HEDAcc: FPGA-based Accelerator for High-order Epistasis Detection
Gaspar Ribeiro, Nuno Neves, Sergio Santander‐Jiménez, Aleksandar D. Ilic · 2021
The manifestation of important genetic diseases is often a consequence of the interactions between Single Nucleotide Polymorphisms (SNPs), also known as epistasis. Detecting epistasis for high-order interactions results in a huge computational complexity, as the number of SNP combinations to be evaluated exponentially grows with the interaction order. To address this challenge, state-of-the-art exhaustive search-based methods for epistasis detection rely on GPUs and FPGAs to provide high-performance solutions tailored for a specific order (second and rarely third-order interactions) and/or specific data-set sizes. In this paper, a novel parameterizable architecture is proposed that enables the deployment of FPGA-based accelerators targeting any order of interactions and any data-set size. By relying on a set of algorithmic and architecture optimizations, the proposed accelerator showed to outperform current FPGA accelerators for second and third-order interactions by as much as 4.6× and 9.5×, respectively. The proposed solution also showed comparable performance to current GPGPU third-order implementations, while consuming up to 8.2× less energy. Finally, the proposed architecture allowed for the implementation of a fourth-order epistasis detection accelerator in an FPGA platform.