Models of decision making using choice-selective sequences

This repository contains the code used to run the Synaptic Plasticity and the Neural Dynamics model from the paper https://www.biorxiv.org/content/10.1101/725382v3.

Installing Python dependencies

I strongly suggest creating a new conda environment before installing all the Python dependencies. Follow these steps to create a conda environment and install all the python dependencies:

• Create a new conda environment - conda create -n env_name python=3.9.4 (replace env_name with the desired environment name).
• Activate the new conda environment - conda activate env_name
• Install all the python dependencies - pip install -r requirements.txt

You are now ready to run all the python scripts. Remember to install Jupyter Notebook or JupyterLab to run the notebooks.

How to Use?

Synaptic Plasticity Model

• To run the Synaptic Plasticity model for the various choice-selective inputs and generate the plots from the paper, run the plots.ipynb notebook located in the SynapticPlasticityModel folder.

Neural Dynamics Model

• To generate the plots from the paper using the saved Neural Dynamics model, run the plots.ipynb notebook located in the NeuralDynamicsModel folder.

• To train the Neural Dynamics model from scratch using the default parameters, run the following command: python train.py

• To generate testing data for the Neural Dynamics model using the default parameters, run the following command: python test.py

• Note that the python test.py file generates testing data for one run. Feel free to generate as many runs of testing data as needed. For the plots in the paper, 50 runs were used to generate the plots.