Causal discovery methods commonly assume that all data is independently and identically distributed (i.i.d.) and that there are no unmeasured confounding variables. In practice, neither is likely to hold, and detecting confounding in non-i.i.d. settings poses a significant challenge. Motivated by this, we explore how to discover confounders from data in multiple environments with causal mechanism shifts. We show that the mechanism changes of observed variables can reveal which variable sets are confounded. Based on this idea, we propose an empirically testable criterion based on mutual information, show under which conditions it can identify confounding, and introduce CoCo to discover confounders from data in multiple contexts. In our experiments, we show that CoCo works well on synthetic and real-world data.

Access to a representative sample from the population is an assumption that underpins all of machine learning. Selection effects can cause observations to instead come from a subpopulation, by which our inferences may be subject to bias. It is therefore important to know whether or not a sample is affected by selection effects. We study under which conditions we can identify selection bias and give results for both parametric and non-parametric families of distributions. Based on these results we develop two practical methods to determine whether or not an observed sample comes from a distribution subject to selection bias. Through extensive evaluation on synthetic and real world data we verify that our methods beat the state of the art both in detecting as well as characterizing selection bias.

In critical applications, causal models are the prime choice for their trustworthiness and explainability. If data is inherently distributed and privacy-sensitive, federated learning allows for collaboratively training a joint model. Existing approaches for federated causal discovery share locally discovered causal model in every iteration, therewith not only revealing local structure but also leading to very high communication costs. Instead, we propose an approach for privacy-preserving federated causal discovery by distributed min-max regret optimization. We prove that max-regret is a consistent scoring criterion that can be used within the well-known Greedy Equivalence Search to discover causal networks in a federated setting and is provably privacy-preserving at the same time. Through extensive experiments, we show that our approach reliably discovers causal networks without ever looking at local data and beats the state of the art both in terms of the quality of discovered causal networks as well as communication efficiency.

Causal discovery, the task of discovering the causal graph over a set of observed variables $X_1,\ldots,X_m$, is a challenging problem. One of the cornerstone assumptions is that of causal sufficiency: that all common causes of all measured variables have been observed. When it does not hold, causal discovery algorithms making this assumption return networks with many spurious edges. In this paper, we propose a nonlinear causal model involving hidden confounders. We show that it is identifiable from only the observed data and propose an efficient method for recovering this causal model. At the heart of our approach is a variational autoencoder which parametrizes both the causal interactions between observed variables as well as the influence of the unobserved confounders. Empirically we show that it outperforms other state-of-the-art methods for causal discovery under latent confounding on synthetic and real-world data.

In many scientific applications, we observe a system in different conditions in which its components may change, rather than in isolation. In our work, we are interested in explaining the generating process of such a multi-context system using a finite mixture of causal mechanisms. Recent work shows that this causal model is identifiable from data, but is limited to settings where the sparse mechanism shift hypothesis holds and only a subset of the causal conditionals change. As this assumption is not easily verifiable in practice, we study the more general principle that mechanism shifts are independent, which we formalize using the algorithmic notion of independence. We introduce an approach for causal discovery beyond partially directed graphs using Gaussian Process models, and give conditions under which we provably identify the correct causal model. In our experiments, we show that our method performs well in a range of synthetic settings, on realistic gene expression simulations, as well as on real-world cell signaling data.

Causal sufficiency is a cornerstone assumption in causal discovery. It is, however, both unlikely to hold in practice as well as unverifiable. When it does not hold, existing methods struggle to return meaningful results. In this paper, we show how to discover the causal network over both observed and unobserved variables. Moreover, we show that the causal model is identifiable in the sparse linear Gaussian case. More generally, we extend the algorithmic Markov condition to include latent confounders. We propose a consistent score based on the Minimum Description Length principle to discover the full causal network, including latent confounders. Based on this score, we develop an effective algorithm that finds those sets of nodes for which the addition of a confounding factor $Z$ is most beneficial, then fits a new causal network over both observed as well as inferred latent variables.

While invariance of causal mechanisms has inspired recent work in both robust machine learning and causal inference, causal mechanisms may also vary over domains due to, for example, population-specific differences, the context of data collection, or intervention. To discover invariant and changing mechanisms from data, we propose extending the algorithmic model for causation to mechanism changes and instantiating it using Minimum Description Length. In essence, for a continuous variable Y in multiple contexts C, we identify variables X as causal if the regression functions g : X → Y have succinct descriptions in all contexts. In empirical evaluations we show that our method, VARIO, finds invariant variable sets, reveals mechanism changes, and discovers causal networks, such as on real-world data that gives insight into the signaling pathways in human immune cells.

Given complex data collections, practitioners can perform non-parametric functional dependency discovery (FDD) to uncover relationships between variables that were previously unknown. However, known FDD methods are applicable to nominal data, and in practice non-nominal variables are discretized, e.g., in a pre-processing step. This is problematic because, as soon as a mix of discrete and continuous variables is involved, the interaction of discretization with the various dependency measures from the literature is poorly understood. In particular, it is unclear whether a given discretization method even leads to a consistent dependency estimate. In this paper, we analyze these fundamental questions and derive formal criteria as to when a discretization process applied to a mixed set of random variables leads to consistent estimates of mutual information. With these insights, we derive an estimator framework applicable to any task that involves estimating mutual information from multivariate and mixed-type data. Last, we extend with this framework a previously proposed FDD approach for reliable dependencies. Experimental evaluation shows that the derived reliable estimator is both computationally and statistically efficient, and leads to effective FDD algorithms for mixed-type data.

Given data over variables (X1, …, Xm, Y) we consider the problem of finding out whether X jointly causes Y or whether they are all confounded by an unobserved latent variable Z. To do so, we take an information-theoretic approach based on Kolmogorov complexity. In a nutshell, we follow the postulate that first encoding the true cause, and then the effects given that cause, results in a shorter description than any other encoding of the observed variables. The ideal score is not computable, and hence we have to approximate it. We propose to do so using the Minimum Description Length (MDL) principle. We compare the MDL scores under the models where X causes Y and where there exists a latent variables Z confounding both X and Y and show our scores are consistent. To find potential confounders we propose using latent factor modeling, in particular, probabilistic PCA (PPCA). Empirical evaluation on both synthetic and real-world data shows that our method, CoCa, performs very well—even when the true generating process of the data is far from the assumptions made by the models we use. Moreover, it is robust as its accuracy goes hand in hand with its confidence.