David A. Bader
David A. Bader
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Interactive Graph Analytics at Scale in Arkouda
Data from many real-world applications often can be abstracted as graphs. However, the increasing graph size makes it impossible for …
Zhihui Du
,
Oliver Alvarado Rodriguez
,
Joseph Patchett
,
David Bader
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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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DOI
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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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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DOI
Parallel community detection for massive graphs
E. Jason Riedy
,
Henning Meyerhenke
,
David Ediger
,
David A. Bader
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DOI
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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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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DOI
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
Cite
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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