Results 1  10
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315
Sequential Monte Carlo Samplers
, 2002
"... In this paper, we propose a general algorithm to sample sequentially from a sequence of probability distributions known up to a normalizing constant and de ned on a common space. A sequence of increasingly large arti cial joint distributions is built; each of these distributions admits a marginal ..."
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Cited by 311 (48 self)
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In this paper, we propose a general algorithm to sample sequentially from a sequence of probability distributions known up to a normalizing constant and de ned on a common space. A sequence of increasingly large arti cial joint distributions is built; each of these distributions admits a marginal which is a distribution of interest. To sample from these distributions, we use sequential Monte Carlo methods. We show that these methods can be interpreted as interacting particle approximations of a nonlinear FeynmanKac ow in distribution space. One interpretation of the FeynmanKac ow corresponds to a nonlinear Markov kernel admitting a speci ed invariant distribution and is a natural nonlinear extension of the standard MetropolisHastings algorithm. Many theoretical results have already been established for such ows and their particle approximations. We demonstrate the use of these algorithms through simulation.
HighOrder Collocation Methods for Differential Equations with Random Inputs
 SIAM Journal on Scientific Computing
"... Abstract. Recently there has been a growing interest in designing efficient methods for the solution of ordinary/partial differential equations with random inputs. To this end, stochastic Galerkin methods appear to be superior to other nonsampling methods and, in many cases, to several sampling met ..."
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Cited by 180 (9 self)
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Abstract. Recently there has been a growing interest in designing efficient methods for the solution of ordinary/partial differential equations with random inputs. To this end, stochastic Galerkin methods appear to be superior to other nonsampling methods and, in many cases, to several sampling methods. However, when the governing equations take complicated forms, numerical implementations of stochastic Galerkin methods can become nontrivial and care is needed to design robust and efficient solvers for the resulting equations. On the other hand, the traditional sampling methods, e.g., Monte Carlo methods, are straightforward to implement, but they do not offer convergence as fast as stochastic Galerkin methods. In this paper, a highorder stochastic collocation approach is proposed. Similar to stochastic Galerkin methods, the collocation methods take advantage of an assumption of smoothness of the solution in random space to achieve fast convergence. However, the numerical implementation of stochastic collocation is trivial, as it requires only repetitive runs of an existing deterministic solver, similar to Monte Carlo methods. The computational cost of the collocation methods depends on the choice of the collocation points, and we present several feasible constructions. One particular choice, based on sparse grids, depends weakly on the dimensionality of the random space and is more suitable for highly accurate computations of practical applications with large dimensional random inputs. Numerical examples are presented to demonstrate the accuracy and efficiency of the stochastic collocation methods. Key words. collocation methods, stochastic inputs, differential equations, uncertainty quantification
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 177 (10 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
Kronecker Graphs: An Approach to Modeling Networks
 JOURNAL OF MACHINE LEARNING RESEARCH 11 (2010) 9851042
, 2010
"... How can we generate realistic networks? In addition, how can we do so with a mathematically tractable model that allows for rigorous analysis of network properties? Real networks exhibit a long list of surprising properties: Heavy tails for the in and outdegree distribution, heavy tails for the ei ..."
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Cited by 122 (3 self)
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How can we generate realistic networks? In addition, how can we do so with a mathematically tractable model that allows for rigorous analysis of network properties? Real networks exhibit a long list of surprising properties: Heavy tails for the in and outdegree distribution, heavy tails for the eigenvalues and eigenvectors, small diameters, and densification and shrinking diameters over time. Current network models and generators either fail to match several of the above properties, are complicated to analyze mathematically, or both. Here we propose a generative model for networks that is both mathematically tractable and can generate networks that have all the above mentioned structural properties. Our main idea here is to use a nonstandard matrix operation, the Kronecker product, to generate graphs which we refer to as “Kronecker graphs”. First, we show that Kronecker graphs naturally obey common network properties. In fact, we rigorously prove that they do so. We also provide empirical evidence showing that Kronecker graphs can effectively model the structure of real networks. We then present KRONFIT, a fast and scalable algorithm for fitting the Kronecker graph generation model to large real networks. A naive approach to fitting would take superexponential
Bayesian Inference for Nonstationary Spatial Covariance Structure via Spatial Deformations
 JOURNAL OF THE ROYAL STATISTICAL SOCIETY, SERIES B
, 2000
"... In geostatistics it is common practice to assume that the underlying spatial process is stationary and isotropic, that is the spatial distribution is unchanged when the origin of the index set is translated and the process is stationary under rotations about the origin. However in environmental p ..."
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Cited by 74 (1 self)
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In geostatistics it is common practice to assume that the underlying spatial process is stationary and isotropic, that is the spatial distribution is unchanged when the origin of the index set is translated and the process is stationary under rotations about the origin. However in environmental problems, it is not very realistic to make such assumptions since local influences in the correlation structure of the spatial process may be clearly found in the data. This paper proposes a Bayesian model wherein the main aim is to address the anisotropy problem. Following Sampson and Guttorp (1992), we define the correlation function of the spatial process by reference to a latent space, denoted by D, where stationarity and isotropy hold. The space where the gauged monitoring sites lie is denoted by G. We adopt a Bayesian approach in which the mapping between G space and D space is represented by an unknown function d(:). A Gaussian process prior distribution is defined for d(:). ...
Scalable modeling of real graphs using Kronecker multiplication
 IN 24TH ICML
, 2007
"... Given a large, real graph, how can we generate a synthetic graph that matches its properties, i.e., it has similar degree distribution, similar (small) diameter, similar spectrum, etc? We propose to use “Kronecker graphs”, which naturally obey all of the above properties, and we present KronFit, a f ..."
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Cited by 73 (9 self)
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Given a large, real graph, how can we generate a synthetic graph that matches its properties, i.e., it has similar degree distribution, similar (small) diameter, similar spectrum, etc? We propose to use “Kronecker graphs”, which naturally obey all of the above properties, and we present KronFit, a fast and scalable algorithm for fitting the Kronecker graph generation model to real networks. A naive approach to fitting would take superexponential time. In contrast, KronFit takes linear time, by exploiting the structure of Kronecker product and by using sampling. Experiments on large real and synthetic graphs show that KronFit indeed mimics very well the patterns found in the target graphs. Once fitted, the model parameters and the resulting synthetic graphs can be used for anonymization, extrapolations, and graph summarization.
Bayes in the sky: Bayesian inference and model selection in cosmology
 Contemp. Phys
"... The application of Bayesian methods in cosmology and astrophysics has flourished over the past decade, spurred by data sets of increasing size and complexity. In many respects, Bayesian methods have proven to be vastly superior to more traditional statistical tools, offering the advantage of higher ..."
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Cited by 58 (6 self)
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The application of Bayesian methods in cosmology and astrophysics has flourished over the past decade, spurred by data sets of increasing size and complexity. In many respects, Bayesian methods have proven to be vastly superior to more traditional statistical tools, offering the advantage of higher efficiency and of a consistent conceptual basis for dealing with the problem of induction in the presence of uncertainty. This trend is likely to continue in the future, when the way we collect, manipulate and analyse observations and compare them with theoretical models will assume an even more central role in cosmology. This review is an introduction to Bayesian methods in cosmology and astrophysics and recent results in the field. I first present Bayesian probability theory and its conceptual underpinnings, Bayes ’ Theorem and the role of priors. I discuss the problem of parameter inference and its general solution, along with numerical techniques such as Monte Carlo Markov Chain methods. I then review the theory and application of Bayesian model comparison, discussing the notions of Bayesian evidence and effective model complexity, and how to compute and interpret those quantities. Recent developments in cosmological parameter extraction and Bayesian cosmological model building are summarized, highlighting the challenges that lie ahead.
Bayesian sequential inference for nonlinear multivariate diffusions
 Statistics and Computing
, 2006
"... In this paper, we adapt recently developed simulationbased sequential algorithms to the problem concerning the Bayesian analysis of discretely observed diffusion processes. The estimation framework involves the introduction of m −1 latent data points between every pair of observations. Sequential ..."
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Cited by 52 (5 self)
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In this paper, we adapt recently developed simulationbased sequential algorithms to the problem concerning the Bayesian analysis of discretely observed diffusion processes. The estimation framework involves the introduction of m −1 latent data points between every pair of observations. Sequential MCMC methods are then used to sample the posterior distribution of the latent data and the model parameters online. The method is applied to the estimation of parameters in a simple stochastic volatility model (SV) of the U.S. shortterm interest rate. We also provide a simulation study to validate our method, using synthetic data generated by the SV model with parameters calibrated to match weekly observations of the U.S. shortterm interest rate. 1
Random Generation of Bayesian Networks
 IN BRAZILIAN SYMP. ON ARTIFICIAL INTELLIGENCE
, 2002
"... This paper presents new methods for generation of random Bayesian networks. Such methods can be used to test inference and learning algorithms for Bayesian networks, and to obtain insights on average properties of such networks. Any method that generates Bayesian networks must first generate dir ..."
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Cited by 36 (6 self)
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This paper presents new methods for generation of random Bayesian networks. Such methods can be used to test inference and learning algorithms for Bayesian networks, and to obtain insights on average properties of such networks. Any method that generates Bayesian networks must first generate directed acyclic graphs (the "structure" of the network) and then, for the generated graph, conditional probability distributions. No algorithm in the literature currently offers guarantees concerning the distribution of generated Bayesian networks. Using tools from the theory of Markov chains, we propose algorithms that can generate uniformly distributed samples of directed acyclic graphs. We introduce methods for the uniform generation of multiconnected and singlyconnected networks for a given number of nodes; constraints on node degree and number of arcs can be easily imposed. After a directed acyclic graph is uniformly generated, the conditional distributions are produced by sampling Dirichlet distributions.