We examine the Bayesian approach to the discovery of directed acyclic causal models and compare it to the constraint-based approach. Both approaches rely on the Causal Markov assumption, but the two differ significantly in theory and practice. An important difference between the approaches is that the constraint-based approach uses categorical information about conditional-independence constraints in the domain, whereas the Bayesian approach weighs the degree to which such constraints hold. As a result, the Bayesian approach has three distinct advantages over its constraint-based counterpart. One, conclusions derived from the Bayesian approach are not susceptible to incorrect categorical decisions about independence facts that can occur with data sets of finite size. Two, using the Bayesian approach, finer distinctions among model structures---both quantitative and qualitative---can be made. Three, information from several models can be combined to make better inferences and to better ...

We present several Markov chain Monte Carlo simulation methods that have been widely used in recent years in econometrics and statistics. Among these is the Gibbs sampler, which has been of particular interest to econometricians. Although the paper summarizes some of the relevant theoretical literature, its emphasis is on the presentation and explanation of applications to important models that are studied in econometrics. We include a discussion of some implementation issues, the use of the methods in connection with the EM algorithm, and how the methods can be helpful in model specification questions. Many of the applications of these methods are of particular interest to Bayesians, but we also point out ways in which frequentist statisticians may find the techniques useful.

This paper provides a practical simulation-based Bayesian and non-Bayesian analysis of correlated binary data using the multivariate probit model. The posterior distribution is simulated by Markov chain Monte Carlo methods and maximum likelihood estimates are obtained by a Monte Carlo version of the EM algorithm. A practical approach for the computation of Bayes factors from the simulation output is also developed. The methods are applied to a dataset with a bivariate binary response, to a four-year longitudinal dataset from the Six Cities study of the health effects of air pollution and to a sevenvariate binary response dataset on the labour supply of married women from the Panel Survey of Income Dynamics.

Richardson and Green (1997) present a method of performing a Bayesian analysis of data from a finite mixture distribution with an unknown number of components. Their method is a Markov Chain Monte Carlo (MCMC) approach, which makes use of the "reversible jump" methodology described by Green (1995). We describe an alternative MCMC method which views the parameters of the model as a (marked) point process, extending methods suggested by Ripley (1977) to create a Markov birth-death process with an appropriate stationary distribution. Our method is easy to implement, even in the case of data in more than one dimension, and we illustrate it on both univariate and bivariate data. Keywords: Bayesian analysis, Birth-death process, Markov process, MCMC, Mixture model, Model Choice, Reversible Jump, Spatial point process 1 Introduction Finite mixture models are typically used to model data where each observation is assumed to have arisen from one of k groups, each group being suitably modelle...

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This paper is concerned with the Bayesian estimation and comparison of flexible, high dimensional multivariate time series models with time varying correlations. The model proposed and considered here combines features of the classical factor model with that of the heavy tailed univariate stochastic volatility model. A unified analysis of the model, and its special cases, is developed that encompasses estimation, filtering and model choice. The centerpieces of the estimation algorithm (which relies on MCMC methods) are (1) a reduced blocking scheme for sampling the free elements of the loading matrix and the factors and (2) a special method for sampling the parameters of the univariate SV process. The resulting algorithm is scalable in terms of series and factors and simulation-efficient. Methods for estimating the log-likelihood function and the filtered values of the time-varying volatilities and correlations are also provided. The performance and effectiveness of the inferential methods are extensively tested using simulated data where models up to 50 dimensions and 688 parameters are fitted and studied. The performance of our model, in relation to multivariate GARCH models, is also evaluated using a real data set of weekly returns on a set of 10 international stock indices. We consider the performance along two dimensions: the ability to correctly estimate the conditional covariance matrix of future returns and the unconditional and conditional coverage of the 5 % and 1% Value-at-Risk (VaR) measures of four pre-defined portfolios.

Factor analysis has been one of the most powerful and flexible tools for assessment of multivariate dependence and codependence. Loosely speaking, it could be argued that the origin of its success rests in its very exploratory nature, where various kinds of data-relationships amongst the variables at study can be iteratively verified and/or refuted. Bayesian inference in factor analytic models has received renewed attention in recent years, partly due to computational advances but also partly to applied focuses generating factor structures as exemplified by recent work in financial time series modeling. The focus of our current work is on exploring questions of uncertainty about the number of latent factors in a multivariate factor model, combined with methodological and computational issues of model specification and model fitting. We explore reversible jump MCMC methods that build on sets of parallel Gibbs sampling-based analyses to generate suitable empirical proposal distributions and that address the challenging problem of finding e#cient proposals in high-dimensional models. Alternative MCMC methods based on bridge sampling are discussed, and these fully Bayesian MCMC approaches are compared with a collection of popular model selection methods in empirical studies.

The linear model with sparsity-favouring prior on the coefficients has important applications in many different domains. In machine learning, most methods to date search for maximum a posteriori sparse solutions and neglect to represent posterior uncertainties. In this paper, we address problems of Bayesian optimal design (or experiment planning), for which accurate estimates of uncertainty are essential. To this end, we employ expectation propagation approximate inference for the linear model with Laplace prior, giving new insight into numerical stability properties and proposing a robust algorithm. We also show how to estimate model hyperparameters by empirical Bayesian maximisation of the marginal likelihood, and propose ideas in order to scale up the method to very large underdetermined problems. We demonstrate the versatility of our framework on the application of gene regulatory network identification from micro-array expression data, where both the Laplace prior and the active experimental design approach are shown to result in significant improvements. We also address the problem of sparse coding of natural images, and show how our framework can be used for compressive sensing tasks. Part of this work appeared in Seeger et al. (2007b). The gene network identification application appears in Steinke et al. (2007).

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This paper provides a novel approach to forecasting time series subject to discrete structural breaks. We propose a Bayesian estimation and prediction procedure that allows for the possibility of new breaks over the forecast horizon, taking account of the size and duration of past breaks (if any) by means of a hierarchical hidden Markov chain model. Predictions are formed by integrating over the hyper parameters from the meta distributions that characterize the stochastic break point process. In an application to US Treasury bill rates, we find that the method leads to better out-of-sample forecasts than alternative methods that ignore breaks, particularly at long horizons.