Code accompanying the paper MultiViewICA https://arxiv.org/pdf/2006.06635.pdf
Documentation: https://hugorichard.github.io/multiviewica/
Clone the repository
git clone https://github.com/hugorichard/multiviewica.git
Move into the multiviewica directory
cd multiviewica
Install MultiView ICA
pip install -e .
For the core algorithms:
- numpy >= 1.16
- scipy >= 1.12
- scikit-learn >= 0.20
- python-picard >= 0.4 (
pip install python-picard)
For the Experiments:
- nibabel (>=2.3.3)
- mne (>=0.20)
- nilearn (>=0.5)
- fastsrm (
pip install fastsrm)
Move into the multiviewica directory
cd multiviewica
Run the experiment on synthetic data
python examples/synthetic_experiment.py
In order to reproduce the figure in the paper, use (might take a long time):
# sigmas: data noise
# m: number of subjects
# k: number of components
# n: number of samples
sigmas = np.logspace(-2, 1, 21)
n_seeds = 100
m, k, n = 10, 15, 1000
Move into the data directory
cd multiviewica/data
Launch the download script (Runtime 34m6.751s)
bash download_data.sh
Mask the data (Runtime 15m27.104s)
python mask_data.py
Move into the real_data_experiments directory
cd multiviewica/real_data_experiments
Run the experiment on masked data (Runtime 30m55.347s)
python reconstruction_experiment.py
This runs the experiment with n_components = 5 and benchmark PCA + GroupICA, PermICA and MultiView ICA with subject specific PCA for dimension reduction in PCA + GroupICA and SRM for PermICA and MultiView ICA.
Move into the real_data_experiment directory
cd multiviewica/real_data_experiments
Run the experiment on masked data (Runtime 17m39.520s)
python timesegment_matching.py
This runs the experiment with n_components = 5 and benchmark PCA + GroupICA, PermICA and MultiView ICA with subject specific PCA for dimension reduction in PCA + GroupICA and SRM for PermICA and MultiView ICA.
If you use this code in your project, please cite:
@inproceedings{NEURIPS2020_de03beff,
author = {Richard, Hugo and Gresele, Luigi and Hyvarinen, Aapo and Thirion, Bertrand and Gramfort, Alexandre and Ablin, Pierre},
booktitle = {Advances in Neural Information Processing Systems},
editor = {H. Larochelle and M. Ranzato and R. Hadsell and M. F. Balcan and H. Lin},
pages = {19149--19162},
publisher = {Curran Associates, Inc.},
title = {Modeling Shared responses in Neuroimaging Studies through MultiView ICA},
url = {https://proceedings.neurips.cc/paper/2020/file/de03beffeed9da5f3639a621bcab5dd4-Paper.pdf},
volume = {33},
year = {2020}
}