Results 1  10
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14
The LikeIt Intelligent String Comparison Facility
 NEC Research Institute
, 1997
"... A highlyefficient ANSIC facility is described for intelligently comparing a query string with a series of database strings. The bipartite weighted matching approach taken tolerates ordering violations that are problematic for simple automaton or string edit distance methodsyet common in practic ..."
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Cited by 18 (0 self)
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A highlyefficient ANSIC facility is described for intelligently comparing a query string with a series of database strings. The bipartite weighted matching approach taken tolerates ordering violations that are problematic for simple automaton or string edit distance methodsyet common in practice. The method is character and polygraph based and does not require that words are properly formed in a query. Database characters are processed at a rate of approximately 2.5 million per second using a 200MHz Pentium Pro processor. A subroutinelevel API is described along with an simple executable utility supporting both commandline and Web interfaces. An optimized Web interface is also reported consisting of a daemon that preloads multiple databases, and a corresponding CGI stub. The daemon may be initiated manually or via inetd. Keywords: String Comparison/Similarity, Text/Database Search/Retrieval, Bipartite Matching/Assignment, Edit Distance. Both authors are with the NEC Research I...
Linear and O(n log n) Time MinimumCost Matching Algorithms for Quasiconvex Tours (Extended Abstract)
"... Samuel R. Buss # Peter N. Yianilos + Abstract Let G be a complete, weighted, undirected, bipartite graph with n red nodes, n # blue nodes, and symmetric cost function c(x, y) . A maximum matching for G consists of min{n, n # edges from distinct red nodes to distinct blue nodes. Our objective is ..."
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Cited by 17 (3 self)
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Samuel R. Buss # Peter N. Yianilos + Abstract Let G be a complete, weighted, undirected, bipartite graph with n red nodes, n # blue nodes, and symmetric cost function c(x, y) . A maximum matching for G consists of min{n, n # edges from distinct red nodes to distinct blue nodes. Our objective is to find a minimumcost maximum matching, i.e. one for which the sum of the edge costs has minimal value. This is the weighted bipartite matching problem; or as it is sometimes called, the assignment problem.
The Geometry of Musical Rhythm
 In Proc. Japan Conference on Discrete and Computational Geometry, LNCS 3742
, 2004
"... Musical rhythm is considered from the point of view of geometry. ..."
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Cited by 15 (6 self)
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Musical rhythm is considered from the point of view of geometry.
Efficient Minimum Cost Matching and Transportation Using Quadrangle Inequality
, 1995
"... We present efficient algorithms for finding a minimum cost perfect matching, and for solving the transportation problem in bipartite graphs, G = (Sinks [ Sources; Sinks 2 Sources), where jSinksj = n, jSourcesj = m, n m, and the cost function obeys the quadrangle inequality. First, we assume tha ..."
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Cited by 12 (0 self)
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We present efficient algorithms for finding a minimum cost perfect matching, and for solving the transportation problem in bipartite graphs, G = (Sinks [ Sources; Sinks 2 Sources), where jSinksj = n, jSourcesj = m, n m, and the cost function obeys the quadrangle inequality. First, we assume that all the sink points and all the source points lie on a curve that is homeomorphic to either a line or a circle and the cost function is given by the Euclidean distance along the curve. We present a linear time algorithm for the matching problem that is simpler than the algorithm of [KL75]. We generalize our method to solve the corresponding transportation problem in O((m+n) log(m +n)) time, improving on the best previously known algorithm of [KL75]. Next, we present an O(n log m)time algorithm for minimum cost matching when the cost array is a bitonic Monge array. An example of this is when the sink points lie on one straight line and the source points lie on another straight line Finally...
An Algorithm for Computing the Restriction Scaffold Assignment Problem in Computational Biology
 in computational biology. Information Processing Letters, 95(Issue 4):466–471
, 2005
"... Let S and T be two finite sets of points on the real line with S + T  = n and S > T . The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every elem ..."
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Cited by 10 (7 self)
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Let S and T be two finite sets of points on the real line with S + T  = n and S > T . The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element s i of S to an element t j of T is s i  t j , i.e., the distance between s i and t j . In 2003 BenDor, Karp, Schwikowski and Shamir [2] published an O(n logn) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n ) time, improving the best previous complexity of O(n ).
The Restriction Scaffold Problem
 Journal of Computational Biology
, 2003
"... Most shotgun sequencing projects undergo a long and costly phase of finishing, in which a partial assembly forms several contigs whose order, orientation and relative distance is unknown. We propose here a new technique that supplements the shotgun assembly data by experimentally simple and commonly ..."
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Cited by 10 (0 self)
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Most shotgun sequencing projects undergo a long and costly phase of finishing, in which a partial assembly forms several contigs whose order, orientation and relative distance is unknown. We propose here a new technique that supplements the shotgun assembly data by experimentally simple and commonly used complete restriction digests of the target. By computationally combining information from the contig sequences and the fragment sizes measured for several different enzymes, we seek to form a "scaffold" on which the contigs will be placed in their correct orientation, order and distance. We give a heuristic search algorithm for solving the problem and report on promising preliminary simulation results. The key to the success of the search scheme is the very rapid solution of two timecritical subproblems that are solved to optimality in linear time.
A Bipartite Matching Approach to Approximate String Comparison and Search
, 1995
"... Approximate string comparison and search is an important part of applications that range from natural language to the interpretation of DNA. This paper presents a bipartite weighted graph matching approach to these problems, based on the authors' linear time matching algorithms # . Our approach's ..."
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Cited by 9 (1 self)
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Approximate string comparison and search is an important part of applications that range from natural language to the interpretation of DNA. This paper presents a bipartite weighted graph matching approach to these problems, based on the authors' linear time matching algorithms # . Our approach's tolerance to permutation of symbols or blocks, distinguishes it from the widely used edit distance and finite state machine methods. A close relationship with the earlier related `proximity comparison' method is established.
An O(n log n)time algorithm for the restriction scaffold assignment problem
 Journal of Computational Biology
"... The assignment problem takes as input two finite point sets S and T and establishes a correspondence between points in S and points in T, such that each point in S maps to exactly one point in T, and each point in T maps to at least one point in S. In this paper we show that this problem has an O(n ..."
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Cited by 4 (3 self)
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The assignment problem takes as input two finite point sets S and T and establishes a correspondence between points in S and points in T, such that each point in S maps to exactly one point in T, and each point in T maps to at least one point in S. In this paper we show that this problem has an O(n log n)time solution, provided that the points in S and T are restricted to lie on a line (linear time, if S and T are presorted). 1
Efficient ManyToMany Point Matching in One Dimension
"... Abstract. Let S and T be two sets of points with total cardinality n. The minimumcost manytomany matching problem matches each point in S to at least one point in T and each point in T to at least one point in S, such that sum of the matching costs is minimized. Here we examine the special case w ..."
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Cited by 3 (0 self)
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Abstract. Let S and T be two sets of points with total cardinality n. The minimumcost manytomany matching problem matches each point in S to at least one point in T and each point in T to at least one point in S, such that sum of the matching costs is minimized. Here we examine the special case where both S and T lie on the line and the cost of matching s ∈ S to t ∈ T is equal to the distance between s and t. In this context, we provide an algorithm that determines a minimumcost manytomany matching in O(n log n) time, improving the previous best time complexity of O(n 2) for the same problem. 1.
FAST TRANSPORT OPTIMIZATION FOR MONGE COSTS ON THE CIRCLE ∗
"... Abstract. Consider the problem of optimally matching two measures on the circle, or equivalently two periodic measures on R, and suppose the cost c(x, y) of matching two points x, y satisfies the Monge condition: c(x1, y1)+c(x2, y2) < c(x1, y2)+c(x2, y1) whenever x1 < x2 and y1 < y2. We introduce a ..."
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Abstract. Consider the problem of optimally matching two measures on the circle, or equivalently two periodic measures on R, and suppose the cost c(x, y) of matching two points x, y satisfies the Monge condition: c(x1, y1)+c(x2, y2) < c(x1, y2)+c(x2, y1) whenever x1 < x2 and y1 < y2. We introduce a notion of locally optimal transport plan, motivated by the weak KAM (Aubry–Mather) theory, and show that all locally optimal transport plans are conjugate to shifts and that the cost of a locally optimal transport plan is a convex function of a shift parameter. This theory is applied to a transportation problem arising in image processing: for two sets of point masses on the circle, both of which have the same total mass, find an optimal transport plan with respect to a given cost function c satisfying the Monge condition. In the circular case the sorting strategy fails to provide a unique candidate solution and a naive approach requires a quadratic number of operations. For the case of N realvalued point masses we present an O(Nlog ǫ) algorithm that approximates the optimal cost within ǫ; when all masses are integer multiples of 1/M, the algorithm gives an exact solution in O(N log M) operations.