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422,874
Application of Phylogenetic Networks in Evolutionary Studies
 SUBMITTED TO MBE 2005
, 2005
"... The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evoluti ..."
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Cited by 867 (15 self)
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The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when
An Efficient Boosting Algorithm for Combining Preferences
, 1999
"... The problem of combining preferences arises in several applications, such as combining the results of different search engines. This work describes an efficient algorithm for combining multiple preferences. We first give a formal framework for the problem. We then describe and analyze a new boosting ..."
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Cited by 707 (18 self)
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The problem of combining preferences arises in several applications, such as combining the results of different search engines. This work describes an efficient algorithm for combining multiple preferences. We first give a formal framework for the problem. We then describe and analyze a new
A learning algorithm for Boltzmann machines
 Cognitive Science
, 1985
"... The computotionol power of massively parallel networks of simple processing elements resides in the communication bandwidth provided by the hardware connections between elements. These connections con allow a significant fraction of the knowledge of the system to be applied to an instance of a probl ..."
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Cited by 586 (13 self)
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problem in o very short time. One kind of computation for which massively porollel networks appear to be well suited is large constraint satisfaction searches, but to use the connections efficiently two conditions must be met: First, a search technique that is suitable for parallel networks must be found
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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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
Simplifications and speedups of the Pseudoflow algorithm
 NETWORKS
, 2013
"... The pseudoflow algorithm for solving the maximum flow and minimum cut problems was devised in Hochbaum (2008). The complexity of the algorithm was shown in (2008) to be O(nm log n). Chandran and Hochbaum, (2009) demonstrated that the pseudoflow algorithm is very efficient in practice, and that the h ..."
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Cited by 3 (3 self)
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The pseudoflow algorithm for solving the maximum flow and minimum cut problems was devised in Hochbaum (2008). The complexity of the algorithm was shown in (2008) to be O(nm log n). Chandran and Hochbaum, (2009) demonstrated that the pseudoflow algorithm is very efficient in practice
Algorithms for Scalable Synchronization on SharedMemory Multiprocessors
 ACM Transactions on Computer Systems
, 1991
"... Busywait techniques are heavily used for mutual exclusion and barrier synchronization in sharedmemory parallel programs. Unfortunately, typical implementations of busywaiting tend to produce large amounts of memory and interconnect contention, introducing performance bottlenecks that become marke ..."
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Cited by 567 (32 self)
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markedly more pronounced as applications scale. We argue that this problem is not fundamental, and that one can in fact construct busywait synchronization algorithms that induce no memory or interconnect contention. The key to these algorithms is for every processor to spin on separate locally
Interior Point Methods in Semidefinite Programming with Applications to Combinatorial Optimization
 SIAM Journal on Optimization
, 1993
"... We study the semidefinite programming problem (SDP), i.e the problem of optimization of a linear function of a symmetric matrix subject to linear equality constraints and the additional condition that the matrix be positive semidefinite. First we review the classical cone duality as specialized to S ..."
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Cited by 557 (12 self)
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mechanical way to algorithms for SDP with proofs of convergence and polynomial time complexity also carrying over in a similar fashion. Finally we study the significance of these results in a variety of combinatorial optimization problems including the general 01 integer programs, the maximum clique
Semantic Similarity in a Taxonomy: An InformationBased Measure and its Application to Problems of Ambiguity in Natural Language
, 1999
"... This article presents a measure of semantic similarityinanisa taxonomy based on the notion of shared information content. Experimental evaluation against a benchmark set of human similarity judgments demonstrates that the measure performs better than the traditional edgecounting approach. The a ..."
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Cited by 601 (9 self)
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. The article presents algorithms that take advantage of taxonomic similarity in resolving syntactic and semantic ambiguity, along with experimental results demonstrating their e#ectiveness. 1. Introduction Evaluating semantic relatedness using network representations is a problem with a long history
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 622 (6 self)
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. The algorithms are tested on a standard LennardJones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers  the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray YMP and C90 algorithm shows
Results 11  20
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422,874