Improving CUDA DNA Analysis Software with Genetic Programming
William B. Langdon, Brian Y.H. Lam, Justyna Petke, Mark Harman · 2015
We genetically improve BarraCUDA using a BNF grammar incorporating C scoping rules with GP. Barracuda maps next generation DNA sequences to the human genome using the Burrows-Wheeler algorithm (BWA) on nVidia Tesla parallel graphics hardware (GPUs). GI using phenotypic tabu search with manually grown code can graft new features giving more than 100 fold speed up on a performance critical kernel without loss of accuracy.