  The gold standard for discovering causal relations is by means of
experimentation. Over the last decades, alternative methods have been proposed
that can infer causal relations between variables from certain statistical
patterns in purely observational data. We introduce Joint Causal Inference
(JCI), a novel approach to causal discovery from multiple data sets from
different contexts that elegantly unifies both approaches. JCI is a causal
modeling framework rather than a specific algorithm, and it can be implemented
using any causal discovery algorithm that can take into account certain
background knowledge. JCI can deal with different types of interventions (e.g.,
perfect, imperfect, stochastic, etc.) in a unified fashion, and does not
require knowledge of intervention targets or types in case of interventional
data. We explain how several well-known causal discovery algorithms can be seen
as addressing special cases of the JCI framework, and we also propose novel
implementations that extend existing causal discovery methods for purely
observational data to the JCI setting. We evaluate different JCI
implementations on synthetic data and on flow cytometry protein expression data
and conclude that JCI implementations can considerably outperform
state-of-the-art causal discovery algorithms.
