arXiv subjects

Joris M. Mooij

Publications and source records attributed to Joris M. Mooij.

At least 19 recordsLinked to original sources

arXiv2026

Are Bayesian networks typically faithful?

Faithfulness is a common assumption in causal inference, often motivated by the fact that the faithful parameters of linear Gaussian and discrete Bayesian networks are typical, and the folklore belief that this should also hold for other classes of Bayesian networks. We address this open question by showing that among all Bayesian networks over a given DAG, the faithful Bayesian networks are indeed `typical': they constitute a dense, open set with respect to the total variation metric. This does not directly imply that faithfulness is typical in restricted classes of Bayesian networks that are often considered in statistical applications. To this end we consider the class of Bayesian networks parametrised by conditional exponential families, for which we show that under regularity conditions, the faithful parameters constitute a dense and open set, the unfaithful parameters have Lebesgue measure zero, and the induced faithful distributions are open and dense in the weak topology. This extends the existing results for linear Gaussian and discrete Bayesian networks. We also show for nonparametric classes of Bayesian networks with uniformly equicontinuous and uniformly bounded conditional densities that the faithful Bayesian networks are open and dense in the weak topology. All these results also hold for Bayesian networks with latent variables, if faithfulness is only required to hold with respect to the latent projection. Finally, for the considered conditional exponential family parametrisations and nonparametric conditional density models, the topological properties of conditional independence imply the existence of a consistent conditional independence test. Together with the topological properties of faithfulness, this implies that sound constraint-based causal discovery algorithms like PC and FCI are consistent on an open and dense -- and hence `typical' -- set of Bayesian networks.

math.ST↗

arXiv2026

Causal Reasoning with Bipartite Graphical Causal Models

Causal Bayesian networks (CBNs) and structural causal models (SCMs) are the dominant frameworks for graphical causal reasoning, but they cannot adequately represent all real-world causal systems. In particular, systems at equilibrium---where feedback mechanisms create cyclic causal dependencies---can exhibit causal semantics that are fundamentally incompatible with these frameworks: different interventions that enforce the same variable value may have different effects, rendering the standard ``perfect intervention'' do($X = x$) ambiguous. We propose bipartite graphical causal models (BGCMs), in which the structure of a system of equations is encoded by a bipartite graph with variable and equation nodes. In this framework, a hard intervention do($f_j : X_v = ξ_v$) specifies which equation is replaced, which variable is targeted, and at what value---resolving the ambiguity of the standard notion. We demonstrate, through a detailed case study of a physical system, that this representation naturally corresponds to distinct real-world interventions. We formulate a Markov property in terms of a new graphical separation criterion (B-separation) that exploits the functional determinism inherent in the equations, and we extend it to settings with non-random inputs. We show how this gives rise to a do-calculus for reasoning about domain invariances. BGCMs strictly generalize CBNs and SCMs while retaining the ability to perform graphical causal reasoning.

cs.AI↗

arXiv2026

Causal Graphs, Markov Properties and Do-calculus for Stochastic Differential Equations

Stochastic differential equations (SDEs) are widely used to model continuous-time dynamical systems, but graphical causal models for them are not yet well-understood. We consider systems of causal SDEs that are equipped with an explicit causal semantics. We pose solvability conditions for systems of causal SDEs such that they have well-defined observational and interventional distributions - even after marginalisation - and provide a general class of Lipschitz semimartingale SDEs that satisfies these conditions. As core results we establish the $σ$-separation Markov property and the do-calculus in terms of the system's causal graph for probabilistic independence and interventions on the level of sample paths. For a class of additive-noise SDEs we prove a stronger $d$-separation Markov property, even if the system is cyclic. As a corollary of the do-calculus, we obtain an explicit causal interpretation of the graph: that the absence of a directed path implies the absence of a causal effect. We further introduce time-split systems, which consider the causal relations between the processes when evaluated on disjoint intervals or time-points, and use them to reason about subsampled time-series, continuous-time Granger non-causality and local independence. Finally, we discuss how constraint-based causal discovery algorithms (PC, FCI, CCD, CCI) apply directly to SDEs within our framework when conditional independence between sample paths can be consistently tested.

math.ST↗

arXiv2026

Dynamic Structural Causal Models

We study a specific type of SCM, called a Dynamic Structural Causal Model (DSCM), whose endogenous variables represent functions of time, which is possibly cyclic and allows for latent confounding. As a motivating use-case, we show that certain systems of Stochastic Differential Equations (SDEs) can be appropriately represented with DSCMs. An immediate consequence of this construction is a graphical Markov property for systems of SDEs. We define a time-splitting operation, allowing us to analyse the concept of local independence (a notion of continuous-time Granger (non-)causality). We also define a subsampling operation, which returns a discrete-time DSCM, and which can be used for mathematical analysis of subsampled time-series. We give suggestions how DSCMs can be used for identification of the causal effect of time-dependent interventions, and how existing constraint-based causal discovery algorithms can be applied to time-series data.

math.ST↗

arXiv2026

Topological Criteria for Hypothesis Testing with Finite-Precision Measurements

We establish topological necessary and sufficient conditions under which a pair of statistical hypotheses can be consistently distinguished when i.i.d. observations are recorded only to finite precision. To accommodate finite-precision data, we introduce finite-precision tests: tests whose decision regions are open in the sample-space topology. We first show that, both for classical and finite-precision tests, the existence of such tests with finite-sample error control, asymptotic error control, or uniform convergence of the errors are all equivalent. A pair of null- and alternative hypotheses $H_0$ and $H_1$ admits a consistent finite-precision test if and only if both are $F_σ$ in the weak topology on the space of probability measures $W := H_0\cup H_1$. The hypotheses admit uniform error control under $H_i$ if and only if $H_i$ is closed in $W$, and admit uniformly consistent testing with bounded precision under metric separation of $H_0$ and $H_1$. These criteria imply that, without regularity assumptions, conditional independence is not consistently testable from finite-precision data when the conditioning space has no isolated points - strengthening existing impossibility results to Polish sample spaces and showing that even pointwise consistency cannot be obtained. We introduce an equicontinuity assumption on the family of conditional distributions under which we recover consistent finite-precision testability of conditional independence with uniform error control under the null, provided sample spaces are Polish and the conditioning space is locally compact. The equicontinuity assumption is itself a finite-precision-testable hypothesis, so the resulting test for conditional independence is, in a precise sense, assumption-free.

math.ST↗

arXiv2026

Complete Causal Identification from Ancestral Graphs under Selection Bias

Many causal discovery algorithms, including the celebrated FCI algorithm, output a Partial Ancestral Graph (PAG). PAGs serve as an abstract graphical representation of the underlying causal structure, modeled by directed acyclic graphs with latent and selection variables. This paper develops a characterization of the set of extended-type conditional independence relations that are invariant across all causal models represented by a PAG. This theory allows us to formulate a general measure-theoretic version of Pearl's causal calculus and a sound and complete identification algorithm for PAGs under selection bias. Our results also apply when PAGs are learned by certain algorithms that integrate observational data with experimental data and incorporate background knowledge.

stat.ME↗

arXiv2026

Testing Partially-Identifiable Causal Queries Using Ternary Tests

We consider hypothesis testing of binary causal queries using observational data. Since the mapping of causal models to the observational distribution that they induce is not one-to-one, in general, causal queries are often only partially identifiable. When binary statistical tests are used for testing partially-identifiable causal queries, their results do not translate in a straightforward manner to the causal hypothesis testing problem. We propose using ternary (three-outcome) statistical tests to test partially-identifiable causal queries. We establish testability requirements that ternary tests must satisfy in terms of uniform consistency and present equivalent topological conditions on the hypotheses. To leverage the existing toolbox of binary tests, we prove that obtaining ternary tests by combining binary tests is complete. Finally, we demonstrate how topological conditions serve as a guide to construct ternary tests for two concrete causal hypothesis testing problems, namely testing the instrumental variable (IV) inequalities and comparing treatment efficacy.

stat.ME↗

arXiv2025

Foundations of Structural Causal Models with Latent Selection

Three distinct phenomena complicate statistical causal analysis: latent common causes, causal cycles, and latent selection. Foundational works on Structural Causal Models (SCMs), e.g., Bongers et al. (2021, Ann. Stat., 49(5): 2885-2915), treat cycles and latent variables, while an analogous account of latent selection is missing. The goal of this article is to develop a theoretical foundation for modeling latent selection with SCMs. To achieve that, we introduce a conditioning operation for SCMs: it maps an SCM with explicit selection mechanisms to one without them while preserving the causal semantics of the selected subpopulation. Graphically, in Directed Mixed Graphs we extend bidirected edge--beyond latent common cause--to also encode latent selection. We prove that the conditioning operation preserves simplicity, acyclicity, and linearity of SCMs, and interacts well with marginalization, conditioning, and interventions. These properties make those three operations valuable tools for causal modeling, reasoning, and learning after abstracting away latent details (latent common causes and selection). Examples show how this abstraction streamlines analysis and clarifies when standard tools (e.g., adjustment, causal calculus, instrumental variables) remain valid under selection bias. We hope that these results deepen the SCM-based understanding of selection bias and become part of the standard causal modeling toolbox to build more reliable causal analysis.

stat.ME↗

arXiv2025

Conditional Forecasts and Proper Scoring Rules for Reliable and Accurate Performative Predictions

Performative predictions are forecasts which influence the outcomes they aim to predict, undermining the existence of correct forecasts and standard methods of elicitation and estimation. We show that conditioning forecasts on covariates that separate them from the outcome renders the target distribution forecast-invariant, guaranteeing well-posedness of the forecasting problem. However, even under this condition, classical proper scoring rules fail to elicit correct forecasts. We prove a general impossibility result and identify two solutions: (i) in decision-theoretic settings, elicitation of correct and incentive-compatible forecasts is possible if forecasts are separating; (ii) scoring with unbiased estimates of the divergence between the forecast and the induced distribution of the target variable yields correct forecasts. Applying these insights to parameter estimation, conditional forecasts and proper scoring rules enable performatively stable estimation of performatively correct parameters, resolving the issues raised by Perdomo et al. (2020). Our results expose fundamental limits of classical forecast evaluation and offer new tools for reliable and accurate forecasting in performative settings.

math.ST↗

arXiv2025

Revisiting the Berkeley Admissions data: Statistical Tests for Causal Hypotheses

Reasoning about fairness through correlation-based notions is rife with pitfalls. The 1973 University of California, Berkeley graduate school admissions case from Bickel et. al. (1975) is a classic example of one such pitfall, namely Simpson's paradox. The discrepancy in admission rates among males and female applicants, in the aggregate data over all departments, vanishes when admission rates per department are examined. We reason about the Berkeley graduate school admissions case through a causal lens. In the process, we introduce a statistical test for causal hypothesis testing based on Pearl's instrumental-variable inequalities (Pearl 1995). We compare different causal notions of fairness that are based on graphical, counterfactual and interventional queries on the causal model, and develop statistical tests for these notions that use only observational data. We study the logical relations between notions, and show that while notions may not be equivalent, their corresponding statistical tests coincide for the case at hand. We believe that a thorough case-based causal analysis helps develop a more principled understanding of both causal hypothesis testing and fairness.

stat.ME↗

arXiv2025

$σ$-Maximal Ancestral Graphs

Maximal Ancestral Graphs (MAGs) provide an abstract representation of Directed Acyclic Graphs (DAGs) with latent (selection) variables. These graphical objects encode information about ancestral relations and d-separations of the DAGs they represent. This abstract representation has been used amongst others to prove the soundness and completeness of the FCI algorithm for causal discovery, and to derive a do-calculus for its output. One significant inherent limitation of MAGs is that they rule out the possibility of cyclic causal relationships. In this work, we address that limitation. We introduce and study a class of graphical objects that we coin ''$σ$-Maximal Ancestral Graphs'' (''$σ$-MAGs''). We show how these graphs provide an abstract representation of (possibly cyclic) Directed Graphs (DGs) with latent (selection) variables, analogously to how MAGs represent DAGs. We study the properties of these objects and provide a characterization of their Markov equivalence classes.

cs.DM↗

arXiv2024

Evaluating and Correcting Performative Effects of Decision Support Systems via Causal Domain Shift

When predicting a target variable $Y$ from features $X$, the prediction $\hat{Y}$ can be performative: an agent might act on this prediction, affecting the value of $Y$ that we eventually observe. Performative predictions are deliberately prevalent in algorithmic decision support, where a Decision Support System (DSS) provides a prediction for an agent to affect the value of the target variable. When deploying a DSS in high-stakes settings (e.g. healthcare, law, predictive policing, or child welfare screening) it is imperative to carefully assess the performative effects of the DSS. In the case that the DSS serves as an alarm for a predicted negative outcome, naive retraining of the prediction model is bound to result in a model that underestimates the risk, due to effective workings of the previous model. In this work, we propose to model the deployment of a DSS as causal domain shift and provide novel cross-domain identification results for the conditional expectation $E[Y | X]$, allowing for pre- and post-hoc assessment of the deployment of the DSS, and for retraining of a model that assesses the risk under a baseline policy where the DSS is not deployed. Using a running example, we empirically show that a repeated regression procedure provides a practical framework for estimating these quantities, even when the data is affected by sample selection bias and selective labelling, offering for a practical, unified solution for multiple forms of target variable bias.

cs.LG↗

arXiv2023

Constraint-Based Causal Discovery using Partial Ancestral Graphs in the presence of Cycles

While feedback loops are known to play important roles in many complex systems, their existence is ignored in a large part of the causal discovery literature, as systems are typically assumed to be acyclic from the outset. When applying causal discovery algorithms designed for the acyclic setting on data generated by a system that involves feedback, one would not expect to obtain correct results. In this work, we show that -- surprisingly -- the output of the Fast Causal Inference (FCI) algorithm is correct if it is applied to observational data generated by a system that involves feedback. More specifically, we prove that for observational data generated by a simple and $σ$-faithful Structural Causal Model (SCM), FCI is sound and complete, and can be used to consistently estimate (i) the presence and absence of causal relations, (ii) the presence and absence of direct causal relations, (iii) the absence of confounders, and (iv) the absence of specific cycles in the causal graph of the SCM. We extend these results to constraint-based causal discovery algorithms that exploit certain forms of background knowledge, including the causally sufficient setting (e.g., the PC algorithm) and the Joint Causal Inference setting (e.g., the FCI-JCI algorithm).

math.ST↗

arXiv2023

Establishing Markov Equivalence in Cyclic Directed Graphs

We present a new, efficient procedure to establish Markov equivalence between directed graphs that may or may not contain cycles under the \textit{d}-separation criterion. It is based on the Cyclic Equivalence Theorem (CET) in the seminal works on cyclic models by Thomas Richardson in the mid '90s, but now rephrased from an ancestral perspective. The resulting characterization leads to a procedure for establishing Markov equivalence between graphs that no longer requires tests for d-separation, leading to a significantly reduced algorithmic complexity. The conceptually simplified characterization may help to reinvigorate theoretical research towards sound and complete cyclic discovery in the presence of latent confounders. This version includes a correction to rule (iv) in Theorem 1, and the subsequent adjustment in part 2 of Algorithm 2.

cs.AI↗

arXiv2023

Correcting for Selection Bias and Missing Response in Regression using Privileged Information

When estimating a regression model, we might have data where some labels are missing, or our data might be biased by a selection mechanism. When the response or selection mechanism is ignorable (i.e., independent of the response variable given the features) one can use off-the-shelf regression methods; in the nonignorable case one typically has to adjust for bias. We observe that privileged information (i.e. information that is only available during training) might render a nonignorable selection mechanism ignorable, and we refer to this scenario as Privilegedly Missing at Random (PMAR). We propose a novel imputation-based regression method, named repeated regression, that is suitable for PMAR. We also consider an importance weighted regression method, and a doubly robust combination of the two. The proposed methods are easy to implement with most popular out-of-the-box regression algorithms. We empirically assess the performance of the proposed methods with extensive simulated experiments and on a synthetically augmented real-world dataset. We conclude that repeated regression can appropriately correct for bias, and can have considerable advantage over weighted regression, especially when extrapolating to regions of the feature space where response is never observed.

math.ST↗

arXiv2023

Causality and independence in perfectly adapted dynamical systems

Perfect adaptation in a dynamical system is the phenomenon that one or more variables have an initial transient response to a persistent change in an external stimulus but revert to their original value as the system converges to equilibrium. With the help of the causal ordering algorithm, one can construct graphical representations of dynamical systems that represent the causal relations between the variables and the conditional independences in the equilibrium distribution. We apply these tools to formulate sufficient graphical conditions for identifying perfect adaptation from a set of first-order differential equations. Furthermore, we give sufficient conditions to test for the presence of perfect adaptation in experimental equilibrium data. We apply this method to a simple model for a protein signalling pathway and test its predictions both in simulations and using real-world protein expression data. We demonstrate that perfect adaptation can lead to misleading orientation of edges in the output of causal discovery algorithms.

cs.AI↗

arXiv2023

Combining Interventional and Observational Data Using Causal Reductions

Unobserved confounding is one of the main challenges when estimating causal effects. We propose a causal reduction method that, given a causal model, replaces an arbitrary number of possibly high-dimensional latent confounders with a single latent confounder that takes values in the same space as the treatment variable, without changing the observational and interventional distributions the causal model entails. This allows us to estimate the causal effect in a principled way from combined data without relying on the common but often unrealistic assumption that all confounders have been observed. We apply our causal reduction in three different settings. In the first setting, we assume the treatment and outcome to be discrete. The causal reduction then implies bounds between the observational and interventional distributions that can be exploited for estimation purposes. In certain cases with highly unbalanced observational samples, the accuracy of the causal effect estimate can be improved by incorporating observational data. Second, for continuous variables and assuming a linear-Gaussian model, we derive equality constraints for the parameters of the observational and interventional distributions. Third, for the general continuous setting (possibly nonlinear and non-Gaussian), we parameterize the reduced causal model using normalizing flows, a flexible class of easily invertible nonlinear transformations. We perform a series of experiments on synthetic data and find that in several cases the number of interventional samples can be reduced when adding observational training samples without sacrificing accuracy.

stat.ML↗

arXiv2022

Causal Bandits without prior knowledge using separating sets

The Causal Bandit is a variant of the classic Bandit problem where an agent must identify the best action in a sequential decision-making process, where the reward distribution of the actions displays a non-trivial dependence structure that is governed by a causal model. Methods proposed for this problem thus far in the literature rely on exact prior knowledge of the full causal graph. We formulate new causal bandit algorithms that no longer necessarily rely on prior causal knowledge. Instead, they utilize an estimator based on separating sets, which we can find using simple conditional independence tests or causal discovery methods. We show that, given a true separating set, for discrete i.i.d. data, this estimator is unbiased, and has variance which is upper bounded by that of the sample mean. We develop algorithms based on Thompson Sampling and UCB for discrete and Gaussian models respectively and show increased performance on simulation data as well as on a bandit drawing from real-world protein signaling data.

cs.AI↗