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.

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

The weights are public. Loading them needs RegRex (formerly enhancer-designer), an internal Allen Institute tool with a public release planned. For early access contact Kasia Kedzierska (kasia.kedzierska@alleninstitute.org).

The checkpoint names its geometry input_length and output_bins, as RegRex does since the DilatedCNN rename. The earlier format (seq_len, output_length) is kept at revision pre-input-length-rename.

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

import regrex as rr

model = rr.Model.from_checkpoint("bg_macaque_dilated_cnn")  # or "AllenInstitute/BG-macaque-dilatedCNN"

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