FenTechSolutions/CausalDiscoveryToolbox

The Causal Discovery Toolbox is a package for causal inference in graphs and in the pairwise settings for Python>=3.5. Tools for graph structure recovery and dependencies are included. The package is based on Numpy, Scikit-learn, Pytorch and R.

It implements lots of algorithms for graph structure recovery (including algorithms from the bnlearn, pcalg packages), mainly based out of observational data.

Check out the documentation here

Please cite us if you use our software

A tutorial is available here

Install it using pip: (See more details on installation below)

pip install cdt

Docker images

Docker images are available, including all the dependencies, and enabled functionalities:

Branch	master	dev
Python 3.6 - CPU
Python 3.6 - GPU

Installation

The packages requires a python version >=3.5, as well as some libraries listed in requirements file. For some additional functionalities, more libraries are needed for these extra functions and options to become available. Here is a quick install guide of the package, starting off with the minimal install up to the full installation.

Note: A (mini/ana)conda framework would help installing all those packages and therefore could be recommended for non-expert users.

Install PyTorch

As some of the key algorithms in the cdt package use the PyTorch package, it is required to install it. Check out their website to install the PyTorch version suited to your hardware configuration: http://pytorch.org

Install the CausalDiscoveryToolbox package

The package is available on PyPi:

pip install cdt

Or you can also install it from source.

$ git clone https://github.com/FenTechSolutions/CausalDiscoveryToolbox.git  # Download the package 
$ cd CausalDiscoveryToolbox
$ pip install -r requirements.txt  # Install the requirements
$ python setup.py install develop --user

The package is then up and running! You can run most of the algorithms in the CausalDiscoveryToolbox, you might get warnings: some additional features are not available

From now on, you can import the library using:

import cdt

Check out the package structure and more info on the package itself here.

Additional : R and R libraries

In order to have access to additional algorithms from various R packages such as bnlearn, kpcalg, pcalg, ... while using the cdt framework, it is required to install R.

Check out how to install all R dependencies in the before-install section of the travis.yml file for debian based distributions. The r-requirements file notes all of the R packages used by the toolbox.

Here is an example of installation script of the R packages on Ubuntu 20.04:

apt-get -qq update
DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
apt-get -qq install dialog apt-utils -y
apt-get install apt-transport-https -y
apt-get install -qq software-properties-common -y
apt-get -qq update
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' -y
apt-get -qq update

apt-get -qq install r-base -y
apt-get -qq install libssl-dev -y
apt-get -qq install libgmp3-dev  -y
apt-get -qq install git -y
apt-get -qq install build-essential  -y
apt-get -qq install libv8-dev  -y
apt-get -qq install libcurl4-openssl-dev -y
apt-get -qq install libgsl-dev -y

Rscript -e 'install.packages(c("V8"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
Rscript -e 'install.packages(c("sfsmisc"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
Rscript -e 'install.packages(c("clue"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/randomForest/randomForest_4.6-14.tar.gz", repos=NULL, type="source")'
Rscript -e 'install.packages(c("lattice"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
Rscript -e 'install.packages(c("devtools"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
Rscript -e 'install.packages(c("MASS"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
Rscript -e 'install.packages("BiocManager")'
Rscript -e 'BiocManager::install(c("igraph"))'
Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/fastICA/fastICA_1.2-2.tar.gz", repos=NULL, type="source")'
Rscript -e 'BiocManager::install(c("SID", "bnlearn", "pcalg", "kpcalg", "glmnet", "mboost"))'
Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/CAM/CAM_1.0.tar.gz", repos=NULL, type="source")'
Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/sparsebnUtils_0.0.8.tar.gz", repos=NULL, type="source")'
Rscript -e 'BiocManager::install(c("ccdrAlgorithm", "discretecdAlgorithm"))'

apt-get -qq install libxml2-dev -y
Rscript -e 'install.packages("devtools")'
Rscript -e 'library(devtools); install_github("cran/CAM"); install_github("cran/momentchi2"); install_github("Diviyan-Kalainathan/RCIT", quiet=TRUE, verbose=FALSE)'
Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/sparsebn/sparsebn_0.1.2.tar.gz", repos=NULL, type="source")'

Overview

General package structure

The following figure shows how the package and its algorithms are structured

   cdt package
   |
   |- independence
   |  |- graph (Infering the skeleton from data)
   |  |  |- Lasso variants (Randomized Lasso[1], Glasso[2], HSICLasso[3])
   |  |  |- FSGNN (CGNN[12] variant for feature selection)
   |  |  |- Skeleton recovery using feature selection algorithms (RFECV[5], LinearSVR[6], RRelief[7], ARD[8,9], DecisionTree)
   |  |
   |  |- stats (pairwise methods for dependency)
   |     |- Correlation (Pearson, Spearman, KendallTau)
   |     |- Kernel based (NormalizedHSIC[10])
   |     |- Mutual information based (MIRegression, Adjusted Mutual Information[11], Normalized mutual information[11])
   |
   |- data
   |  |- CausalPairGenerator (Generate causal pairs)
   |  |- AcyclicGraphGenerator (Generate FCM-based graphs)
   |  |- load_dataset (load standard benchmark datasets)
   |
   |- causality
   |  |- graph (methods for graph inference)
   |  |  |- CGNN[12]
   |  |  |- PC[13]
   |  |  |- GES[13]
   |  |  |- GIES[13]
   |  |  |- LiNGAM[13]
   |  |  |- CAM[13]
   |  |  |- GS[23]
   |  |  |- IAMB[24]
   |  |  |- MMPC[25]
   |  |  |- SAM[26]
   |  |  |- CCDr[27]
   |  |
   |  |- pairwise (methods for pairwise inference)
   |     |- ANM[14] (Additive Noise Model)
   |     |- IGCI[15] (Information Geometric Causal Inference)
   |     |- RCC[16] (Randomized Causation Coefficient)
   |     |- NCC[17] (Neural Causation Coefficient)
   |     |- GNN[12] (Generative Neural Network -- Part of CGNN )
   |     |- Bivariate fit (Baseline method of regression)
   |     |- Jarfo[20]
   |     |- CDS[20]
   |     |- RECI[28]
   |
   |- metrics (Implements the metrics for graph scoring)
   |  |- Precision Recall
   |  |- SHD
   |  |- SID [29]
   |
   |- utils
      |- Settings -> SETTINGS class (hardware settings)
      |- loss -> MMD loss [21, 22] & various other loss functions
      |- io -> for importing data formats
      |- graph -> graph utilities

Hardware and algorithm settings

The toolbox has a SETTINGS class that defines the hardware settings. Those settings are unique and their default parameters are defined in cdt/utils/Settings.

These parameters are accessible and overridable via accessing the class:

import cdt
cdt.SETTINGS

Moreover, the hardware parameters are detected and defined automatically (including number of GPUs, CPUs, available optional packages) at the import of the package using the cdt.utils.Settings.autoset_settings method, run at startup.

The graph class

The whole package revolves around using the DiGraph and Graph classes from the networkx package.

References

[1] Wang, S., Nan, B., Rosset, S., & Zhu, J. (2011). Random lasso. The annals of applied statistics, 5(1), 468.
[2] Friedman, J., Hastie, T., & Tibshirani, R. (2008). Sparse inverse covariance estimation with the graphical lasso. Biostatistics, 9(3), 432-441.
[3] Yamada, M., Jitkrittum, W., Sigal, L., Xing, E. P., & Sugiyama, M. (2014). High-dimensional feature selection by feature-wise kernelized lasso. Neural computation, 26(1), 185-207.
[4] Feizi, S., Marbach, D., Médard, M., & Kellis, M. (2013). Network deconvolution as a general method to distinguish direct dependencies in networks. Nature biotechnology, 31(8), 726-733.
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[7] Kira, K., & Rendell, L. A. (1992, July). The feature selection problem: Traditional methods and a new algorithm. In Aaai (Vol. 2, pp. 129-134).
[8] MacKay, D. J. (1992). Bayesian interpolation. Neural Computation, 4, 415–447.
[9] Neal, R. M. (1996). Bayesian learning for neural networks. No. 118 in Lecture Notes in Statistics. New York: Springer.
[10] Gretton, A., Bousquet, O., Smola, A., & Scholkopf, B. (2005, October). Measuring statistical dependence with Hilbert-Schmidt norms. In ALT (Vol. 16, pp. 63-78).
[11] Vinh, N. X., Epps, J., & Bailey, J. (2010). Information theoretic measures for clusterings comparison: Variants, properties, normalization and correction for chance. Journal of Machine Learning Research, 11(Oct), 2837-2854.
[12] Goudet, O., Kalainathan, D., Caillou, P., Lopez-Paz, D., Guyon, I., Sebag, M., ... & Tubaro, P. (2017). Learning functional causal models with generative neural networks. arXiv preprint arXiv:1709.05321.
[13] Spirtes, P., Glymour, C., Scheines, R. (2000). Causation, Prediction, and Search. MIT press.
[14] Hoyer, P. O., Janzing, D., Mooij, J. M., Peters, J., & Schölkopf, B. (2009). Nonlinear causal discovery with additive noise models. In Advances in neural information processing systems (pp. 689-696).
[15] Janzing, D., Mooij, J., Zhang, K., Lemeire, J., Zscheischler, J., Daniušis, P., ... & Schölkopf, B. (2012). Information-geometric approach to inferring causal directions. Artificial Intelligence, 182, 1-31.
[16] Lopez-Paz, D., Muandet, K., Schölkopf, B., & Tolstikhin, I. (2015, June). Towards a learning theory of cause-effect inference. In International Conference on Machine Learning (pp. 1452-1461).
[17] Lopez-Paz, D., Nishihara, R., Chintala, S., Schölkopf, B., & Bottou, L. (2017, July). Discovering causal signals in images. In Proceedings of CVPR.
[18] Stegle, O., Janzing, D., Zhang, K., Mooij, J. M., & Schölkopf, B. (2010). Probabilistic latent variable models for distinguishing between cause and effect. In Advances in Neural Information Processing Systems (pp. 1687-1695).
[19] Zhang, K., & Hyvärinen, A. (2009, June). On the identifiability of the post-nonlinear causal model. In Proceedings of the twenty-fifth conference on uncertainty in artificial intelligence (pp. 647-655). AUAI Press.
[20] Fonollosa, J. A. (2016). Conditional distribution variability measures for causality detection. arXiv preprint arXiv:1601.06680.
[21] Gretton, A., Borgwardt, K. M., Rasch, M. J., Schölkopf, B., & Smola, A. (2012). A kernel two-sample test. Journal of Machine Learning Research, 13(Mar), 723-773.
[22] Li, Y., Swersky, K., & Zemel, R. (2015). Generative moment matching networks. In Proceedings of the 32nd International Conference on Machine Learning (ICML-15) (pp. 1718-1727).
[23] Margaritis D (2003). Learning Bayesian Network Model Structure from Data . Ph.D. thesis, School of Computer Science, Carnegie-Mellon University, Pittsburgh, PA. Available as Technical Report CMU-CS-03-153
[24] Tsamardinos I, Aliferis CF, Statnikov A (2003). “Algorithms for Large Scale Markov Blanket Discovery”. In “Proceedings of the Sixteenth International Florida Artificial Intelligence Research Society Conference”, pp. 376-381. AAAI Press.
[25] Tsamardinos I, Aliferis CF, Statnikov A (2003). “Time and Sample Efficient Discovery of Markov Blankets and Direct Causal Relations”. In “KDD ’03: Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining”, pp. 673-678. ACM. Tsamardinos I, Brown LE, Aliferis CF (2006). “The Max-Min Hill-Climbing Bayesian Network Structure Learning Algorithm”. Machine Learning,65(1), 31-78.
[26] Kalainathan, Diviyan & Goudet, Olivier & Guyon, Isabelle & Lopez-Paz, David & Sebag, Michèle. (2018). SAM: Structural Agnostic Model, Causal Discovery and Penalized Adversarial Learning.
[27] Aragam, B., & Zhou, Q. (2015). Concave penalized estimation of sparse Gaussian Bayesian networks. Journal of Machine Learning Research, 16, 2273-2328.
[28] Bloebaum, P., Janzing, D., Washio, T., Shimizu, S., & Schoelkopf, B. (2018, March). Cause-Effect Inference by Comparing Regression Errors. In International Conference on Artificial Intelligence and Statistics (pp. 900-909).
[29] Structural Intervention Distance (SID) for Evaluating Causal Graphs, Jonas Peters, Peter Bühlmann: https://arxiv.org/abs/1306.1043

FenTechSolutions / CausalDiscoveryToolbox