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33
Towards A Discipline Of Experimental Algorithmics
"... The last 20 years have seen enormous progress in the design of algorithms, but very little of it has been put into practice, even within academia; indeed, the gap between theory and practice has continuously widened over these years. Moreover, many of the recently developed algorithms are very hard ..."
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Cited by 36 (8 self)
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The last 20 years have seen enormous progress in the design of algorithms, but very little of it has been put into practice, even within academia; indeed, the gap between theory and practice has continuously widened over these years. Moreover, many of the recently developed algorithms are very hard to characterize theoretically and, as initially described, suffer from large runningtime coefficients. Thus the algorithms and data structures community needs to return to implementation as the standard of value; we call such an approach Experimental Algorithmics. Experimental Algorithmics studies algorithms and data structures by joining experimental studies with the more traditional theoretical analyses. Experimentation with algorithms and data structures is proving indispensable in the assessment of heuristics for hard problems, in the design of test cases, in the characterization of asymptotic behavior of complex algorithms, in the comparison of competing designs for tractabl...
A Fast, Parallel Spanning Tree Algorithm for Symmetric Multiprocessors (SMPs) (Extended Abstract)
, 2004
"... Our study in this paper focuses on implementing parallel spanning tree algorithms on SMPs. Spanning tree is an important problem in the sense that it is the building block for many other parallel graph algorithms and also because it is representative of a large class of irregular combinatorial probl ..."
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Cited by 30 (11 self)
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Our study in this paper focuses on implementing parallel spanning tree algorithms on SMPs. Spanning tree is an important problem in the sense that it is the building block for many other parallel graph algorithms and also because it is representative of a large class of irregular combinatorial problems that have simple and efficient sequential implementations and fast PRAM algorithms, but often have no known efficient parallel implementations. In this paper we present a new randomized algorithm and implementation with superior performance that for the firsttime achieves parallel speedup on arbitrary graphs (both regular and irregular topologies) when compared with the best sequential implementation for finding a spanning tree. This new algorithm uses several techniques to give an expected running time that scales linearly with the number p of processors for suitably large inputs (n> p 2). As the spanning tree problem is notoriously hard for any parallel implementation to achieve reasonable speedup, our study may shed new light on implementing PRAM algorithms for sharedmemory parallel computers. The main results of this paper are 1. A new and practical spanning tree algorithm for symmetric multiprocessors that exhibits parallel speedups on graphs with regular and irregular topologies; and 2. An experimental study of parallel spanning tree algorithms that reveals the superior performance of our new approach compared with the previous algorithms. The source code for these algorithms is freelyavailable from our web site hpc.ece.unm.edu.
HighPerformance Algorithm Engineering for Computational Phylogenetics
 J. Supercomputing
, 2002
"... A phylogeny is the evolutionary history of a group of organisms; systematists (and other biologists) attempt to reconstruct this history from various forms of data about contemporary organisms. Phylogeny reconstruction is a crucial step in the understanding of evolution as well as an important tool ..."
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Cited by 22 (7 self)
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A phylogeny is the evolutionary history of a group of organisms; systematists (and other biologists) attempt to reconstruct this history from various forms of data about contemporary organisms. Phylogeny reconstruction is a crucial step in the understanding of evolution as well as an important tool in biological, pharmaceutical, and medical research. Phylogeny reconstruction from molecular data is very difficult: almost all optimization models give rise to NPhard (and thus computationally intractable) problems. Yet approximations must be of very high quality in order to avoid outright biological nonsense. Thus many biologists have been willing to run farms of processors for many months in order to analyze just one dataset. Highperformance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing phylogenetic algorithms, as well as help designers produce better algorithms. We present an overview of algorithm engineering techniques, illustrating them with an application to the "breakpoint analysis" method of Sankoff et al., which resulted in the GRAPPA software suite. GRAPPA demonstrated a speedup in running time by over eight orders of magnitude over the original implementation on a variety of real and simulated datasets. We show how these algorithmic engineering techniques are directly applicable to a large variety of challenging combinatorial problems in computational biology.
Fast SharedMemory Algorithms for Computing the Minimum Spanning Forest of Sparse Graphs
, 2006
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Practical Parallel Algorithms for Minimum Spanning Trees
 In Workshop on Advances in Parallel and Distributed Systems
, 1998
"... We study parallel algorithms for computing the minimum spanning tree of a weighted undirected graph G with n vertices and m edges. We consider an input graph G with m=n p, where p is the number of processors. For this case, we show that simple algorithms with dataindependent communication patterns ..."
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Cited by 17 (0 self)
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We study parallel algorithms for computing the minimum spanning tree of a weighted undirected graph G with n vertices and m edges. We consider an input graph G with m=n p, where p is the number of processors. For this case, we show that simple algorithms with dataindependent communication patterns are efficient, both in theory and in practice. The algorithms are evaluated theoretically using Valiant's BSP model of parallel computation and empirically through implementation results.
Adapting Radix Sort to the Memory Hierarchy
 In ALENEX, Workshop on Algorithm Engineering and Experimentation
, 2000
"... this paper, we focus on one such: the integer sorting algorithm least signicant bit (LSB) radix sort. LSB radix sort sorts wbit integer keys with an rbit radix in O(dw=re(n+2 ..."
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Cited by 15 (2 self)
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this paper, we focus on one such: the integer sorting algorithm least signicant bit (LSB) radix sort. LSB radix sort sorts wbit integer keys with an rbit radix in O(dw=re(n+2
Engineering an External Memory Minimum Spanning Tree Algorithm
 IN PROC. 3RD IFIP INTL. CONF. ON THEORETICAL COMPUTER SCIENCE
, 2004
"... We develop an external memory algorithm for computing minimum spanning trees. The algorithm is considerably simpler than previously known external memory algorithms for this problem and needs a factor of at least four less I/Os for realistic inputs. Our implementation indicates that this algorithm ..."
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Cited by 14 (3 self)
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We develop an external memory algorithm for computing minimum spanning trees. The algorithm is considerably simpler than previously known external memory algorithms for this problem and needs a factor of at least four less I/Os for realistic inputs. Our implementation indicates that this algorithm processes graphs only limited by the disk capacity of most current machines in time no more than a factor 2–5 of a good internal algorithm with sufficient memory space.
Graph and Hashing Algorithms for Modern Architectures: Design and Performance
 PROC. 2ND WORKSHOP ON ALGORITHM ENG. WAE 98, MAXPLANCK INST. FÜR INFORMATIK, 1998, IN TR MPII981019
, 1998
"... We study the eects of caches on basic graph and hashing algorithms and show how cache effects inuence the best solutions to these problems. We study the performance of basic data structures for storing lists of values and use these results to design and evaluate algorithms for hashing, BreadthFi ..."
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Cited by 12 (0 self)
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We study the eects of caches on basic graph and hashing algorithms and show how cache effects inuence the best solutions to these problems. We study the performance of basic data structures for storing lists of values and use these results to design and evaluate algorithms for hashing, BreadthFirstSearch (BFS) and DepthFirstSearch (DFS). For the basic
A shortest path algorithm for realweighted undirected graphs
 in 13th ACMSIAM Symp. on Discrete Algs
, 1985
"... Abstract. We present a new scheme for computing shortest paths on realweighted undirected graphs in the fundamental comparisonaddition model. In an efficient preprocessing phase our algorithm creates a linearsize structure that facilitates singlesource shortest path computations in O(m log α) ti ..."
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Cited by 12 (3 self)
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Abstract. We present a new scheme for computing shortest paths on realweighted undirected graphs in the fundamental comparisonaddition model. In an efficient preprocessing phase our algorithm creates a linearsize structure that facilitates singlesource shortest path computations in O(m log α) time, where α = α(m, n) is the very slowly growing inverseAckermann function, m the number of edges, and n the number of vertices. As special cases our algorithm implies new bounds on both the allpairs and singlesource shortest paths problems. We solve the allpairs problem in O(mnlog α(m, n)) time and, if the ratio between the maximum and minimum edge lengths is bounded by n (log n)O(1) , we can solve the singlesource problem in O(m + nlog log n) time. Both these results are theoretical improvements over Dijkstra’s algorithm, which was the previous best for real weighted undirected graphs. Our algorithm takes the hierarchybased approach invented by Thorup. Key words. singlesource shortest paths, allpairs shortest paths, undirected graphs, Dijkstra’s
Experimental Evaluation of a New Shortest Path Algorithm (Extended Abstract)
, 2002
"... We evaluate the practical eciency of a new shortest path algorithm for undirected graphs which was developed by the rst two authors. This algorithm works on the fundamental comparisonaddition model. Theoretically, this new algorithm outperforms Dijkstra's algorithm on sparse graphs for the al ..."
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Cited by 12 (4 self)
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We evaluate the practical eciency of a new shortest path algorithm for undirected graphs which was developed by the rst two authors. This algorithm works on the fundamental comparisonaddition model. Theoretically, this new algorithm outperforms Dijkstra's algorithm on sparse graphs for the allpairs shortest path problem, and more generally, for the problem of computing singlesource shortest paths from !(1) different sources. Our extensive experimental analysis demonstrates that this is also the case in practice. We present results which show the new algorithm to run faster than Dijkstra's on a variety of sparse graphs when the number of vertices ranges from a few thousand to a few million, and when computing singlesource shortest paths from as few as three different sources.