README.md

---
title: BERT Metagenome Embeddings
emoji: 🧬
colorFrom: gray
colorTo: gray
sdk: docker
pinned: false
license: mit
short_description: Extract DNA sequence embeddings from pretrained BERT
---

# bert-embedding

Extract embeddings from DNA sequences using a BERT model pretrained on metagenomic sequences.

## Model

| | |
|---|---|
| architecture | BERT, 24 layers, 768 hidden, 12 heads |
| parameters | ~430M |
| input | DNA sequence (min 1000 bp) |
| output | 768-dim embedding |
| source | [genomenet/bert-metagenome](https://huggingface.co/genomenet/bert-metagenome) |

## Deployment

```bash
cd /vol/hpcprojects/pmuench/crispr_tool/bert-embedding
git add -A && git commit -m "update" && git push
```

## Acknowledgements

- BMBF de.NBI / GenomeNet
- DFG SPP 2141
- HZI BIFO