Reconfigurable Hardware Acceleration of Canonical Graph Labelling

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 resource usage and speed with changing algorithm parameters and input data-sets. The hardware labelling unit is over 100 times faster than a quad Opteron 2.2GHz for graphs with few vertex invariants, and at least 10 times faster for graphs that are easier to label.

• Type: Conference
• Year: 2007
• Where: ARC
• Authors: David B. Thomas, Wayne Luk, Michael Stumpf
• Keywords: ARC 2007, Canonical Labelling Algorithm, Graph Labelling Algorithm, Hardware, Labelling Algorithm