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SODA
2012
ACM
212views Algorithms» more  SODA 2012»
13 years 8 days ago
Parallelism and time in hierarchical self-assembly
We study the role that parallelism plays in time complexariants of Winfree’s abstract Tile Assembly Model (aTAM), a model of molecular algorithmic self-assembly. In the “hiera...
Ho-Lin Chen, David Doty
HPCS
2005
IEEE
15 years 3 months ago
High Performance Derivative-Free Optimization Applied to Biomedical Image Registration
Abstract— Optimization of a similarity metric is an essential component in most medical image registration approaches based on image intensities. In this paper, two new, determin...
Mark P. Wachowiak, Terry M. Peters
TCS
1998
14 years 9 months ago
ERCW PRAMs and Optical Communication
This paper presents algorithms and lower bounds for several fundamental problems on the Exclusive Read, Concurrent Write Parallel Random Access Machine (ERCW PRAM) and some result...
Philip D. MacKenzie, Vijaya Ramachandran
BIBM
2008
IEEE
110views Bioinformatics» more  BIBM 2008»
15 years 4 months ago
Genome Alignments Using MPI-LAGAN
We develop a parallel algorithm for a widely used whole genome alignment method called LAGAN. We use the MPI-based protocol to develop parallel solutions for two phases of the alg...
Ruinan Zhang, Huzefa Rangwala, George Karypis
IPPS
2008
IEEE
15 years 4 months ago
On the representation and multiplication of hypersparse matrices
Multicore processors are marking the beginning of a new era of computing where massive parallelism is available and necessary. Slightly slower but easy to parallelize kernels are ...
Aydin Buluç, John R. Gilbert