Results 1  10
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220
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...
Consistency of spectral clustering
, 2004
"... Consistency is a key property of statistical algorithms, when the data is drawn from some underlying probability distribution. Surprisingly, despite decades of work, little is known about consistency of most clustering algorithms. In this paper we investigate consistency of a popular family of spe ..."
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Cited by 567 (15 self)
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Consistency is a key property of statistical algorithms, when the data is drawn from some underlying probability distribution. Surprisingly, despite decades of work, little is known about consistency of most clustering algorithms. In this paper we investigate consistency of a popular family of spectral clustering algorithms, which cluster the data with the help of eigenvectors of graph Laplacian matrices. We show that one of the two of major classes of spectral clustering (normalized clustering) converges under some very general conditions, while the other (unnormalized), is only consistent under strong additional assumptions, which, as we demonstrate, are not always satisfied in real data. We conclude that our analysis provides strong evidence for the superiority of normalized spectral clustering in practical applications. We believe that methods used in our analysis will provide a basis for future exploration of Laplacianbased methods in a statistical setting.
Fast Multilevel Implementation of Recursive Spectral Bisection for Partitioning Unstructured Problems, Concurrency: Practice and Experience 6
, 1994
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Multiclass spectral clustering
 In Proc. Int. Conf. Computer Vision
, 2003
"... We propose a principled account on multiclass spectral clustering. Given a discrete clustering formulation, we first solve a relaxed continuous optimization problem by eigendecomposition. We clarify the role of eigenvectors as a generator of all optimal solutions through orthonormal transforms. We t ..."
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Cited by 262 (7 self)
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We propose a principled account on multiclass spectral clustering. Given a discrete clustering formulation, we first solve a relaxed continuous optimization problem by eigendecomposition. We clarify the role of eigenvectors as a generator of all optimal solutions through orthonormal transforms. We then solve an optimal discretization problem, which seeks a discrete solution closest to the continuous optima. The discretization is efficiently computed in an iterative fashion using singular value decomposition and nonmaximum suppression. The resulting discrete solutions are nearly globaloptimal. Our method is robust to random initialization and converges faster than other clustering methods. Experiments on real image segmentation are reported. optima consist not only of the eigenvectors, but of a whole family spanned by the eigenvectors through orthonormal transforms. The goal is to find the right orthonormal transform that leads to a discretization. ˜X normalize
Spectral Partitioning Works: Planar graphs and finite element meshes
 In IEEE Symposium on Foundations of Computer Science
, 1996
"... Spectral partitioning methods use the Fiedler vectorthe eigenvector of the secondsmallest eigenvalue of the Laplacian matrixto find a small separator of a graph. These methods are important components of many scientific numerical algorithms and have been demonstrated by experiment to work extr ..."
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Cited by 199 (10 self)
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Spectral partitioning methods use the Fiedler vectorthe eigenvector of the secondsmallest eigenvalue of the Laplacian matrixto find a small separator of a graph. These methods are important components of many scientific numerical algorithms and have been demonstrated by experiment to work extremely well. In this paper, we show that spectral partitioning methods work well on boundeddegree planar graphs and finite element meshes the classes of graphs to which they are usually applied. While naive spectral bisection does not necessarily work, we prove that spectral partitioning techniques can be used to produce separators whose ratio of vertices removed to edges cut is O( p n) for boundeddegree planar graphs and twodimensional meshes and O i n 1=d j for wellshaped ddimensional meshes. The heart of our analysis is an upper bound on the secondsmallest eigenvalues of the Laplacian matrices of these graphs. 1. Introduction Spectral partitioning has become one of the mos...
METIS  Unstructured Graph Partitioning and Sparse Matrix Ordering System, Version 2.0
, 1995
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Some Applications of Laplace Eigenvalues of Graphs
 GRAPH SYMMETRY: ALGEBRAIC METHODS AND APPLICATIONS, VOLUME 497 OF NATO ASI SERIES C
, 1997
"... In the last decade important relations between Laplace eigenvalues and eigenvectors of graphs and several other graph parameters were discovered. In these notes we present some of these results and discuss their consequences. Attention is given to the partition and the isoperimetric properties of ..."
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Cited by 129 (0 self)
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In the last decade important relations between Laplace eigenvalues and eigenvectors of graphs and several other graph parameters were discovered. In these notes we present some of these results and discuss their consequences. Attention is given to the partition and the isoperimetric properties of graphs, the maxcut problem and its relation to semidefinite programming, rapid mixing of Markov chains, and to extensions of the results to infinite graphs.
Geometric Mesh Partitioning: Implementation and Experiments
"... We investigate a method of dividing an irregular mesh into equalsized pieces with few interconnecting edges. The method’s novel feature is that it exploits the geometric coordinates of the mesh vertices. It is based on theoretical work of Miller, Teng, Thurston, and Vavasis, who showed that certain ..."
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Cited by 112 (20 self)
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We investigate a method of dividing an irregular mesh into equalsized pieces with few interconnecting edges. The method’s novel feature is that it exploits the geometric coordinates of the mesh vertices. It is based on theoretical work of Miller, Teng, Thurston, and Vavasis, who showed that certain classes of “wellshaped” finite element meshes have good separators. The geometric method is quite simple to implement: we describe a Matlab code for it in some detail. The method is also quite efficient and effective: we compare it with some other methods, including spectral bisection.
A Solver for the Network Testbed Mapping Problem
 SIGCOMM Computer Communications Review
, 2002
"... this paper, we explore this problem, which we call the network testbed mapping problem. We describe the interesting challenges that characterize this problem, and explore its application to other spaces, such as distributed simulation. We present the design, implementation, and evaluation of a solve ..."
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Cited by 110 (12 self)
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this paper, we explore this problem, which we call the network testbed mapping problem. We describe the interesting challenges that characterize this problem, and explore its application to other spaces, such as distributed simulation. We present the design, implementation, and evaluation of a solver for this problem, which is currently in use on the Netbed network testbed. It builds on simulated annealing to find very good solutions in a few seconds for our historical workload, and scales gracefully on large wellconnected synthetic topologies