Latent Diffusion for Neural Spiking Data

This repository contains research code for the NeurIPS 2024 paper:
Latent Diffusion for Neural Spiking Data
by Kapoor*, Schulz*, Vetter, Pei, Gao†, and Macke† (2024).

Installation

To run the scripts make sure to first install all the requirements. We recommend creating a conda environment first. A GPU is recommend but not necessary.

git clone git@github.com:mackelab/LDNS.git
cd LDNS
conda create --name ldns python=3.9
conda activate ldns
pip install -e . # install from requirements.txt
# optional: install jupyter notebook
pip install jupyter

Downloading human and monkey data

If you want to run the experiments on the human and monkey data, download and store the datasets:

• Monkey data: https://dandiarchive.org/dandiset/000128 (download using dandi download DANDI:000128/0.220113.0400 in data/monkey)
• Human data (Willet et al, 2023): https://datadryad.org/stash/downloads/file_stream/2547369 (download in data/human, then unzip using tar -xvf data/human/2547369)

Running the experiments

The core model and data loading code is in the ldns directory. Training and evaluation is done in .ipynb files in the notebooks directory.

Dataset	Train and Evaluate	Notebook
Lorenz system	train ae	notebooks/train_autoencoder_Lorenz.ipynb
	train diffusion	notebooks/train_diffusion_Lorenz.ipynb
	evaluate	notebooks/plotting_diffusion_Lorenz.ipynb
	LFADS length gen	notebooks/LFADS_Lorenz_length_generalization.ipynb
Human BCI data	train ae	notebooks/train_autoencoder_human.ipynb
	train diffusion	notebooks/train_diffusion_human.ipynb`
	evaluate	notebooks/plotting_diffusion_human.ipynb`
Monkey reach data	train ae	notebooks/train_autoencoder_monkey.ipynb
	train diffusion (unconditional)	notebooks/train_diffusion_monkey.ipynb
	train diffusion (angle-conditioned)	notebooks/train_and_plot_diffusion_monkey_angle_conditioned.ipynb
	train diffusion (velocity-conditioned)	notebooks/train_and_plot_diffusion_monkey_velocity_conditioned.ipynb
	train spike history	notebooks/train_spike_history_monkey.ipynb
	evaluate (unconditional)	notebooks/plotting_diffusion_monkey_unconditional_with_baselines.ipynb

Checkpoints and spike samples

For better reproducibility, we provide the checkpoints and spike samples for the experiments in this OneDrive link. Please download the artifacts and spike samples in the exp/stored_models and exp/stored_spike_samples directory, and appropriately change the paths in the plotting notebooks.

Baselines for the Lorenz and Monkey Reach Data

In the paper, we compared LDNS to a number of VAE-based baselines. The code for these baselines can be found in the baselines directory.

The code for LFADS (Pandarinath et al, 2018) can be found in the baselines/lfads directory. We quantitatively compare LFADS samples with LDNS on the unconditional Monkey reach data, and in supplementary material, qualitatively compare the length generalization of LFADS with LDNS on the Lorenz dataset.

We additionally use TNDM (Hennig et al, 2021) and pi-VAE (Zhou et al, 2020) as baselines for the unconditional monkey reach data in supplementary material. The code for TNDM can be found in the baselines/tndm directory, and the code for pi-VAE can be found in the baselines/pivae.py file.

After training, rates are sampled and stored by running code in baselines/lfads/sample_lfads.ipynb, and the TNDM and pi-VAE samples are stored in baselines/tndm/tndm_reach.ipynb and baselines/pivae.py respectively. We use these samples for comparisons in the corresponding analysis notebooks in the notebooks directory.

The spike samples are provided in the link above.

Citation

@inproceedings{kapoorschulz2024ldns,
	author = {Jaivardhan Kapoor and Auguste Schulz and Julius Vetter and Felix C Pei and Richard Gao and Jakob H. Macke},  
	title = {Latent Diffusion for Neural Spiking Data},  
	journal = {Advances in Neural Information Processing Systems},
	year = {2024}  
}

Contact

Please open a Github issue for any questions, or send an email to jaivardhan.kapoor@uni-tuebingen.de or auguste.schulz@uni-tuebingen.de.