On Computing Transitive-Closure Equivalence Sets Using a Hybrid GA-DP Approach

Abstract

The computation of transitive-closure equivalence sets has recently emerged as an important step for building static and dynamic models for biological DNA sequencing.We present a hybrid method of integrating genetic algorithm (GA) with dynamic programming (DP), and offer an efficient FPGA (field programmable gate array) implementation platform for the required computation. The dynamic programming calculation of transitive closure makes use of the Floyd-Warshall algorithm that forms the basic fitness evaluation in genetic algorithm, for selecting candidate chromosome strings generated by applying basic genetic operators. The complete high-level design is developed using Xilinx's System Generator tool, which provides an efficient generation of VHDL code for verification on targeted FPGA hardware such as the Virtex-800. Successful testing results for finding 5-node equivalence sets for a 30-node genetic network are reported.