Chapter

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 …
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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 …
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Benchmarking for Graph Clustering and Partitioning
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Engineering Algorithms for Computational Biology
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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, …
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Sorting Signed Permutations by Reversal (Reversal Distance)
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Benchmarking for Graph Clustering and Partitioning
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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 …
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Parallel community detection for massive graphs
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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 …
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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 …
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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 …
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Graph Algorithms
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Hybrid Programming With SIMPLE
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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 …
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Spanning Tree, Minimum Weight
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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 …
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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 …
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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 …
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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 …
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Engineering Algorithms for Computational Biology
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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, …
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Sorting Signed Permutations by Reversal (Reversal Distance)
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Design of Multithreaded Algorithms for Combinatorial Problems
Graph theoretic and combinatorial problems arise in several traditional and emerging scientific disciplines such as VLSI design, …
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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, …
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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 …
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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 …
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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 …
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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 …
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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 …
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