Parallel Computing Techniques for Performance Enhancement of a cDNA Microarray Gridding Algorithm

Stamos Katsigiannis, Dimitris Maroulis

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

cDNA microarrays are a powerful tool for studying gene expression levels. A challenging and complex task of microarray image analysis is the creation of a grid that matches the spots in the image. Proposed methods and tools usually require human intervention, leading to variations of the gene expression results. Furthermore, while automatic methods are available, they present high computational complexity. In this work, the authors present a performance enhancement via GPU computing techniques of an automatic gridding method, previously proposed by their research group. Complex steps of the algorithm were computed in parallel by utilizing the NVIDIA CUDA architecture that allows the use of NVIDIA GPUs for general purpose parallel computations. Experiments showed that the proposed approach achieves higher utilization of the available computational resources, leading to enhanced performance and significantly reduced computational time.
Original languageEnglish
Title of host publicationSignal Processing and Information Technology(ISSPIT), 2013 IEEE International Symposium on
PublisherIEEE
Pages446-451
ISBN (Electronic)978-1-4799-4796-6
ISBN (Print)978-1-4799-4795-9
DOIs
Publication statusPublished - 2013
Externally publishedYes

Publication series

Name
PublisherIEEE
ISSN (Print)2162-7843

Keywords

  • cDNA microarray gridding
  • GPU computing
  • genetic algorithm
  • CUDA

Cite this

Katsigiannis, S., & Maroulis, D. (2013). Parallel Computing Techniques for Performance Enhancement of a cDNA Microarray Gridding Algorithm. In Signal Processing and Information Technology(ISSPIT), 2013 IEEE International Symposium on (pp. 446-451). IEEE. https://doi.org/10.1109/ISSPIT.2013.6781922
Katsigiannis, Stamos ; Maroulis, Dimitris. / Parallel Computing Techniques for Performance Enhancement of a cDNA Microarray Gridding Algorithm. Signal Processing and Information Technology(ISSPIT), 2013 IEEE International Symposium on. IEEE, 2013. pp. 446-451
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Katsigiannis, S & Maroulis, D 2013, Parallel Computing Techniques for Performance Enhancement of a cDNA Microarray Gridding Algorithm. in Signal Processing and Information Technology(ISSPIT), 2013 IEEE International Symposium on. IEEE, pp. 446-451. https://doi.org/10.1109/ISSPIT.2013.6781922

Parallel Computing Techniques for Performance Enhancement of a cDNA Microarray Gridding Algorithm. / Katsigiannis, Stamos; Maroulis, Dimitris.

Signal Processing and Information Technology(ISSPIT), 2013 IEEE International Symposium on. IEEE, 2013. p. 446-451.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AB - cDNA microarrays are a powerful tool for studying gene expression levels. A challenging and complex task of microarray image analysis is the creation of a grid that matches the spots in the image. Proposed methods and tools usually require human intervention, leading to variations of the gene expression results. Furthermore, while automatic methods are available, they present high computational complexity. In this work, the authors present a performance enhancement via GPU computing techniques of an automatic gridding method, previously proposed by their research group. Complex steps of the algorithm were computed in parallel by utilizing the NVIDIA CUDA architecture that allows the use of NVIDIA GPUs for general purpose parallel computations. Experiments showed that the proposed approach achieves higher utilization of the available computational resources, leading to enhanced performance and significantly reduced computational time.

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Katsigiannis S, Maroulis D. Parallel Computing Techniques for Performance Enhancement of a cDNA Microarray Gridding Algorithm. In Signal Processing and Information Technology(ISSPIT), 2013 IEEE International Symposium on. IEEE. 2013. p. 446-451 https://doi.org/10.1109/ISSPIT.2013.6781922