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CAM4: In-Memory Viral Pathogen Genome Classification Using Similarity Search Dynamic Content-Addressable Memory

Abstract:

Wepresent CAM4, a novel embedded dynamic storage-based similarity search content addressable memory. CAM4 is designated for in-memory computational genomics applications, particularly the identification and classification of pathogen DNA. CAM4 employs a novel gain cell design and one-hot encoding of DNA bases to address retention time variations, and mitigate potential data loss from pulldown leakage and soft errors in embedded DRAM. CAM4 features performance overhead-free refresh and data upload, allowing simultaneous search and refresh without performance degradation. CAM4 offers approximate search versatility in scenarios with a variety of industrial sequencers with different error profiles. When classifying DNA reads with a 10% error rate, it achieves, on average, a 25% higher F<inf>1</inf> score compared to MetaCache-GPU and Kraken2 DNA classification tools. Simulated at 1 GHz, CAM4 provides 1, 412× and 1, 040× average speedup over MetaCache-GPU and Kraken2 respectively.