---
library_name: regrex
license: other
license_name: allen-institute-software-license
license_link: LICENSE
tags:
- pytorch
- lightning
- genomics
- regrex
- neuroscience
- regulatory-genomics
- sequence-to-function
- basal-ganglia
- macaque
- dilated_cnn
---

# AllenInstitute/BG-macaque-dilatedCNN

Dilated CNN trained on macaque (*Macaca mulatta*) basal ganglia chromatin accessibility across 58 cell-type tracks. Part of the DNA sequence-modeling resources for the basal ganglia cell atlas. Published in [Johansen, Fu et al., 2025](https://doi.org/10.64898/2025.12.15.694496).

### Background
Learns cis-regulatory sequence logic underlying basal ganglia cell-type specialization from snATAC-seq accessibility profiles. Use it to score candidate enhancers, run in silico mutagenesis, or guide cell-type-specific sequence design.

### Availability
Currently private. RegRex (formerly `enhancer-designer`) is an internal Allen Institute tool with a public release planned. For early access contact Kasia Kedzierska (kasia.kedzierska@alleninstitute.org).

## Model Details

- **Architecture:** dilated_cnn
- **Species:** macaque
- **Number of tracks:** 58
- **Framework:** PyTorch Lightning
- **Checkpoint format:** Lightning .ckpt

## Target Tracks

- AMY-SLEA-BNST_D1_GABA
- AMY-SLEA-BNST_GABA
- Astrocyte
- BAM
- BF_SKOR1_Glut
- COP
- Endo
- Ependymal
- GPe-NDB-SI_LHX6-LHX8-GBX1_GABA
- GPe_MEIS2-SOX6_GABA
- ... (48 more)

## Usage

```python
from regrex.models import load_model

model = load_model("AllenInstitute/BG-macaque-dilatedCNN")
```