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A fast and high quality multilevel scheme for partitioning irregular graphs
 SIAM JOURNAL ON SCIENTIFIC COMPUTING
, 1998
"... Recently, a number of researchers have investigated a class of graph partitioning algorithms that reduce the size of the graph by collapsing vertices and edges, partition the smaller graph, and then uncoarsen it to construct a partition for the original graph [Bui and Jones, Proc. ..."
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Cited by 1189 (15 self)
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Recently, a number of researchers have investigated a class of graph partitioning algorithms that reduce the size of the graph by collapsing vertices and edges, partition the smaller graph, and then uncoarsen it to construct a partition for the original graph [Bui and Jones, Proc.
Greedy Randomized Adaptive Search Procedures
, 2002
"... GRASP is a multistart metaheuristic for combinatorial problems, in which each iteration consists basically of two phases: construction and local search. The construction phase builds a feasible solution, whose neighborhood is investigated until a local minimum is found during the local search phas ..."
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Cited by 647 (82 self)
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GRASP is a multistart metaheuristic for combinatorial problems, in which each iteration consists basically of two phases: construction and local search. The construction phase builds a feasible solution, whose neighborhood is investigated until a local minimum is found during the local search phase. The best overall solution is kept as the result. In this chapter, we first describe the basic components of GRASP. Successful implementation techniques and parameter tuning strategies are discussed and illustrated by numerical results obtained for different applications. Enhanced or alternative solution construction mechanisms and techniques to speed up the search are also described: Reactive GRASP, cost perturbations, bias functions, memory and learning, local search on partially constructed solutions, hashing, and filtering. We also discuss in detail implementation strategies of memorybased intensification and postoptimization techniques using pathrelinking. Hybridizations with other metaheuristics, parallelization strategies, and applications are also reviewed.
A LinearTime Heuristic for Improving Network Partitions
, 1982
"... An iterative mincut heuristic for partitioning networks is presented whose worst case computation time, per pass, grows linearly with the size of the network. In practice, only a very small number of passes are typically needed, leading to a fast approximation algorithm for mincut partitioning. To d ..."
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Cited by 524 (0 self)
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An iterative mincut heuristic for partitioning networks is presented whose worst case computation time, per pass, grows linearly with the size of the network. In practice, only a very small number of passes are typically needed, leading to a fast approximation algorithm for mincut partitioning. To deal with cells of various sizes, the algorithm progresses by moving one cell at a time between the blocks of the partition while maintaining a desired balance based on the size of the blocks rather than the number of cells per block. Efficient data structures are used to avoid unnecessary searching for the best cell to move and to minimize unnecessary updating of cells affected by each move.
Coclustering documents and words using Bipartite Spectral Graph Partitioning
, 2001
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Arb: A software environment for sequence data
 Nucleic Acids Res
, 2004
"... The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed ..."
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Cited by 421 (10 self)
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The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database ®elds assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, pro®le and ®lter calculation, phylogenetic analyses, speci®c hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.
Survey of clustering data mining techniques
, 2002
"... Accrue Software, Inc. Clustering is a division of data into groups of similar objects. Representing the data by fewer clusters necessarily loses certain fine details, but achieves simplification. It models data by its clusters. Data modeling puts clustering in a historical perspective rooted in math ..."
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Cited by 408 (0 self)
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Accrue Software, Inc. Clustering is a division of data into groups of similar objects. Representing the data by fewer clusters necessarily loses certain fine details, but achieves simplification. It models data by its clusters. Data modeling puts clustering in a historical perspective rooted in mathematics, statistics, and numerical analysis. From a machine learning perspective clusters correspond to hidden patterns, the search for clusters is unsupervised learning, and the resulting system represents a data concept. From a practical perspective clustering plays an outstanding role in data mining applications such as scientific data exploration, information retrieval and text mining, spatial database applications, Web analysis, CRM, marketing, medical diagnostics, computational biology, and many others. Clustering is the subject of active research in several fields such as statistics, pattern recognition, and machine learning. This survey focuses on clustering in data mining. Data mining adds to clustering the complications of very large datasets with very many attributes of different types. This imposes unique
Partitioning of Unstructured Problems for Parallel Processing
, 1991
"... Many large scale computational problems are based on unstructured computational domains. Primary examples are unstructured grid calculations based on finite volume methods in computational fluid dynamics, or structural analysis problems based on finite element approximations. Here we will address th ..."
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Cited by 344 (16 self)
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Many large scale computational problems are based on unstructured computational domains. Primary examples are unstructured grid calculations based on finite volume methods in computational fluid dynamics, or structural analysis problems based on finite element approximations. Here we will address the question of how to distribute such unstructured computational domains over a large number of processors in a MIMD machine with distributed memory. A graph theoretical framework for these problems will be established. Based on this framework three decomposition algorithms will be introduced. In particular a new decomposition algorithm will be discussed, which is based on the computation of an eigenvector of the Laplacian matrix associated with the graph. Numerical comparisons on large scale two and three dimensional problems demonstrate the superiority of the new spectral bisection algorithm.
Multilevel hypergraph partitioning: Application in VLSI domain
 IEEE TRANS. VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS
, 1999
"... In this paper, we present a new hypergraphpartitioning algorithm that is based on the multilevel paradigm. In the multilevel paradigm, a sequence of successively coarser hypergraphs is constructed. A bisection of the smallest hypergraph is computed and it is used to obtain a bisection of the origina ..."
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Cited by 315 (22 self)
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In this paper, we present a new hypergraphpartitioning algorithm that is based on the multilevel paradigm. In the multilevel paradigm, a sequence of successively coarser hypergraphs is constructed. A bisection of the smallest hypergraph is computed and it is used to obtain a bisection of the original hypergraph by successively projecting and refining the bisection to the next level finer hypergraph. We have developed new hypergraph coarsening strategies within the multilevel framework. We evaluate their performance both in terms of the size of the hyperedge cut on the bisection, as well as on the run time for a number of very large scale integration circuits. Our experiments show that our multilevel hypergraphpartitioning algorithm produces highquality partitioning in a relatively small amount of time. The quality of the partitionings produced by our scheme are on the average 6%–23 % better than those produced by other stateoftheart schemes. Furthermore, our partitioning algorithm is significantly faster, often requiring 4–10 times less time than that required by the other schemes. Our multilevel hypergraphpartitioning algorithm scales very well for large hypergraphs. Hypergraphs with over 100 000 vertices can be bisected in a few minutes on today’s workstations. Also, on the large hypergraphs, our scheme outperforms other schemes (in hyperedge cut) quite consistently with larger margins (9%–30%).
Comparing community structure identification
 Journal of Statistical Mechanics: Theory and Experiment
, 2005
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