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187
Bayes Factors
, 1995
"... In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null ..."
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Cited by 1826 (74 self)
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In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is onehalf. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this paper we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology and psychology.
Simulating Normalized Constants: From Importance Sampling to Bridge Sampling to Path Sampling
, 1998
"... Computing (ratios of) normalizing constants of probability models is a fundamental computational problem for many statistical and scientific studies. Monte Carlo simulation is an effective technique, especially with complex and highdimensional models. This paper aims to bring to the attention of ..."
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Cited by 233 (5 self)
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Computing (ratios of) normalizing constants of probability models is a fundamental computational problem for many statistical and scientific studies. Monte Carlo simulation is an effective technique, especially with complex and highdimensional models. This paper aims to bring to the attention of general statistical audiences of some effective methods originating from theoretical physics and at the same time to explore these methods from a more statistical perspective, through establishing theoretical connections and illustrating their uses with statistical problems. We show that the acceptance ratio method and thermodynamic integration are natural generalizations of importance sampling, which is most familiar to statistical audiences. The former generalizes importance sampling through the use of a single “bridge ” density and is thus a case of bridge sampling in the sense of Meng and Wong. Thermodynamic integration, which is also known in the numerical analysis literature as Ogata’s method for highdimensional integration, corresponds to the use of infinitely many and continuously connected bridges (and thus a “path”). Our path sampling formulation offers more flexibility and thus potential efficiency to thermodynamic integration, and the search of optimal paths turns out to have close connections with the Jeffreys prior density and the Rao and Hellinger distances between two densities. We provide an informative theoretical example as well as two empirical examples (involving 17 to 70dimensional integrations) to illustrate the potential and implementation of path sampling. We also discuss some open problems.
Marginal Likelihood From the MetropolisHastings Output
 OUTPUT,JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 2001
"... This article provides a framework for estimating the marginal likelihood for the purpose of Bayesian model comparisons. The approach extends and completes the method presented in Chib (1995) by overcoming the problems associated with the presence of intractable full conditional densities. The propos ..."
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Cited by 217 (16 self)
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This article provides a framework for estimating the marginal likelihood for the purpose of Bayesian model comparisons. The approach extends and completes the method presented in Chib (1995) by overcoming the problems associated with the presence of intractable full conditional densities. The proposed method is developed in the context of MCMC chains produced by the Metropolis–Hastings algorithm, whose building blocks are used both for sampling and marginal likelihood estimation, thus economizing on prerun tuning effort and programming. Experiments involving the logit model for binary data, hierarchical random effects model for clustered Gaussian data, Poisson regression model for clustered count data, and the multivariate probit model for correlated binary data, are used to illustrate the performance and implementation of the method. These examples demonstrate that the method is practical and widely applicable.
Bayesian Model Assessment In Factor Analysis
, 2004
"... 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 datarelationships amongst the variable ..."
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Cited by 104 (10 self)
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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 datarelationships 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 samplingbased analyses to generate suitable empirical proposal distributions and that address the challenging problem of finding e#cient proposals in highdimensional 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.
An efficient Markov chain Monte Carlo method for distributions with intractable normalising constants
 Biometrika
, 2006
"... Maximum likelihood parameter estimation and sampling from Bayesian posterior distributions are problematic when the probability density for the parameter of interest involves an intractable normalising constant which is also a function of that parameter. In this paper, an auxiliary variable method i ..."
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Cited by 89 (4 self)
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Maximum likelihood parameter estimation and sampling from Bayesian posterior distributions are problematic when the probability density for the parameter of interest involves an intractable normalising constant which is also a function of that parameter. In this paper, an auxiliary variable method is presented which requires only that independent samples can be drawn from the unnormalised density at any particular parameter value. The proposal distribution is constructed so that the normalising constant cancels from the Metropolis–Hastings ratio. The method is illustrated by producing posterior samples for parameters of the Ising model given a particular lattice realisation.
Inference in Curved Exponential Family Models for Networks
 Journal of Computational and Graphical Statistics
, 2006
"... Network data arise in a wide variety of applications. Although descriptive statistics for networks abound in the literature, the science of fitting statistical models to complex network data is still in its infancy. The models considered in this article are based on exponential families; therefore, ..."
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Cited by 80 (11 self)
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Network data arise in a wide variety of applications. Although descriptive statistics for networks abound in the literature, the science of fitting statistical models to complex network data is still in its infancy. The models considered in this article are based on exponential families; therefore, we refer to them as exponential random graph models (ERGMs). Although ERGMs are easy to postulate, maximum likelihood estimation of parameters in these models is very difficult. In this article, we first review the method of maximum likelihood estimation using Markov chain Monte Carlo in the context of fitting linear ERGMs. We then extend this methodology to the situation where the model comes from a curved exponential family. The curved exponential family methodology is applied to new specifications of ERGMs, proposed by Snijders et al. (2004), having nonlinear parameters to represent structural properties of networks such as transitivity and heterogeneity of degrees. We review the difficult topic of implementing likelihood ratio tests for these models, then apply all these modelfitting and testing techniques to the estimation of linear and nonlinear parameters for a collaboration network between partners in a New England law firm.
Estimating Bayes Factors via Posterior Simulation with the LaplaceMetropolis Estimator
 Journal of the American Statistical Association
, 1994
"... The key quantity needed for Bayesian hypothesis testing and model selection is the marginal likelihood for a model, also known as the integrated likelihood, or the marginal probability of the data. In this paper we describe a way to use posterior simulation output to estimate marginal likelihoods. W ..."
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Cited by 60 (11 self)
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The key quantity needed for Bayesian hypothesis testing and model selection is the marginal likelihood for a model, also known as the integrated likelihood, or the marginal probability of the data. In this paper we describe a way to use posterior simulation output to estimate marginal likelihoods. We describe the basic LaplaceMetropolis estimator for models without random effects. For models with random effects the compound LaplaceMetropolis estimator is introduced. This estimator is applied to data from the World Fertility Survey and shown to give accurate results. Batching of simulation output is used to assess the uncertainty involved in using the compound LaplaceMetropolis estimator. The method allows us to test for the effects of independent variables in a random effects model, and also to test for the presence of the random effects. KEY WORDS: LaplaceMetropolis estimator; Random effects models; Marginal likelihoods; Posterior simulation; World Fertility Survey. 1 Introduction...
Estimating and understanding exponential random graph models
, 2011
"... We introduce a new method for estimating the parameters of exponential random graph models. The method is based on a largedeviations approximation to the normalizing constant shown to be consistent using theory developed by Chatterjee and Varadhan [15]. The theory explains a host of difficulties e ..."
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Cited by 50 (1 self)
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We introduce a new method for estimating the parameters of exponential random graph models. The method is based on a largedeviations approximation to the normalizing constant shown to be consistent using theory developed by Chatterjee and Varadhan [15]. The theory explains a host of difficulties encountered by applied workers: many distinct models have essentially the same MLE, rendering the problems “practically” illposed. We give the first rigorous proofs of “degeneracy” observed in these models. Here, almost all graphs have essentially no edges or are essentially complete. We supplement recent work of Bhamidi, Bresler and Sly [6] showing that for many models, the extra sufficient statistics are useless: most realizations look like the results of a simple Erdős–Rényi model. We also find classes of models where the limiting graphs differ from Erdős–Rényi graphs and begin to make the link to models where the natural parameters alternate in sign.
EQUIENERGY SAMPLER WITH APPLICATIONS IN STATISTICAL INFERENCE AND STATISTICAL MECHANICS
, 2006
"... We introduce a new sampling algorithm, the equienergy sampler, for efficient statistical sampling and estimation. Complementary to the widely used temperaturedomain methods, the equienergy sampler, utilizing the temperature–energy duality, targets the energy directly. The focus on the energy func ..."
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Cited by 47 (5 self)
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We introduce a new sampling algorithm, the equienergy sampler, for efficient statistical sampling and estimation. Complementary to the widely used temperaturedomain methods, the equienergy sampler, utilizing the temperature–energy duality, targets the energy directly. The focus on the energy function not only facilitates efficient sampling, but also provides a powerful means for statistical estimation, for example, the calculation of the density of states and microcanonical averages in statistical mechanics. The equienergy sampler is applied to a variety of problems, including exponential regression in statistics, motif sampling in computational biology and protein folding in biophysics.