Repository accompanying the paper Persistent homology for high-dimensional data based on spectral methods

Compute the persistent homology of a toy dataset with compute_ph.py, of toy datasets with outliers with compute_ph_outliers.py and that of a single-cell dataset with compute_ph_real_data.py. Changing the dataset in the top of the script allows to compute the persistent homology of different datasets.

cd scripts
python compute_ph.py

Create the figures of the paper with the various fig_*.ipynb notebooks. The notebooks create the following figures:

• Figure 1: fig_1.ipynb
• Figure 2: fig_ph.ipynb
• Figure 3: fig_vary_dim_mds.ipynb
• Figure 4: fig_spectral.ipynb
• Figure 5: fig_circle.ipynb
• Figure 6: fig_datasets.ipynb
• Figure 7: fig_dims.ipynb
• Figure 8, 9: fig_real_data.ipynb
• Figure S1: fig_dims.ipynb
• Figure S3, S4: fig_spectral.ipynb
• Figure S5: fig_real_data.ipynb
• Figure S6, S7: spectral.ipynb
• Figure S8, S9: fig_toy_datasets.ipynb
• Figure S10: fig_sc_datasets.ipynb
• Figure S11: fig_sensitivity.ipynb
• Figure S12: fig_outliers.ipynb
• Figure S13, S14: fig_high_dim_UMAP.ipynb
• Figure S15: fig_real_data.ipynb
• Figure S16: fig_circle.ipynb
• Figure S17: fig_datasets.ipynb
• Figure S18: fig_circle.ipynb
• Figures S19-S26, S28: fig_all_methods_on_toy.ipynb
• Figure S27: fig_torus_high_n.ipynb
• Figure S29: fig_real_data.ipynb
• Figure S30: fig_Lp.ipynb

Clone the repository

git clone https://github.com/berenslab/eff-ph.git

Create a conda python environment

cd eff-ph
conda env create -f environment.yml

Install the utils:

cd ../eff-ph
python setup.py install

Clone the repository ripser and compile it:

cd ..
git clone -b representative-cycles https://github.com/Ripser/ripser.git
cd risper
make

Clone the repository vis_utils

cd ..
git clone https://github.com/sdamrich/vis_utils.git --branch eff-ph-arxiv-v1 --single-branch

Create the conda R environment (for loading some single-cell datasets)

cd vis_utils
conda create -f r_env.yml

Install vis_utils

conda activate eff-ph
python setup.py install