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294
An introduction to variational methods for graphical models
 TO APPEAR: M. I. JORDAN, (ED.), LEARNING IN GRAPHICAL MODELS
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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 770 (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.
DecisionTheoretic Planning: Structural Assumptions and Computational Leverage
 JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH
, 1999
"... Planning under uncertainty is a central problem in the study of automated sequential decision making, and has been addressed by researchers in many different fields, including AI planning, decision analysis, operations research, control theory and economics. While the assumptions and perspectives ..."
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Cited by 515 (4 self)
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Planning under uncertainty is a central problem in the study of automated sequential decision making, and has been addressed by researchers in many different fields, including AI planning, decision analysis, operations research, control theory and economics. While the assumptions and perspectives adopted in these areas often differ in substantial ways, many planning problems of interest to researchers in these fields can be modeled as Markov decision processes (MDPs) and analyzed using the techniques of decision theory. This paper presents an overview and synthesis of MDPrelated methods, showing how they provide a unifying framework for modeling many classes of planning problems studied in AI. It also describes structural properties of MDPs that, when exhibited by particular classes of problems, can be exploited in the construction of optimal or approximately optimal policies or plans. Planning problems commonly possess structure in the reward and value functions used to de...
The generalized distributive law
 Information Theory, IEEE Transactions on
"... Abstract—In this semitutorial paper we discuss a general message passing algorithm, which we call the generalized distributive law (GDL). The GDL is a synthesis of the work of many authors in the information theory, digital communications, signal processing, statistics, and artificial intelligence ..."
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Cited by 359 (2 self)
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Abstract—In this semitutorial paper we discuss a general message passing algorithm, which we call the generalized distributive law (GDL). The GDL is a synthesis of the work of many authors in the information theory, digital communications, signal processing, statistics, and artificial intelligence communities. It includes as special cases the Baum–Welch algorithm, the fast Fourier transform (FFT) on any finite Abelian group, the Gallager–Tanner–Wiberg decoding algorithm, Viterbi’s algorithm, the BCJR algorithm, Pearl’s “belief propagation ” algorithm, the Shafer–Shenoy probability propagation algorithm, and the turbo decoding algorithm. Although this algorithm is guaranteed to give exact answers only in certain cases (the “junction tree ” condition), unfortunately not including the cases of GTW with cycles or turbo decoding, there is much experimental evidence, and a few theorems, suggesting that it often works approximately even when it is not supposed to. Index Terms—Belief propagation, distributive law, graphical models, junction trees, turbo codes. I.
Bucket Elimination: A Unifying Framework for Reasoning
"... Bucket elimination is an algorithmic framework that generalizes dynamic programming to accommodate many problemsolving and reasoning tasks. Algorithms such as directionalresolution for propositional satisfiability, adaptiveconsistency for constraint satisfaction, Fourier and Gaussian elimination ..."
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Cited by 298 (58 self)
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Bucket elimination is an algorithmic framework that generalizes dynamic programming to accommodate many problemsolving and reasoning tasks. Algorithms such as directionalresolution for propositional satisfiability, adaptiveconsistency for constraint satisfaction, Fourier and Gaussian elimination for solving linear equalities and inequalities, and dynamic programming for combinatorial optimization, can all be accommodated within the bucket elimination framework. Many probabilistic inference tasks can likewise be expressed as bucketelimination algorithms. These include: belief updating, finding the most probable explanation, and expected utility maximization. These algorithms share the same performance guarantees; all are time and space exponential in the inducedwidth of the problem's interaction graph. While elimination strategies have extensive demands on memory, a contrasting class of algorithms called "conditioning search" require only linear space. Algorithms in this class split a problem into subproblems by instantiating a subset of variables, called a conditioning set, or a cutset. Typical examples of conditioning search algorithms are: backtracking (in constraint satisfaction), and branch and bound (for combinatorial optimization). The paper presents the bucketelimination framework as a unifying theme across probabilistic and deterministic reasoning tasks and show how conditioning search can be augmented to systematically trade space for time.
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 250 (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 223 (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
Exploiting Causal Independence in Bayesian Network Inference
 Journal of Artificial Intelligence Research
, 1996
"... A new method is proposed for exploiting causal independencies in exact Bayesian network inference. ..."
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Cited by 181 (10 self)
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A new method is proposed for exploiting causal independencies in exact Bayesian network inference.
Collective classification in network data
, 2008
"... Numerous realworld applications produce networked data such as web data (hypertext documents connected via hyperlinks) and communication networks (people connected via communication links). A recent focus in machine learning research has been to extend traditional machine learning classification te ..."
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Cited by 178 (32 self)
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Numerous realworld applications produce networked data such as web data (hypertext documents connected via hyperlinks) and communication networks (people connected via communication links). A recent focus in machine learning research has been to extend traditional machine learning classification techniques to classify nodes in such data. In this report, we attempt to provide a brief introduction to this area of research and how it has progressed during the past decade. We introduce four of the most widely used inference algorithms for classifying networked data and empirically compare them on both synthetic and realworld data.
Representing and querying correlated tuples in probabilistic databases
 In ICDE
, 2007
"... Probabilistic databases have received considerable attention recently due to the need for storing uncertain data produced by many real world applications. The widespread use of probabilistic databases is hampered by two limitations: (1) current probabilistic databases make simplistic assumptions abo ..."
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Cited by 142 (11 self)
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Probabilistic databases have received considerable attention recently due to the need for storing uncertain data produced by many real world applications. The widespread use of probabilistic databases is hampered by two limitations: (1) current probabilistic databases make simplistic assumptions about the data (e.g., complete independence among tuples) that make it difficult to use them in applications that naturally produce correlated data, and (2) most probabilistic databases can only answer a restricted subset of the queries that can be expressed using traditional query languages. We address both these limitations by proposing a framework that can represent not only probabilistic tuples, but also correlations that may be present among them. Our proposed framework naturally lends itself to the possible world semantics thus preserving the precise query semantics extant in current probabilistic databases. We develop an efficient strategy for query evaluation over such probabilistic databases by casting the query processing problem as an inference problem in an appropriately constructed probabilistic graphical model. We present several optimizations specific to probabilistic databases that enable efficient query evaluation. We validate our approach by presenting an experimental evaluation that illustrates the effectiveness of our techniques at answering various queries using real and synthetic datasets. 1