superposition of two dependent nonhomogenous Poisson processes is studied by means of a bivariate Poisson distribution. This particular distribution presents a new likelihood function which takes into account the correlation between the two nonhomogenous Poisson processes. A numerical example using Markov Chain Monte Carlo method with data augmentation is considered.     

BAYESIAN HIDDEN MARKOV MODELS FOR LONGITUDINAL COUNTS

This paper describes a Bayesian approach to modelling carcinogenity in animal studies where the data consist of counts of the number of tumours present over time. It compares two autoregressive hidden Markov models. One of them models the transitions between three latent states: an inactive transient state, a multiplying state for increasing counts and a reducing state for decreasing counts. The second model introduces a fourth tied state to describe non‐zero observations that are neither increasing nor decreasing. Both these models can model the length of stay upon entry of a state. A discrete constant hazards waiting time distribution is used to model the time to onset of tumour growth. Our models describe between‐animal‐variability by a single hierarchy of random effects and the within‐animal variation by first‐order serial dependence. They can be extended to higher‐order serial dependence and multi‐level hierarchies. Analysis of data from animal experiments comparing the influence of two genes leads to conclusions that differ from those of Dunson (2000). The observed data likelihood defines an information criterion to assess the predictive properties of the three‐ and four‐state models. The deviance information criterion is appropriately defined for discrete parameters.     

BETTER PRIORS FOR BAYESIAN BETTORS

Consider the game where a Bayesian investor places a series of bets on the outcomes of a sequence of tosses of a coin with odds set by a Bayesian bookie. It is shown that at each toss the investor can have non-negative expected winnings even though after many tosses the two posterior distributions are nearly equivalent.     

BAYESIAN ANALYSIS OF THE LINEAR REGRESSION MODEL WITH NON-NORMAL DISTURBANCES

This paper considers the Bayesian analysis of a linear regression model with identically independently distributed non-normal disturbances. The distribution of disturbances is approximated by an Edgeworth series distribution with cumulants, of order higher than fourth, negligible. The posterior distribution of the regression coefficients vector is obtained under the assumption of a g-prior distribution for the parameters of the model. The Bayes estimator and its Bayes risk of the estimator are derived under a quadratic loss structure.     

BAYESIAN ANALYSIS OF VECTOR ARFIMA PROCESSES

A general framework is presented for Bayesian inference of multivariate time series exhibiting long-range dependence. The series are modelled using a vector autoregressive fractionally integrated moving-average (VARFIMA) process, which can capture both short-term correlation structure and long-range dependence characteristics of the individual series, as well as interdependence and feedback relationships between the series. To facilitate a sampling-based Bayesian approach, the exact joint posterior density is derived for the parameters, in a form that is computationally simpler than direct evaluation of the likelihood, and a modified Gibbs sampling algorithm is used to generate samples from the complete conditional distribution associated with each parameter. The paper also shows how an approximate form of the joint posterior density may be used for long time series. The procedure is illustrated using sea surface temperatures measured at three locations along the central California coast. These series are believed to be interdependent due to similarities in local atmospheric conditions at the different locations, and previous studies have found that they exhibit ‘long memory’ when studied individually. The approach adopted here permits investigation of the effects on model estimation of the interdependence and feedback relationships between the series.     

ANALYSIS OF HEAD INJURIES USING A BAYESIAN VECTOR GENERALIZED ADDITIVE MODEL

The potential of cycle helmets to reduce head injury remains controversial. Although several case‐control studies have been published, ecological analyses of head injury remain commonplace, presumably because of the availability of data and policy‐makers’ preference for ‘whole population’ studies. Given that such population‐level analysis will be conducted, this paper models the odds ratio between different road‐user groups over time. We use a Bayesian implementation of a vector generalized additive model in order to examine the odds ratio for head injury when comparing male cyclists with female cyclists, male pedestrians with male cyclists, and female pedestrians with female cyclists over a period when helmet‐wearing rates were thought to diverge by gender.     

MULTIPERIOD FORECASTING ANALYSIS OF A DYNAMIC MODEL FOR A SMALL SAMPLE

In this paper we derive the formulae for the bias and mean squared forecast error (MSFE) of the least squares forecast several periods ahead in the context of a dynamic model. Since the expressions are in terms of integrals, we have also obtained the numerical value of the bias and MSFE for different values of parameters and different disturbance structures. The results confirm some earlier studies (based on the AR(1) model), for example Lahiri (1975) and Hoque et al. (1988).     

A BAYESIAN HIERARCHICAL MODEL FOR POISSON RATE AND REPORTING-PROBABILITY INFERENCE USING DOUBLE SAMPLING

We analyse a combination of errant count data subject to under‐reported counts and inerrant count data to estimate multiple Poisson rates and reporting probabilities of cervical cancer for four European countries. Our analysis uses a Bayesian hierarchical model. Using a simulation study, we demonstrate the efficacy of our new simultaneous inference method and compare the utility of our method with an empirical Bayes approach developed by Fader and Hardie (J. Appl. Statist., 2000).     

A SEMIPARAMETRIC MIXTURE MODEL FOR THE ANALYSIS OF COMPETING RISKS DATA

This paper deals with the regression analysis of failure time data when there are censoring and multiple types of failures. We propose a semiparametric generalization of a parametric mixture model of Larson & Dinse (1985), for which the marginal probabilities of the various failure types are logistic functions of the covariates. Given the type of failure, the conditional distribution of the time to failure follows a proportional hazards model. A marginal like lihood approach to estimating regression parameters is suggested, whereby the baseline hazard functions are eliminated as nuisance parameters. The Monte Carlo method is used to approximate the marginal likelihood; the resulting function is maximized easily using existing software. Some guidelines for choosing the number of Monte Carlo replications are given. Fixing the regression parameters at their estimated values, the full likelihood is maximized via an EM algorithm to estimate the baseline survivor functions. The methods suggested are illustrated using the Stanford heart transplant data.     

A BAYESIAN METHOD FOR THE CHOICE OF THE SAMPLE SIZE IN EQUIVALENCE TRIALS

In this paper we consider a Bayesian predictive approach to sample size determination in equivalence trials. Equivalence experiments are conducted to show that the unknown difference between two parameters is small. For instance, in clinical practice this kind of experiment aims to determine whether the effects of two medical interventions are therapeutically similar. We declare an experiment successful if an interval estimate of the effects‐difference is included in a set of values of the parameter of interest indicating a negligible difference between treatment effects (equivalence interval). We derive two alternative criteria for the selection of the optimal sample size, one based on the predictive expectation of the interval limits and the other based on the predictive probability that these limits fall in the equivalence interval. Moreover, for both criteria we derive a robust version with respect to the choice of the prior distribution. Numerical results are provided and an application is illustrated when the normal model with conjugate prior distributions is assumed.     

BAYESIAN TESTS FOR SOME PRECISE HYPOTHESES ON MULTI-NORMAL MEANS

Bayesian counterparts of some standard tests concerning the means of multi-normal distribution are discussed. In particular the hypothesis that the multi-normal mean is equal to a specified value, and the hypothesis that the means are equal. Lower bounds on the Bayes factor in favour of the null hypothesis are obtained over the class of conjugate priors. The P-value, or observed significance level of the standard sampling-theoretic test procedure are compared with the posterior probability. The results correspond closely with those of Good (1967), Berger & Sellke (1987), Pepple (1988) and others and illustrate the conflict between posterior probabilities and P-values as measures of evidence.     

ASSOCIATIONS BETWEEN AIR POLLUTION AND HOSPITAL VISITS FOR CARDIOVASCULAR DISEASES IN THE ELDERLY IN SYDNEY USING BAYESIAN STATISTICAL METHODS

Using generalized linear models (GLMs), Jalaludin  et al. (2006;  J. Exposure Analysis and Epidemiology   16 , 225–237) studied the association between the daily number of visits to emergency departments for cardiovascular disease by the elderly (65+) and five measures of ambient air pollution. Bayesian methods provide an alternative approach to classical time series modelling and are starting to be more widely used. This paper considers Bayesian methods using the dataset used by Jalaludin  et al.  (2006) , and compares the results from Bayesian methods with those obtained by Jalaludin  et al.  (2006) using GLM methods.     

A BAYESIAN SIMULATION APPROACH TO INFERENCE ON A MULTI‐STATE LATENT FACTOR INTENSITY MODEL

The influence of economic conditions on the movement of a variable between states (for example a change in credit rating from A to B) can be modelled using a multi‐state latent factor intensity framework. Estimation of this type of model is, however, not straightforward, as transition probabilities are involved and the model contains a few highly analytically intractable distributions. In this paper, a Bayesian approach is adopted to manage the distributions. The innovation in the sampling algorithm used to obtain the posterior distributions of the model parameters includes a particle filter step and a Metropolis–Hastings step within a Gibbs sampler. The feasibility and accuracy of the proposed sampling algorithm is supported with a few simulated examples. The paper contains an application concerning what caused 1049 firms to change their credit ratings over a span of ten years.     

BAYESIAN DETECTION AND ANALYSIS OF CHANGING TRANSITION MATRICES OF STATIONARY MARKOV CHAINS

This paper considers the detection of abrupt changes in the transition matrix of a Markov chain from a Bayesian viewpoint. It derives Bayes factors and posterior probabilities for unknown numbers of change‐points, as well as the positions of the change‐points, assuming non‐informative but proper priors on the parameters and fixed upper bound. The Markov chain Monte Carlo approach proposed by Chib in 1998 for estimating multiple change‐points models is adapted for the Markov chain model. It is especially useful when there are many possible change‐points. The method can be applied in a wide variety of disciplines and is particularly relevant in the social and behavioural sciences, for analysing the effects of events on the attitudes of people.     

AN ALGORITHMIC APPROACH TO BAYESIAN LINEAR MODEL CALCULATIONS

A framework is described for organizing and understanding the computations necessary to obtain the posterior mean of a vector of linear effects in a normal linear model, conditional on the parameters that determine covariance structure. The approach has two major uses; firstly, as a pedagogical tool in the derivation of formulae, and secondly, as a practical tool for developing computational strategies without needing complicated matrix formulae that are often unwieldy in complex hierarchical models. The proposed technique is based upon symbolic application of the sweep operator SWP to an appropriate tableau of means and covariances. The method is illustrated with standard linear model specifications, including the so-called mixed model, with both fixed and random effects.     

NON‐PARAMETRIC BAYESIAN INFERENCE FOR INHOMOGENEOUS MARKOV POINT PROCESSES

With reference to a specific dataset, we consider how to perform a flexible non‐parametric Bayesian analysis of an inhomogeneous point pattern modelled by a Markov point process, with a location‐dependent first‐order term and pairwise interaction only. A priori we assume that the first‐order term is a shot noise process, and that the interaction function for a pair of points depends only on the distance between the two points and is a piecewise linear function modelled by a marked Poisson process. Simulation of the resulting posterior distribution using a Metropolis–Hastings algorithm in the ‘conventional’ way involves evaluating ratios of unknown normalizing constants. We avoid this problem by applying a recently introduced auxiliary variable technique. In the present setting, the auxiliary variable used is an example of a partially ordered Markov point process model.     

BAYESIAN SUBSET SELECTION AND MODEL AVERAGING USING A CENTRED AND DISPERSED PRIOR FOR THE ERROR VARIANCE

This article proposes a new data‐based prior distribution for the error variance in a Gaussian linear regression model, when the model is used for Bayesian variable selection and model averaging. For a given subset of variables in the model, this prior has a mode that is an unbiased estimator of the error variance but is suitably dispersed to make it uninformative relative to the marginal likelihood. The advantage of this empirical Bayes prior for the error variance is that it is centred and dispersed sensibly and avoids the arbitrary specification of hyperparameters. The performance of the new prior is compared to that of a prior proposed previously in the literature using several simulated examples and two loss functions. For each example our paper also reports results for the model that orthogonalizes the predictor variables before performing subset selection. A real example is also investigated. The empirical results suggest that for both the simulated and real data, the performance of the estimators based on the prior proposed in our article compares favourably with that of a prior used previously in the literature.