Large-scale microarray data analysis using GPU-accelerated linear algebra libraries.

摘要

The biological datasets produced as a result of high-throughput genomic research such as specifically microarrays, contain vast amounts of knowledge for entire genome and their expression affiliations. Gene clustering from such data is a challenging task due to the huge data size and high complexity of the algorithms as well as the visualization needs. Most of the existing analysis methods for genome-wide gene expression profiles are sequential programs using greedy algorithms and require subjective human decision. Recently, Zhu et al. proposed a parallel Random matrix theory (RMT) based approach for generating transcriptional networks, which is much more resistant to high level of noise in the data [9] without human intervention. Nowadays GPUs are designed to be used more efficiently for general purpose computing [1] and are vastly superior to CPUs [6] in terms of threading performance. Our kernel functions running on GPU utilizes the functions from both the libraries of Compute Unified Basic Linear Algebra Subroutines (CUBLAS) and Compute Unified Linear Algebra (CULA) which implements the Linear Algebra Package (LAPACK). Our experiment results show that GPU program can achieve an average speed-up of 2∼3 times for some simulated datasets.