├── .codecov.yml ├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE.md ├── README.md ├── cdt ├── __init__.py ├── causality │ ├── __init__.py │ ├── graph │ │ ├── CAM.py │ │ ├── CCDr.py │ │ ├── CGNN.py │ │ ├── GES.py │ │ ├── GIES.py │ │ ├── LiNGAM.py │ │ ├── PC.py │ │ ├── R_templates │ │ │ ├── CCDr.R │ │ │ ├── bnlearn.R │ │ │ ├── cam.R │ │ │ ├── ges.R │ │ │ ├── gies.R │ │ │ ├── lingam.R │ │ │ └── pc.R │ │ ├── SAM.py │ │ ├── SAMv1.py │ │ ├── __init__.py │ │ ├── bnlearn.py │ │ └── model.py │ └── pairwise │ │ ├── ANM.py │ │ ├── Bivariate_fit.py │ │ ├── CDS.py │ │ ├── GNN.py │ │ ├── IGCI.py │ │ ├── Jarfo.py │ │ ├── Jarfo_model │ │ ├── README.md │ │ ├── SETTINGS.json │ │ ├── __init__.py │ │ ├── estimator.py │ │ ├── features.py │ │ ├── hsic.py │ │ ├── train.py │ │ └── util.py │ │ ├── NCC.py │ │ ├── RCC.py │ │ ├── RECI.py │ │ ├── __init__.py │ │ └── model.py ├── data │ ├── __init__.py │ ├── acyclic_graph_generator.py │ ├── causal_mechanisms.py │ ├── causal_pair_generator.py │ ├── loader.py │ └── resources │ │ ├── Tuebingen_pairs.csv │ │ ├── Tuebingen_targets.csv │ │ ├── cyto_full_data.csv │ │ ├── cyto_full_target.csv │ │ ├── goldstandard_insilico100_multifactorial_1.csv │ │ ├── goldstandard_insilico100_multifactorial_2.csv │ │ ├── goldstandard_insilico100_multifactorial_3.csv │ │ ├── goldstandard_insilico100_multifactorial_4.csv │ │ └── goldstandard_insilico100_multifactorial_5.csv ├── independence │ ├── __init__.py │ ├── graph │ │ ├── FSGNN.py │ │ ├── FSRegression.py │ │ ├── HSICLasso.py │ │ ├── Lasso.py │ │ ├── __init__.py │ │ └── model.py │ └── stats │ │ ├── __init__.py │ │ ├── all_types.py │ │ ├── model.py │ │ └── numerical.py ├── metrics.py ├── timeseries │ ├── __init__.py │ ├── graph │ │ ├── VARLiNGAM.py │ │ └── __init__.py │ └── pairwise │ │ └── __init__.py └── utils │ ├── R.py │ ├── R_templates │ ├── cpdag.R │ ├── sid.R │ └── test_import.R │ ├── Settings.py │ ├── __init__.py │ ├── graph.py │ ├── io.py │ ├── loss.py │ ├── parallel.py │ └── torch.py ├── docs ├── .doctrees │ ├── index.doctree │ └── installation-link.doctree ├── .nojekyll ├── .old.index ├── Makefile ├── _static │ └── custom.css ├── banner.png ├── causality.rst ├── conf.py ├── data.rst ├── developer.rst ├── favicon.png ├── html │ ├── .doctrees │ │ ├── causality.doctree │ │ ├── data.doctree │ │ ├── developer.doctree │ │ ├── environment.pickle │ │ ├── generators.doctree │ │ ├── independence.doctree │ │ ├── index.doctree │ │ ├── metrics.doctree │ │ ├── settings.doctree │ │ ├── tutorial.doctree │ │ ├── tutorial_1.doctree │ │ ├── tutorial_2.doctree │ │ └── utils.doctree │ ├── .nojekyll │ ├── _images │ │ └── banner.png │ ├── _modules │ │ ├── cdt │ │ │ ├── causality │ │ │ │ ├── graph │ │ │ │ │ ├── CAM.html │ │ │ │ │ ├── CCDr.html │ │ │ │ │ ├── CGNN.html │ │ │ │ │ ├── GES.html │ │ │ │ │ ├── GIES.html │ │ │ │ │ ├── LiNGAM.html │ │ │ │ │ ├── PC.html │ │ │ │ │ ├── SAM.html │ │ │ │ │ ├── SAMv1.html │ │ │ │ │ ├── bnlearn.html │ │ │ │ │ └── model.html │ │ │ │ └── pairwise │ │ │ │ │ ├── ANM.html │ │ │ │ │ ├── Bivariate_fit.html │ │ │ │ │ ├── CDS.html │ │ │ │ │ ├── GNN.html │ │ │ │ │ ├── IGCI.html │ │ │ │ │ ├── Jarfo.html │ │ │ │ │ ├── NCC.html │ │ │ │ │ ├── RCC.html │ │ │ │ │ ├── RECI.html │ │ │ │ │ └── model.html │ │ │ ├── data │ │ │ │ ├── acyclic_graph_generator.html │ │ │ │ ├── causal_pair_generator.html │ │ │ │ └── loader.html │ │ │ ├── independence │ │ │ │ ├── graph │ │ │ │ │ ├── FSGNN.html │ │ │ │ │ ├── FSRegression.html │ │ │ │ │ ├── Lasso.html │ │ │ │ │ └── model.html │ │ │ │ └── stats │ │ │ │ │ ├── all_types.html │ │ │ │ │ ├── model.html │ │ │ │ │ └── numerical.html │ │ │ ├── metrics.html │ │ │ └── utils │ │ │ │ ├── R.html │ │ │ │ ├── Settings.html │ │ │ │ ├── graph.html │ │ │ │ ├── io.html │ │ │ │ ├── loss.html │ │ │ │ ├── metrics.html │ │ │ │ ├── parallel.html │ │ │ │ └── torch.html │ │ └── index.html │ ├── _sources │ │ ├── causality.rst.txt │ │ ├── data.rst.txt │ │ ├── developer.rst.txt │ │ ├── generators.rst.txt │ │ ├── independence.rst.txt │ │ ├── index.md.txt │ │ ├── index.rst.txt │ │ ├── metrics.rst.txt │ │ ├── settings.rst.txt │ │ ├── tutorial.rst.txt │ │ ├── tutorial_1.rst.txt │ │ ├── tutorial_2.rst.txt │ │ └── utils.rst.txt │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── banner.png │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── favicon.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Inconsolata.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ ├── jquery-3.2.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ ├── causality.html │ ├── data.html │ ├── developer.html │ ├── generators.html │ ├── genindex.html │ ├── independence.html │ ├── index.html │ ├── metrics.html │ ├── objects.inv │ ├── py-modindex.html │ ├── search.html │ ├── searchindex.js │ ├── settings.html │ ├── tutorial.html │ ├── tutorial_1.html │ ├── tutorial_2.html │ └── utils.html ├── independence.rst ├── index.html ├── index.md ├── index.rst ├── make.bat ├── metrics.rst ├── settings.rst ├── tutorial.rst ├── tutorial_1.rst ├── tutorial_2.rst └── utils.rst ├── documentation.md ├── examples └── example_cgnn.ipynb ├── install-deps ├── Dockerfile-env ├── Dockerfile-env-1.1 └── install-dependencies.sh ├── installation_instructions.md ├── nv-Dockerfile ├── pytest.ini ├── r_requirements.txt ├── rel_travis.enc ├── requirements.txt ├── setup.py └── tests ├── datasets ├── Example_graph_confounders_numdata.csv ├── 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