# Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN

arXiv: https://arxiv.org/abs/2507.16978 · HTML: https://mlsanity.com/paper/2507.16978/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 21 references that are in the map.
- First posted on arXiv 22 Jul 2025.

## Builds on (most cited first, 7 of 7)

- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- [Billion-scale similarity search with GPUs](https://mlsanity.com/paper/1702.08734/) (2017)
- [Improving language models by retrieving from trillions of tokens](https://mlsanity.com/paper/2112.04426/) (2021)
- [Approximate Nearest Neighbor Negative Contrastive Learning for Dense Text Retrieval](https://mlsanity.com/paper/2007.00808/) (2020)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)

## Built on by (most cited first, 1 of 1)

- [Adaptive Multimodal Agents-Based Framework for Automatic Workflow Execution](https://mlsanity.com/paper/2605.28607/) (2026)

## Abstract (arXiv)

The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a foundational task in bioinformatics for detecting homology, functional similarity, and novelty among genomic and proteomic sequences. Although tools like BLAST have been widely used and remain effective in many scenarios, they suffer from limitations such as high computational cost and poor performance on divergent sequences. In this work, we explore embedding-based similarity search methods that learn latent representations capturing deeper structural and functional patterns beyond raw sequence alignment. We systematically evaluate two state-of-the-art vector search libraries, FAISS and ScaNN, on biologically meaningful gene embeddings. Unlike prior studies, our analysis focuses on bioinformatics-specific embeddings and benchmarks their utility for detecting novel sequences, including those from uncharacterized taxa or genes lacking known homologs. Our results highlight both computational advantages (in memory and runtime efficiency) and improved retrieval quality, offering a promising alternative to traditional alignment-heavy tools.