arXiv subjects

Marloes H. Maathuis

Publications and source records attributed to Marloes H. Maathuis.

At least 19 recordsLinked to original sources

arXiv2025

Root cause discovery via permutations and Cholesky decomposition

This work is motivated by the following problem: Can we identify the disease-causing gene in a patient affected by a monogenic disorder? This problem is an instance of root cause discovery. In particular, we aim to identify the intervened variable in one interventional sample using a set of observational samples as reference. We consider a linear structural equation model where the causal ordering is unknown. We begin by examining a simple method that uses squared z-scores and characterize the conditions under which this method succeeds and fails, showing that it generally cannot identify the root cause. We then prove, without additional assumptions, that the root cause is identifiable even if the causal ordering is not. Two key ingredients of this identifiability result are the use of permutations and the Cholesky decomposition, which allow us to exploit an invariant property across different permutations to discover the root cause. Furthermore, we characterize permutations that yield the correct root cause and, based on this, propose a valid method for root cause discovery. We also adapt this approach to high-dimensional settings. Finally, we evaluate the performance of our methods through simulations and apply the high-dimensional method to discover disease-causing genes in the gene expression dataset that motivates this work.

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arXiv2024

Simultaneous false discovery proportion bounds via knockoffs and closed testing

We propose new methods to obtain simultaneous false discovery proportion bounds for knockoff-based approaches. We first investigate an approach based on Janson and Su's $k$-familywise error rate control method and interpolation. We then generalize it by considering a collection of $k$ values, and show that the bound of Katsevich and Ramdas is a special case of this method and can be uniformly improved. Next, we further generalize the method by using closed testing with a multi-weighted-sum local test statistic. This allows us to obtain a further uniform improvement and other generalizations over previous methods. We also develop an efficient shortcut for its implementation. We compare the performance of our proposed methods in simulations and apply them to a data set from the UK Biobank.

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arXiv2023

A Graphical Approach to Treatment Effect Estimation with Observational Network Data

We propose an easy-to-use adjustment estimator for the effect of a treatment based on observational data from a single (social) network of units. The approach allows for interactions among units within the network, called interference, and for observed confounding. We define a simplified causal graph that does not differentiate between units, called generic graph. Using valid adjustment sets determined in the generic graph, we can identify the treatment effect and build a corresponding estimator. We establish the estimator's consistency and its convergence to a Gaussian limiting distribution at the parametric rate under certain regularity conditions that restrict the growth of dependencies among units. We empirically verify the theoretical properties of our estimator through a simulation study and apply it to estimate the effect of a strict facial-mask policy on the spread of COVID-19 in Switzerland.

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arXiv2023

Graphical tools for selecting conditional instrumental sets

We consider the efficient estimation of total causal effects in the presence of unmeasured confounding using conditional instrumental sets. Specifically, we consider the two-stage least squares estimator in the setting of a linear structural equation model with correlated errors that is compatible with a known acyclic directed mixed graph. To set the stage for our results, we characterize the class of linearly valid conditional instrumental sets that yield consistent two-stage least squares estimators for the target total effect and derive a new asymptotic variance formula for these estimators. Equipped with these results, we provide three graphical tools for selecting more efficient linearly valid conditional instrumental sets. First, a graphical criterion that for certain pairs of linearly valid conditional instrumental sets identifies which of the two corresponding estimators has the smaller asymptotic variance. Second, an algorithm that greedily adds covariates that reduce the asymptotic variance to a given linearly valid conditional instrumental set. Third, a linearly valid conditional instrumental set for which the corresponding estimator has the smallest asymptotic variance that can be ensured with a graphical criterion.

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arXiv2023

Estimation and Inference of Extremal Quantile Treatment Effects for Heavy-Tailed Distributions

Causal inference for extreme events has many potential applications in fields such as climate science, medicine and economics. We study the extremal quantile treatment effect of a binary treatment on a continuous, heavy-tailed outcome. Existing methods are limited to the case where the quantile of interest is within the range of the observations. For applications in risk assessment, however, the most relevant cases relate to extremal quantiles that go beyond the data range. We introduce an estimator of the extremal quantile treatment effect that relies on asymptotic tail approximation, and use a new causal Hill estimator for the extreme value indices of potential outcome distributions. We establish asymptotic normality of the estimators and propose a consistent variance estimator to achieve valid statistical inference. We illustrate the performance of our method in simulation studies, and apply it to a real data set to estimate the extremal quantile treatment effect of college education on wage.

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arXiv2021

GGM knockoff filter: False Discovery Rate Control for Gaussian Graphical Models

We propose a new method to learn the structure of a Gaussian graphical model with finite sample false discovery rate control. Our method builds on the knockoff framework of Barber and Candès for linear models. We extend their approach to the graphical model setting by using a local (node-based) and a global (graph-based) step: we construct knockoffs and feature statistics for each node locally, and then solve a global optimization problem to determine a threshold for each node. We then estimate the neighborhood of each node, by comparing its feature statistics to its threshold, resulting in our graph estimate. Our proposed method is very flexible, in the sense that there is freedom in the choice of knockoffs, feature statistics, and the way in which the final graph estimate is obtained. For any given data set, it is not clear a priori what choices of these hyperparameters are optimal. We therefore use a sample-splitting-recycling procedure that first uses half of the samples to select the hyperparameters, and then learns the graph using all samples, in such a way that the finite sample FDR control still holds. We compare our method to several competitors in simulations and on a real data set.

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arXiv2021

Profiling Compliers in Instrumental Variables Designs

Instrumental variable (IV) analyses are becoming common in health services research and epidemiology. IV analyses can be used both to analyze randomized trials with noncompliance and as a form of natural experiment. In these analyses, investigators often adopt a monotonicity assumption, which implies that the relevant effect only applies to a subset of the study population known as compliers. Since the estimated effect is not the average treatment effect of the study population, it is important to compare the characteristics of compliers and non-compliers. Profiling compliers and non-compliers is necessary to understand what subpopulation the researcher is making inferences about, and an important first step in evaluating the external validity (or lack thereof) of the IV estimate for compliers. Here, we discuss the assumptions necessary for profiling, which are weaker than the assumptions necessary for identifying the local average treatment effect if the instrument is randomly assigned. We then outline a simple and general method to characterize compliers and noncompliers using baseline covariates. Next, we extend current methods by deriving standard errors for these estimates. We demonstrate these methods using an IV known as tendency to operate (TTO) from health services research.

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arXiv2020

On efficient adjustment in causal graphs

We consider estimation of a total causal effect from observational data via covariate adjustment. Ideally, adjustment sets are selected based on a given causal graph, reflecting knowledge of the underlying causal structure. Valid adjustment sets are, however, not unique. Recent research has introduced a graphical criterion for an 'optimal' valid adjustment set (O-set). For a given graph, adjustment by the O-set yields the smallest asymptotic variance compared to other adjustment sets in certain parametric and non-parametric models. In this paper, we provide three new results on the O-set. First, we give a novel, more intuitive graphical characterisation: We show that the O-set is the parent set of the outcome node(s) in a suitable latent projection graph, which we call the forbidden projection. An important property is that the forbidden projection preserves all information relevant to total causal effect estimation via covariate adjustment, making it a useful methodological tool in its own right. Second, we extend the existing IDA algorithm to use the O-set, and argue that the algorithm remains semi-local. This is implemented in the R-package pcalg. Third, we present assumptions under which the O-set can be viewed as the target set of popular non-graphical variable selection algorithms such as stepwise backward selection.

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arXiv2020

Graphical Criteria for Efficient Total Effect Estimation via Adjustment in Causal Linear Models

Covariate adjustment is a commonly used method for total causal effect estimation. In recent years, graphical criteria have been developed to identify all valid adjustment sets, that is, all covariate sets that can be used for this purpose. Different valid adjustment sets typically provide total effect estimates of varying accuracies. Restricting ourselves to causal linear models, we introduce a graphical criterion to compare the asymptotic variances provided by certain valid adjustment sets. We employ this result to develop two further graphical tools. First, we introduce a simple variance reducing pruning procedure for any given valid adjustment set. Second, we give a graphical characterization of a valid adjustment set that provides the optimal asymptotic variance among all valid adjustment sets. Our results depend only on the graphical structure and not on the specific error variances or edge coefficients of the underlying causal linear model. They can be applied to directed acyclic graphs (DAGs), completed partially directed acyclic graphs (CPDAGs) and maximally oriented partially directed acyclic graphs (maximal PDAGs). We present simulations and a real data example to support our results and show their practical applicability.

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arXiv2020

Evaluation of Causal Structure Learning Algorithms via Risk Estimation

Recent years have seen many advances in methods for causal structure learning from data. The empirical assessment of such methods, however, is much less developed. Motivated by this gap, we pose the following question: how can one assess, in a given problem setting, the practical efficacy of one or more causal structure learning methods? We formalize the problem in a decision-theoretic framework, via a notion of expected loss or risk for the causal setting. We introduce a theoretical notion of causal risk as well as sample quantities that can be computed from data, and study the relationship between the two, both theoretically and through an extensive simulation study. Our results provide an assumptions-light framework for assessing causal structure learning methods that can be applied in a range of practical use-cases.

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arXiv2018

Robust causal structure learning with some hidden variables

We introduce a new method to estimate the Markov equivalence class of a directed acyclic graph (DAG) in the presence of hidden variables, in settings where the underlying DAG among the observed variables is sparse, and there are a few hidden variables that have a direct effect on many of the observed ones. Building on the so-called low rank plus sparse framework, we suggest a two-stage approach which first removes the effect of the hidden variables, and then estimates the Markov equivalence class of the underlying DAG under the assumption that there are no remaining hidden variables. This approach is consistent in certain high-dimensional regimes and performs favourably when compared to the state of the art, both in terms of graphical structure recovery and total causal effect estimation.

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arXiv2018

Complete Graphical Characterization and Construction of Adjustment Sets in Markov Equivalence Classes of Ancestral Graphs

We present a graphical criterion for covariate adjustment that is sound and complete for four different classes of causal graphical models: directed acyclic graphs (DAGs), maximum ancestral graphs (MAGs), completed partially directed acyclic graphs (CPDAGs), and partial ancestral graphs (PAGs). Our criterion unifies covariate adjustment for a large set of graph classes. Moreover, we define an explicit set that satisfies our criterion, if there is any set that satisfies our criterion. We also give efficient algorithms for constructing all sets that fulfill our criterion, implemented in the R package dagitty. Finally, we discuss the relationship between our criterion and other criteria for adjustment, and we provide new soundness and completeness proofs for the adjustment criterion for DAGs.

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arXiv2018

High-dimensional consistency in score-based and hybrid structure learning

Main approaches for learning Bayesian networks can be classified as constraint-based, score-based or hybrid methods. Although high-dimensional consistency results are available for constraint-based methods like the PC algorithm, such results have not been proved for score-based or hybrid methods, and most of the hybrid methods have not even shown to be consistent in the classical setting where the number of variables remains fixed and the sample size tends to infinity. In this paper, we show that consistency of hybrid methods based on greedy equivalence search (GES) can be achieved in the classical setting with adaptive restrictions on the search space that depend on the current state of the algorithm. Moreover, we prove consistency of GES and adaptively restricted GES (ARGES) in several sparse high-dimensional settings. ARGES scales well to sparse graphs with thousands of variables and our simulation study indicates that both GES and ARGES generally outperform the PC algorithm.

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arXiv2017

Distributional Equivalence and Structure Learning for Bow-free Acyclic Path Diagrams

We consider the problem of structure learning for bow-free acyclic path diagrams (BAPs). BAPs can be viewed as a generalization of linear Gaussian DAG models that allow for certain hidden variables. We present a first method for this problem using a greedy score-based search algorithm. We also prove some necessary and some sufficient conditions for distributional equivalence of BAPs which are used in an algorithmic ap- proach to compute (nearly) equivalent model structures. This allows us to infer lower bounds of causal effects. We also present applications to real and simulated datasets using our publicly available R-package.

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arXiv2017

Structure Learning of Linear Gaussian Structural Equation Models with Weak Edges

We consider structure learning of linear Gaussian structural equation models with weak edges. Since the presence of weak edges can lead to a loss of edge orientations in the true underlying CPDAG, we define a new graphical object that can contain more edge orientations. We show that this object can be recovered from observational data under a type of strong faithfulness assumption. We present a new algorithm for this purpose, called aggregated greedy equivalence search (AGES), that aggregates the solution path of the greedy equivalence search (GES) algorithm for varying values of the penalty parameter. We prove consistency of AGES and demonstrate its performance in a simulation study and on single cell data from Sachs et al. (2005). The algorithm will be made available in the R-package pcalg.

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arXiv2017

Causal Structure Learning

Graphical models can represent a multivariate distribution in a convenient and accessible form as a graph. Causal models can be viewed as a special class of graphical models that not only represent the distribution of the observed system but also the distributions under external interventions. They hence enable predictions under hypothetical interventions, which is important for decision making. The challenging task of learning causal models from data always relies on some underlying assumptions. We discuss several recently proposed structure learning algorithms and their assumptions, and compare their empirical performance under various scenarios.

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arXiv2016

Structure Learning in Graphical Modeling

A graphical model is a statistical model that is associated to a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models admit computationally convenient factorization properties and have long been a valuable tool for tractable modeling of multivariate distributions. More recently, applications such as reconstructing gene regulatory networks from gene expression data have driven major advances in structure learning, that is, estimating the graph underlying a model. We review some of these advances and discuss methods such as the graphical lasso and neighborhood selection for undirected graphical models (or Markov random fields), and the PC algorithm and score-based search methods for directed graphical models (or Bayesian networks). We further review extensions that account for effects of latent variables and heterogeneous data sources.

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arXiv2016

Estimating the effect of joint interventions from observational data in sparse high-dimensional settings

We consider the estimation of joint causal effects from observational data. In particular, we propose new methods to estimate the effect of multiple simultaneous interventions (e.g., multiple gene knockouts), under the assumption that the observational data come from an unknown linear structural equation model with independent errors. We derive asymptotic variances of our estimators when the underlying causal structure is partly known, as well as high-dimensional consistency when the causal structure is fully unknown and the joint distribution is multivariate Gaussian. We also propose a generalization of our methodology to the class of nonparanormal distributions. We evaluate the estimators in simulation studies and also illustrate them on data from the DREAM4 challenge.

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