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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 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.
Dynamic Bayesian Networks: Representation, Inference and Learning
, 2002
"... Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have bee ..."
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Cited by 564 (3 self)
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Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have been used for problems ranging from tracking planes and missiles to predicting the economy. However, HMMs
and KFMs are limited in their “expressive power”. Dynamic Bayesian Networks (DBNs) generalize HMMs by allowing the state space to be represented in factored form, instead of as a single discrete random variable. DBNs generalize KFMs by allowing arbitrary probability distributions, not just (unimodal) linearGaussian. In this thesis, I will discuss how to represent many different kinds of models as DBNs, how to perform exact and approximate inference in DBNs, and how to learn DBN models from sequential data.
In particular, the main novel technical contributions of this thesis are as follows: a way of representing
Hierarchical HMMs as DBNs, which enables inference to be done in O(T) time instead of O(T 3), where T is the length of the sequence; an exact smoothing algorithm that takes O(log T) space instead of O(T); a simple way of using the junction tree algorithm for online inference in DBNs; new complexity bounds on exact online inference in DBNs; a new deterministic approximate inference algorithm called factored frontier; an analysis of the relationship between the BK algorithm and loopy belief propagation; a way of
applying RaoBlackwellised particle filtering to DBNs in general, and the SLAM (simultaneous localization
and mapping) problem in particular; a way of extending the structural EM algorithm to DBNs; and a variety of different applications of DBNs. However, perhaps the main value of the thesis is its catholic presentation of the field of sequential data modelling.
High dimensional graphs and variable selection with the Lasso
 ANNALS OF STATISTICS
, 2006
"... The pattern of zero entries in the inverse covariance matrix of a multivariate normal distribution corresponds to conditional independence restrictions between variables. Covariance selection aims at estimating those structural zeros from data. We show that neighborhood selection with the Lasso is a ..."
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Cited by 399 (21 self)
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The pattern of zero entries in the inverse covariance matrix of a multivariate normal distribution corresponds to conditional independence restrictions between variables. Covariance selection aims at estimating those structural zeros from data. We show that neighborhood selection with the Lasso is a computationally attractive alternative to standard covariance selection for sparse highdimensional graphs. Neighborhood selection estimates the conditional independence restrictions separately for each node in the graph and is hence equivalent to variable selection for Gaussian linear models. We show that the proposed neighborhood selection scheme is consistent for sparse highdimensional graphs. Consistency hinges on the choice of the penalty parameter. The oracle value for optimal prediction does not lead to a consistent neighborhood estimate. Controlling instead the probability of falsely joining some distinct connectivity components of the graph, consistent estimation for sparse graphs is achieved (with exponential rates), even when the number of variables grows as the number of observations raised to an arbitrary power.
Convolution Kernels on Discrete Structures
, 1999
"... We introduce a new method of constructing kernels on sets whose elements are discrete structures like strings, trees and graphs. The method can be applied iteratively to build a kernel on an infinite set from kernels involving generators of the set. The family of kernels generated generalizes the fa ..."
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Cited by 368 (0 self)
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We introduce a new method of constructing kernels on sets whose elements are discrete structures like strings, trees and graphs. The method can be applied iteratively to build a kernel on an infinite set from kernels involving generators of the set. The family of kernels generated generalizes the family of radial basis kernels. It can also be used to define kernels in the form of joint Gibbs probability distributions. Kernels can be built from hidden Markov random elds, generalized regular expressions, pairHMMs, or ANOVA decompositions. Uses of the method lead to open problems involving the theory of infinitely divisible positive definite functions. Fundamentals of this theory and the theory of reproducing kernel Hilbert spaces are reviewed and applied in establishing the validity of the method.
Nonparametric Belief Propagation
 IN CVPR
, 2002
"... In applications of graphical models arising in fields such as computer vision, the hidden variables of interest are most naturally specified by continuous, nonGaussian distributions. However, due to the limitations of existing inf#6F6F3 algorithms, it is of#]k necessary tof#3# coarse, ..."
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Cited by 208 (25 self)
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In applications of graphical models arising in fields such as computer vision, the hidden variables of interest are most naturally specified by continuous, nonGaussian distributions. However, due to the limitations of existing inf#6F6F3 algorithms, it is of#]k necessary tof#3# coarse, discrete approximations to such models. In this paper, we develop a nonparametric belief propagation (NBP) algorithm, which uses stochastic methods to propagate kernelbased approximations to the true continuous messages. Each NBP message update is based on an efficient sampling procedure which can accomodate an extremely broad class of potentialf#l3]k[[z3 allowing easy adaptation to new application areas. We validate our method using comparisons to continuous BP for Gaussian networks, and an application to the stereo vision problem.
Algebraic Algorithms for Sampling from Conditional Distributions
 Annals of Statistics
, 1995
"... We construct Markov chain algorithms for sampling from discrete exponential families conditional on a sufficient statistic. Examples include generating tables with fixed row and column sums and higher dimensional analogs. The algorithms involve finding bases for associated polynomial ideals and so a ..."
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Cited by 192 (16 self)
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We construct Markov chain algorithms for sampling from discrete exponential families conditional on a sufficient statistic. Examples include generating tables with fixed row and column sums and higher dimensional analogs. The algorithms involve finding bases for associated polynomial ideals and so an excursion into computational algebraic geometry.
On the Optimality of Solutions of the MaxProduct Belief Propagation Algorithm in Arbitrary Graphs
, 2001
"... Graphical models, suchasBayesian networks and Markov random fields, represent statistical dependencies of variables by a graph. The maxproduct "belief propagation" algorithm is a localmessage passing algorithm on this graph that is known to converge to a unique fixed point when the graph is a tr ..."
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Cited by 185 (15 self)
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Graphical models, suchasBayesian networks and Markov random fields, represent statistical dependencies of variables by a graph. The maxproduct "belief propagation" algorithm is a localmessage passing algorithm on this graph that is known to converge to a unique fixed point when the graph is a tree. Furthermore, when the graph is a tree, the assignment based on the fixedpoint yields the most probable a posteriori (MAP) values of the unobserved variables given the observed ones. Recently, good
Correctness of Local Probability Propagation in Graphical Models with Loops
, 2000
"... This article analyzes the behavior of local propagation rules in graphical models with a loop. ..."
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Cited by 178 (9 self)
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This article analyzes the behavior of local propagation rules in graphical models with a loop.
Dependency networks for inference, collaborative filtering, and data visualization
 Journal of Machine Learning Research
"... We describe a graphical model for probabilistic relationshipsan alternative tothe Bayesian networkcalled a dependency network. The graph of a dependency network, unlike aBayesian network, is potentially cyclic. The probability component of a dependency network, like aBayesian network, is a set of ..."
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Cited by 159 (10 self)
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We describe a graphical model for probabilistic relationshipsan alternative tothe Bayesian networkcalled a dependency network. The graph of a dependency network, unlike aBayesian network, is potentially cyclic. The probability component of a dependency network, like aBayesian network, is a set of conditional distributions, one for each nodegiven its parents. We identify several basic properties of this representation and describe a computationally e cient procedure for learning the graph and probability components from data. We describe the application of this representation to probabilistic inference, collaborative ltering (the task of predicting preferences), and the visualization of acausal predictive relationships.
Model selection through sparse maximum likelihood estimation
 Journal of Machine Learning Research
, 2008
"... We consider the problem of estimating the parameters of a Gaussian or binary distribution in such a way that the resulting undirected graphical model is sparse. Our approach is to solve a maximum likelihood problem with an added ℓ1norm penalty term. The problem as formulated is convex but the memor ..."
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Cited by 158 (1 self)
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We consider the problem of estimating the parameters of a Gaussian or binary distribution in such a way that the resulting undirected graphical model is sparse. Our approach is to solve a maximum likelihood problem with an added ℓ1norm penalty term. The problem as formulated is convex but the memory requirements and complexity of existing interior point methods are prohibitive for problems with more than tens of nodes. We present two new algorithms for solving problems with at least a thousand nodes in the Gaussian case. Our first algorithm uses block coordinate descent, and can be interpreted as recursive ℓ1norm penalized regression. Our second algorithm, based on Nesterov’s first order method, yields a complexity estimate with a better dependence on problem size than existing interior point methods. Using a log determinant relaxation of the log partition function (Wainwright and Jordan, 2006), we show that these same algorithms can be used to solve an approximate sparse maximum likelihood problem for the binary case. We test our algorithms on synthetic data, as well as on gene expression and senate voting records data.