Sparsity Controllable Hyperdimensional Computing for Genome Sequence Matching Acceleration

Abstract

In this paper, we propose a Hyper-Dimensional genome analysis platform. Instead of working with original sequences, our method maps the genome sequences into high-dimensional space and performs sequence matching with simple and parallel similarity searches. At the algorithm level, we revisit the sequence searching with brain-like memorization that Hyper-Dimensional computing natively supports. Instead of working on the original data, we map all data points into high-dimensional space, enabling the main sequence searching operations to process in a hardware-friendly way. We accordingly design a density-aware FPGA implementation. Our solution searches the similarity of an encoded query and large-scale genome library through different chunks. We exploit the holographic representation of patterns to stop search operations on libraries with a lower chance of a match. This translates our computation from dense to highly sparse just after a few chuck-based searches. Our evaluation shows that our accelerator can provide 46× speedup and 188× energy efficiency improvement compared to a state-of-the-art GPU implementation. Results show that our accelerator achieves up to 3440.6 GCUPS using a single Xilinx Alveo U280 board. © 2023 IEEE.