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1,363
Comparing community structure identification
 Journal of Statistical Mechanics: Theory and Experiment
, 2005
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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 ..."
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Cited by 192 (30 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]).
The Maximum Clique Problem
, 1999
"... Contents 1 Introduction 2 1.1 Notations and Definitions . . . . . . . . . . . . . . . . . . . . . . . . 3 2 Problem Formulations 4 2.1 Integer Programming Formulations . . . . . . . . . . . . . . . . . . . 5 2.2 Continuous Formulations . . . . . . . . . . . . . . . . . . . . . . . . 8 3 Computation ..."
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Cited by 186 (21 self)
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Contents 1 Introduction 2 1.1 Notations and Definitions . . . . . . . . . . . . . . . . . . . . . . . . 3 2 Problem Formulations 4 2.1 Integer Programming Formulations . . . . . . . . . . . . . . . . . . . 5 2.2 Continuous Formulations . . . . . . . . . . . . . . . . . . . . . . . . 8 3 Computational Complexity 12 4 Bounds and Estimates 15 5 Exact Algorithms 19 5.1 Enumerative Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . 19 5.2 Exact Algorithms for the Unweighted Case . . . . . . . . . . . . . . 21 5.3 Exact Algorithms for the Weighted Case . . . . . . . . . . . . . . . . 25 6 Heuristics 27 6.1 Sequential Greedy Heuristics . . . . . . . . . . . . . . . . . . . . . . 28 6.2 Local Search Heuristics . . . . . . . . . . . . . . . . . . . . . . . . . 29 6.3 Advanced Search Heuristics . . . . . . . . . . . . . . . . . . . . . . . 30 6.3.1 Simulated annealing . . . . . . . . . . . . . . . . . . . . . . . 30 6.3.2 Neural networks . . . . . . . . . . . . . . . . . . . . . . . .
MAP estimation via agreement on trees: Messagepassing and linear programming
, 2002
"... We develop and analyze methods for computing provably optimal maximum a posteriori (MAP) configurations for a subclass of Markov random fields defined on graphs with cycles. By decomposing the original distribution into a convex combination of treestructured distributions, we obtain an upper bound ..."
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Cited by 179 (9 self)
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We develop and analyze methods for computing provably optimal maximum a posteriori (MAP) configurations for a subclass of Markov random fields defined on graphs with cycles. By decomposing the original distribution into a convex combination of treestructured distributions, we obtain an upper bound on the optimal value of the original problem (i.e., the log probability of the MAP assignment) in terms of the combined optimal values of the tree problems. We prove that this upper bound is tight if and only if all the tree distributions share an optimal configuration in common. An important implication is that any such shared configuration must also be a MAP configuration for the original distribution. Next we develop two approaches to attempting to obtain tight upper bounds: (a) a treerelaxed linear program (LP), which is derived from the Lagrangian dual of the upper bounds; and (b) a treereweighted maxproduct messagepassing algorithm that is related to but distinct from the maxproduct algorithm. In this way, we establish a connection between a certain LP relaxation of the modefinding problem, and a reweighted form of the maxproduct (minsum) messagepassing algorithm.
Efficient Testing of Large Graphs
 Combinatorica
"... Let P be a property of graphs. An test for P is a randomized algorithm which, given the ability to make queries whether a desired pair of vertices of an input graph G with n vertices are adjacent or not, distinguishes, with high probability, between the case of G satisfying P and the case that it h ..."
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Cited by 167 (46 self)
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Let P be a property of graphs. An test for P is a randomized algorithm which, given the ability to make queries whether a desired pair of vertices of an input graph G with n vertices are adjacent or not, distinguishes, with high probability, between the case of G satisfying P and the case that it has to be modified by adding and removing more than n 2 edges to make it satisfy P . The property P is called testable, if for every there exists an test for P whose total number of queries is independent of the size of the input graph. Goldreich, Goldwasser and Ron [8] showed that certain graph properties admit an test. In this paper we make a first step towards a logical characterization of all testable graph properties, and show that properties describable by a very general type of coloring problem are testable. We use this theorem to prove that first order graph properties not containing a quantifier alternation of type "89" are always testable, while we show that some properties containing this alternation are not. Our results are proven using a combinatorial lemma, a special case of which, that may be of independent interest, is the following. A graph H is called unavoidable in G if all graphs that differ from G in no more than jGj 2 places contain an induced copy of H . A graph H is called abundant in G if G contains at least jGj jHj induced copies of H. If H is unavoidable in G then it is also ( ; jHj)abundant.
Approximation Algorithms for Disjoint Paths Problems
, 1996
"... The construction of disjoint paths in a network is a basic issue in combinatorial optimization: given a network, and specified pairs of nodes in it, we are interested in finding disjoint paths between as many of these pairs as possible. This leads to a variety of classical NPcomplete problems for w ..."
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Cited by 157 (0 self)
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The construction of disjoint paths in a network is a basic issue in combinatorial optimization: given a network, and specified pairs of nodes in it, we are interested in finding disjoint paths between as many of these pairs as possible. This leads to a variety of classical NPcomplete problems for which very little is known from the point of view of approximation algorithms. It has recently been brought into focus in work on problems such as VLSI layout and routing in highspeed networks; in these settings, the current lack of understanding of the disjoint paths problem is often an obstacle to the design of practical heuristics.
The Expression Of Graph Properties And Graph Transformations In Monadic SecondOrder Logic
, 1997
"... By considering graphs as logical structures, one... ..."
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Cited by 152 (40 self)
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By considering graphs as logical structures, one...
MAP estimation via agreement on (hyper)trees: Messagepassing and linear programming approaches
 IEEE Transactions on Information Theory
, 2002
"... We develop an approach for computing provably exact maximum a posteriori (MAP) configurations for a subclass of problems on graphs with cycles. By decomposing the original problem into a convex combination of treestructured problems, we obtain an upper bound on the optimal value of the original ..."
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Cited by 132 (11 self)
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We develop an approach for computing provably exact maximum a posteriori (MAP) configurations for a subclass of problems on graphs with cycles. By decomposing the original problem into a convex combination of treestructured problems, we obtain an upper bound on the optimal value of the original problem (i.e., the log probability of the MAP assignment) in terms of the combined optimal values of the tree problems. We prove that this upper bound is met with equality if and only if the tree problems share an optimal configuration in common. An important implication is that any such shared configuration must also be a MAP configuration for the original problem. Next we present and analyze two methods for attempting to obtain tight upper bounds: (a) a treereweighted messagepassing algorithm that is related to but distinct from the maxproduct (minsum) algorithm; and (b) a treerelaxed linear program (LP), which is derived from the Lagrangian dual of the upper bounds. Finally, we discuss the conditions that govern when the relaxation is tight, in which case the MAP configuration can be obtained. The analysis described here generalizes naturally to convex combinations of hypertreestructured distributions.
Connectivity of wireless multihop networks in a shadow fading environment
, 2003
"... Authors ’ preprint of an article accepted for ACM/Kluwer Wireless Networks, special issue on selected papers from ACM MSWiM 2003, to be published 2005. Abstract. This article analyzes the connectivity of multihop radio networks in a lognormal shadow fading environment. Assuming the nodes have equal ..."
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Cited by 127 (6 self)
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Authors ’ preprint of an article accepted for ACM/Kluwer Wireless Networks, special issue on selected papers from ACM MSWiM 2003, to be published 2005. Abstract. This article analyzes the connectivity of multihop radio networks in a lognormal shadow fading environment. Assuming the nodes have equal transmission capabilities and are randomly distributed according to a homogeneous Poisson process, we give a tight lower bound for the minimum node density that is necessary to obtain an almost surely connected subnetwork on a bounded area of given size. We derive an explicit expression for this bound, compute it in a variety of scenarios, and verify its tightness by simulation. The numerical results can be used for the practical design and simulation of wireless sensor and ad hoc networks. In addition, they give insight into how fading affects the topology of multihop networks. It is explained why a high fading variance helps the network to become connected.
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 113 (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.