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BMCBI
2007
233views more  BMCBI 2007»
13 years 7 months ago
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
Background: To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching s...
Isaac T. S. Li, Warren Shum, Kevin Truong
FPL
2008
Springer
150views Hardware» more  FPL 2008»
13 years 9 months ago
Compiler generated systolic arrays for wavefront algorithm acceleration on FPGAs
Wavefront algorithms, such as the Smith-Waterman algorithm, are commonly used in bioinformatics for exact local and global sequence alignment. These algorithms are highly computat...
Betul Buyukkurt, Walid A. Najjar
NICSO
2010
Springer
13 years 11 months ago
Accelerated Genetic Algorithms with Markov Chains
t] Based on the mutation matrix formalism and past statistics of genetic algorithm, a Markov Chain transition probability matrix is introduced to provide a guided search for comple...
Guan Wang, Chen Chen, Kwok Yip Szeto
ICDM
2005
IEEE
109views Data Mining» more  ICDM 2005»
14 years 1 months ago
Triple Jump Acceleration for the EM Algorithm
This paper presents the triple jump framework for accelerating the EM algorithm and other bound optimization methods. The idea is to extrapolate the third search point based on th...
Han-Shen Huang, Bou-Ho Yang, Chun-Nan Hsu
VLSISP
2011
358views Database» more  VLSISP 2011»
13 years 2 months ago
Accelerating Machine-Learning Algorithms on FPGAs using Pattern-Based Decomposition
Machine-learning algorithms are employed in a wide variety of applications to extract useful information from data sets, and many are known to suffer from superlinear increases in ...
Karthik Nagarajan, Brian Holland, Alan D. George, ...