A Heterogeneous Platform for 3D NAND-Based In-Memory Hyperdimensional Computing Engine for Genome Sequencing Applications

Hyperdimensional (HD) computing is a promising paradigm for large-scale genome sequencing. In prior work, we proposed a 3D NAND-based HD computing engine as an energy-efficient solution for sequencing several gigabytes or terabytes of genomic data. In this work, we introduce an improved HD computing engine for genome sequencing that leverages heterogeneous 3D integration techniques. We employ Cu-Cu hybrid bonding and CMOS under array (CuA) technologies to integrate the digital logic tier with the 3D NAND-based associative memory tier. We benchmark the performance of the proposed hardware design using a dataset of 10,575 microorganism genomes. The results indicate the robustness of the classification accuracy despite device non-idealities. Compared to conventional methods, the proposed design reduces the system-level energy consumption by
$1000\times $
, provided the data is not offloaded from the solid-state drive to the computing units.