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IPPS
2009
IEEE
16 years 1 months ago
Dynamic parallelization for RNA structure comparison
In this paper we describe the parallelization of a dynamic programming algorithm used to find common RNA secondary structures including pseudoknots and similar structures. The se...
Eric Snow, Eric Aubanel, Patricia Evans
SIAMSC
2008
129views more  SIAMSC 2008»
15 years 6 months ago
Bottom-Up Construction and 2: 1 Balance Refinement of Linear Octrees in Parallel
Abstract. In this article, we propose new parallel algorithms for the construction and 2:1 balance refinement of large linear octrees on distributed memory machines. Such octrees a...
Hari Sundar, Rahul S. Sampath, George Biros
PDP
2010
IEEE
15 years 12 months ago
DAG Scheduling Using a Lookahead Variant of the Heterogeneous Earliest Finish Time Algorithm
Abstract—Among the numerous DAG scheduling heuristics suitable for heterogeneous systems, the Heterogeneous Earliest Finish Time (HEFT) heuristic is known to give good results in...
Luiz F. Bittencourt, Rizos Sakellariou, Edmundo R....
IPPS
1999
IEEE
15 years 11 months ago
A Graph Based Method for Generating the Fiedler Vector of Irregular Problems
In this paper we present new algorithms for spectral graph partitioning. Previously, the best partitioning methods were based on a combination of Combinatorial algorithms and appli...
Michael Holzrichter, Suely Oliveira
ESCIENCE
2006
IEEE
16 years 21 days ago
Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems
Bioinformatics algorithms such as sequence alignment methods based on profile-HMM (Hidden Markov Model) are popular but CPU-intensive. If large amounts of data are processed, a s...
Heinz Stockinger, Marco Pagni, Lorenzo Cerutti, La...