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Gibbs Sampling Methods for StickBreaking Priors
"... ... In this paper we present two general types of Gibbs samplers that can be used to fit posteriors of Bayesian hierarchical models based on stickbreaking priors. The first type of Gibbs sampler, referred to as a Polya urn Gibbs sampler, is a generalized version of a widely used Gibbs sampling meth ..."
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Cited by 212 (17 self)
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... In this paper we present two general types of Gibbs samplers that can be used to fit posteriors of Bayesian hierarchical models based on stickbreaking priors. The first type of Gibbs sampler, referred to as a Polya urn Gibbs sampler, is a generalized version of a widely used Gibbs sampling method currently employed for Dirichlet process computing. This method applies to stickbreaking priors with a known P'olya urn characterization; that is priors with an explicit and simple prediction rule. Our second method, the blocked Gibbs sampler, is based on a entirely different approach that works by directly sampling values from the posterior of the random measure. The blocked Gibbs sampler can be viewed as a more general approach as it works without requiring an explicit prediction rule. We find that the blocked Gibbs avoids some of the limitations seen with the Polya urn approach and should be simpler for nonexperts to use.
Infinite Latent Feature Models and the Indian Buffet Process
, 2005
"... We define a probability distribution over equivalence classes of binary matrices with a finite number of rows and an unbounded number of columns. This distribution ..."
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Cited by 180 (38 self)
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We define a probability distribution over equivalence classes of binary matrices with a finite number of rows and an unbounded number of columns. This distribution
A SplitMerge Markov Chain Monte Carlo Procedure for the Dirichlet Process Mixture Model
 Journal of Computational and Graphical Statistics
, 2000
"... . We propose a splitmerge Markov chain algorithm to address the problem of inefficient sampling for conjugate Dirichlet process mixture models. Traditional Markov chain Monte Carlo methods for Bayesian mixture models, such as Gibbs sampling, can become trapped in isolated modes corresponding to an ..."
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Cited by 91 (0 self)
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. We propose a splitmerge Markov chain algorithm to address the problem of inefficient sampling for conjugate Dirichlet process mixture models. Traditional Markov chain Monte Carlo methods for Bayesian mixture models, such as Gibbs sampling, can become trapped in isolated modes corresponding to an inappropriate clustering of data points. This article describes a MetropolisHastings procedure that can escape such local modes by splitting or merging mixture components. Our MetropolisHastings algorithm employs a new technique in which an appropriate proposal for splitting or merging components is obtained by using a restricted Gibbs sampling scan. We demonstrate empirically that our method outperforms the Gibbs sampler in situations where two or more components are similar in structure. Key words: Dirichlet process mixture model, Markov chain Monte Carlo, MetropolisHastings algorithm, Gibbs sampler, splitmerge updates 1 Introduction Mixture models are often applied to density estim...
Modelling heterogeneity with and without the Dirichlet process
, 2001
"... We investigate the relationships between Dirichlet process (DP) based models and allocation models for a variable number of components, based on exchangeable distributions. It is shown that the DP partition distribution is a limiting case of a Dirichlet± multinomial allocation model. Comparisons of ..."
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Cited by 68 (3 self)
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We investigate the relationships between Dirichlet process (DP) based models and allocation models for a variable number of components, based on exchangeable distributions. It is shown that the DP partition distribution is a limiting case of a Dirichlet± multinomial allocation model. Comparisons of posterior performance of DP and allocation models are made in the Bayesian paradigm and illustrated in the context of univariate mixture models. It is shown in particular that the unbalancedness of the allocation distribution, present in the prior DP model, persists a posteriori. Exploiting the model connections, a new MCMC sampler for general DP based models is introduced, which uses split/merge moves in a reversible jump framework. Performance of this new sampler relative to that of some traditional samplers for DP processes is then explored.
Sequential Importance Sampling for Nonparametric Bayes Models: The Next Generation
 Journal of Statistics
, 1998
"... this paper, we exploit the similarities between the Gibbs sampler and the SIS, bringing over the improvements for Gibbs sampling algorithms to the SIS setting for nonparametric Bayes problems. These improvements result in an improved sampler and help satisfy questions of Diaconis (1995) pertaining t ..."
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Cited by 67 (5 self)
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this paper, we exploit the similarities between the Gibbs sampler and the SIS, bringing over the improvements for Gibbs sampling algorithms to the SIS setting for nonparametric Bayes problems. These improvements result in an improved sampler and help satisfy questions of Diaconis (1995) pertaining to convergence. Such an effort can see wide applications in many other problems related to dynamic systems where the SIS is useful (Berzuini et al. 1996; Liu and Chen 1996). Section 2 describes the specific model that we consider. For illustration we focus discussion on the betabinomial model, although the methods are applicable to other conjugate families. In Section 3, we describe the first generation of the SIS and Gibbs sampler in this context, and present the necessary conditional distributions upon which the techniques rely. Section 4 describes the alterations that create the second generation techniques, and provides specific algorithms for the model we consider. Section 5 presents a comparison of the techniques on a large set of data. Section 6 provides theory that ensures the proposed methods work and that is generally applicable to many other problems using importance sampling approaches. The final section presents discussion. 2 The Model
Poisson/gamma random field models for spatial statistics
 BIOMETRIKA
, 1998
"... Doubly stochastic Bayesian hierarchical models are introduced to account for uncertainty and spatial variation in the underlying intensity measure for point process models. Inhomogeneous gamma process random fields and, more generally, Markov random fields with infinitely divisible distributions are ..."
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Cited by 47 (12 self)
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Doubly stochastic Bayesian hierarchical models are introduced to account for uncertainty and spatial variation in the underlying intensity measure for point process models. Inhomogeneous gamma process random fields and, more generally, Markov random fields with infinitely divisible distributions are used to construct positively autocorrelated intensity measures for spatial Poisson point processes; these in turn are used to model the number and location of individual events. A data augmentation scheme and Markov chain Monte Carlo numerical methods are employed to generate samples from Bayesian posterior and predictive distributions. The methods are developed in both continuous and discrete settings, and are applied to a problem in forest ecology.
Generalized spatial Dirichlet process models
, 2007
"... Many models for the study of pointreferenced data explicitly introduce spatial random effects to capture residual spatial association. These spatial effects are customarily modelled as a zeromean stationary Gaussian process. The spatial Dirichlet process introduced by Gelfand et al. (2005) produces ..."
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Cited by 30 (1 self)
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Many models for the study of pointreferenced data explicitly introduce spatial random effects to capture residual spatial association. These spatial effects are customarily modelled as a zeromean stationary Gaussian process. The spatial Dirichlet process introduced by Gelfand et al. (2005) produces a random spatial process which is neither Gaussian nor stationary. Rather, it varies about a process that is assumed to be stationary and Gaussian. The spatial Dirichlet process arises as a probabilityweighted collection of random surfaces. This can be limiting for modelling and inferential purposes since it insists that a process realization must be one of these surfaces. We introduce a random distribution for the spatial effects that allows different surface selection at different sites. Moreover, we can specify the model so that the marginal distribution of the effect at each site still comes from a Dirichlet process. The development is offered constructively, providing a multivariate extension of the stickbreaking representation of the weights. We then introduce mixing using this generalized spatial Dirichlet process. We illustrate with a simulated dataset of independent replications and note that we can embed the generalized process within a dynamic model specification to eliminate the independence assumption.
A computational approach for full nonparametric Bayesian inference under Dirichlet process mixture models
 Journal of Computational and Graphical Statistics
, 2002
"... Widely used parametric generalizedlinear models are, unfortunately,a somewhat limited class of speci � cations. Nonparametric aspects are often introduced to enrich this class, resultingin semiparametricmodels. Focusing on single or ksample problems,many classical nonparametricapproachesare limited ..."
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Cited by 27 (7 self)
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Widely used parametric generalizedlinear models are, unfortunately,a somewhat limited class of speci � cations. Nonparametric aspects are often introduced to enrich this class, resultingin semiparametricmodels. Focusing on single or ksample problems,many classical nonparametricapproachesare limited to hypothesistesting. Those that allow estimation are limited to certain functionals of the underlying distributions. Moreover, the associated inference often relies upon asymptotics when nonparametric speci � cations are often most appealing for smaller sample sizes. Bayesian nonparametricapproachesavoid asymptotics but have, to date, been limited in the range of inference. Working with Dirichlet process priors, we overcome the limitations of existing simulationbasedmodel � tting approaches which yield inference that is con � ned to posterior moments of linear functionals of the population distribution.This article provides a computationalapproach to obtain the entire posterior distribution for more general functionals. We illustrate with three applications: investigation of extreme value distributions associated with a single population, comparison of medians in a ksample problem, and comparison of survival times from different populations under fairly heavy censoring.
Approximate Dirichlet Process Computing in Finite Normal Mixtures: Smoothing and Prior Information
 JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
, 2000
"... ..."
Bayesian Inference for Semiparametric Binary Regression
 JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 1996
"... We propose a regression model for binary response data which places no structural restrictions on the link function except monotonicity and known location and scale. Predictors enter linearly. We demonstrate Bayesian inference calculations in this model. By modifying the Dirichlet process, we obtain ..."
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Cited by 24 (2 self)
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We propose a regression model for binary response data which places no structural restrictions on the link function except monotonicity and known location and scale. Predictors enter linearly. We demonstrate Bayesian inference calculations in this model. By modifying the Dirichlet process, we obtain a natural prior measure over this semiparametric model, and we use Polya sequence theory to formulate this measure in terms of a finite number of unobserved variables. A Markov chain Monte Carlo algorithm is designed for posterior simulation, and the methodology is applied to data on radiotherapy treatments for cancer.