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Factor Graphs and the SumProduct Algorithm
 IEEE TRANSACTIONS ON INFORMATION THEORY
, 1998
"... A factor graph is a bipartite graph that expresses how a "global" function of many variables factors into a product of "local" functions. Factor graphs subsume many other graphical models including Bayesian networks, Markov random fields, and Tanner graphs. Following one simple c ..."
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Cited by 1787 (72 self)
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A factor graph is a bipartite graph that expresses how a "global" function of many variables factors into a product of "local" functions. Factor graphs subsume many other graphical models including Bayesian networks, Markov random fields, and Tanner graphs. Following one simple computational rule, the sumproduct algorithm operates in factor graphs to computeeither exactly or approximatelyvarious marginal functions by distributed messagepassing in the graph. A wide variety of algorithms developed in artificial intelligence, signal processing, and digital communications can be derived as specific instances of the sumproduct algorithm, including the forward/backward algorithm, the Viterbi algorithm, the iterative "turbo" decoding algorithm, Pearl's belief propagation algorithm for Bayesian networks, the Kalman filter, and certain fast Fourier transform algorithms.
An introduction to variational methods for graphical models
 TO APPEAR: M. I. JORDAN, (ED.), LEARNING IN GRAPHICAL MODELS
"... ..."
Cognitive networks
 in Proc. of IEEE DySPAN 2005
, 2005
"... Abstract — This paper presents a definition and framework for a novel type of adaptive data network: the cognitive network. In a cognitive network, the collection of elements that make up the network observes network conditions and then, using prior knowledge gained from previous interactions with t ..."
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Cited by 1090 (7 self)
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Abstract — This paper presents a definition and framework for a novel type of adaptive data network: the cognitive network. In a cognitive network, the collection of elements that make up the network observes network conditions and then, using prior knowledge gained from previous interactions with the network, plans, decides and acts on this information. Cognitive networks are different from other “intelligent ” communication technologies because these actions are taken with respect to the endtoend goals of a data flow. In addition to the cognitive aspects of the network, a specification language is needed to translate the user’s endtoend goals into a form understandable by the cognitive process. The cognitive network also depends on a Software Adaptable Network that has both an external interface accessible to the cognitive network and network status sensors. These devices are used to provide control and feedback. The paper concludes by presenting a simple case study to illustrate a cognitive network and its framework. I.
Using Bayesian networks to analyze expression data
 Journal of Computational Biology
, 2000
"... DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biologica ..."
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Cited by 1076 (18 self)
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DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graphbased model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cellcycle measurements of Spellman et al. (1998). Key words: gene expression, microarrays, Bayesian methods. 1.
Turbo decoding as an instance of Pearl’s belief propagation algorithm
 IEEE Journal on Selected Areas in Communications
, 1998
"... Abstract—In this paper, we will describe the close connection between the now celebrated iterative turbo decoding algorithm of Berrou et al. and an algorithm that has been well known in the artificial intelligence community for a decade, but which is relatively unknown to information theorists: Pear ..."
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Cited by 420 (16 self)
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Abstract—In this paper, we will describe the close connection between the now celebrated iterative turbo decoding algorithm of Berrou et al. and an algorithm that has been well known in the artificial intelligence community for a decade, but which is relatively unknown to information theorists: Pearl’s belief propagation algorithm. We shall see that if Pearl’s algorithm is applied to the “belief network ” of a parallel concatenation of two or more codes, the turbo decoding algorithm immediately results. Unfortunately, however, this belief diagram has loops, and Pearl only proved that his algorithm works when there are no loops, so an explanation of the excellent experimental performance of turbo decoding is still lacking. However, we shall also show that Pearl’s algorithm can be used to routinely derive previously known iterative, but suboptimal, decoding algorithms for a number of other errorcontrol systems, including Gallager’s
Probabilistic Boolean networks: a rulebased uncertainty model for gene regulatory networks
, 2002
"... Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rulebased dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selec ..."
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Cited by 382 (58 self)
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Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rulebased dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selection; and (iv ) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes.
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 364 (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.
Learning Bayesian network structure from massive datasets: the “sparse candidate” algorithm
 In Proceedings of the 15th Conference on Uncertainty in Artificial Intelligence (UAI
, 1999
"... Learning Bayesian networks is often cast as an optimization problem, where the computational task is to find a structure that maximizes a statistically motivated score. By and large, existing learning tools address this optimization problem using standard heuristic search techniques. Since the sear ..."
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Cited by 248 (8 self)
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Learning Bayesian networks is often cast as an optimization problem, where the computational task is to find a structure that maximizes a statistically motivated score. By and large, existing learning tools address this optimization problem using standard heuristic search techniques. Since the search space is extremely large, such search procedures can spend most of the time examining candidates that are extremely unreasonable. This problem becomes critical when we deal with data sets that are large either in the number of instances, or the number of attributes. In this paper, we introduce an algorithm that achieves faster learning by restricting the search space. This iterative algorithm restricts the parents of each variable to belong to a small subset of candidates. We then search for a network that satisfies these constraints. The learned network is then used for selecting better candidates for the next iteration. We evaluate this algorithm both on synthetic and reallife data. Our results show that it is significantly faster than alternative search procedures without loss of quality in the learned structures. 1
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 gra ..."
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Cited by 242 (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