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ZemlianovaRNN

Overview

This repository contains the PyTorch implementation of the model described in the 2024 paper "A Recurrent Neural Network for Rhythmic Timing" by Klavdia Zemlianova, Amit Bose, & John Rinzel. The model is designed to explore and demonstrate the neural mechanisms behind rhythmic timing.

Features

  • ZemlianovaRNN Implementation: Fully implemented model based on the 2024 paper, designed to explore neural mechanisms of rhythmic timing.
  • Dynamic Configuration: Model parameters can be dynamically configured using YAML files or overridden via command-line arguments with Fire.
  • Training and Evaluation Scripts: Scripts to train the models and evaluate their performance are included, with the ability to plot and save results for further analysis.
  • GPU Support: Efficient training with CUDA, automatically adjusting based on available hardware.
  • Vanilla RNN Implementation: Also a standard RNN model which can be used as a baseline or for comparison.

Getting Started

Prerequisites

Ensure you have Python 3.6+ and PyTorch installed. Dependencies can be installed via pip:

pip install -r requirements.txt

Training the Model

To train the ZemlianovaRNN model, use:

python train.py --model_type ZemlianovaRNN

This will save a best_model.pth when the training is complete. It will also create a folder called plots with examples of model activity for each of the periods included in the training set.

Saving Model Outputs for Analysis After Training

After training, you can run inference on the model to save outputs for further analysis using:

python drive_model_and_save_outputs.py

This script processes inputs based on the configured periods, detects peaks in the model’s output, and saves the model outputs, hidden states, and plots. These are stored in a directory named model_outputs. Each file is named to indicate which saved model activity corresponds to a specific stimulus period, making it easier to track and analyze the results.

Analyzing and Visualizing Model Outputs

Further analysis and visualization can be conducted by running:

python plot_fig1.py

This generates detailed plots illustrating the normalized firing rates and PCA trajectories:

  • Normalized Firing Rates: Units' firing rates are normalized between 0 and 1 and sorted by their maximal firing rate during the initial inter-tap interval (ITI). Units are colored by type—excitatory units in red and inhibitory in blue. Tap times are marked by vertical lines. Normalized Firing Rates

  • PCA Trajectory Analysis:

    • Left Panel: Shows unit trajectories in the top 3 PCA space, colored by stimulus frequency from low to high. Tap times are indicated by black circles.
    • Middle Panel: Displays the relationship between the mean and standard deviation of trajectory lengths, calculated per cycle for each stimulus period.
    • Right Panel: Simulated inter-tap intervals (ITIs) for varying context cues, with trained points marked in yellow. PCA and Model Activity Analysis

  • Reduced Model Analysis:

python plot_fig3.py

This generates plots reduced model analysis, similar to figure 3 in the paper: RNN Dynamics CC Values

  • Top row: The activity of the reduced model varibles simulated for different context cues.
  • Bottom row:
    • Left plot: Oscillations periods vs context cue.
    • Central plot: Bifurcation diagram. Red points indicate stable fixed points, while black denote unstable ones. In the oscillatory regime, the max and min z are plotted in green. dashed lines indicate the critical, bifurcation points, and dotted lines correspond to the simulations plotted above.
    • Right Plot: Different (0.197, 0.3, 0.5, 0.8 and 1.2) oscillatory trajectories, with color indicating the periods.
python plot_fig5.py

This generates plots of the RNN dynamics (aiming to reproduce figure 5 in the paper):

  • Different context cue values: Two dimensional depiction of the RNN dynamics for different values of context cue on a projection plane that is chosen by principal components analysis. Red curves indicate the trajectories, and the heatmap shows the speed magnitude. RNN Dynamics CC Values
  • Oscillatory trajectory: Here the same plot is shown on different times for the same trajectory, simulated with context cue amplitude of 0.5, for which the outcome is in the oscillatory regime. RNN Dynamics CC Values

Configuration

Modify the config.yaml file to set up different experimental settings or model parameters.

Training the Vanilla RNN

To train the Vanilla RNN model, use the following command:

python train.py --model_type RNN

Contributing

Contributions to the development of ZemlianovaRNN are welcome. Please submit a pull request or open an issue to discuss proposed changes or additions.

Cite

If you use this code please cite the original paper:

@article{zemlianova2024recurrent,
  title={A Recurrent Neural Network for Rhythmic Timing},
  author={Zemlianova, Klavdia and Bose, Amitabha and Rinzel, John},
  journal={bioRxiv},
  pages={2024--05},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}