Prior work has shown that causal structure can be uniquely identified from observational data when these follow a structural equation model whose error terms have equal variances. We show that this fact is implied by an ordering among (conditional) variances. We demonstrate that ordering estimates of these variances yields a simple yet state-of-the-art method for causal structure learning that is readily extendable to high-dimensional problems.
This paper presents a new open source Python framework for causal discovery from observational data and domain background knowledge, aimed at causal graph and causal mechanism modeling. The 'cdt' package implements the end-to-end approach, recovering the direct dependencies (the skeleton of the causal graph) and the causal relationships between variables. It includes algorithms from the 'Bnlearn' and 'Pcalg' packages, together with algorithms for pairwise causal discovery such as ANM. 'cdt' is available under the MIT License at https://github.com/Diviyan-Kalainathan/CausalDiscoveryToolbox.
Causal variance decompositions for a given disease-specific quality indicator can be used to quantify differences in performance between hospitals or health care providers. While variance decompositions can demonstrate variation in quality of care, causal mediation analysis can be used to study care pathways leading to the differences in performance between the institutions. This raises the question of whether the two approaches can be combined to decompose between-hospital variation in an outcome type indicator to that mediated through a given process (indirect effect) and remaining variation…
The SINDy algorithm has been successfully used to identify the governing equations of dynamical systems from time series data. In this paper, we argue that this makes SINDy a potentially useful tool for causal discovery and that existing tools for causal discovery can be used to dramatically improve the performance of SINDy as tool for robust sparse modeling and system identification. We then demonstrate empirically that augmenting the SINDy algorithm with tools from causal discovery can provides engineers with a tool for learning causally robust governing equations.
We consider the problem of causal discovery (structure learning) from heterogeneous observational data. Most existing methods assume a homogeneous sampling scheme, which leads to misleading conclusions when violated in many applications. To this end, we propose a novel approach that exploits data heterogeneity to infer possibly cyclic causal structures from causally insufficient systems. The core idea is to model the direct causal effects as functions of exogenous covariates that properly explain data heterogeneity. We investigate structure identifiability properties of the proposed model. Str…
Causal questions are omnipresent in many scientific problems. While much progress has been made in the analysis of causal relationships between random variables, these methods are not well suited if the causal mechanisms only manifest themselves in extremes. This work aims to connect the two fields of causal inference and extreme value theory. We define the causal tail coefficient that captures asymmetries in the extremal dependence of two random variables. In the population case, the causal tail coefficient is shown to reveal the causal structure if the distribution follows a linear structura…
Causal Variance Decompositions for Measuring Health Inequalities
Dalla Lana School of Public Health, University of Toronto（多伦多大学达拉斯·兰纳公共卫生学院）；Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network（安大略健康网络公主玛格丽特癌症中心生物统计系）；Department of Radiation Oncology, Princess Margaret Hospital, University Health Network（安大略健康网络公主玛格丽特医院放射肿瘤学系）
IE University（IE大学）；Universitat de València（瓦伦西亚大学）
Causal discovery algorithms aim at untangling complex causal relationships from data. Here, we study causal discovery and inference methods based on staged tree models, which can represent complex and asymmetric causal relationships between categorical variables. We provide a first graphical representation of the equivalence class of a staged tree, by looking only at a specific subset of its underlying independences. We further define a new pre-metric, inspired by the widely used structural intervention distance, to quantify the closeness between two staged trees in terms of their correspondin…
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constra…
Rensselaer Polytechnic Institute（伦斯勒理工学院）；Northeast Normal University（东北师范大学）
Causal discovery is to learn cause-effect relationships among variables given observational data and is important for many applications. Existing causal discovery methods assume data sufficiency, which may not be the case in many real world datasets. As a result, many existing causal discovery methods can fail under limited data. In this work, we propose Bayesian-augmented frequentist independence tests to improve the performance of constraint-based causal discovery methods under insufficient data: 1) We firstly introduce a Bayesian method to estimate mutual information (MI), based on which we…
Causal reasoning is a crucial part of science and human intelligence. In order to discover causal relationships from data, we need structure discovery methods. We provide a review of background theory and a survey of methods for structure discovery. We primarily focus on modern, continuous optimization methods, and provide reference to further resources such as benchmark datasets and software packages. Finally, we discuss the assumptive leap required to take us from structure to causality.
The Robustness of Differentiable Causal Discovery in Misspecified Scenarios
School of Mathematics, Southeast University, Nanjing 210096, China（数学学院，东南大学，南京210096，中国）；School of Cyber Science and Engineering, Southeast University, Nanjing 210096, China（网络科学与工程学院，东南大学，南京210096，中国）
Causal discovery for quantitative data has been extensively studied but less is known for categorical data. We propose a novel causal model for categorical data based on a new classification model, termed classification with optimal label permutation (COLP). By design, COLP is a parsimonious classifier, which gives rise to a provably identifiable causal model. A simple learning algorithm via comparing likelihood functions of causal and anti-causal models suffices to learn the causal direction. Through experiments with synthetic and real data, we demonstrate the favorable performance of the pro…
Causal discovery for purely observational, categorical data is a long-standing challenging problem. Unlike continuous data, the vast majority of existing methods for categorical data focus on inferring the Markov equivalence class only, which leaves the direction of some causal relationships undetermined. This paper proposes an identifiable ordinal causal discovery method that exploits the ordinal information contained in many real-world applications to uniquely identify the causal structure. The proposed method is applicable beyond ordinal data via data discretization. Through real-world and …
CUTS+: High-dimensional Causal Discovery from Irregular Time-series
Tsinghua University（清华大学）；Institute for Brain and Cognitive Science, Tsinghua University (THUIBCS)（清华大学脑与认知科学研究院（THUIBCS））；Chinese PLA General Hospital（中国人民解放军总医院）
Causal processes in nature may contain cycles, and real datasets may violate causal sufficiency as well as contain selection bias. No constraint-based causal discovery algorithm can currently handle cycles, latent variables and selection bias (CLS) simultaneously. I therefore introduce an algorithm called Cyclic Causal Inference (CCI) that makes sound inferences with a conditional independence oracle under CLS, provided that we can represent the cyclic causal process as a non-recursive linear structural equation model with independent errors. Empirical results show that CCI outperforms CCD in …
We study the performance of Local Causal Discovery (LCD), a simple and efficient constraint-based method for causal discovery, in predicting causal effects in large-scale gene expression data. We construct practical estimators specific to the high-dimensional regime. Inspired by the ICP algorithm, we use an optional preselection method and two different statistical tests. Empirically, the resulting LCD estimator is seen to closely approach the accuracy of ICP, the state-of-the-art method, while it is algorithmically simpler and computationally more efficient.
A Versatile Causal Discovery Framework to Allow Causally-Related Hidden Variables
University of California San Diego（加州大学圣地亚哥分校）；Carnegie Mellon University（卡内基梅隆大学）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）；KDDI Research（KDDI研究所）
Carnegie Mellon University（卡内基梅隆大学）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）；University of California, San Diego（加利福尼亚大学圣迭戈分校）；Guangdong University of Technology（广东工业大学）；University of Melbourne（墨尔本大学）；Shiga University（滋贺大学）；RIKEN（理化学研究所）
University of Waterloo（滑铁卢大学）；ATS Automation（ATS自动化公司）
Causal discovery between collections of time-series data can help diagnose causes of symptoms and hopefully prevent faults before they occur. However, reliable causal discovery can be very challenging, especially when the data acquisition rate varies (i.e., non-uniform data sampling), or in the presence of missing data points (e.g., sparse data sampling). To address these issues, we proposed a new system comprised of two parts, the first part fills missing data with a Gaussian Process Regression, and the second part leverages an Echo State Network, which is a type of reservoir computer (i.e., …
Causal inference can estimate causal effects, but unless data are collected experimentally, statistical analyses must rely on pre-specified causal models. Causal discovery algorithms are empirical methods for constructing such causal models from data. Several asymptotically correct methods already exist, but they generally struggle on smaller samples. Moreover, most methods focus on very sparse causal models, which may not always be a realistic representation of real-life data generating mechanisms. Finally, while causal relationships suggested by the methods often hold true, their claims abou…
Benchmarking Bayesian Causal Discovery Methods for Downstream Treatment Effect Estimation
Technical University of Munich（慕尼黑工业大学）；Mila - Quebec AI Institute（米拉 - 魁北克人工智能研究所）；ServiceNow Research（ServiceNow研究院）；Université de Montréal（蒙特利尔大学）；Helmholtz AI（亥姆霍兹人工智能研究所）
Selecting powerful predictors for an outcome is a cornerstone task for machine learning. However, some types of questions can only be answered by identifying the predictors that causally affect the outcome. A recent approach to this causal inference problem leverages the invariance property of a causal mechanism across differing experimental environments (Peters et al., 2016; Heinze-Deml et al., 2018). This method, invariant causal prediction (ICP), has a substantial computational defect -- the runtime scales exponentially with the number of possible causal variables. In this work, we show tha…
Tsinghua University（清华大学）；Institute for Brain and Cognitive Science, Tsinghua University (THUIBCS)（清华大学脑与认知科学研究所）；Chinese PLA General Hospital（中国人民解放军总医院）
Causal discovery from time-series data has been a central task in machine learning. Recently, Granger causality inference is gaining momentum due to its good explainability and high compatibility with emerging deep neural networks. However, most existing methods assume structured input data and degenerate greatly when encountering data with randomly missing entries or non-uniform sampling frequencies, which hampers their applications in real scenarios. To address this issue, here we present CUTS, a neural Granger causal discovery algorithm to jointly impute unobserved data points and build cau…
Feedzai（Feedzai公司）；Instituto Superior Técnico, Universidade de Lisboa（里斯本大学高等技术学院）；DCC, Faculdade de Ciêncidas da Universidade do Porto（波尔图大学理学院数据与计算机科学系）；Instituto de Telecomunicações（电信研究所）
Causal discovery algorithms estimate causal graphs from observational data. This can provide a valuable complement to analyses focussing on the causal relation between individual treatment-outcome pairs. Constraint-based causal discovery algorithms rely on conditional independence testing when building the graph. Until recently, these algorithms have been unable to handle missing values. In this paper, we investigate two alternative solutions: Test-wise deletion and multiple imputation. We establish necessary and sufficient conditions for the recoverability of causal structures under test-wise…
University of Maryland, Baltimore County（马里兰大学巴尔的摩县分校）
Conventional temporal causal discovery (CD) methods suffer from high dimensionality, fail to identify lagged causal relationships, and often ignore dynamics in relations. In this study, we present a novel constraint-based CD approach for autocorrelated and non-stationary time series data (eCDANs) capable of detecting lagged and contemporaneous causal relationships along with temporal changes. eCDANs addresses high dimensionality by optimizing the conditioning sets while conducting conditional independence (CI) tests and identifies the changes in causal relations by introducing a surrogate vari…
The mainstream of research in genetics, epigenetics and imaging data analysis focuses on statistical association or exploring statistical dependence between variables. Despite their significant progresses in genetic research, understanding the etiology and mechanism of complex phenotypes remains elusive. Using association analysis as a major analytical platform for the complex data analysis is a key issue that hampers the theoretic development of genomic science and its application in practice. Causal inference is an essential component for the discovery of mechanical relationships among compl…
It is crucial to consider the social and ethical consequences of AI and ML based decisions for the safe and acceptable use of these emerging technologies. Fairness, in particular, guarantees that the ML decisions do not result in discrimination against individuals or minorities. Identifying and measuring reliably fairness/discrimination is better achieved using causality which considers the causal relation, beyond mere association, between the sensitive attribute (e.g. gender, race, religion, etc.) and the decision (e.g. job hiring, loan granting, etc.). The big impediment to the use of causal…
Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）；Universiteit van Amsterdam（阿姆斯特丹大学）
Causal discovery is a major task with the utmost importance for machine learning since causal structures can enable models to go beyond pure correlation-based inference and significantly boost their performance. However, finding causal structures from data poses a significant challenge both in computational effort and accuracy, let alone its impossibility without interventions in general. In this paper, we develop a meta-reinforcement learning algorithm that performs causal discovery by learning to perform interventions such that it can construct an explicit causal graph. Apart from being usef…
ETH Zürich（苏黎世联邦理工学院）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；IBM Research Zürich（苏黎世IBM研究院）
Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experi…
Exploring Multi-Modal Data with Tool-Augmented LLM Agents for Precise Causal Discovery
University of Houston（德克萨斯大学休斯顿分校）；NEC Laboratories America（NEC美国实验室）；Florida International University（佛罗里达国际大学）；North Carolina State University（北卡罗来纳州立大学）
University of Amsterdam（阿姆斯特丹大学）；University of Toronto（多伦多大学）；Vector Institute（向量研究所）
On time-series data, most causal discovery methods fit a new model whenever they encounter samples from a new underlying causal graph. However, these samples often share relevant information which is lost when following this approach. Specifically, different samples may share the dynamics which describe the effects of their causal relations. We propose Amortized Causal Discovery, a novel framework that leverages such shared dynamics to learn to infer causal relations from time-series data. This enables us to train a single, amortized model that infers causal relations across samples with diffe…
