Top-Scoring Pair and Top-Scoring Triple on the Graphics Processing Unit (GPU)

We have implemented the relative expression classification algorithms the top-scoring pair  (TSP) and top-scoring triplet (TST) for the graphics processing unit (GPU). The GPU is a specialized hardware most commonly associated with gaming applications. However, with the NVIDIA’s release of the Compute Unified Device Architecture (CUDA), the GPU became a general-purpose computational device now widely used in computational biology.  The GPU architecture emphasizes massive parallelism, in which thousands of parallel threads execute simultaneously.  Algorithms that can exploit such parallelism, such as relative expression algorithms, will yield impressive speedups when implemented on GPU hardware. My implementations of TSP and TST run 200-300X faster than the corresponding CPU implementations of these algorithms, greatly accelerating the pace of discovery.



Data and Software File(s):
ZIP file containing Matlab and Standalone Source Code, Executables, and Test Data