  Conditional independence testing is a fundamental problem underlying causal
discovery and a particularly challenging task in the presence of nonlinear and
high-dimensional dependencies. Here a fully non-parametric test for continuous
data based on conditional mutual information combined with a local permutation
scheme is presented. Through a nearest neighbor approach, the test efficiently
adapts also to non-smooth distributions due to strongly nonlinear dependencies.
Numerical experiments demonstrate that the test reliably simulates the null
distribution even for small sample sizes and with high-dimensional conditioning
sets. The test is better calibrated than kernel-based tests utilizing an
analytical approximation of the null distribution, especially for non-smooth
densities, and reaches the same or higher power levels. Combining the local
permutation scheme with the kernel tests leads to better calibration, but
suffers in power. For smaller sample sizes and lower dimensions, the test is
faster than random fourier feature-based kernel tests if the permutation scheme
is (embarrassingly) parallelized, but the runtime increases more sharply with
sample size and dimensionality. Thus, more theoretical research to analytically
approximate the null distribution and speed up the estimation for larger sample
sizes is desirable.
