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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.
Bayesian analysis of multivariate stochastic volatility with skew distribution  [PDF]
Jouchi Nakajima
Statistics , 2012,
Abstract: Multivariate stochastic volatility models with skew distributions are proposed. Exploiting Cholesky stochastic volatility modeling, univariate stochastic volatility processes with leverage effect and generalized hyperbolic skew t-distributions are embedded to multivariate analysis with time-varying correlations. Bayesian prior works allow this approach to provide parsimonious skew structure and to easily scale up for high-dimensional problem. Analyses of daily stock returns are illustrated. Empirical results show that the time-varying correlations and the sparse skew structure contribute to improved prediction performance and VaR forecasts.
A comparison of nonlinear population Monte Carlo and particle Markov chain Monte Carlo algorithms for Bayesian inference in stochastic kinetic models  [PDF]
Eugenia Koblents,Joaquín Míguez
Statistics , 2014,
Abstract: In this paper we address the problem of Monte Carlo approximation of posterior probability distributions in stochastic kinetic models (SKMs). SKMs are multivariate Markov jump processes that model the interactions among species in biochemical systems according to a set of uncertain parameters. Markov chain Monte Carlo (MCMC) methods have been typically preferred for this Bayesian inference problem. Specifically, the particle MCMC (pMCMC) method has been recently shown to be an effective, while computationally demanding, method applicable to this problem. Within the pMCMC framework, importance sampling (IS) has been used only as the basis of the sequential Monte Carlo (SMC) approximation of the acceptance ratio in the Metropolis-Hastings kernel. However, the recently proposed nonlinear population Monte Carlo (NPMC) algorithm, based on an iterative IS scheme, has also been shown to be effective as a Bayesian inference tool for low dimensional (predator-prey) SKMs. In this paper, we provide an extensive performance comparison of pMCMC versus NPMC, when applied to the challenging prokaryotic autoregulatory network. We show how the NPMC method can greatly outperform the pMCMC algorithm in this scenario, with an overall moderate computational effort. We complement the numerical comparison of the two techniques with an asymptotic convergence analysis of the nonlinear IS scheme at the core of the proposed method when the importance weights can only be computed approximately.
Bayesian Inference in Monte-Carlo Tree Search  [PDF]
Gerald Tesauro,V T Rajan,Richard Segal
Computer Science , 2012,
Abstract: Monte-Carlo Tree Search (MCTS) methods are drawing great interest after yielding breakthrough results in computer Go. This paper proposes a Bayesian approach to MCTS that is inspired by distributionfree approaches such as UCT [13], yet significantly differs in important respects. The Bayesian framework allows potentially much more accurate (Bayes-optimal) estimation of node values and node uncertainties from a limited number of simulation trials. We further propose propagating inference in the tree via fast analytic Gaussian approximation methods: this can make the overhead of Bayesian inference manageable in domains such as Go, while preserving high accuracy of expected-value estimates. We find substantial empirical outperformance of UCT in an idealized bandit-tree test environment, where we can obtain valuable insights by comparing with known ground truth. Additionally we rigorously prove on-policy and off-policy convergence of the proposed methods.
Informative Bayesian inference for the skew-normal distribution  [PDF]
Antonio Canale,Bruno Scarpa
Statistics , 2013,
Abstract: Motivated by the analysis of the distribution of university grades, which is usually asymmetric, we discuss two informative priors for the shape parameter of the skew-normal distribution, showing that they lead to closed-form full-conditional posterior distributions, particularly useful in MCMC computation. Gibbs sampling algorithms are discussed for the joint vector of parameters, given independent prior distributions for the location and scale parameters. Simulation studies are performed to assess the performance of Gibbs samplers and to compare the choice of informative priors against a non-informative one. The method is used to analyze the grades of the basic statistics examination of the first-year undergraduate students at the School of Economics, University of Padua, Italy.
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.
Exact Bayesian inference in spatio-temporal Cox processes driven by multivariate Gaussian processes  [PDF]
Flávio B. Gon?alves,Dani Gamerman
Statistics , 2015,
Abstract: In this paper we present a novel inference methodology to perform Bayesian inference for spatio-temporal Cox processes where the intensity function depends on a multivariate Gaussian process. Dynamic Gaussian processes are introduced to allow for evolution of the intensity function over discrete time. The novelty of the method lies on the fact that no discretisation error is involved despite the non-tractability of the likelihood function and infinite dimensionality of the problem. The method is based on a Markov chain Monte Carlo algorithm that samples from the joint posterior distribution of the parameters and latent variables of the model. A particular choice of the dominating measure to obtain the likelihood function is shown to be crucial to devise a valid MCMC. The models are defined in a general and flexible way but they are amenable to direct sampling from the relevant distributions, due to careful characterisation of its components. The models also allow for the inclusion of regression covariates and/or temporal components to explain the variability of the intensity function. These components may be subject to relevant interaction with space and/or time. Simulated examples illustrate the methodology, followed by concluding remarks.
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.
Limitations of Markov chain Monte Carlo algorithms for Bayesian Inference of phylogeny  [PDF]
Elchanan Mossel,Eric Vigoda
Quantitative Biology , 2005, DOI: 10.1214/105051600000000538
Abstract: Markov chain Monte Carlo algorithms play a key role in the Bayesian approach to phylogenetic inference. In this paper, we present the first theoretical work analyzing the rate of convergence of several Markov chains widely used in phylogenetic inference. We analyze simple, realistic examples where these Markov chains fail to converge quickly. In particular, the data studied are generated from a pair of trees, under a standard evolutionary model. We prove that many of the popular Markov chains take exponentially long to reach their stationary distribution. Our construction is pertinent since it is well known that phylogenetic trees for genes may differ within a single organism. Our results shed a cautionary light on phylogenetic analysis using Bayesian inference and highlight future directions for potential theoretical work.
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.
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