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README.md

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+---
+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](https://github.com/jaxleyverse/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
+
+```bibtex
+@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
+
+- Simulation parameters from [Ramaswamy et al. 2018](https://www.frontiersin.org/articles/10.3389/fncir.2018.00077/full)
+- Real data from [Allen Brain Observatory](https://portal.brain-map.org/)
+- Simulation engine: [Jaxley](https://github.com/jaxleyverse/jaxley) (Deistler et al., Nature Methods 2025)
+- Compute: [Modal](https://modal.com/) cloud GPUs (~$230 total)
+- Built with NeuroPeek AI Agents

data/allen_epochs.tar.gz

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data/v14a_circuits.tar.gz

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data/v14c_circuits.tar.gz

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