Inferring Genome-Wide Gene Regulatory Networks with GPU or CPU Parallel Algorithm

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International Journal of Advanced Network, Monitoring and Controls

Xi'an Technological University

Subject: Computer Science, Software Engineering

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eISSN: 2470-8038

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VOLUME 2 , ISSUE 3 (September 2017) > List of articles

Inferring Genome-Wide Gene Regulatory Networks with GPU or CPU Parallel Algorithm

Ming Zheng / Mugui Zhuo / Shugong Zhang / Guixia Liu *

Keywords : Gene regulatory network, CPU/GPU cooperative computing, Efficient access cache, Parallel algorithm

Citation Information : International Journal of Advanced Network, Monitoring and Controls. Volume 2, Issue 3, Pages 15-19, DOI: https://doi.org/10.1109/iccnea.2017.84

License : (CC BY-NC-ND 4.0)

Published Online: 10-April-2018

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ABSTRACT

Expression of gene block, with the GPU parallel thread structure characteristic calculation, according to the structural characteristics of GPU thread design of double parallel mode, and the use of texture cache memory to achieve high efficiency; on the basis of CPU two level cache capacity of basic blocks further subdivided into sub blocks to improve the cache hit rate, the technology to reduce the number of memory accesses the use of data, reduce the thread migration in the core between the use of thread binding technology; according to the calculated capacity allocation of multi-core CPU and GPU CPU and GPU gene in the mutual information calculation task to calculate the load balance of CPU and GPU; in the design of the new threshold calculation algorithm based on the design and implementation of memory efficient construction of global gene control network CPU /GPU parallel algorithm. The experimental results show that compared with the existing algorithms, this algorithm speed is more obvious, and is able to build more large-scale global gene regulation Control network.

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