https://github.com/genentech/regLM

Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
https://github.com/genentech/regLM

Last synced: 4 months ago
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Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.

Host: GitHub
URL: https://github.com/genentech/regLM
Owner: Genentech
License: mit
Created: 2023-10-02T02:39:49.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2024-10-04T18:29:29.000Z (over 1 year ago)
Last Synced: 2025-03-27T14:48:06.343Z (10 months ago)
Language: Jupyter Notebook
Homepage:
Size: 4.15 MB
Stars: 38
Watchers: 7
Forks: 3
Open Issues: 1
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
- Authors: AUTHORS.md

top-pharma50 - **genentech/regLM** - based autoregressive language models on DNA sequences.<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 20 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> Jupyter Notebook <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> MIT License <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-02-19 04:41:23 | (Ranked by starred repositories)

README

# regLM
regLM is a toolkit for training hyenaDNA-based autoregressive language models on DNA sequences and generating novel regulatory elements.

![regLM schematic](fig1.png)

## Documentation

[Documentation](https://genentech.github.io/regLM)

## Tutorials

[Tutorials](tutorials)

## Installation

### 1. Install HyenaDNA
To use regLM, first install HyenaDNA from GitHub following the instructions: https://github.com/HazyResearch/hyena-dna

### 2. Install regLM
```
git clone https://github.com/Genentech/regLM.git
cd regLM
pip install .
```

## Publication

https://genome.cshlp.org/content/early/2024/09/24/gr.279142.124.abstract

Lal, A., Garfield, D., Biancalani, T., & Eraslan, G. (2024). Designing realistic regulatory DNA with autoregressive language models. Genome Research.