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Learning in graphical models
, 2004
"... Statistical applications in fields such as bioinformatics, information retrieval, speech processing, image processing and communications often involve largescale models in which thousands or millions of random variables are linked in complex ways. Graphical models provide a general methodology for ..."
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Cited by 614 (10 self)
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Statistical applications in fields such as bioinformatics, information retrieval, speech processing, image processing and communications often involve largescale models in which thousands or millions of random variables are linked in complex ways. Graphical models provide a general methodology for approaching these problems, and indeed many of the models developed by researchers in these applied fields are instances of the general graphical model formalism. We review some of the basic ideas underlying graphical models, including the algorithmic ideas that allow graphical models to be deployed in largescale data analysis problems. We also present examples of graphical models in bioinformatics, errorcontrol coding and language processing. Key words and phrases: Probabilistic graphical models, junction tree algorithm, sumproduct algorithm, Markov chain Monte Carlo, variational inference, bioinformatics, errorcontrol coding.
Implementing approximate Bayesian inference for latent Gaussian models using integrated nested Laplace approximations: A manual for the inlaprogram
, 2008
"... Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalised) linear models, (generalised) additive models, smoothingspline models, statespace models, semiparametric regression, spatial and spatiotemp ..."
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Cited by 79 (16 self)
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Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalised) linear models, (generalised) additive models, smoothingspline models, statespace models, semiparametric regression, spatial and spatiotemporal models, logGaussian Coxprocesses, geostatistical and geoadditive models. In this paper we consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models, where the latent field is Gaussian, controlled by a few hyperparameters and with nonGaussian response variables. The posterior marginals are not available in closed form due to the nonGaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, both in terms of convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations
Variational Approximations in Bayesian Model Selection for Finite Mixture Distributions
 COMPUTATIONAL STATISTICS AND DATA ANALYSIS
, 2006
"... Variational methods for model comparison have become popular in the neural computing/machine learning literature. In this paper we explore their application to the Bayesian analysis of mixtures of Gaussians. We also consider how the Deviance Information Criterion, or DIC, devised by Spiegelhalter e ..."
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Cited by 12 (3 self)
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Variational methods for model comparison have become popular in the neural computing/machine learning literature. In this paper we explore their application to the Bayesian analysis of mixtures of Gaussians. We also consider how the Deviance Information Criterion, or DIC, devised by Spiegelhalter et al. (2002), can be extended to these types of model by exploiting the use of variational approximations. We illustrate the results of using variational methods for model selection and the calculation of a DIC using real and simulated data. Using the variational approximation, one can simultaneously estimate component parameters and the model complexity. It turns out that, if one starts o# with a large number of components, superfluous components are eliminated as the method converges to a solution, thereby leading to an automatic choice of model complexity, the appropriateness of which is reflected in the DIC values.
Computational advances for and from Bayesian analysis
 Statist. Sci
, 2004
"... Abstract. The emergence in the past years of Bayesian analysis in many methodological and applied fields as the solution to the modeling of complex problems cannot be dissociated from major changes in its computational implementation. We show in this review how the advances in Bayesian analysis and ..."
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Cited by 10 (0 self)
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Abstract. The emergence in the past years of Bayesian analysis in many methodological and applied fields as the solution to the modeling of complex problems cannot be dissociated from major changes in its computational implementation. We show in this review how the advances in Bayesian analysis and statistical computation are intermingled. Key words and phrases: Monte Carlo methods, importance sampling, Markov chain Monte Carlo (MCMC) algorithms.
Statistical challenges of highdimensional data
 52 SPIKE AND SLAB PRIORS FOR BAYESIAN GROUP FEATURE SELECTION
, 1906
"... Modern applications of statistical theory and methods can involve extremely large datasets, often with huge numbers of measurements on each of a comparatively small number of experimental units. New methodology and accompanying theory have emerged in response: the goal of this theme issue is to ill ..."
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Cited by 8 (0 self)
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Modern applications of statistical theory and methods can involve extremely large datasets, often with huge numbers of measurements on each of a comparatively small number of experimental units. New methodology and accompanying theory have emerged in response: the goal of this theme issue is to illustrate a number of these recent developments. This overview article introduces the difficulties that arise with highdimensional data in the context of the very familiar linear statistical model: we give a taste of what can nevertheless be achieved when the parameter vector of interest is sparse, that is, contains many zero elements. We describe other ways of identifying lowdimensional subspaces of the data space that contain all useful information. The topic of classification is then reviewed along with the problem of identifying, from within a very large set, the variables that help to classify observations. Brief mention is made of the visualization of highdimensional data and ways to handle computational problems in Bayesian analysis are described. At appropriate points, reference is made to the other papers in the issue.
Lessons in Uncertainty Quantification for Turbulent Dynamical System
 DCDSA
"... Abstract. The modus operandi of modern applied mathematics in developing very recent mathematical strategies for uncertainty quantification in partially observed highdimensional turbulent dynamical systems is emphasized here. The approach involves the synergy of rigorous mathematical guidelines wit ..."
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Cited by 3 (0 self)
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Abstract. The modus operandi of modern applied mathematics in developing very recent mathematical strategies for uncertainty quantification in partially observed highdimensional turbulent dynamical systems is emphasized here. The approach involves the synergy of rigorous mathematical guidelines with a suite of physically relevant and progressively more complex test models which are mathematically tractable while possessing such important features as the twoway coupling between the resolved dynamics and the turbulent fluxes, intermittency and positive Lyapunov exponents, eddy diffusivity parameterization and turbulent spectra. A large number of new theoretical and computational phenomena which arise in the emerging statisticalstochastic framework for quantifying and mitigating model error in imperfect predictions, such as the existence of information barriers to model improvement, are developed and reviewed here with the intention to introduce mathematicians, applied mathematicians, and scientists to these remarkable emerging topics with increasing practical importance. 1. Introduction. The ‘inevitable reality
doi:10.1155/2011/506583 Research Article
"... Copyright © 2011 Rhydon Jackson et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Machine learning was applied to a challenging ..."
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Copyright © 2011 Rhydon Jackson et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Machine learning was applied to a challenging and biologically significant protein classification problem: the prediction of avonoid UGT acceptor regioselectivity from primary sequence. Novel indices characterizing graphical models of residues were proposed and found to be widely distributed among existing amino acid indices and to cluster residues appropriately. UGT subsequences biochemically linked to regioselectivity were modeled as sets of index sequences. Several learning techniques incorporating these UGT models were compared with classifications based on standard sequence alignment scores. These techniques included an application of time series distance functions to protein classification. Time series distances defined on the index sequences were used in nearest neighbor and support vector machine classifiers. Additionally, Bayesian neural network classifiers were applied to the index sequences. The experiments identified improvements over the nearest neighbor and support vector machine classifications relying on standard alignment similarity scores, as well as strong correlations between specific subsequences and regioselectivities. 1.
The EM algorithm, variational approximations and expectation propagation for mixtures
, 2011
"... ..."
neural networks
"... Predicting expected progeny difference for marbling score in Angus cattle using artificial ..."
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Predicting expected progeny difference for marbling score in Angus cattle using artificial