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47
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 598 (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.
The Bayes Net Toolbox for MATLAB
 Computing Science and Statistics
, 2001
"... The Bayes Net Toolbox (BNT) is an opensource Matlab package for directed graphical models. BNT supports many kinds of nodes (probability distributions), exact and approximate inference, parameter and structure learning, and static and dynamic models. BNT is widely used in teaching and research: the ..."
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Cited by 186 (1 self)
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The Bayes Net Toolbox (BNT) is an opensource Matlab package for directed graphical models. BNT supports many kinds of nodes (probability distributions), exact and approximate inference, parameter and structure learning, and static and dynamic models. BNT is widely used in teaching and research: the web page has received over 28,000 hits since May 2000. In this paper, we discuss a broad spectrum of issues related to graphical models (directed and undirected), and describe, at a highlevel, how BNT was designed to cope with them all. We also compare BNT to other software packages for graphical models, and to the nascent OpenBayes effort.
Modelling gene expression data using dynamic bayesian networks
, 1999
"... Recently, there has been much interest in reverse engineering genetic networks from time series data. In this paper, we show that most of the proposed discrete time models — including the boolean network model [Kau93, SS96], the linear model of D’haeseleer et al. [DWFS99], and the nonlinear model of ..."
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Cited by 170 (1 self)
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Recently, there has been much interest in reverse engineering genetic networks from time series data. In this paper, we show that most of the proposed discrete time models — including the boolean network model [Kau93, SS96], the linear model of D’haeseleer et al. [DWFS99], and the nonlinear model of Weaver et al. [WWS99] — are all special cases of a general class of models called Dynamic Bayesian Networks (DBNs). The advantages of DBNs include the ability to model stochasticity, to incorporate prior knowledge, and to handle hidden variables and missing data in a principled way. This paper provides a review of techniques for learning DBNs. Keywords: Genetic networks, boolean networks, Bayesian networks, neural networks, reverse engineering, machine learning. 1
Tutorial on Variational Approximation Methods
 In Advanced Mean Field Methods: Theory and Practice
, 2000
"... We provide an introduction to the theory and use of variational methods for inference and estimation in the context of graphical models. Variational methods become useful as ecient approximate methods when the structure of the graph model no longer admits feasible exact probabilistic calculations. T ..."
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Cited by 76 (1 self)
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We provide an introduction to the theory and use of variational methods for inference and estimation in the context of graphical models. Variational methods become useful as ecient approximate methods when the structure of the graph model no longer admits feasible exact probabilistic calculations. The emphasis of this tutorial is on illustrating how inference and estimation problems can be transformed into variational form along with describing the resulting approximation algorithms and their properties insofar as these are currently known. 1 Introduction The term variational methods refers to a large collection of optimization techniques. The classical context for these methods involves nding the extremum of an integral depending on an unknown function and its derivatives. This classical de nition, however, and the accompanying calculus of variation no longer adequately characterizes modern variational methods. Modern variational approaches have become indispensable tools in...
Hybrid Bayesian Networks for Reasoning about Complex Systems
, 2002
"... Many realworld systems are naturally modeled as hybrid stochastic processes, i.e., stochastic processes that contain both discrete and continuous variables. Examples include speech recognition, target tracking, and monitoring of physical systems. The task is usually to perform probabilistic inferen ..."
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Cited by 50 (0 self)
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Many realworld systems are naturally modeled as hybrid stochastic processes, i.e., stochastic processes that contain both discrete and continuous variables. Examples include speech recognition, target tracking, and monitoring of physical systems. The task is usually to perform probabilistic inference, i.e., infer the hidden state of the system given some noisy observations. For example, we can ask what is the probability that a certain word was pronounced given the readings of our microphone, what is the probability that a submarine is trying to surface given our sonar data, and what is the probability of a valve being open given our pressure and flow readings. Bayesian networks are
Variational Approximations between Mean Field Theory and the Junction Tree Algorithm
 In Uncertainty in Artificial Intelligence
, 2000
"... Recently, variational approximations such as the mean field approximation have received much interest. We extend the standard mean field method by using an approximating distribution that factorises into cluster potentials. This includes undirected graphs, directed acyclic graphs and junction ..."
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Cited by 45 (1 self)
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Recently, variational approximations such as the mean field approximation have received much interest. We extend the standard mean field method by using an approximating distribution that factorises into cluster potentials. This includes undirected graphs, directed acyclic graphs and junction trees. We derive generalised mean field equations to optimise the cluster potentials. We show that the method bridges the gap between the standard mean field approximation and the exact junction tree algorithm. In addition, we address the problem of how to choose the structure and the free parameters of the approximating distribution. From the generalised mean field equations we derive rules to simplify the approximation in advance without affecting the potential accuracy of the model class. We also show how the method fits into some other variational approximations that are currently popular. 1 INTRODUCTION Graphical models, such as Bayesian networks, Markov fields, and Bolt...
Building Blocks For Hierarchical Latent Variable Models
 In Proc. 3rd Int. Conf. on Independent Component Analysis and Signal Separation (ICA2001
, 2001
"... We introduce building blocks from which a large variety of latent variable models can be built. The blocks include continuous and discrete variables, summation, addition, nonlinearity and switching. Ensemble learning provides a cost function which can be used for updating the variables as well as op ..."
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Cited by 29 (17 self)
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We introduce building blocks from which a large variety of latent variable models can be built. The blocks include continuous and discrete variables, summation, addition, nonlinearity and switching. Ensemble learning provides a cost function which can be used for updating the variables as well as optimising the model structure. The blocks are designed to fit together and to yield efficient update rules. Emphasis is on local computation which results in linear computational complexity. We propose and test a structure with a hierachical nonlinear model for variances and means.
Inference and Learning in Hybrid Bayesian Networks
, 1998
"... We survey the literature on methods for inference and learning in Bayesian Networks composed of discrete and continuous nodes, in which the continuous nodes have a multivariate Gaussian distribution, whose mean and variance depends on the values of the discrete nodes. We also briefly consider hybrid ..."
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Cited by 26 (2 self)
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We survey the literature on methods for inference and learning in Bayesian Networks composed of discrete and continuous nodes, in which the continuous nodes have a multivariate Gaussian distribution, whose mean and variance depends on the values of the discrete nodes. We also briefly consider hybrid Dynamic Bayesian Networks, an extension of switching Kalman filters. This report is meant to summarize what is known at a sufficient level of detail to enable someone to implement the algorithms, but without dwelling on formalities.
Exact inference in networks with discrete children of continuous parents
 in: J. Breese, D. Koller (Eds.), Uncertainty in Artificial Intelligence
, 2001
"... Many real life domains contain a mixture of discrete and continuous variables and can be modeled as hybrid Bayesian Networks (BNs). An important subclass of hybrid BNs are conditional linear Gaussian (CLG) networks, where the conditional distribution of the continuous variables given an assignment t ..."
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Cited by 25 (2 self)
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Many real life domains contain a mixture of discrete and continuous variables and can be modeled as hybrid Bayesian Networks (BNs). An important subclass of hybrid BNs are conditional linear Gaussian (CLG) networks, where the conditional distribution of the continuous variables given an assignment to the discrete variables is a multivariate Gaussian. Lauritzen’s extension to the clique tree algorithm can be used for exact inference in CLG networks. However, many domains include discrete variables that depend on continuous ones, and CLG networks do not allow such dependencies to be represented. In this paper, we propose the first “exact ” inference algorithm for augmented CLG networks — CLG networks augmented by allowing discrete children of continuous parents. Our algorithm is based on Lauritzen’s algorithm, and is exact in a similar sense: it computes the exact distributions over the discrete nodes, and the exact first and second moments of the continuous ones, up to inaccuracies resulting from numerical integration used within the algorithm. In the special case of softmax CPDs, we show that integration can often be done efficiently, and that using the first two moments leads to a particularly accurate approximation. We show empirically that our algorithm achieves substantially higher accuracy at lower cost than previous algorithms for this task. 1
Approximating probability density functions with mixtures of truncated exponentials
 Proceedings of the Tenth Conference on Information Processing and Management of Uncertainty in KnowledgeBased Systems (IPMU04), 2004
, 2006
"... Mixtures of truncated exponentials (MTE) potentials are an alternative to discretization and Monte Carlo methods for solving hybrid Bayesian networks. Any probability density function (PDF) can be approximated by an MTE potential, which can always be marginalized in closed form. This allows propagat ..."
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Cited by 23 (14 self)
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Mixtures of truncated exponentials (MTE) potentials are an alternative to discretization and Monte Carlo methods for solving hybrid Bayesian networks. Any probability density function (PDF) can be approximated by an MTE potential, which can always be marginalized in closed form. This allows propagation to be done exactly using the ShenoyShafer architecture for computing marginals, with no restrictions on the construction of a join tree. This paper presents MTE potentials that approximate standard PDF’s and applications of these potentials for solving inference problems in hybrid Bayesian networks. These approximations will extend the types of inference problems that can be modeled with Bayesian networks, as demonstrated using three examples.