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» Dynamic Programming and Fast Matrix Multiplication
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ESA
2006
Springer
105views Algorithms» more  ESA 2006»
13 years 8 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 9 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 10 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 4 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 8 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...