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49
Simple linear work suffix array construction
, 2003
"... Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more exp ..."
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Cited by 149 (6 self)
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Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more explicit structure. We narrow this gap between theory and practice with a simple lineartime construction algorithm for suffix arrays. The simplicity is demonstrated with a C++ implementation of 50 effective lines of code. The algorithm is called DC3, which stems from the central underlying concept of difference cover. This view leads to a generalized algorithm, DC, that allows a spaceefficient implementation and, moreover, supports the choice of a space–time tradeoff. For any v ∈ [1, √ n], it runs in O(vn) time using O(n / √ v) space in addition to the input string and the suffix array. We also present variants of the algorithm for several parallel and hierarchical memory models of computation. The algorithms for BSP and EREWPRAM models are asymptotically faster than all previous suffix tree or array construction algorithms.
Improved Parallel Integer Sorting without Concurrent Writing
, 1992
"... We show that n integers in the range 1 : : n can be sorted stably on an EREW PRAM using O(t) time and O(n( p log n log log n + (log n) 2 =t)) operations, for arbitrary given t log n log log n, and on a CREW PRAM using O(t) time and O(n( p log n + log n=2 t=logn )) operations, for arbitrary ..."
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Cited by 41 (4 self)
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We show that n integers in the range 1 : : n can be sorted stably on an EREW PRAM using O(t) time and O(n( p log n log log n + (log n) 2 =t)) operations, for arbitrary given t log n log log n, and on a CREW PRAM using O(t) time and O(n( p log n + log n=2 t=logn )) operations, for arbitrary given t log n. In addition, we are able to sort n arbitrary integers on a randomized CREW PRAM within the same resource bounds with high probability. In each case our algorithm is a factor of almost \Theta( p log n) closer to optimality than all previous algorithms for the stated problem in the stated model, and our third result matches the operation count of the best previous sequential algorithm. We also show that n integers in the range 1 : : m can be sorted in O((log n) 2 ) time with O(n) operations on an EREW PRAM using a nonstandard word length of O(log n log log n log m) bits, thereby greatly improving the upper bound on the word length necessary to sort integers with a linear t...
Parallel Algorithms with Optimal Speedup for Bounded Treewidth
 Proceedings 22nd International Colloquium on Automata, Languages and Programming
, 1995
"... We describe the first parallel algorithm with optimal speedup for constructing minimumwidth tree decompositions of graphs of bounded treewidth. On nvertex input graphs, the algorithm works in O((logn)^2) time using O(n) operations on the EREW PRAM. We also give faster parallel algorithms with opti ..."
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Cited by 33 (10 self)
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We describe the first parallel algorithm with optimal speedup for constructing minimumwidth tree decompositions of graphs of bounded treewidth. On nvertex input graphs, the algorithm works in O((logn)^2) time using O(n) operations on the EREW PRAM. We also give faster parallel algorithms with optimal speedup for the problem of deciding whether the treewidth of an input graph is bounded by a given constant and for a variety of problems on graphs of bounded treewidth, including all decision problems expressible in monadic secondorder logic. On nvertex input graphs, the algorithms use O(n) operations together with O(log n log n) time on the EREW PRAM, or O(log n) time on the CRCW PRAM.
Efficient LowContention Parallel Algorithms
 the 1994 ACM Symp. on Parallel Algorithms and Architectures
, 1994
"... The queueread, queuewrite (qrqw) parallel random access machine (pram) model permits concurrent reading and writing to shared memory locations, but at a cost proportional to the number of readers/writers to any one memory location in a given step. The qrqw pram model reflects the contention prope ..."
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Cited by 30 (11 self)
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The queueread, queuewrite (qrqw) parallel random access machine (pram) model permits concurrent reading and writing to shared memory locations, but at a cost proportional to the number of readers/writers to any one memory location in a given step. The qrqw pram model reflects the contention properties of most commercially available parallel machines more accurately than either the wellstudied crcw pram or erew pram models, and can be efficiently emulated with only logarithmic slowdown on hypercubetype noncombining networks. This paper describes fast, lowcontention, workoptimal, randomized qrqw pram algorithms for the fundamental problems of load balancing, multiple compaction, generating a random permutation, parallel hashing, and distributive sorting. These logarithmic or sublogarithmic time algorithms considerably improve upon the best known erew pram algorithms for these problems, while avoiding the highcontention steps typical of crcw pram algorithms. An illustrative expe...
Finding Triconnected Components By Local Replacement
, 1993
"... . We present a parallel algorithm for finding triconnected components on a CRCW PRAM. The time complexity of our algorithm is O(log n) and the processortime product is O((m + n) log log n) where n is the number of vertices, and m is the number of edges of the input graph. Our algorithm, like other ..."
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Cited by 29 (6 self)
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. We present a parallel algorithm for finding triconnected components on a CRCW PRAM. The time complexity of our algorithm is O(log n) and the processortime product is O((m + n) log log n) where n is the number of vertices, and m is the number of edges of the input graph. Our algorithm, like other parallel algorithms for this problem, is based on open ear decomposition but it employs a new technique, local replacement, to improve the complexity. Only the need to use the subroutines for connected components and integer sorting, for which no optimal parallel algorithm that runs in O(log n) time is known, prevents our algorithm from achieving optimality. 1. Introduction. A connected graph G = (V; E) is kvertex connected if it has at least (k + 1) vertices and removal of any (k \Gamma 1) vertices leaves the graph connected. Designing efficient algorithms for determining the connectivity of graphs has been a subject of great interest in the last two decades. Applications of graph connect...
Implementations of Randomized Sorting on Large Parallel Machines
"... Flashsort [RV83,86] and Samplesort [HC83] are related parallel sorting algorithms proposed in the literature. Both utilize a sophisticated randomized sampling technique to form a splitter set, but Samplesort distributes the splitter set to each processor while Flashsort uses splitterdirected routin ..."
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Cited by 28 (1 self)
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Flashsort [RV83,86] and Samplesort [HC83] are related parallel sorting algorithms proposed in the literature. Both utilize a sophisticated randomized sampling technique to form a splitter set, but Samplesort distributes the splitter set to each processor while Flashsort uses splitterdirected routing. In this
Efficient parallel algorithms for chordal graphs
"... We give the first efficient parallel algorithms for recognizing chordal graphs, finding a maximum clique and a maximum independent set in a chordal graph, finding an optimal coloring of a chordal graph, finding a breadthfirst search tree and a depthfirst search tree of a chordal graph, recognizing ..."
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Cited by 26 (0 self)
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We give the first efficient parallel algorithms for recognizing chordal graphs, finding a maximum clique and a maximum independent set in a chordal graph, finding an optimal coloring of a chordal graph, finding a breadthfirst search tree and a depthfirst search tree of a chordal graph, recognizing interval graphs, and testing interval graphs for isomorphism. The key to our results is an efficient parallel algorithm for finding a perfect elimination ordering.
Parallel Open Ear Decomposition with Applications to Graph Biconnectivity and Triconnectivity
 Synthesis of Parallel Algorithms
, 1992
"... This report deals with a parallel algorithmic technique that has proved to be very useful in the design of efficient parallel algorithms for several problems on undirected graphs. We describe this method for searching undirected graphs, called "open ear decomposition", and we relate this decompos ..."
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Cited by 25 (9 self)
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This report deals with a parallel algorithmic technique that has proved to be very useful in the design of efficient parallel algorithms for several problems on undirected graphs. We describe this method for searching undirected graphs, called "open ear decomposition", and we relate this decomposition to graph biconnectivity. We present an efficient parallel algorithm for finding this decomposition and we relate it to a sequential algorithm based on depthfirst search. We then apply open ear decomposition to obtain an efficient parallel algorithm for testing graph triconnectivity and for finding the triconnnected components of a graph.
On Parallel Hashing and Integer Sorting
, 1991
"... The problem of sorting n integers from a restricted range [1::m], where m is superpolynomial in n, is considered. An o(n log n) randomized algorithm is given. Our algorithm takes O(n log log m) expected time and O(n) space. (Thus, for m = n polylog(n) we have an O(n log log n) algorithm.) The al ..."
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Cited by 25 (9 self)
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The problem of sorting n integers from a restricted range [1::m], where m is superpolynomial in n, is considered. An o(n log n) randomized algorithm is given. Our algorithm takes O(n log log m) expected time and O(n) space. (Thus, for m = n polylog(n) we have an O(n log log n) algorithm.) The algorithm is parallelizable. The resulting parallel algorithm achieves optimal speed up. Some features of the algorithm make us believe that it is relevant for practical applications. A result of independent interest is a parallel hashing technique. The expected construction time is logarithmic using an optimal number of processors, and searching for a value takes O(1) time in the worst case. This technique enables drastic reduction of space requirements for the price of using randomness. Applicability of the technique is demonstrated for the parallel sorting algorithm, and for some parallel string matching algorithms. The parallel sorting algorithm is designed for a strong and non standard mo...
Randomized Parallel Algorithms For Trapezoidal Diagrams
, 1992
"... We describe randomized parallel algorithms for building trapezoidal diagrams of line segments in the plane. The algorithms are designed for a CRCW PRAM. For general segments, we give an algorithm requiring optimal O(A + n log n) expected work and optimal O(logn) time, where A is the number of inters ..."
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Cited by 23 (0 self)
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We describe randomized parallel algorithms for building trapezoidal diagrams of line segments in the plane. The algorithms are designed for a CRCW PRAM. For general segments, we give an algorithm requiring optimal O(A + n log n) expected work and optimal O(logn) time, where A is the number of intersecting pairs of segments. If the segments form a simple chain, we give an algorithm requiring optimal O(n) expected work and O(logn log log n log n) expected time a , and a simpler algorithm requiring O(n log n) expected work. The serial algorithm corresponding to the latter is among the simplest known algorithms requiring O(n log n) expected operations. For a set of segments forming K chains, we give an algorithm requiring O(A + n log n + K log n) expected work and O(logn log log n log n) expected time. The parallel time bounds require the assumption that enough processors are available, with processor allocations every log n steps. Keywords: randomized, parallel, trapez...