# M5: A Whole Genome Bacterial Encoder at Single Nucleotide Resolution

arXiv: https://arxiv.org/abs/2407.03392 · HTML: https://mlsanity.com/paper/2407.03392/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 19 references that are in the map.
- First posted on arXiv 3 Jul 2024.

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [ReZero is All You Need: Fast Convergence at Large Depth](https://mlsanity.com/paper/2003.04887/) (2020)
- [Repeat After Me: Transformers are Better than State Space Models at Copying](https://mlsanity.com/paper/2402.01032/) (2024)
- [Transformer Dissection: A Unified Understanding of Transformer's Attention via the Lens of Kernel](https://mlsanity.com/paper/1908.11775/) (2019)
- [Simple linear attention language models balance the recall-throughput tradeoff](https://mlsanity.com/paper/2402.18668/) (2024)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [The Hedgehog & the Porcupine: Expressive Linear Attentions with Softmax Mimicry](https://mlsanity.com/paper/2402.04347/) (2024)
- [Fast Attention Requires Bounded Entries](https://mlsanity.com/paper/2302.13214/) (2023)
- [BEND: Benchmarking DNA Language Models on biologically meaningful tasks](https://mlsanity.com/paper/2311.12570/) (2023)

## Abstract (arXiv)

A linear attention mechanism is described to extend the context length of an encoder only transformer, called M5 in this report, to a multi-million single nucleotide resolution foundation model pretrained on bacterial whole genomes. The linear attention mechanism used approximates a full quadratic attention mechanism tightly and has a simple and lightweight implementation for the use case when the key-query embedding dimensionality is low. The M5-small model is entirely trained and tested on one A100 GPU with 40gb of memory up to 196K nucleotides during training and 2M nucleotides during testing. We test the performance of the M5-small model and record notable improvements in performance as whole genome bacterial sequence lengths are increased as well as demonstrating the stability of the full multi-head attention approximation used as sequence length is increased.