CUDA-based multi-core implementation of MDS-based bioinformatics algorithms

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2009
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Fester
Strickert, Marc
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GROSSE, Ivo, ed., Steffen NEUMANN, ed., Stefan POSCH, ed., Falk SCHREIBER, ed., Peter STADLER, ed.. German conference on bioinformatics 2009. Bonn: Gesellschaft für Informatik, 2009, pp. 67-79. Lecture Notes in Informatics. P-157. ISSN 1617-5468. ISBN 978-3-88579-251-2
Zusammenfassung

Solving problems in bioinformatics often needs extensive computational power. Current trends in processor architecture, especially massive multi-core processors for graphic cards, combine a large number of cores into a single chip to improve the overall performance. The Compute Unified Device Architecture (CUDA) provides programming interfaces to make full use of the computing power of graphics processing units. We present a way to use CUDA for substantial performance improvement of methods based on multi-dimensional scaling (MDS). The suitability of the CUDA architecture as a high-performance computing platform is studied by adapting a MDS algorithm on specific hardware properties. We show how typical bioinformatics problems related to dimension reduction and network layout benefit from the multi-core implementation of the MDS algorithm. CUDA-based methods are introduced and compared to standard solutions, demonstrating 50-fold acceleration and above.

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German conference on bioinformatics 2009, 28. Sept. 2009 - 30. Sept. 2009, Halle-Wittenberg
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ISO 690FESTER, , Falk SCHREIBER, Marc STRICKERT, 2009. CUDA-based multi-core implementation of MDS-based bioinformatics algorithms. German conference on bioinformatics 2009. Halle-Wittenberg, 28. Sept. 2009 - 30. Sept. 2009. In: GROSSE, Ivo, ed., Steffen NEUMANN, ed., Stefan POSCH, ed., Falk SCHREIBER, ed., Peter STADLER, ed.. German conference on bioinformatics 2009. Bonn: Gesellschaft für Informatik, 2009, pp. 67-79. Lecture Notes in Informatics. P-157. ISSN 1617-5468. ISBN 978-3-88579-251-2
BibTex
@inproceedings{Fester2009CUDAb-40247,
  year={2009},
  title={CUDA-based multi-core implementation of MDS-based bioinformatics algorithms},
  url={http://subs.emis.de/LNI/Proceedings/Proceedings157/67.pdf},
  number={P-157},
  isbn={978-3-88579-251-2},
  issn={1617-5468},
  publisher={Gesellschaft für Informatik},
  address={Bonn},
  series={Lecture Notes in Informatics},
  booktitle={German conference on bioinformatics 2009},
  pages={67--79},
  editor={Grosse, Ivo and Neumann, Steffen and Posch, Stefan and Schreiber, Falk and Stadler, Peter},
  author={Fester and Schreiber, Falk and Strickert, Marc}
}
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