FPGA-accelerated Bayesian learning for construction of gene regulatory networks

Abstract

Rapid advances in biological technologies, such as DNA microarrays, have enabled biologists to measure the expression levels of thousand of genes simultaneously under different conditions. This leads to a growing need to find methods that extract valuable information, fast and reliably, from this large amount of data. Recently, the advantages of using Bayesian networks for the reconstruction of gene regulatory networks from microarray data have been shown. However, these methods are very computationally intensive. Here, we explore the inherent parallelism of Bayesian learning and propose a hardware design that can be used for the reconstruction of such networks. The evaluation of the proposed design in a VirtexII demonstrates a speed up of the algorithm by 76 times over a software implementation in a Pentium 4.