DSHD-CAM: High-Throughput RRAM CAM Leveraging Dynamic Shifted Hamming Distance for Genome Analysis

Genome analysis has been critical in various applications, such as infectious disease control. High throughput is an essential requirement for genome analysis in data-intensive scenarios, which requires acceleration by content-addressable memory (CAM) with parallel comparison capability. However, existing genome analysis CAMs still face inadequate throughput issues due to large cell area, excessive array storage redundancy, and inefficient comparison algorithms. To address these issues, we propose a high-throughput dynamic shifted Hamming distance (SHD) resistive random access memory (RRAM)-based CAM (DSHD-CAM) that leverages the characteristics of genome analysis. First, we propose a compact RRAM-based CAM cell utilizing one-hot encoding and time-domain computation to minimize cell area. Second, we propose a dense CAM array utilizing an efficient storage scheme to reduce array storage redundancy. Third, we propose a dynamic SHD search algorithm filtering out low-match-potential cases to reduce search latency. Compared to the state-of-the-art (SOTA), DSHD-CAM achieves an average of$7.58\times $higher throughput under the same area constraints while maintaining competitive sensitivity and precision.