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ach-cortical-circuits

Tasks:
Tabular Regression
Languages:
English
Size:
10K<n<100K
Tags:
neuroscience
computational-neuroscience
acetylcholine
neuromodulation
sim-to-real
jaxley
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metadata 
license: mit
task_categories:
  - tabular-regression
language:
  - en
tags:
  - neuroscience
  - computational-neuroscience
  - acetylcholine
  - neuromodulation
  - sim-to-real
  - jaxley
  - allen-brain-observatory
  - neuropixels
  - biophysical-simulation
size_categories:
  - 10K<n<100K

ACh Cortical Circuits: Cross-Cortical Transfer Dataset

15,000 simulated cortical microcircuits with acetylcholine (ACh) modulation + 2,678 real mouse V1 recording epochs from the Allen Brain Observatory.

Dataset Description

This dataset accompanies the paper "Cross-Cortical Transfer of Cholinergic Modulation Principles via Biophysical Simulation Surrogates" (CAISc 2026).

Simulated Circuits (15,000 total)

Three mechanistic variants of ACh modulation, each with 5,000 circuits × 11 ACh levels = 55,000 simulations per variant:

Variant ACh Mechanism File
v14a Synaptic suppression only (E2 dose-response) v14a_circuits.tar.gz
v14b Depolarization only (OU mean shift) v14b_circuits.tar.gz
v14c Both mechanisms combined v14c_circuits.tar.gz

Parameters source: Ramaswamy, Colangelo & Markram (2018), Frontiers in Neural Circuits — rat somatosensory cortex (S1).

Simulator: Jaxley (JAX-based, GPU-accelerated)

Each circuit JSON contains:

  • Circuit parameters (n_neurons, connectivity, synaptic conductances, OU noise params)
  • ACh level (0.0 to 1.0 in 0.1 steps)
  • 11 population statistics (firing rate, CV ISI, Fano factor, synchrony index, pairwise correlation, peak frequency, spectral power, etc.)

Allen Brain Observatory Epochs (2,678 total)

Real mouse V1 (area VISp) neural recordings from the Allen Brain Observatory Visual Coding Neuropixels dataset:

  • 2,325 running epochs + 353 stationary epochs
  • 44 sessions, 16 with both behavioral states
  • Quality filtered (presence_ratio > 0.95, ISI violations < 0.5)
  • Same 11 population statistics as simulated data

File: allen_epochs.tar.gz

Model Checkpoints

12 trained surrogate models (3 architectures × 3 ACh variants + 3 baselines):

  • CircuitTransformer (222K params)
  • CircuitMLP (5.6K params)
  • XGBoost

File: checkpoints.tar.gz

Key Results

Statistic Model S (syn) Model D (depol) Model SD (both)
Pairwise correlation 75.0% 25.0% 25.0%
Mean firing rate 12.5% 87.5% 87.5%
Spectral power 68.8% 68.8% 68.8%

Key finding: Synaptic suppression captures correlation structure; depolarization captures rate modulation. The mechanisms are dissociable in sim-to-real transfer.

Citation 

@inproceedings{neuropeek2026crosstransfer,
  title={Cross-Cortical Transfer of Cholinergic Modulation Principles via Biophysical Simulation Surrogates},
  author={NeuroPeek AI and Basak, Sohan},
  booktitle={1st Conference for AI Scientists (CAISc 2026)},
  year={2026}
}

License

MIT

Acknowledgments