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872
Multiple Shrinkage and Subset Selection in Wavelets
, 1997
"... This paper discusses Bayesian methods for multiple shrinkage estimation in wavelets. Wavelets are used in applications for data denoising, via shrinkage of the coefficients towards zero, and for data compression, by shrinkage and setting small coefficients to zero. We approach wavelet shrinkage by u ..."
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Cited by 127 (16 self)
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This paper discusses Bayesian methods for multiple shrinkage estimation in wavelets. Wavelets are used in applications for data denoising, via shrinkage of the coefficients towards zero, and for data compression, by shrinkage and setting small coefficients to zero. We approach wavelet shrinkage by using Bayesian hierarchical models, assigning a positive prior probability to the wavelet coefficients being zero. The resulting estimator for the wavelet coefficients is a multiple shrinkage estimator that exhibits a wide variety of nonlinear shrinkage patterns. We discuss fast computational implementations, with a focus on easytocompute analytic approximations as well as importance sampling and Markov chain Monte Carlo methods. Multiple shrinkage estimators prove to have excellent mean squared error performance in reconstructing standard test functions. We demonstrate this in simulated test examples, comparing various implementations of multiple shrinkage to commonly used shrinkage rules. Finally, we illustrate our approach with an application to the socalled "glint" data.
Analysis of multivariate probit models
 BIOMETRIKA
, 1998
"... This paper provides a practical simulationbased Bayesian and nonBayesian 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 ..."
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Cited by 124 (8 self)
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This paper provides a practical simulationbased Bayesian and nonBayesian 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 fouryear 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.
Practical Bayesian Density Estimation Using Mixtures Of Normals
 Journal of the American Statistical Association
, 1995
"... this paper, we propose some solutions to these problems. Our goal is to come up with a simple, practical method for estimating the density. This is an interesting problem in its own right, as well as a first step towards solving other inference problems, such as providing more flexible distributions ..."
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Cited by 124 (2 self)
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this paper, we propose some solutions to these problems. Our goal is to come up with a simple, practical method for estimating the density. This is an interesting problem in its own right, as well as a first step towards solving other inference problems, such as providing more flexible distributions in hierarchical models. To see why the posterior is improper under the usual reference prior, we write the model in the following way. Let Z = (Z 1 ; : : : ; Z n ) and X = (X 1 ; : : : ; X n ). The Z
Markov Chain Monte Carlo Estimation of Exponential Random Graph Models
 Journal of Social Structure
, 2002
"... This paper is about estimating the parameters of the exponential random graph model, also known as the p # model, using frequentist Markov chain Monte Carlo (MCMC) methods. The exponential random graph model is simulated using Gibbs or MetropolisHastings sampling. The estimation procedures consider ..."
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Cited by 118 (17 self)
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This paper is about estimating the parameters of the exponential random graph model, also known as the p # model, using frequentist Markov chain Monte Carlo (MCMC) methods. The exponential random graph model is simulated using Gibbs or MetropolisHastings sampling. The estimation procedures considered are based on the RobbinsMonro algorithm for approximating a solution to the likelihood equation.
Bayesian phylogenetic analysis of combined data
 Syst. Biol
, 2004
"... Abstract. — The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameterrich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new typ ..."
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Cited by 117 (5 self)
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Abstract. — The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameterrich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes (nuclear and mitochondrial, ribosomal and protein coding). Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene. Bayesian MCMC analysis deals efficiently with complex models: convergence occurs faster and more predictably for complex models, mixing is adequate for all parameters even under very complex models, and the parameter update cycle is virtually unaffected by model partitioning across sites. Morphology contributed only 5 % of the characters in the data set but nevertheless influenced the combineddata tree, supporting the utility of morphological data in multigene analyses. We used Bayesian criteria (Bayes factors) to show that process heterogeneity across data partitions is a significant model component, although not as important as amongsite rate variation. More complex evolutionary models are associated with more topological uncertainty and less conflict between morphology and molecules. Bayes factors sometimes favor simpler models over considerably more
An exact likelihood analysis of the multinomial probit model
, 1994
"... We develop new methods for conducting a finite sample, likelihoodbased analysis of the multinomial probit model. Using a variant of the Gibbs sampler, an algorithm is developed to draw from the exact posterior of the multinomial probit model with correlated errors. This approach avoids direct evalu ..."
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Cited by 117 (5 self)
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We develop new methods for conducting a finite sample, likelihoodbased analysis of the multinomial probit model. Using a variant of the Gibbs sampler, an algorithm is developed to draw from the exact posterior of the multinomial probit model with correlated errors. This approach avoids direct evaluation of the likelihood and, thus, avoids the problems associated with calculating choice probabilities which affect both the standard likelihood and method of simulated moments approaches. Both simulated and actual consumer panel data are used to fit sixdimensional choice models. We also develop methods for analyzing random coefficient and multiperiod probit models.
Markov Chain Monte Carlo Simulation Methods in Econometrics
, 1993
"... 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 literat ..."
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Cited by 116 (5 self)
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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.
General state space Markov chains and MCMC algorithm
 PROBABILITY SURVEYS
, 2004
"... This paper surveys various results about Markov chains on general (noncountable) state spaces. It begins with an introduction to Markov chain Monte Carlo (MCMC) algorithms, which provide the motivation and context for the theory which follows. Then, sufficient conditions for geometric and uniform e ..."
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Cited by 112 (28 self)
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This paper surveys various results about Markov chains on general (noncountable) state spaces. It begins with an introduction to Markov chain Monte Carlo (MCMC) algorithms, which provide the motivation and context for the theory which follows. Then, sufficient conditions for geometric and uniform ergodicity are presented, along with quantitative bounds on the rate of convergence to stationarity. Many of these results are proved using direct coupling constructions based on minorisation and drift conditions. Necessary and sufficient conditions for Central Limit Theorems (CLTs) are also presented, in some cases proved via the Poisson Equation or direct regeneration constructions. Finally, optimal scaling and weak convergence results for MetropolisHastings algorithms are discussed. None of the results presented is new, though many of the proofs are. We also describe some Open Problems.
Bayesian phylogenetic inference via Markov chain Monte Carlo methods
 Biometrics
, 1999
"... SUMMARY. We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cop ..."
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Cited by 112 (4 self)
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SUMMARY. We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cophenetic matrix form suggests a simple and effective proposal distribution for selecting candidate trees close to the current tree in the chain. We illustrate the algorithm with restriction site data on 9 plant species, then extend to DNA sequences from 32 species of fish. The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution.
An Adaptive Metropolis algorithm
 Bernoulli
, 1998
"... A proper choice of a proposal distribution for MCMC methods, e.g. for the MetropolisHastings algorithm, is well known to be a crucial factor for the convergence of the algorithm. In this paper we introduce an adaptive Metropolis Algorithm (AM), where the Gaussian proposal distribution is updated al ..."
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Cited by 105 (4 self)
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A proper choice of a proposal distribution for MCMC methods, e.g. for the MetropolisHastings algorithm, is well known to be a crucial factor for the convergence of the algorithm. In this paper we introduce an adaptive Metropolis Algorithm (AM), where the Gaussian proposal distribution is updated along the process using the full information cumulated so far. Due to the adaptive nature of the process, the AM algorithm is nonMarkovian, but we establish here that it has the correct ergodic properties. We also include the results of our numerical tests, which indicate that the AM algorithm competes well with traditional MetropolisHastings algorithms, and demonstrate that AM provides an easy to use algorithm for practical computation. 1991 Mathematics Subject Classification: 65C05, 65U05. Keywords: adaptive MCMC, comparison, convergence, ergodicity, Markov Chain Monte Carlo, MetropolisHastings algorithm 1 Introduction It is generally acknowledged that the choice of an effective proposal...