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LogP: Towards a Realistic Model of Parallel Computation
, 1993
"... A vast body of theoretical research has focused either on overly simplistic models of parallel computation, notably the PRAM, or overly specific models that have few representatives in the real world. Both kinds of models encourage exploitation of formal loopholes, rather than rewarding developme ..."
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Cited by 562 (15 self)
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parallel algorithms and to offer guidelines to machine designers. Such a model must strike a balance between detail and simplicity in order to reveal important bottlenecks without making analysis of interesting problems intractable. The model is based on four parameters that specify abstractly
Fast Effective Rule Induction
, 1995
"... Many existing rule learning systems are computationally expensive on large noisy datasets. In this paper we evaluate the recentlyproposed rule learning algorithm IREP on a large and diverse collection of benchmark problems. We show that while IREP is extremely efficient, it frequently gives error r ..."
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Cited by 1257 (21 self)
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Many existing rule learning systems are computationally expensive on large noisy datasets. In this paper we evaluate the recentlyproposed rule learning algorithm IREP on a large and diverse collection of benchmark problems. We show that while IREP is extremely efficient, it frequently gives error rates higher than those of C4.5 and C4.5rules. We then propose a number of modifications resulting in an algorithm RIPPERk that is very competitive with C4.5rules with respect to error rates, but much more efficient on large samples. RIPPERk obtains error rates lower than or equivalent to C4.5rules on 22 of 37 benchmark problems, scales nearly linearly with the number of training examples, and can efficiently process noisy datasets containing hundreds of thousands of examples.
The Omega Test: a fast and practical integer programming algorithm for dependence analysis
 Communications of the ACM
, 1992
"... The Omega testi s ani nteger programmi ng algori thm that can determi ne whether a dependence exi sts between two array references, and i so, under what condi7: ns. Conventi nalwi[A m holds thati nteger programmiB techni:36 are far too expensi e to be used for dependence analysi6 except as a method ..."
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Cited by 521 (15 self)
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The Omega testi s ani nteger programmi ng algori thm that can determi ne whether a dependence exi sts between two array references, and i so, under what condi7: ns. Conventi nalwi[A m holds thati nteger programmiB techni:36 are far too expensi e to be used for dependence analysi6 except as a method
Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)
"... Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and bas ..."
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Cited by 812 (119 self)
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Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions
FAST VOLUME RENDERING USING A SHEARWARP FACTORIZATION OF THE VIEWING TRANSFORMATION
, 1995
"... Volume rendering is a technique for visualizing 3D arrays of sampled data. It has applications in areas such as medical imaging and scientific visualization, but its use has been limited by its high computational expense. Early implementations of volume rendering used bruteforce techniques that req ..."
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Cited by 541 (2 self)
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that require on the order of 100 seconds to render typical data sets on a workstation. Algorithms with optimizations that exploit coherence in the data have reduced rendering times to the range of ten seconds but are still not fast enough for interactive visualization applications. In this thesis we present a
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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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 dynamics models which can be difficult to parallelize efficiently  those with shortrange forces where the neighbors of each atom change rapidly. They can be implemented on any distributedmemory parallel machine which allows for messagepassing of data between independently executing processors. 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 that the current generation of parallel machines is competitive with conventi...
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
, 2003
"... The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The ..."
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Cited by 2109 (30 self)
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The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements
FastMap: A Fast Algorithm for Indexing, DataMining and Visualization of Traditional and Multimedia Datasets
, 1995
"... A very promising idea for fast searching in traditional and multimedia databases is to map objects into points in kd space, using k featureextraction functions, provided by a domain expert [25]. Thus, we can subsequently use highly finetuned spatial access methods (SAMs), to answer several types ..."
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Cited by 497 (23 self)
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A very promising idea for fast searching in traditional and multimedia databases is to map objects into points in kd space, using k featureextraction functions, provided by a domain expert [25]. Thus, we can subsequently use highly finetuned spatial access methods (SAMs), to answer several
ModelBased Clustering, Discriminant Analysis, and Density Estimation
 JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 2000
"... Cluster analysis is the automated search for groups of related observations in a data set. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures and most clustering methods available in commercial software are also of this type. However, there is little ..."
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Cited by 557 (28 self)
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Cluster analysis is the automated search for groups of related observations in a data set. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures and most clustering methods available in commercial software are also of this type. However
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