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Constructing String Graphs in External Memory
"... Abstract. In this paper we present an efficient external memory algorithm to compute the string graph from a collection of reads, which is a fundamental data representation used for sequence assembly. Our algorithm builds upon some recent results on lightweight BurrowsWheeler Transform (BWT) and Lo ..."
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Abstract. In this paper we present an efficient external memory algorithm to compute the string graph from a collection of reads, which is a fundamental data representation used for sequence assembly. Our algorithm builds upon some recent results on lightweight BurrowsWheeler Transform (BWT
A Guided Tour to Approximate String Matching
 ACM COMPUTING SURVEYS
, 1999
"... We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining t ..."
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Cited by 584 (38 self)
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We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining
Composable memory transactions
 In Symposium on Principles and Practice of Parallel Programming (PPoPP
, 2005
"... Atomic blocks allow programmers to delimit sections of code as ‘atomic’, leaving the language’s implementation to enforce atomicity. Existing work has shown how to implement atomic blocks over wordbased transactional memory that provides scalable multiprocessor performance without requiring changes ..."
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Cited by 506 (42 self)
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Atomic blocks allow programmers to delimit sections of code as ‘atomic’, leaving the language’s implementation to enforce atomicity. Existing work has shown how to implement atomic blocks over wordbased transactional memory that provides scalable multiprocessor performance without requiring
ChernSimons Gauge Theory as a String Theory
, 2003
"... Certain two dimensional topological field theories can be interpreted as string theory backgrounds in which the usual decoupling of ghosts and matter does not hold. Like ordinary string models, these can sometimes be given spacetime interpretations. For instance, threedimensional ChernSimons gaug ..."
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Cited by 551 (14 self)
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Certain two dimensional topological field theories can be interpreted as string theory backgrounds in which the usual decoupling of ghosts and matter does not hold. Like ordinary string models, these can sometimes be given spacetime interpretations. For instance, threedimensional Chern
String theory and noncommutative geometry
 JHEP
, 1999
"... We extend earlier ideas about the appearance of noncommutative geometry in string theory with a nonzero Bfield. We identify a limit in which the entire string dynamics is described by a minimally coupled (supersymmetric) gauge theory on a noncommutative space, and discuss the corrections away from ..."
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Cited by 801 (8 self)
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We extend earlier ideas about the appearance of noncommutative geometry in string theory with a nonzero Bfield. We identify a limit in which the entire string dynamics is described by a minimally coupled (supersymmetric) gauge theory on a noncommutative space, and discuss the corrections away from
Community detection in graphs
, 2009
"... The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of th ..."
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Cited by 801 (1 self)
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The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices
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
Interprocedural Slicing Using Dependence Graphs
 ACM TRANSACTIONS ON PROGRAMMING LANGUAGES AND SYSTEMS
, 1990
"... ... This paper concerns the problem of interprocedural slicinggenerating a slice of an entire program, where the slice crosses the boundaries of procedure calls. To solve this problem, we introduce a new kind of graph to represent programs, called a system dependence graph, which extends previou ..."
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Cited by 822 (85 self)
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... This paper concerns the problem of interprocedural slicinggenerating a slice of an entire program, where the slice crosses the boundaries of procedure calls. To solve this problem, we introduce a new kind of graph to represent programs, called a system dependence graph, which extends
A theory of memory retrieval
 PSYCHOL. REV
, 1978
"... A theory of memory retrieval is developed and is shown to apply over a range of experimental paradigms. Access to memory traces is viewed in terms of a resonance metaphor. The probe item evokes the search set on the basis of probememory item relatedness, just as a ringing tuning fork evokes sympath ..."
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Cited by 728 (81 self)
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A theory of memory retrieval is developed and is shown to apply over a range of experimental paradigms. Access to memory traces is viewed in terms of a resonance metaphor. The probe item evokes the search set on the basis of probememory item relatedness, just as a ringing tuning fork evokes
Results 1  10
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796,329