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59
Graph visualization and navigation in information visualization: a survey
 IEEE Transactions on Visualization and Computer Graphics
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A New Class of Upper Bounds on the Log Partition Function
 In Uncertainty in Artificial Intelligence
, 2002
"... Bounds on the log partition function are important in a variety of contexts, including approximate inference, model fitting, decision theory, and large deviations analysis [11, 5, 4]. We introduce a new class of upper bounds on the log partition function, based on convex combinations of distribution ..."
Abstract

Cited by 159 (27 self)
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Bounds on the log partition function are important in a variety of contexts, including approximate inference, model fitting, decision theory, and large deviations analysis [11, 5, 4]. We introduce a new class of upper bounds on the log partition function, based on convex combinations of distributions in the exponential domain, that is applicable to an arbitrary undirected graphical model. In the special case of convex combinations of treestructured distributions, we obtain a family of variational problems, similar to the Bethe free energy, but distinguished by the following desirable properties: (i) they are convex, and have a unique global minimum; and (ii) the global minimum gives an upper bound on the log partition function. The global minimum is defined by stationary conditions very similar to those defining xed points of belief propagation (BP) or treebased reparameterization [see 13, 14]. As with BP fixed points, the elements of the minimizing argument can be used as approximations to the marginals of the original model. The analysis described here can be extended to structures of higher treewidth (e.g., hypertrees), thereby making connections with more advanced approximations (e.g., Kikuchi and variants [15, 10]).
TreeBased Reparameterization Framework for Analysis of Belief Propagation and Related Algorithms
, 2001
"... We present a treebased reparameterization framework that provides a new conceptual view of a large class of algorithms for computing approximate marginals in graphs with cycles. This class includes the belief propagation or sumproduct algorithm [39, 36], as well as a rich set of variations and ext ..."
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Cited by 102 (21 self)
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We present a treebased reparameterization framework that provides a new conceptual view of a large class of algorithms for computing approximate marginals in graphs with cycles. This class includes the belief propagation or sumproduct algorithm [39, 36], as well as a rich set of variations and extensions of belief propagation. Algorithms in this class can be formulated as a sequence of reparameterization updates, each of which entails refactorizing a portion of the distribution corresponding to an acyclic subgraph (i.e., a tree). The ultimate goal is to obtain an alternative but equivalent factorization using functions that represent (exact or approximate) marginal distributions on cliques of the graph. Our framework highlights an important property of BP and the entire class of reparameterization algorithms: the distribution on the full graph is not changed. The perspective of treebased updates gives rise to a simple and intuitive characterization of the fixed points in terms of tree consistency. We develop interpretations of these results in terms of information geometry. The invariance of the distribution, in conjunction with the fixed point characterization, enables us to derive an exact relation between the exact marginals on an arbitrary graph with cycles, and the approximations provided by belief propagation, and more broadly, any algorithm that minimizes the Bethe free energy. We also develop bounds on this approximation error, which illuminate the conditions that govern their accuracy. Finally, we show how the reparameterization perspective extends naturally to more structured approximations (e.g., Kikuchi and variants [52, 37]) that operate over higher order cliques.
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC
 Bioinformatics
, 2005
"... Motivation: Pathway Hunter Tool (PHT) (Syed Asad Rahman et al., 2004) is a fast, robust, and user friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PH ..."
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Cited by 25 (2 self)
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Motivation: Pathway Hunter Tool (PHT) (Syed Asad Rahman et al., 2004) is a fast, robust, and user friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PHT, the user can also calculate the average shortest path (Jungnickel, 2002), average alternate path and the top 10 hubs in the metabolic network. The comparative study of metabolic connectivity and the cross talk between metabolic pathways between various sequenced genomes is possible. Results: A new algorithm for finding the biochemically valid connectivity between metabolites in a metabolic network was developed and implemented. A predefined manual assignment of side metabolites (like ATP, ADP, Water, CO2 etc) and main metabolites is not necessary as the new concept uses chemical structure information (global and local similarity) between metabolites for identification of the shortest path. Availability: Pathway Hunter Tool (PHT) is accessible at
Spatial networks
 Physics Reports
"... Complex systems are very often organized under the form of networks where nodes and edges are embedded in space. Transportation and mobility networks, Internet, mobile phone networks, power grids, social and contact networks, neural networks, are all examples where space is relevant and where topolo ..."
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Cited by 14 (1 self)
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Complex systems are very often organized under the form of networks where nodes and edges are embedded in space. Transportation and mobility networks, Internet, mobile phone networks, power grids, social and contact networks, neural networks, are all examples where space is relevant and where topology alone does not contain all the information. Characterizing and understanding
On The Performance Of Heuristics For Broadcast Scheduling
, 2004
"... In the Broadcast Scheduling Problem (BSP), a finite set of stations are to be scheduled in a time division multiple access (TDMA) frame. In a TDMA frame, time is divided into equal length transmission slots. Unconstrained message transmission can result in a collision of messages, rendering them use ..."
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Cited by 9 (8 self)
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In the Broadcast Scheduling Problem (BSP), a finite set of stations are to be scheduled in a time division multiple access (TDMA) frame. In a TDMA frame, time is divided into equal length transmission slots. Unconstrained message transmission can result in a collision of messages, rendering them useless. Therefore, the objective of the BSP is to provide a collision free broadcast schedule which minimizes the total frame length and maximizes the slot utilization within the frame. In this chapter, we introduce the BSP, show that it is NP complete, and discuss several heuristics which have been applied to the problem. The heuristics are tested on over 60 networks of varying sizes and densities and the results are compared.
Parameterized Complexity of Candidate Control in Elections and Related Digraph Problems
"... Abstract. There are different ways for an external agent to influence the outcome of an election. We concentrate on “control ” by adding or deleting candidates of an election. Our main focus is to investigate the parameterized complexity of various control problems for different voting systems. To t ..."
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Cited by 8 (3 self)
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Abstract. There are different ways for an external agent to influence the outcome of an election. We concentrate on “control ” by adding or deleting candidates of an election. Our main focus is to investigate the parameterized complexity of various control problems for different voting systems. To this end, we introduce natural digraph problems that may be of independent interest. They help in determining the parameterized complexity of control for different voting systems including Llull, Copeland, and plurality votings. Devising several parameterized reductions, we provide a parameterized complexity overview of the digraph and control problems with respect to natural parameters. 1
DAG Drawing from an Information Visualization Perspective
, 1999
"... When dealing with a graph, any visualization strategy must rely on a layout procedure at least to initiate the process. Because the visualization process evolves within an interactive environment the choice of this layout procedure is critical and will often be based on efficiency. This paper com ..."
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Cited by 7 (2 self)
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When dealing with a graph, any visualization strategy must rely on a layout procedure at least to initiate the process. Because the visualization process evolves within an interactive environment the choice of this layout procedure is critical and will often be based on efficiency. This paper compares two popular layout strategies, one based on the extraction of a spanning tree, the other based on edge crossing minimization of directed acyclic graphs. The comparison is made based on a large number of experimental evidence gathered through random graph generation. The main conclusion of these experiments is that, contrary to the popular belief, usage of edge crossing minimization algorithms may be extremely useful and advantageous, even under the heavy requirements of information visualization.
The AI Conference Paper Assignment Problem
"... The Conference Paper Assignment Problem (CPAP) is the problem of assigning reviewers to conference paper submissions in a manner intended to minimize whingeing. It is assumed that papers are reviewed by members of a preset program committee (PC), each of whom has the opportunity to bid on papers pri ..."
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Cited by 6 (0 self)
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The Conference Paper Assignment Problem (CPAP) is the problem of assigning reviewers to conference paper submissions in a manner intended to minimize whingeing. It is assumed that papers are reviewed by members of a preset program committee (PC), each of whom has the opportunity to bid on papers prior to the assignment algorithm being run. In this survey, we show that CPAP is in P if the only information given is individual program committee members ’ preferences for individual papers. However, if both preferences and expertise