We study causal discovery from observational data in linear Gaussian systems affected by \emph{mixed latent confounding}, where some unobserved factors act broadly across many variables while others influence only small subsets. This setting is common in practice and poses a challenge for existing methods: differentiable and score-based DAG learners can misinterpret global latent effects as causal edges, while latent-variable graphical models recover only undirected structure.
We propose \textsc{DCL-DECOR}, a modular, precision-led pipeline that separates these roles. The method first isolates pervasive latent effects by decomposing the observed precision matrix into a structured component and a low-rank component. The structured component corresponds to the conditional distribution after accounting for pervasive confounders and retains only local dependence induced by the causal graph and localized confounding. A correlated-noise DAG learner is then applied to this deconfounded representation to recover directed edges while modeling remaining structured error correlations, followed by a simple reconciliation step to enforce bow-freeness.
We provide identifiability results that characterize the recoverable causal target under mixed confounding and show how the overall problem reduces to well-studied subproblems with modular guarantees. Synthetic experiments that vary the strength and dimensionality of pervasive confounding demonstrate consistent improvements in directed edge recovery over applying correlated-noise DAG learning directly to the confounded data.
Causal Gaussian Processes for Robust Treatment Effect Evaluation with Unobserved Confounding
Department of Electrical Engineering and Computer Science, Syracuse University（Syracuse大学电气工程与计算机科学系）；Department of Computer Science, Columbia University（哥伦比亚大学计算机科学系）
Center for Frontier AI Research, Agency for Science, Technology, and Research (A*STAR)（科技研究局前沿人工智能研究中心）；Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR)（科技研究局高性能计算研究所）；Southern University of Science and Technology (SUSTech)（南方科技大学）；Australian Artificial Intelligence Institute, University of Technology Sydney (UTS)（悉尼科技大学澳大利亚人工智能研究院）
University of Cambridge（剑桥大学）；The Alan Turing Institute（艾伦·图灵研究所）；University of California Los Angeles（加州大学洛杉矶分校）
Unobserved confounding is one of the greatest challenges for causal discovery. The case in which unobserved variables have a widespread effect on many of the observed ones is particularly difficult because most pairs of variables are conditionally dependent given any other subset, rendering the causal effect unidentifiable. In this paper we show that beyond conditional independencies, under the principle of independent mechanisms, unobserved confounding in this setting leaves a statistical footprint in the observed data distribution that allows for disentangling spurious and causal effects. Us…
Causal modeling has been recognized as a potential solution to many challenging problems in machine learning (ML). Here, we describe how a recently proposed counterfactual approach developed to deconfound linear structural causal models can still be used to deconfound the feature representations learned by deep neural network (DNN) models. The key insight is that by training an accurate DNN using softmax activation at the classification layer, and then adopting the representation learned by the last layer prior to the output layer as our features, we have that, by construction, the learned fea…
MPI for Intelligent Systems（马克斯·普朗克智能系统研究所）；University of Cambridge（剑桥大学）；Microsoft Research（微软研究院）；University of Oxford（牛津大学）；The Alan Turing Institute（艾伦·图灵研究所）；University College London（伦敦大学学院）
Causal approaches to fairness have seen substantial recent interest, both from the machine learning community and from wider parties interested in ethical prediction algorithms. In no small part, this has been due to the fact that causal models allow one to simultaneously leverage data and expert knowledge to remove discriminatory effects from predictions. However, one of the primary assumptions in causal modeling is that you know the causal graph. This introduces a new opportunity for bias, caused by misspecifying the causal model. One common way for misspecification to occur is via unmeasure…
HIIT（赫尔辛基信息技术研究所）；University of Helsinki（赫尔辛基大学）；Washington University in St. Louis（圣路易斯华盛顿大学）
Given a set of experiments in which varying subsets of observed variables are subject to intervention, we consider the problem of identifiability of causal models exhibiting latent confounding. While identifiability is trivial when each experiment intervenes on a large number of variables, the situation is more complicated when only one or a few variables are subject to intervention per experiment. For linear causal models with latent variables Hyttinen et al. (2010) gave precise conditions for when such data are sufficient to identify the full model. While their result cannot be extended to d…
We propose a method to classify the causal relationship between two discrete variables given only the joint distribution of the variables, acknowledging that the method is subject to an inherent baseline error. We assume that the causal system is acyclicity, but we do allow for hidden common causes. Our algorithm presupposes that the probability distributions $P(C)$ of a cause $C$ is independent from the probability distribution $P(E\mid C)$ of the cause-effect mechanism. While our classifier is trained with a Bayesian assumption of flat hyperpriors, we do not make this assumption about our te…
Latent variables often mask cause-effect relationships in observational data which provokes spurious links that may be misinterpreted as causal. This problem sparks great interest in the fields such as climate science and economics. We propose to estimate confounded causal links of time series using Sequential Causal Effect Variational Autoencoder (SCEVAE) while applying Knockoff interventions. Knockoff variables have the same distribution as the originals and preserve the correlation to other variables. This allows for counterfactuals that are more faithful to the observational distribution. …
Causal Discovery of Linear Non-Gaussian Causal Models with Unobserved Confounding
TUM School of Computation, Information and Technology（慕尼黑工业大学计算、信息与技术学院）；Technical University of Munich（慕尼黑工业大学）；University of British Columbia（不列颠哥伦比亚大学）；Munich Center for Machine Learning（慕尼黑机器学习中心）
ProximalFM: Amortized Proximal Causal Inference under Hidden Confounding
University of Oxford（牛津大学）；Harvard University（哈佛大学）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Perelman School of Medicine, University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）；Vector Institute（向量研究所）；University College London（伦敦大学学院）
Johns Hopkins University（约翰斯·霍普金斯大学）；University of Texas at Austin（德克萨斯大学奥斯汀分校）；Columbia University（哥伦比亚大学）
The data drawn from biological, economic, and social systems are often confounded due to the presence of unmeasured variables. Prior work in causal discovery has focused on discrete search procedures for selecting acyclic directed mixed graphs (ADMGs), specifically ancestral ADMGs, that encode ordinary conditional independence constraints among the observed variables of the system. However, confounded systems also exhibit more general equality restrictions that cannot be represented via these graphs, placing a limit on the kinds of structures that can be learned using ancestral ADMGs. In this …
University of Tübingen（蒂宾根大学）；Technical University of Munich（慕尼黑工业大学）；Munich Data Science Institute（慕尼黑数据科学研究所）
We study the problem of learning causal models from observational data through the lens of interpolation and its counterpart -- regularization. A large volume of recent theoretical, as well as empirical work, suggests that, in highly complex model classes, interpolating estimators can have good statistical generalization properties and can even be optimal for statistical learning. Motivated by an analogy between statistical and causal learning recently highlighted by Janzing (2019), we investigate whether interpolating estimators can also learn good causal models. To this end, we consider a si…
In recommendation systems, the existence of the missing-not-at-random (MNAR) problem results in the selection bias issue, degrading the recommendation performance ultimately. A common practice to address MNAR is to treat missing entries from the so-called "exposure" perspective, i.e., modeling how an item is exposed (provided) to a user. Most of the existing approaches use heuristic models or re-weighting strategy on observed ratings to mimic the missing-at-random setting. However, little research has been done to reveal how the ratings are missing from a causal perspective. To bridge the gap,…
New York University（纽约大学）；Columbia University（哥伦比亚大学）
Causal inference from observational data requires assumptions. These assumptions range from measuring confounders to identifying instruments. Traditionally, causal inference assumptions have focused on estimation of effects for a single treatment. In this work, we construct techniques for estimation with multiple treatments in the presence of unobserved confounding. We develop two assumptions based on shared confounding between treatments and independence of treatments given the confounder. Together, these assumptions lead to a confounder estimator regularized by mutual information. For this e…
University of Toronto（多伦多大学）；Vector Institute（向量研究所）；Harvard University（哈佛大学）；MIT（麻省理工学院）
Machine learning models achieve state-of-the-art performance on many supervised learning tasks. However, prior evidence suggests that these models may learn to rely on shortcut biases or spurious correlations (intuitively, correlations that do not hold in the test as they hold in train) for good predictive performance. Such models cannot be trusted in deployment environments to provide accurate predictions. While viewing the problem from a causal lens is known to be useful, the seamless integration of causation techniques into machine learning pipelines remains cumbersome and expensive. In thi…
Institute for Analytical Sociology（分析社会学研究所）；Linköping University（林雪平大学）；Chalmers University of Technology（查尔姆斯理工大学）
Observational studies of causal effects require adjustment for confounding factors. In the tabular setting, where these factors are well-defined, separate random variables, the effect of confounding is well understood. However, in public policy, ecology, and in medicine, decisions are often made in non-tabular settings, informed by patterns or objects detected in images (e.g., maps, satellite or tomography imagery). Using such imagery for causal inference presents an opportunity because objects in the image may be related to the treatment and outcome of interest. In these cases, we rely on the…
Layer 6 AI, TD Bank Group（道明银行集团Layer 6 AI）；Harvard University（哈佛大学）；University of Toronto（多伦多大学）；Vector Institute（向量研究所）
Reliable treatment effect estimation from observational data depends on the availability of all confounding information. While much work has targeted treatment effect estimation from observational data, there is relatively little work in the setting of confounding variable missingness, where collecting more information on confounders is often costly or time-consuming. In this work, we frame this challenge as a problem of feature acquisition of confounding features for causal inference. Our goal is to prioritize acquiring values for a fixed and known subset of missing confounders in samples tha…
Unobserved confounding is a central barrier to drawing causal inferences from observational data. Several authors have recently proposed that this barrier can be overcome in the case where one attempts to infer the effects of several variables simultaneously. In this paper, we present two simple, analytical counterexamples that challenge the general claims that are central to these approaches. In addition, we show that nonparametric identification is impossible in this setting. We discuss practical implications, and suggest alternatives to the methods that have been proposed so far in this lin…
Cornell University（康奈尔大学）；Cornell Tech（康奈尔理工学院）；New York University（纽约大学）；Technion（以色列理工学院）
Observational data is increasingly used as a means for making individual-level causal predictions and intervention recommendations. The foremost challenge of causal inference from observational data is hidden confounding, whose presence cannot be tested in data and can invalidate any causal conclusion. Experimental data does not suffer from confounding but is usually limited in both scope and scale. We introduce a novel method of using limited experimental data to correct the hidden confounding in causal effect models trained on larger observational data, even if the observational data does no…
We address the problem of inferring the causal effect of an exposure on an outcome across space, using observational data. The data is possibly subject to unmeasured confounding variables which, in a standard approach, must be adjusted for by estimating a nuisance function. Here we develop a method that eliminates the nuisance function, while mitigating the resulting errors-in-variables. The result is a robust and accurate inference method for spatially varying heterogeneous causal effects. The properties of the method are demonstrated on synthetic as well as real data from Germany and the US.
Inferring causal relationships in observational time series data is an important task when interventions cannot be performed. Granger causality is a popular framework to infer potential causal mechanisms between different time series. The original definition of Granger causality is restricted to linear processes and leads to spurious conclusions in the presence of a latent confounder. In this work, we harness the expressive power of recurrent neural networks and propose a deep learning-based approach to model non-linear Granger causality by directly accounting for latent confounders. Our appro…
We propose a method to distinguish causal influence from hidden confounding in the following scenario: given a target variable Y, potential causal drivers X, and a large number of background features, we propose a novel criterion for identifying causal relationship based on the stability of regression coefficients of X on Y with respect to selecting different background features. To this end, we propose a statistic V measuring the coefficient's variability. We prove, subject to a symmetry assumption for the background influence, that V converges to zero if and only if X contains no causal driv…
Confounding bias, missing data, and selection bias are three common obstacles to valid causal inference in the data sciences. Covariate adjustment is the most pervasive technique for recovering casual effects from confounding bias. In this paper, we introduce a covariate adjustment formulation for controlling confounding bias in the presence of missing-not-at-random data and develop a necessary and sufficient condition for recovering causal effects using the adjustment. We also introduce an adjustment formulation for controlling both confounding and selection biases in the presence of missing …
We consider causal inference in the presence of unobserved confounding. We study the case where a proxy is available for the unobserved confounding in the form of a network connecting the units. For example, the link structure of a social network carries information about its members. We show how to effectively use the proxy to do causal inference. The main idea is to reduce the causal estimation problem to a semi-supervised prediction of both the treatments and outcomes. Networks admit high-quality embedding models that can be used for this semi-supervised prediction. We show that the method …
Neuroimaging datasets keep growing in size to address increasingly complex medical questions. However, even the largest datasets today alone are too small for training complex machine learning models. A potential solution is to increase sample size by pooling scans from several datasets. In this work, we combine 12,207 MRI scans from 15 studies and show that simple pooling is often ill-advised due to introducing various types of biases in the training data. First, we systematically define these biases. Second, we detect bias by experimentally showing that scans can be correctly assigned to the…
Harvard T.H. Chan School of Public Health（哈佛大学陈曾熙公共卫生学院）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）
Estimating the causal effects of a spatially-varying intervention on a spatially-varying outcome may be subject to non-local confounding (NLC), a phenomenon that can bias estimates when the treatments and outcomes of a given unit are dictated in part by the covariates of other nearby units. In particular, NLC is a challenge for evaluating the effects of environmental policies and climate events on health-related outcomes such as air pollution exposure. This paper first formalizes NLC using the potential outcomes framework, providing a comparison with the related phenomenon of causal interferen…
University of Tübingen（图宾根大学）；Technical University of Munich（慕尼黑工业大学）；Munich Data Science Institute（慕尼黑数据科学研究所）
Regression on observational data can fail to capture a causal relationship in the presence of unobserved confounding. Confounding strength measures this mismatch, but estimating it requires itself additional assumptions. A common assumption is the independence of causal mechanisms, which relies on concentration phenomena in high dimensions. While high dimensions enable the estimation of confounding strength, they also necessitate adapted estimators. In this paper, we derive the asymptotic behavior of the confounding strength estimator by Janzing and Schölkopf (2018) and show that it is general…
University of Oxford（牛津大学）；Technion – Israel Institute of Technology（以色列理工学院）
We study the problem of learning conditional average treatment effects (CATE) from high-dimensional, observational data with unobserved confounders. Unobserved confounders introduce ignorance -- a level of unidentifiability -- about an individual's response to treatment by inducing bias in CATE estimates. We present a new parametric interval estimator suited for high-dimensional data, that estimates a range of possible CATE values when given a predefined bound on the level of hidden confounding. Further, previous interval estimators do not account for ignorance about the CATE associated with s…
This paper considers an extension of the linear non-Gaussian acyclic model (LiNGAM) that determines the causal order among variables from a dataset when the variables are expressed by a set of linear equations, including noise. In particular, we assume that the variables are binary. The existing LiNGAM assumes that no confounding is present, which is restrictive in practice. Based on the concept of independent component analysis (ICA), this paper proposes an extended framework in which the mutual information among the noises is minimized. Another significant contribution is to reduce the reali…
