On 400 bp microbial gene fragments, embedding-based nearest-neighbor search with FAISS and ScaNN outperforms nucleotide MMseqs2 in speed and accuracy; tuned FAISS configurations also beat ScaNN.
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Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
On 400 bp microbial gene fragments, embedding-based nearest-neighbor search with FAISS and ScaNN outperforms nucleotide MMseqs2 in speed and accuracy; tuned FAISS configurations also beat ScaNN.