Finding cause-effect relationships is of key importance in science. Causal discovery aims to recover a graph from data that succinctly describes these cause-effect relationships. However, current methods face several challenges, especially when dealing with high-dimensional data and complex dependencies. Incorporating prior knowledge about the system can aid causal discovery. In this work, we leverage Cluster-DAGs as a prior knowledge framework to warm-start causal discovery. We show that Cluster-DAGs offer greater flexibility than existing approaches based on tiered background knowledge and introduce two modified constraint-based algorithms, Cluster-PC and Cluster-FCI, for causal discovery in the fully and partially observed setting, respectively. Empirical evaluation on simulated data demonstrates that Cluster-PC and Cluster-FCI outperform their respective baselines without prior knowledge.

Identifying causal effects is one prominent task throughout empirical sciences.

Identifying causal effects is one prominent task throughout empirical sciences.

Unbiased data synthesis is crucial for evaluating causal discovery algorithms in the presence of unobserved confounding, given the scarcity of real-world datasets. A common approach, implicit parameterization, encodes unobserved confounding by modifying the off-diagonal entries of the idiosyncratic covariance matrix while preserving positive definiteness. Within this approach, state-of-the-art protocols have two distinct issues that hinder unbiased sampling from the complete space of causal models: first, the use of diagonally dominant constructions, which restrict the spectrum of partial correlation matrices; and second, the restriction of possible graphical structures when sampling bidirected edges, unnecessarily ruling out valid causal models. To address these limitations, we propose an improved explicit modeling approach for unobserved confounding, leveraging block-hierarchical ancestral generation of ground truth causal graphs. Algorithms for converting the ground truth DAG into ancestral graph is provided so that the output of causal discovery algorithms could be compared with. We prove that our approach fully covers the space of causal models, including those generated by the implicit parameterization, thus enabling more robust evaluation of methods for causal discovery and inference.

As one transitions from statistical to causal learning, one is seeking the most appropriate causal model. Dynamic Bayesian networks are a popular model, where a weighted directed acyclic graph represents the causal relationships. Stochastic processes are represented by its vertices, and weighted oriented edges suggest the strength of the causal relationships. When there are confounders, one would like to utilize both oriented edges (when the direction of causality is clear) and edges that are not oriented (when there is a confounder), yielding mixed graphs. A little-studied extension of acyclicity to this mixed-graph setting is known as maximally ancestral graphs. We propose a score-based learning algorithm for learning maximally ancestral graphs. A mixed-integer quadratic program is formulated, and an algorithmic approach is proposed, in which the pre-generation of exponentially many constraints is avoided by generating only violated constraints in the so-called branch-and-cut (``lazy constraint'') method. Comparing the novel approach to the state-of-the-art, we show that the proposed approach turns out to produce more accurate results when applied to small and medium-sized synthetic instances containing up to 25 variables.

We propose a greedy search-and-score algorithm for ancestral graphs, which include directed as well as bidirected edges, originating from unobserved latent variables. The normalized likelihood score of ancestral graphs is estimated in terms of multivariate information over relevant ``ac-connected subsets'' of vertices, C, that are connected through collider paths confined to the ancestor set of C. For computational efficiency, the proposed two-step algorithm relies on local information scores limited to the close surrounding vertices of each node (step 1) and edge (step 2). This computational strategy, although restricted to information contributions from ac-connected subsets containing up to two-collider paths, is shown to outperform state-of-the-art causal discovery methods on challenging benchmark datasets.

We study the problem of restricting Markov equivalence classes of maximal ancestral graphs (MAGs) containing certain edge marks, which we refer to as expert knowledge. MAGs forming a Markov equivalence class can be uniquely represented by an essential ancestral graph. We seek to learn the restriction of the essential ancestral graph containing the proposed expert knowledge. Our contributions are several-fold. First, we prove certain properties for the entire Markov equivalence class including a conjecture from Ali et al. (2009). Second, we present three sound graphical orientation rules, two of which generalize previously known rules, for adding expert knowledge to an essential graph. We also show that some orientation rules of Zhang (2008) are not needed for restricting the Markov equivalence class with expert knowledge. We provide an algorithm for including this expert knowledge and show that our algorithm is complete in certain settings i.e., in these settings, the output of our algorithm is a restricted essential ancestral graph. We conjecture this algorithm is complete generally. Outside of our specified settings, we provide an algorithm for checking whether a graph is a restricted essential graph and discuss its runtime. This work can be seen as a generalization of Meek (1995).

Causal discovery is an essential part of causal inference (Spirtes et al., 2000; Peters et al., 2017), but estimating causal effects is extremely challenging if the underlying causal graph is unknown. Algorithms for learning causal graphs are many and varied, using different parametric structure, classes of graphical models, and assumptions about whether all relevant variables are measured (Spirtes et al., 2000; Kaltenpoth and Vreeken, 2023; Claassen and Bucur, 2022; Nowzohour et al., 2017; Zhang and Hyvarinen, 2009; Peters et al., 2017). In this paper, we consider only nonparametric assumptions, i.e. conditional independences in distributions that are represented by graphs. The primary graphical model used in causal inference is the directed acyclic graph, also known as a DAG. These offer a clear interpretation and are straightforward to conduct inference with, and are associated with probabilistic distributions by encoding conditional independence constraints.

Structure learning is the crux of causal inference. Notably, causal discovery (CD) algorithms are brittle when data is scarce, possibly inferring imprecise causal relations that contradict expert knowledge -- especially when considering latent confounders. To aggravate the issue, most CD methods do not provide uncertainty estimates, making it hard for users to interpret results and improve the inference process. Surprisingly, while CD is a human-centered affair, no works have focused on building methods that both 1) output uncertainty estimates that can be verified by experts and 2) interact with those experts to iteratively refine CD. To solve these issues, we start by proposing to sample (causal) ancestral graphs proportionally to a belief distribution based on a score function, such as the Bayesian information criterion (BIC), using generative flow networks. Then, we leverage the diversity in candidate graphs and introduce an optimal experimental design to iteratively probe the expert about the relations among variables, effectively reducing the uncertainty of our belief over ancestral graphs. Finally, we update our samples to incorporate human feedback via importance sampling. Importantly, our method does not require causal sufficiency (i.e., unobserved confounders may exist). Experiments with synthetic observational data show that our method can accurately sample from distributions over ancestral graphs and that we can greatly improve inference quality with human aid.

Instrumental variable (IV) is a powerful approach to inferring the causal effect of a treatment on an outcome of interest from observational data even when there exist latent confounders between the treatment and the outcome. However, existing IV methods require that an IV is selected and justified with domain knowledge. An invalid IV may lead to biased estimates. Hence, discovering a valid IV is critical to the applications of IV methods. In this paper, we study and design a data-driven algorithm to discover valid IVs from data under mild assumptions. We develop the theory based on partial ancestral graphs (PAGs) to support the search for a set of candidate Ancestral IVs (AIVs), and for each possible AIV, the identification of its conditioning set. Based on the theory, we propose a data-driven algorithm to discover a pair of IVs from data. The experiments on synthetic and real-world datasets show that the developed IV discovery algorithm estimates accurate estimates of causal effects in comparison with the state-of-the-art IV based causal effect estimators.