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16
Sequential Monte Carlo Methods for Dynamic Systems
 Journal of the American Statistical Association
, 1998
"... A general framework for using Monte Carlo methods in dynamic systems is provided and its wide applications indicated. Under this framework, several currently available techniques are studied and generalized to accommodate more complex features. All of these methods are partial combinations of three ..."
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Cited by 650 (12 self)
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A general framework for using Monte Carlo methods in dynamic systems is provided and its wide applications indicated. Under this framework, several currently available techniques are studied and generalized to accommodate more complex features. All of these methods are partial combinations of three ingredients: importance sampling and resampling, rejection sampling, and Markov chain iterations. We deliver a guideline on how they should be used and under what circumstance each method is most suitable. Through the analysis of differences and connections, we consolidate these methods into a generic algorithm by combining desirable features. In addition, we propose a general use of RaoBlackwellization to improve performances. Examples from econometrics and engineering are presented to demonstrate the importance of RaoBlackwellization and to compare different Monte Carlo procedures. Keywords: Blind deconvolution; Bootstrap filter; Gibbs sampling; Hidden Markov model; Kalman filter; Markov...
On sequential simulationbased methods for bayesian filtering
, 1998
"... Abstract. In this report, we present an overview of sequential simulationbased methods for Bayesian filtering of nonlinear and nonGaussian dynamic models. It includes in a general framework numerous methods proposed independently in various areas of science and proposes some original developments. ..."
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Cited by 252 (13 self)
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Abstract. In this report, we present an overview of sequential simulationbased methods for Bayesian filtering of nonlinear and nonGaussian dynamic models. It includes in a general framework numerous methods proposed independently in various areas of science and proposes some original developments.
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 229 (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.
Simulating ratios of normalizing constants via a simple identity: A theoretical exploration
 Statistica Sinica
, 1996
"... Abstract: Let pi(w),i =1, 2, be two densities with common support where each density is known up to a normalizing constant: pi(w) =qi(w)/ci. We have draws from each density (e.g., via Markov chain Monte Carlo), and we want to use these draws to simulate the ratio of the normalizing constants, c1/c2. ..."
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Cited by 180 (3 self)
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Abstract: Let pi(w),i =1, 2, be two densities with common support where each density is known up to a normalizing constant: pi(w) =qi(w)/ci. We have draws from each density (e.g., via Markov chain Monte Carlo), and we want to use these draws to simulate the ratio of the normalizing constants, c1/c2. Such a computational problem is often encountered in likelihood and Bayesian inference, and arises in fields such as physics and genetics. Many methods proposed in statistical and other literature (e.g., computational physics) for dealing with this problem are based on various special cases of the following simple identity: c1 c2 = E2[q1(w)α(w)] E1[q2(w)α(w)]. Here Ei denotes the expectation with respect to pi (i =1, 2), and α is an arbitrary function such that the denominator is nonzero. A main purpose of this paper is to provide a theoretical study of the usefulness of this identity, with focus on (asymptotically) optimal and practical choices of α. Using a simple but informative example, we demonstrate that with sensible (not necessarily optimal) choices of α, we can reduce the simulation error by orders of magnitude when compared to the conventional importance sampling method, which corresponds to α =1/q2. We also introduce several generalizations of this identity for handling more complicated settings (e.g., estimating several ratios simultaneously) and pose several open problems that appear to have practical as well as theoretical value. Furthermore, we discuss related theoretical and empirical work.
Marginal Likelihood and Bayes Factors for Dirichlet Process Mixture Models
 Journal of the American Statistical Association
, 2003
"... We present a method for comparing semiparametric Bayesian models, constructed under the Dirichlet process mixture (DPM) framework, with alternative semiparameteric or parameteric Bayesian models. A distinctive feature of the method is that it can be applied to semiparametric models containing covari ..."
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Cited by 37 (5 self)
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We present a method for comparing semiparametric Bayesian models, constructed under the Dirichlet process mixture (DPM) framework, with alternative semiparameteric or parameteric Bayesian models. A distinctive feature of the method is that it can be applied to semiparametric models containing covariates and hierarchical prior structures, and is apparently the rst method of its kind. Formally, the method is based on the marginal likelihood estimation approach of Chib (1995) and requires estimation of the likelihood and posterior ordinates of the DPM model at a single highdensity point. An interesting computation is involved in the estimation of the likelihood ordinate, which is devised via collapsed sequential importance sampling. Extensive experiments with synthetic and real data involving semiparametric binary data regression models and hierarchical longitudinal mixedeffects models are used to illustrate the implementation, performance, and applicability of the method.
Blocking Gibbs Sampling for Linkage Analysis in Large Pedigrees with Many Loops
 AMERICAN JOURNAL OF HUMAN GENETICS
, 1996
"... We will apply the method of blocking Gibbs sampling to a problem of great importance and complexity  linkage analysis. Blocking Gibbs combines exact local computations with Gibbs sampling in a way that complements the strengths of both. The method is able to handle problems with very high complexi ..."
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Cited by 28 (2 self)
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We will apply the method of blocking Gibbs sampling to a problem of great importance and complexity  linkage analysis. Blocking Gibbs combines exact local computations with Gibbs sampling in a way that complements the strengths of both. The method is able to handle problems with very high complexity such as linkage analysis in large pedigrees with many loops; a task that no other known method is able to handle. New developments of the method are outlined, and it is applied to a highly complex linkage problem.
Population Monte Carlo algorithms Trans
 Jpn. Soc. Artif. Intell
, 2001
"... Abstract: In this paper, we give a crossdisciplinary survey on “populationbased ” Monte Carlo algorithms. These algorithms consist of a set of “walkers ” or “particles ” for the representation of a highdimensional vector and the computation is carried out by a random walk and split/deletion of th ..."
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Cited by 13 (0 self)
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Abstract: In this paper, we give a crossdisciplinary survey on “populationbased ” Monte Carlo algorithms. These algorithms consist of a set of “walkers ” or “particles ” for the representation of a highdimensional vector and the computation is carried out by a random walk and split/deletion of these objects. The algorithms are developed in various fields in physics and statistical sciences and called by lots of different terms – “Quantum Monte Carlo”, “Transfer Matrix Monte Carlo”, “Monte Carlo Filter (Particle Filter)”,“Sequential Monte Carlo ” and “PERM ” etc. Here we discuss them in a coherent framework. We also
Multipoint linkage analyses for disease mapping in extended pedigrees: A Markov chain Monte Carlo approach
, 2002
"... Multipoint linkage analyses ofgenetic data on extended pedigrees can involve exact computations which are infeasible. Markov chain Monte Carlo methods represent an attractive alternative, greatly extending the range of models and data sets for which analysis is practical. In this paper, several adva ..."
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Cited by 3 (1 self)
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Multipoint linkage analyses ofgenetic data on extended pedigrees can involve exact computations which are infeasible. Markov chain Monte Carlo methods represent an attractive alternative, greatly extending the range of models and data sets for which analysis is practical. In this paper, several advances in Markov chain Monte Carlo theory, namely joint updates of latent variables across loci and meioses, integrated proposals, MetropolisHastings restarts via sequential imputation and Rao Blackwellized estimators, are incorporated into a sampling strategy which mixes well and produces accurate results in real time. The methodology is demonstrated through its application to several data sets originating from a study of earlyonset Alzheimer's disease in families of VolgaGerman ethnic origin.
Linkage Analysis With Sequential Imputation
 GENET EPIDEMIOL
, 2003
"... ... In this article, we propose a Monte Carlo method for linkage analysis based on sequential imputation. Unlike exact methods, sequential imputation can handle large pedigrees with a moderate number of loci in its current implementation. This Monte Carlo method is an application of importance sampl ..."
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Cited by 2 (2 self)
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... In this article, we propose a Monte Carlo method for linkage analysis based on sequential imputation. Unlike exact methods, sequential imputation can handle large pedigrees with a moderate number of loci in its current implementation. This Monte Carlo method is an application of importance sampling, in which we sequentially impute ordered genotypes locus by locus, and then impute inheritance vectors conditioned on these genotypes. The resulting inheritance vectors, together with the importance sampling weights, are used to derive a consistent estimator of any linkage statistic of interest. The linkage statistic can be parametric or nonparametric; we focus on nonparametric linkage statistics. We demonstrate that accurate estimates can be achieved within a reasonable computing time. A simulation study illustrates the potential gain in power using our method for multilocus linkage analysis with large pedigrees. We simulated data at six markers under three models. We analyzed them using both sequential imputation and GENEHUNTER. GENEHUNTER had to drop between 3854% of pedigree members, whereas our method was able to use all pedigree members. The power gains of using all pedigree members were substantial under 2 of the 3 models. We implemented sequential imputation for multilocus linkage analysis in a userfriendly software package called SIMPLE.