David A. Bader
David A. Bader
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6
High-Performance Phylogenetic Inference
Software tools based on the maximum likelihood method and Bayesian methods are widely used for phylogenetic tree inference. This …
David A. Bader
,
Kamesh Madduri
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Benchmarking for Graph Clustering and Partitioning
David A. Bader
,
Andrea Kappes
,
Henning Meyerhenke
,
Peter Sanders
,
Christian Schulz
,
Dorothea Wagner
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Engineering Algorithms for Computational Biology
David A. Bader
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DOI
High Performance Algorithm Engineering for Large-Scale Problems
Algorithm engineering refers to the process required to transform a pencil-and-paper algorithm into a robust, efficient, well tested, …
David A. Bader
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DOI
Sorting Signed Permutations by Reversal (Reversal Distance)
David A. Bader
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DOI
Benchmarking for Graph Clustering and Partitioning
David A. Bader
,
Henning Meyerhenke
,
Peter Sanders
,
Christian Schulz
,
Andrea Kappes
,
Dorothea Wagner
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DOI
Evaluating Multicore Processors and Accelerators for Dense Numerical Computations
In this chapter, we empirically evaluate fundamental design trade-offs among current multicore processors and accelerator technologies …
Seunghwa Kang
,
Nitin Arora
,
Aashay Shringarpure
,
Richard W. Vuduc
,
David A. Bader
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Parallel Community Detection for Massive Graphs
Tackling the current volume of graph-structured data requires parallel tools. We extend our work on analyzing such massive graph data …
E. Jason Riedy
,
Henning Meyerhenke
,
David Ediger
,
David A. Bader
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Parallel community detection for massive graphs
E. Jason Riedy
,
Henning Meyerhenke
,
David Ediger
,
David A. Bader
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Computational Challenges in Emerging Combinatorial Scientific Computing Applications
In this chapter, we describe several novel uses of combinatorial techniques that have found widespread use in realms outside …
David A. Bader
,
Kamesh Madduri
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Fundamental Questions in the Analysis of Large Graphs
Graphs are a general approach for representing information that spans the widest possible range of computing applications. They are …
Jeremy Kepner
,
David A. Bader
,
Robert Bond
,
Nadya Bliss
,
Christos Faloutsos
,
Bruce Hendrickson
,
John Gilbert
,
Eric Robinson
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Graph Algorithms
David A. Bader
,
Guojing Cong
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Hybrid Programming With SIMPLE
Guojing Cong
,
David A. Bader
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Large-Scale Network Analysis
Centrality analysis deals with the identification of critical vertices and edges in real-world graph abstractions. Graph-theoretic …
David A. Bader
,
Christine Heitsch
,
Kamesh Madduri
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Spanning Tree, Minimum Weight
David A. Bader
,
Guojing Cong
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SWARM: A Parallel Programming Framework for Multicore Processors
S oftW are and A lgorithms for R unning on M ulti-core (SWARM) is a portable open-source parallel library of basic primitives for …
David A. Bader
,
Guojing Cong
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Combinatorial Algorithm Design on the Cell/B.E. Processor
Combinatorial algorithms play a subtle, yet important, role in traditional scientific computing. Perhaps the most well-known example is …
David A. Bader
,
Virat Agarwal
,
Kamesh Madduri
,
Fabrizio Petrini
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Designing Fast Fourier Transform for the IBM Cell Broadband Engine
The Cell Broadband Engine (or the Cell/B.E.) [6, 16, 17, 34] is a novel high-performance architecture designed by Sony, Toshiba, and …
Virat Agarwal
,
David A. Bader
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The Case of the Fast Financial Feed
Traditional scientific HPC applications running on high-end computing platforms are not the only class of applications dependent on the …
Virat Agarwal
,
Lin Duan
,
Lurng-Kuo Liu
,
Michael Perrone
,
Fabrizio Petrini
,
Davide Pasetto
,
David A. Bader
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DOI
Engineering Algorithms for Computational Biology
David A. Bader
PDF
Cite
DOI
High Performance Algorithm Engineering for Large-scale Problems
Algorithm engineering refers to the process required to transform a pencil-and-paper algorithm into a robust, efficient, well tested, …
David A. Bader
PDF
Cite
DOI
Sorting Signed Permutations by Reversal (Reversal Distance)
David A. Bader
PDF
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DOI
Design of Multithreaded Algorithms for Combinatorial Problems
Graph theoretic and combinatorial problems arise in several traditional and emerging scientific disciplines such as VLSI design, …
David A. Bader
,
Kamesh Madduri
,
Guojing Cong
,
John Feo
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DOI
Efficient Parallel Graph Algorithms for Shared-memory Multiprocessors
Graph theoretic and combinatorial problems arise in several traditional and emerging scientific disciplines such as VLSI design, …
David A. Bader
,
Guojing Cong
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DOI
Multithreaded Algorithms for Processing Massive Graphs
In this chapter, we consider the applicability of a non-traditional massively multithreaded architecture, the Cray MTA-2 [13], as a …
Kamesh Madduri
,
David A. Bader
,
Jonathan W. Berry
,
Joseph R. Crobak
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High-Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony
All biological disciplines are united by the idea that species share a common history. These relationships are crucial to the …
David A. Bader
,
Mi Yan
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High-Performance Phylogeny Reconstruction Under Maximum Parsimony
This chapter contains sections titled: Introduction Maximum Parsimony Exact MP: Parallel Branch and Bound MP Heuristics: Disk-Covering …
Tiffani L. Williams
,
David A. Bader
,
Bernard M. E. Moret
,
Mi Yan
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Parallel Algorithm Design for Branch and Bound
Large and/or computationally expensive optimization problems sometimes require parallel or high-performance computing systems to …
David A. Bader
,
William E. Hart
,
Cynthia A. Phillips
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Algorithm Engineering for Parallel Computation
The emerging discipline of algorithm engineering has primarily focused on transforming pencil-and-paper sequential algorithms into …
David A. Bader
,
Bernard M. E. Moret
,
Peter Sanders
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