causalicp 0.1.1

Python implementation of the Invariant Causal Prediction (ICP) algorithm for causal discovery.

Invariant Causal Prediction (ICP) Algorithm for Causal Discovery

This is a Python implementation of the Invariant Causal Prediction (ICP) algorithm from the 2016 paper "Causal inference using invariant prediction: identification and confidence intervals" by Jonas Peters, Peter Bühlmann and Nicolai Meinshausen.

At the point of writing, and to the best of my knowledge, the only other publicly available implementation of the algorithm is in the R package written by the original authors.

Installation

You can clone this repo or install the python package via pip:

pip install causalicp

The package is still at its infancy and its API is subject to change. However, this will be done with care: non backward-compatible changes to the API are reflected by a change to the minor or major version number,

e.g. code written using causalicp==0.1.2 will run with causalicp==0.1.3, but may not run with causalicp==0.2.0.

The code has been written with an emphasis on readability and on keeping the dependency footprint to a minimum; to this end, the only dependencies outside the standard library are numpy, scipy and termcolor.

Documentation

You can find the complete documentation at https://icp.readthedocs.io/en/latest/. For completeness, we include here an overview and an example.

Running the algorithm: causalicp.fit

To run the algorithm, the function fit is provided:

causalicp.fit(data, target, alpha=0.05, sets=None, precompute=True, verbose=False, color=True):

Parameters

• data (numpy.ndarray or list of array-like): The data from all experimental settings. Each element of the list/array is a 2-dimensional array with a sample from a different setting, where columns correspond to variables and rows to observations (data-points). The data also contains the response variable, which is specified with the target parameter.
• target (int) The index of the response or target variable of interest.
• alpha (float, default=0.05 The level of the test procedure, taken from [0,1]. Defaults to 0.05.
• sets (list of set or None, default=None): The sets for which ICP will test invariance. An error is raised if a set is not a subset of {0,...,p-1} or it contains the target, where p is the total number of variables (including the target). If None all possible subsets of predictors will be considered.
• precompute (bool, default=True): Wether to precompute the sample covariance matrix to speed up linear regression during the testing of each predictor set. For large sample sizes this drastically reduces the overall execution time, but it may result in numerical instabilities for highly correlated data. If set to False, for each set of predictors the regression is done using an iterative least-squares solver on the raw data.
• verbose (bool, default=False): If ICP should run in verbose mode, i.e. displaying information about completion and the result of tests.
• color (bool, default=True): If the output produced when verbose=True should be color encoded (not recommended if your terminal does not support ANSII color formatting), see termcolor.

Raises

• ValueError: If the value of some of the parameters is not appropriate, e.g. alpha is negative, data contains samples with different number of variables, or sets contains invalid sets.
• TypeError : If the type of some of the parameters was not expected (see examples below).

Returns

The result of the algorithm is returned in a causalicp.Result object, with the following attributes:

• p (int): The total number of variables in the data (including the response/target).
• target (int): The index of the response/target.
• estimate (set or None): The estimated parental set returned by ICP, or None if all sets of predictors were rejected.
• accepted_sets (list of set): A list containing the accepted sets of predictors.
• rejected_sets (list of set): A list containing the rejected sets of predictors.
• pvalues (dict of (int, float)): A dictionary containing the p-value for the causal effect of each individual predictor. The target/response is included in the dictionary and has value nan.
• conf_intervals (numpy.ndarray or None): A 2 x p array of floats representing the confidence interval for the causal effect of each variable. Each column corresponds to a variable, and the first and second row correspond to the lower and upper limit of the interval, respectively. The column corresponding to the target/response is set to nan.

An example

We generate interventional data from a linear-Gaussian SCM using sempler (not a dependency of causalicp).

import sempler, sempler.generators
import numpy as np
np.random.seed(12)

# Generate a random graph and construct a linear-Gaussian SCM
W = sempler.generators.dag_avg_deg(4, 2.5, 0.5, 2)
scm = sempler.LGANM(W, (-1,1), (1,2))

# Generate a sample for setting 1: Observational setting
data = [scm.sample(n=100)]

# Setting 2: Shift-intervention on X1
data += [scm.sample(n=130, shift_interventions = {1: (3.1, 5.4)})]

# Setting 3: Do-intervention on X2
data += [scm.sample(n=98, do_interventions = {2: (-1, 3)})]

Running ICP for the response variable 3, at a significance level of 0.05.

import causalicp as icp
result = icp.fit(data, 3, alpha=0.05, precompute=True, verbose=True, color=False)

# Output:

# Tested sets and their p-values:
#   set() rejected : 2.355990957880749e-10
#   {0} rejected : 7.698846116207467e-16
#   {1} rejected : 4.573866047163566e-09
#   {2} rejected : 8.374476052441259e-08
#   {0, 1} accepted : 0.7330408066181638
#   {0, 2} rejected : 2.062882130448634e-15
#   {1, 2} accepted : 0.8433000000649277
#   {0, 1, 2} accepted : 1
# Estimated parental set: {1}

The estimate, accepted sets, etc. are attributes of the causalicp.Result object:

result.estimate
# {1}

result.accepted_sets
# [{0, 1}, {1, 2}, {0, 1, 2}]

result.rejected_sets
# [set(), {0}, {1}, {2}, {0, 2}]

result.pvalues
# {0: 0.8433000000649277, 1: 8.374476052441259e-08, 2: 0.7330408066181638, 3: nan}

result.conf_intervals
# array([[0.        , 0.57167295, 0.        ,        nan],
#        [2.11059461, 0.7865869 , 3.87380337,        nan]])

Code structure

The code is divided in two modules:

• icp.py which contains the implementation of the algorithm (fit function) and the definition of the Result object.
• data.py which contains a class to manage the multi-environment data and perform the linear regression for each set in an efficient way.

Tests

Unit tests and doctests are included. Additionally, the output of the overall procedure has been checked over tens of thousands of random graphs against that of the R package by the original authors. Of course, this doesn't mean there are no bugs, but hopefully it means they are less likely :)

The tests can be run with make tests. This will also execute the doctests, generate 1000 random SCMs + interventions, and run the R implementation on them for comparison. You can add SUITE=<module_name> to run a particular module only. There are, however, additional dependencies to run the tests. You can find these in requirements_tests.txt and R_requirements_tests.txt.

Feedback

I hope you find this useful! Feedback and (constructive) criticism is always welcome, just shoot me an email :)