Results 1  10
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325
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 612 (11 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.
An Introduction to MCMC for Machine Learning
, 2003
"... This purpose of this introductory paper is threefold. First, it introduces the Monte Carlo method with emphasis on probabilistic machine learning. Second, it reviews the main building blocks of modern Markov chain Monte Carlo simulation, thereby providing and introduction to the remaining papers of ..."
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Cited by 222 (2 self)
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This purpose of this introductory paper is threefold. First, it introduces the Monte Carlo method with emphasis on probabilistic machine learning. Second, it reviews the main building blocks of modern Markov chain Monte Carlo simulation, thereby providing and introduction to the remaining papers of this special issue. Lastly, it discusses new interesting research horizons.
Image Parsing: Unifying Segmentation, Detection, and Recognition
, 2005
"... In this paper we present a Bayesian framework for parsing images into their constituent visual patterns. The parsing algorithm optimizes the posterior probability and outputs a scene representation in a "parsing graph", in a spirit similar to parsing sentences in speech and natural language. The ..."
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Cited by 160 (18 self)
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In this paper we present a Bayesian framework for parsing images into their constituent visual patterns. The parsing algorithm optimizes the posterior probability and outputs a scene representation in a "parsing graph", in a spirit similar to parsing sentences in speech and natural language. The algorithm constructs the parsing graph and reconfigures it dynamically using a set of reversible Markov chain jumps. This computational framework integrates two popular inference approaches  generative (topdown) methods and discriminative (bottomup) methods. The former formulates the posterior probability in terms of generative models for images defined by likelihood functions and priors. The latter computes discriminative probabilities based on a sequence (cascade) of bottomup tests/filters.
Fastest Mixing Markov Chain on A Graph
 SIAM REVIEW
, 2003
"... We consider a symmetric random walk on a connected graph, where each edge is labeled with the probability of transition between the two adjacent vertices. The associated Markov chain has a uniform equilibrium distribution; the rate of convergence to this distribution, i.e. the mixing rate of the Mar ..."
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Cited by 90 (15 self)
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We consider a symmetric random walk on a connected graph, where each edge is labeled with the probability of transition between the two adjacent vertices. The associated Markov chain has a uniform equilibrium distribution; the rate of convergence to this distribution, i.e. the mixing rate of the Markov chain, is determined by the second largest (in magnitude) eigenvalue of the transition matrix. In this paper we address the problem of assigning probabilities to the edges of the graph in such a way as to minimize the second largest magnitude eigenvalue, i.e., the problem of finding the fastest mixing Markov chain on the graph. We show that
A Stochastic Grammar of Images
 Foundations and Trends in Computer Graphics and Vision
, 2006
"... This exploratory paper quests for a stochastic and context sensitive grammar of images. The grammar should achieve the following four objectives and thus serves as a unified framework of representation, learning, and recognition for a large number of object categories. (i) The grammar represents bot ..."
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Cited by 81 (17 self)
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This exploratory paper quests for a stochastic and context sensitive grammar of images. The grammar should achieve the following four objectives and thus serves as a unified framework of representation, learning, and recognition for a large number of object categories. (i) The grammar represents both the hierarchical decompositions from scenes, to objects, parts, primitives and pixels by terminal and nonterminal nodes and the contexts for spatial and functional relations by horizontal links between the nodes. It formulates each object category as the set of all possible valid configurations produced by the grammar. (ii) The grammar is embodied in a simple And–Or graph representation where each Ornode points to alternative subconfigurations and an Andnode is decomposed into a number of components. This representation supports recursive topdown/bottomup procedures for image parsing under the Bayesian framework and make it convenient to scale
A tutorial on particle filtering and smoothing: fifteen years later
 OXFORD HANDBOOK OF NONLINEAR FILTERING
, 2011
"... Optimal estimation problems for nonlinear nonGaussian statespace models do not typically admit analytic solutions. Since their introduction in 1993, particle filtering methods have become a very popular class of algorithms to solve these estimation problems numerically in an online manner, i.e. r ..."
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Cited by 72 (9 self)
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Optimal estimation problems for nonlinear nonGaussian statespace models do not typically admit analytic solutions. Since their introduction in 1993, particle filtering methods have become a very popular class of algorithms to solve these estimation problems numerically in an online manner, i.e. recursively as observations become available, and are now routinely used in fields as diverse as computer vision, econometrics, robotics and navigation. The objective of this tutorial is to provide a complete, uptodate survey of this field as of 2008. Basic and advanced particle methods for filtering as well as smoothing are presented.
Random sampling from a search engine’s index
 In Proceedings of the 15th International World Wide Web Conference (WWW
, 2006
"... We revisit a problem introduced by Bharat and Broder almost a decade ago: how to sample random pages from the corpus of documents indexed by a search engine, using only the search engine’s public interface? Such a primitive is particularly useful in creating objective benchmarks for search engines. ..."
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Cited by 63 (6 self)
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We revisit a problem introduced by Bharat and Broder almost a decade ago: how to sample random pages from the corpus of documents indexed by a search engine, using only the search engine’s public interface? Such a primitive is particularly useful in creating objective benchmarks for search engines. The technique of Bharat and Broder suffers from a wellrecorded bias: it favors long documents. In this paper we introduce two novel sampling algorithms: a lexiconbased algorithm and a random walk algorithm. Our algorithms produce biased samples, but each sample is accompanied by a weight, which represents its bias. The samples, in conjunction with the weights, are then used to simulate nearuniform samples. To this end, we resort to four wellknown Monte Carlo simulation methods: rejection sampling, importance sampling, the MetropolisHastings algorithm, and the Maximum Degree method. The limited access to search engines force our algorithms to use bias weights that are only “approximate”. We characterize analytically the effect of approximate bias weights on Monte Carlo methods and conclude that our algorithms are guaranteed to produce nearuniform samples from the search engine’s corpus. Our study of approximate Monte Carlo methods could be of independent interest. Experiments on a corpus of 2.4 million documents substantiate our analytical findings and show that our algorithms do not have significant bias towards long documents. We use our algorithms to collect comparative statistics about the corpora of the Google, MSN Search, and Yahoo! search engines.
Marginalized particle filters for mixed linear/nonlinear statespace models
 IEEE Transactions on Signal Processing
, 2005
"... Abstract—The particle filter offers a general numerical tool to approximate the posterior density function for the state in nonlinear and nonGaussian filtering problems. While the particle filter is fairly easy to implement and tune, its main drawback is that it is quite computer intensive, with th ..."
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Cited by 62 (23 self)
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Abstract—The particle filter offers a general numerical tool to approximate the posterior density function for the state in nonlinear and nonGaussian filtering problems. While the particle filter is fairly easy to implement and tune, its main drawback is that it is quite computer intensive, with the computational complexity increasing quickly with the state dimension. One remedy to this problem is to marginalize out the states appearing linearly in the dynamics. The result is that one Kalman filter is associated with each particle. The main contribution in this paper is the derivation of the details for the marginalized particle filter for a general nonlinear statespace model. Several important special cases occurring in typical signal processing applications will also be discussed. The marginalized particle filter is applied to an integrated navigation system for aircraft. It is demonstrated that the complete highdimensional system can be based on a particle filter using marginalization for all but three states. Excellent performance on real flight data is reported. Index Terms—Kalman filter, marginalization, navigation systems, nonlinear systems, particle filter, state estimation. I.
Parameter estimation for text analysis
, 2004
"... Abstract. Presents parameter estimation methods common with discrete probability distributions, which is of particular interest in text modeling. Starting with maximum likelihood, a posteriori and Bayesian estimation, central concepts like conjugate distributions and Bayesian networks are reviewed. ..."
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Cited by 59 (0 self)
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Abstract. Presents parameter estimation methods common with discrete probability distributions, which is of particular interest in text modeling. Starting with maximum likelihood, a posteriori and Bayesian estimation, central concepts like conjugate distributions and Bayesian networks are reviewed. As an application, the model of latent Dirichlet allocation (LDA) is explained in detail with a full derivation of an approximate inference algorithm based on Gibbs sampling, including a discussion of Dirichlet hyperparameter estimation. Finally, analysis methods of LDA models are discussed.
An integrated probabilistic model for functional prediction of proteins
 J. Comp. Biol
, 2003
"... We develop an integrated probabilistic model to combine protein physical interactions, genetic interactions, highly correlated gene expression networks, protein complex data, and domain structures of individual proteins to predict protein functions. The model is an extension of our previous model fo ..."
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Cited by 57 (0 self)
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We develop an integrated probabilistic model to combine protein physical interactions, genetic interactions, highly correlated gene expression networks, protein complex data, and domain structures of individual proteins to predict protein functions. The model is an extension of our previous model for protein function prediction based on Markovian random field theory. The model is flexible in that other protein pairwise relationship information and features of individual proteins can be easily incorporated. Two features distinguish the integrated approach from other available methods for protein function prediction. One is that the integrated approach uses all available sources of information with different weights for different sources of data. It is a global approach that takes the whole network into consideration. The second feature is that the posterior probability that a protein has the function of interest is assigned. The posterior probability indicates how confident we are about assigning the function to the protein. We apply our integrated approach to predict functions of yeast proteins based upon MIPS protein function classifications and upon the interaction networks based on MIPS physical and genetic interactions, gene expression profiles, tandem affinity purification (TAP) protein complex data, and protein domain information. We study the recall and precision of the integrated approach using different sources of information by the leaveoneout approach. In contrast to using MIPS physical interactions only, the integrated approach combining all of the information increases the recall from 57 % to 87% when the precision is set at 57%—an increase of 30%. Key words: function prediction, Pfam domain, protein–protein interaction, Markov random field,