Conference Proceedings

Reconfigurable hardware acceleration of canonical graph labelling

DB Thomas, W Luk, M Stumpf

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Published : 2007


Many important algorithms in computational biology and related subjects rely on the ability to extract and to identify sub-graphs of larger graphs; an example is to find common functional structures within Protein Interaction Networks. However, the increasing size of both the graphs to be searched and the target sub-graphs requires the use of large numbers of parallel conventional CPUs. This paper proposes an architecture to allow acceleration of sub-graph identification through reconfigurable hardware, using a canonical graph labelling algorithm. A practical implementation of the canonical labelling algorithm in the Virtex-4 reconfigurable architecture is presented, examining the scaling of..

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University of Melbourne Researchers

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