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Experiments and Evaluations for BrainUnit

This repository contains code and experiments for evaluating the BrainUnit framework. The experiments focus on training and visualizing neural network models.

Table of Contents

Installation

To install the required dependencies, use pip:

pip install -r requirements.txt

Project Structure

├── 01-hh-neurons/
├── 02-mutiscale-network/
│   └── results/
├── 03-hh-fitting/
├── 04-task-training/
│   ├── results/
│   ├── task_training.py
│   └── verification.py
├── archive/
├── .gitignore
├── README.md
└── requirements.txt
  • 01-hh-neurons/: Contains experiments related to Hodgkin-Huxley neurons.
  • 02-mutiscale-network/: Contains results related to multiscale network experiments.
  • 03-hh-fitting/: Contains experiments related to fitting Hodgkin-Huxley models.
  • 04-task-training/: Contains the main training script and results.
  • archive/: Directory for archived files.
  • .gitignore: Specifies files and directories to be ignored by Git.
  • README.md: This file.
  • requirements.txt: Lists the dependencies required for the project.

Usage

For the Hodgkin-Huxley neuron experiments, defined in 01-hh-neurons/ directory, to run the script, execute:

python dendritex-sim.py

For the multiscale spiking network experiments, defined in 02-multiscale-network/ directory, to run the script, execute:

python large_scale_COBA_EI-bst.py  # with physical units
python large_scale_COBA_EI-bp.py  # without physical units

For the Hodgkin-Huxley model fitting experiments, defined in 03-hh-fitting/ directory, to run the script, execute:

python brian2_hh_fitting.py  # fitting with brian2
python neuron_fitting_of_hh_model.py  # fitting with dendritex

For the cognitive task training task, defined in 04-task-training/ directory, to run the training script, execute:

python task_training.py

Contributing

Contributions are welcome! Please open an issue or submit a pull request for any improvements or bug fixes.

Citation

If you use this code in your research, please consider citing the following paper:

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