TY - GEN
T1 - On accelerating iterative algorithms with CUDA
T2 - 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
AU - Du, Zhihui
AU - Yin, Zhaoming
AU - Liu, Wenjie
AU - Bader, David
PY - 2010
Y1 - 2010
N2 - The accuracy of Conditional Random Fields (CRF) is achieved at the cost of huge amount of computation to train model. In this paper we designed the parallelized algorithm for the Gradient Ascent based CRF training methods for biological sequence alignment. Our contribution is mainly on two aspects: 1) We flexibly parallelized the different iterative computation patterns, and the according optimization methods are presented. 2) As for the Gibbs Sampling based training method, we designed a way to automatically predict the iteration round, so that the parallel algorithm could be run in a more efficient manner. In the experiment, these parallel algorithms achieved valuable accelerations comparing to the serial version.
AB - The accuracy of Conditional Random Fields (CRF) is achieved at the cost of huge amount of computation to train model. In this paper we designed the parallelized algorithm for the Gradient Ascent based CRF training methods for biological sequence alignment. Our contribution is mainly on two aspects: 1) We flexibly parallelized the different iterative computation patterns, and the according optimization methods are presented. 2) As for the Gibbs Sampling based training method, we designed a way to automatically predict the iteration round, so that the parallel algorithm could be run in a more efficient manner. In the experiment, these parallel algorithms achieved valuable accelerations comparing to the serial version.
KW - Biological sequence alignment
KW - Conditional random fields
KW - GPGPU
UR - http://www.scopus.com/inward/record.url?scp=79952013800&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79952013800&partnerID=8YFLogxK
U2 - 10.1109/BIBMW.2010.5703859
DO - 10.1109/BIBMW.2010.5703859
M3 - Conference contribution
AN - SCOPUS:79952013800
SN - 9781424483044
T3 - 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
SP - 543
EP - 548
BT - 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
Y2 - 18 December 2010 through 21 December 2010
ER -