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» Dynamic Programming and Fast Matrix Multiplication
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ESA
2006
Springer
105views Algorithms» more  ESA 2006»
13 years 9 months ago
Dynamic Programming and Fast Matrix Multiplication
Abstract. We give a novel general approach for solving NP-hard optimization problems that combines dynamic programming and fast matrix multiplication. The technique is based on red...
Frederic Dorn
CPM
1998
Springer
209views Combinatorics» more  CPM 1998»
13 years 10 months ago
A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming
The approximate string matching problem is to find all locations at which a query of length m matches a substring of a text of length n with k-or-fewer differences. Simple and prac...
Gene Myers
CP
2003
Springer
13 years 11 months ago
A SAT-Based Approach to Multiple Sequence Alignment
Multiple sequence alignment is a central problem in Bioinformatics. A known integer programming approach is to apply branch-and-cut to exponentially large graph-theoretic models. T...
Steven David Prestwich, Desmond G. Higgins, Orla O...
COCO
2011
Springer
221views Algorithms» more  COCO 2011»
12 years 5 months ago
Non-uniform ACC Circuit Lower Bounds
The class ACC consists of circuit families with constant depth over unbounded fan-in AND, OR, NOT, and MODm gates, where m > 1 is an arbitrary constant. We prove: • NTIME[2n ...
Ryan Williams
GCB
2004
Springer
223views Biometrics» more  GCB 2004»
13 years 9 months ago
PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays
: In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs. In this paper, we present a new nonheuristic algorithm, ...
Michael Beckstette, Dirk Strothmann, Robert Homann...