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Bayesian Inference for Gaussian Mixed Graph Models  [PDF]
Ricardo Silva,Zoubin Ghahramani
Computer Science , 2012,
Abstract: We introduce priors and algorithms to perform Bayesian inference in Gaussian models defined by acyclic directed mixed graphs. Such a class of graphs, composed of directed and bi-directed edges, is a representation of conditional independencies that is closed under marginalization and arises naturally from causal models which allow for unmeasured confounding. Monte Carlo methods and a variational approximation for such models are presented. Our algorithms for Bayesian inference allow the evaluation of posterior distributions for several quantities of interest, including causal effects that are not identifiable from data alone but could otherwise be inferred where informative prior knowledge about confounding is available.
Bayesian multivariate mixed-scale density estimation  [PDF]
Antonio Canale,David B. Dunson
Statistics , 2011,
Abstract: Although continuous density estimation has received abundant attention in the Bayesian nonparametrics literature, there is limited theory on multivariate mixed scale density estimation. In this note, we consider a general framework to jointly model continuous, count and categorical variables under a nonparametric prior, which is induced through rounding latent variables having an unknown density with respect to Lebesgue measure. For the proposed class of priors, we provide sufficient conditions for large support, strong consistency and rates of posterior contraction. These conditions allow one to convert sufficient conditions obtained in the setting of multivariate continuous density estimation to the mixed scale case. To illustrate the procedure a rounded multivariate nonparametric mixture of Gaussians is introduced and applied to a crime and communities dataset.
Bayesian Inference Methods for Univariate and Multivariate GARCH Models: a Survey  [PDF]
Audron? Virbickait?,M. Concepción Ausín,Pedro Galeano
Statistics , 2014, DOI: 10.1111/joes.12046
Abstract: This survey reviews the existing literature on the most relevant Bayesian inference methods for univariate and multivariate GARCH models. The advantages and drawbacks of each procedure are outlined as well as the advantages of the Bayesian approach versus classical procedures. The paper makes emphasis on recent Bayesian non-parametric approaches for GARCH models that avoid imposing arbitrary parametric distributional assumptions. These novel approaches implicitly assume infinite mixture of Gaussian distributions on the standardized returns which have been shown to be more flexible and describe better the uncertainty about future volatilities. Finally, the survey presents an illustration using real data to show the flexibility and usefulness of the non-parametric approach.
Bayesian inference on dependence in multivariate longitudinal data  [PDF]
Hongxia Yang,Fan Li,Enrique F. Schisterman,Sunni L. Mumford,David Dunson
Statistics , 2012,
Abstract: In many applications, it is of interest to assess the dependence structure in multivariate longitudinal data. Discovering such dependence is challenging due to the dimensionality involved. By concatenating the random effects from component models for each response, dependence within and across longitudinal responses can be characterized through a large random effects covariance matrix. Motivated by the common problems in estimating this matrix, especially the off-diagonal elements, we propose a Bayesian approach that relies on shrinkage priors for parameters in a modified Cholesky decomposition. Without adjustment, such priors and previous related approaches are order-dependent and tend to shrink strongly toward an ARtype structure. We propose moment-matching (MM) priors to mitigate such problems. Efficient Gibbs samplers are developed for posterior computation. The methods are illustrated through simulated examples and are applied to a longitudinal epidemiologic study of hormones and oxidative stress.
Bayesian inference for diffusion driven mixed-effects models  [PDF]
Gavin A. Whitaker,Andrew Golightly,Richard J. Boys,Chris Sherlock
Statistics , 2015,
Abstract: Stochastic differential equations (SDEs) provide a natural framework for modelling intrinsic stochasticity inherent in many continuous-time physical processes. When such processes are observed in multiple individuals or experimental units, SDE driven mixed-effects models allow the quantification of between (as well as within) individual variation. Performing Bayesian inference for such models, using discrete time data that may be incomplete and subject to measurement error is a challenging problem and is the focus of this paper. We extend a recently proposed MCMC scheme to include the SDE driven mixed-effects framework. Fundamental to our approach is the development of a novel construct that allows for efficient sampling of conditioned SDEs that may exhibit nonlinear dynamics between observation times. We apply the resulting scheme to synthetic data generated from a simple SDE model of orange tree growth, and real data consisting of observations on aphid numbers recorded under a variety of different treatment regimes. In addition, we provide a systematic comparison of our approach with an inference scheme based on a tractable approximation of the SDE, that is, the linear noise approximation.
Bayesian inference for general Gaussian graphical models with application to multivariate lattice data  [PDF]
Adrian Dobra,Alex Lenkoski,Abel Rodriguez
Statistics , 2010,
Abstract: We introduce efficient Markov chain Monte Carlo methods for inference and model determination in multivariate and matrix-variate Gaussian graphical models. Our framework is based on the G-Wishart prior for the precision matrix associated with graphs that can be decomposable or non-decomposable. We extend our sampling algorithms to a novel class of conditionally autoregressive models for sparse estimation in multivariate lattice data, with a special emphasis on the analysis of spatial data. These models embed a great deal of flexibility in estimating both the correlation structure across outcomes and the spatial correlation structure, thereby allowing for adaptive smoothing and spatial autocorrelation parameters. Our methods are illustrated using simulated and real-world examples, including an application to cancer mortality surveillance.
Bayesian semiparametric inference for multivariate doubly-interval-censored data  [PDF]
Alejandro Jara,Emmanuel Lesaffre,Maria De Iorio,Fernando Quintana
Statistics , 2011, DOI: 10.1214/10-AOAS368
Abstract: Based on a data set obtained in a dental longitudinal study, conducted in Flanders (Belgium), the joint time to caries distribution of permanent first molars was modeled as a function of covariates. This involves an analysis of multivariate continuous doubly-interval-censored data since: (i) the emergence time of a tooth and the time it experiences caries were recorded yearly, and (ii) events on teeth of the same child are dependent. To model the joint distribution of the emergence times and the times to caries, we propose a dependent Bayesian semiparametric model. A major feature of the proposed approach is that survival curves can be estimated without imposing assumptions such as proportional hazards, additive hazards, proportional odds or accelerated failure time.
Bayesian Inference for the Multivariate Extended-Skew Normal Distribution  [PDF]
Mathieu Gerber,Florian Pelgrin
Statistics , 2015,
Abstract: The multivariate extended skew-normal distribution allows for accommodating raw data which are skewed and heavy tailed, and has at least three appealing statistical properties, namely closure under conditioning, affine transformations, and marginalization. In this paper we propose a Bayesian computational approach based on a sequential Monte Carlo (SMC) sampler to estimate such distributions. The practical implementation of each step of the algorithm is discussed and the elicitation of prior distributions takes into consideration some unusual behaviour of the likelihood function and the corresponding Fisher information matrix. Using Monte Carlo simulations, we provide strong evidence regarding the performances of the SMC sampler as well as some new insights regarding the parametrizations of the extended skew-normal distribution. A generalization to the extended skew-normal sample selection model is also presented. Finally we proceed with the analysis of two real datasets.
A Multivariate Discretization Method for Learning Bayesian Networks from Mixed Data  [PDF]
Stefano Monti,Gregory F. Cooper
Computer Science , 2013,
Abstract: In this paper we address the problem of discretization in the context of learning Bayesian networks (BNs) from data containing both continuous and discrete variables. We describe a new technique for multivariate discretization, whereby each continuous variable is discretized while taking into account its interaction with the other variables. The technique is based on the use of a Bayesian scoring metric that scores the discretization policy for a continuous variable given a BN structure and the observed data. Since the metric is relative to the BN structure currently being evaluated, the discretization of a variable needs to be dynamically adjusted as the BN structure changes.
Bayesian inference for the multivariate skew-normal model: a Population Monte Carlo approach  [PDF]
Brunero Liseo,Antonio Parisi
Statistics , 2013,
Abstract: Frequentist and likelihood methods of inference based on the multivariate skew-normal model encounter several technical difficulties with this model. In spite of the popularity of this class of densities, there are no broadly satisfactory solutions for estimation and testing problems. A general population Monte Carlo algorithm is proposed which: 1) exploits the latent structure stochastic representation of skew-normal random variables to provide a full Bayesian analysis of the model and 2) accounts for the presence of constraints in the parameter space. The proposed approach can be defined as weakly informative, since the prior distribution approximates the actual reference prior for the shape parameter vector. Results are compared with the existing classical solutions and the practical implementation of the algorithm is illustrated via a simulation study and a real data example. A generalization to the matrix variate regression model with skew-normal error is also presented.
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