Constraint-based Causal Discovery for Non-Linear Structural Causal Models with Cycles and Latent Confounders

We address the problem of causal discovery from data, making use of the recently proposed causal modeling framework of modular structural causal models (mSCM) to handle cycles, latent confounders and non-linearities. We introduce {\sigma}-connection graphs ({\sigma}-CG), a new class of mixed graphs (containing undirected, bidirected and directed edges) with additional structure, and extend the concept of {\sigma}-separation, the appropriate generalization of the well-known notion of d-separation in this setting, to apply to {\sigma}-CGs. We prove the closedness of {\sigma}-separation under marginalisation and conditioning and exploit this to implement a test of {\sigma}-separation on a {\sigma}-CG. This then leads us to the first causal discovery algorithm that can handle non-linear functional relations, latent confounders, cyclic causal relationships, and data from different (stochastic) perfect interventions. As a proof of concept, we show on synthetic data how well the algorithm recovers features of the causal graph of modular structural causal models.Comment: Accepted for publication in Conference on Uncertainty in Artificial Intelligence 201

Robustness of Model Predictions under Extension

Often, mathematical models of the real world are simplified representations of complex systems. A caveat to using models for analysis is that predicted causal effects and conditional independences may not be robust under model extensions, and therefore applicability of such models is limited. In this work, we consider conditions under which qualitative model predictions are preserved when two models are combined. We show how to use the technique of causal ordering to efficiently assess the robustness of qualitative model predictions and characterize a large class of model extensions that preserve these predictions. For dynamical systems at equilibrium, we demonstrate how novel insights help to select appropriate model extensions and to reason about the presence of feedback loops. We apply our ideas to a viral infection model with immune responses.Comment: Accepted for oral presentation at the Causal Discovery & Causality-Inspired Machine Learning Workshop at Neural Information Processing Systems, 202

Constraint-based Causal Discovery for Non-Linear Structural Causal Models with Cycles and Latent Confounders

We address the problem of causal discovery from data, making use of the recently proposed causal modeling framework of modular structural causal models (mSCM) to handle cycles, latent confounders and non-linearities. We introduce σ-connection graphs (σ-CG), a new class of mixed graphs (containing undirected, bidirected and directed edges) with additional structure, and extend the concept of σ-separation, the appropriate generalization of the well-known notion of d-separation in this setting, to apply to σ-CGs. We prove the closedness of σ-separation under marginalisation and conditioning and exploit this to implement a test of σ-separation on a σ-CG. This then leads us to the first causal discovery algorithm that can handle non-linear functional relations, latent confounders, cyclic causal relationships, and data from different (stochastic) perfect interventions. As a proof of concept, we show on synthetic data how well the algorithm recovers features of the causal graph of modular structural causal models

A Survey on Causal Discovery: Theory and Practice

Understanding the laws that govern a phenomenon is the core of scientific progress. This is especially true when the goal is to model the interplay between different aspects in a causal fashion. Indeed, causal inference itself is specifically designed to quantify the underlying relationships that connect a cause to its effect. Causal discovery is a branch of the broader field of causality in which causal graphs is recovered from data (whenever possible), enabling the identification and estimation of causal effects. In this paper, we explore recent advancements in a unified manner, provide a consistent overview of existing algorithms developed under different settings, report useful tools and data, present real-world applications to understand why and how these methods can be fruitfully exploited

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. The causal ordering algorithm can be used to construct an equilibrium causal ordering graph that represents causal relations and a Markov ordering graph that implies conditional independences from a set of equilibrium equations. Based on this, we formulate sufficient graphical conditions to identify 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 our ideas to a simple model for a protein signalling pathway and test its predictions both in simulations and on real-world protein expression data. We demonstrate that perfect adaptation in this model can explain why the presence and orientation of edges in the output of causal discovery algorithms does not always appear to agree with the direction of edges in biological consensus networks.Comment: 32 page

D'ya like DAGs? A Survey on Structure Learning and Causal Discovery

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.Comment: 35 page

Improving Evaluation Methods for Causal Modeling

Causal modeling is central to many areas of artificial intelligence, including complex reasoning, planning, knowledge-base construction, robotics, explanation, and fairness. Active communities of researchers in machine learning, statistics, social science, and other fields develop and enhance algorithms that learn causal models from data, and this work has produced a series of impressive technical advances. However, evaluation techniques for causal modeling algorithms have remained somewhat primitive, limiting what we can learn from the experimental studies of algorithm performance, constraining the types of algorithms and model representations that researchers consider, and creating a gap between theory and practice. We argue for expanding the standard techniques for evaluating algorithms that construct causal models. Specifically, we argue for the addition of evaluation techniques that use interventional measures rather than structural or observational measures, and that evaluate with those measures on empirical data rather than synthetic data. We survey the current practice in evaluation and show that, while the evaluation techniques we advocate are rarely used in practice, they are feasible and produce substantially different results than using structural measures and synthetic data. We also provide a protocol for generating observational-style data sets from experimental data, allowing the creation of a large number of data sets suitable for evaluation of causal modeling algorithms. We then perform a large-scale evaluation of seven causal modeling methods over 37 data sets, drawn from randomized controlled trials, as well as simulators, real-world computational systems, and observational data sets augmented with a synthetic response variable. We find notable performance differences when comparing across data from different sources. This difference demonstrates the importance of using data from a variety of sources when evaluating any causal modeling methods