Human genetics research is lengthy and slow, and one primary cause of that is the slow combinatorial algorithms used. Researchers at Dartmouth have just published a paper where they implemented these algorithms on NVidia graphics cards with CUDA, with amazing results.
One such algorithm is Multifactor Dimensionality Reduction (MDR). Expert knowledge guided evolutionary computing wrappers around MDR have previously been shown to be a powerful way to efficiently analyze datasets for interactions. Evolutionary computing can effectively address some of the challenges these datasets present. Unfortunately examining the statistical significance of results requires permutation testing, which increases the computation requirements by a factor of 1000. Here we implement an expert knowledge guided ant system on graphics processing units (GPUs) and show that the GPU implementation makes the rigorous statistical analysis of large datasets practical.
The paper was recently published in GECCO’09, and can be viewed below.
