We would like to thank the reviewers for their comments and constructive feedback. Below, we address the main issues raised and clarify some misunderstandings. Also, the work of Y ang et al. (2018) characterizes soft interventions in systems without latent variables. Mooij et al. (2013) discussed interventions of this nature in the context of equilibrium in cyclic causal models. Usage of MAGs: The reviewer's observation only holds for hard interventions.

Invariant causal prediction (ICP) is a popular technique for finding causal parents (direct causes) of a target via exploiting distribution shifts and invariance testing (Peters et al., 2016). However, since ICP needs to run an exponential number of tests and fails to identify parents when distribution shifts only affect a few variables, applying ICP to practical large scale problems is challenging. We propose MMSE-ICP and fastICP, two approaches which employ an error inequality to address the identifiability problem of ICP. The inequality states that the minimum prediction error of the predictor using causal parents is the smallest among all predictors which do not use descendants. fastICP is an efficient approximation tailored for large problems as it exploits the inequality and a heuristic to run fewer tests. MMSE-ICP and fastICP not only outperform competitive baselines in many simulations but also achieve state-of-the-art result on a large scale real data benchmark.

Making predictions in an unseen environment given data from multiple training environments is a challenging task. We approach this problem from an invariance perspective, focusing on binary classification to shed light on general nonlinear data generation mechanisms. We identify a unique form of invariance that exists solely in a binary setting that allows us to train models invariant over environments. We provide sufficient conditions for such invariance and show it is robust even when environmental conditions vary greatly. Our formulation admits a causal interpretation, allowing us to compare it with various frameworks. Finally, we propose a heuristic prediction method and conduct experiments using real and synthetic datasets.

Discovering causal relationships from observational data is a fundamental yet challenging task. Invariant causal prediction (ICP, Peters et al., 2016) is a method for causal feature selection which requires data from heterogeneous settings and exploits that causal models are invariant. ICP has been extended to general additive noise models and to nonparametric settings using conditional independence tests. However, the latter often suffer from low power (or poor type I error control) and additive noise models are not suitable for applications in which the response is not measured on a continuous scale, but reflects categories or counts. Here, we develop transformation-model (TRAM) based ICP, allowing for continuous, categorical, count-type, and uninformatively censored responses (these model classes, generally, do not allow for identifiability when there is no exogenous heterogeneity). As an invariance test, we propose TRAM-GCM based on the expected conditional covariance between environments and score residuals with uniform asymptotic level guarantees. For the special case of linear shift TRAMs, we also consider TRAM-Wald, which tests invariance based on the Wald statistic. We provide an open-source R package 'tramicp' and evaluate our approach on simulated data and in a case study investigating causal features of survival in critically ill patients.

We consider the problem of estimating the differences between two causal directed acyclic graph (DAG) models with a shared topological order given i.i.d. This is of interest for example in genomics, where changes in the structure or edge weights of the underlying causal graphs reflect alterations in the gene regulatory networks. We here provide the first provably consistent method for directly estimating the differences in a pair of causal DAGs without separately learning two possibly large and dense DAG models and computing their difference. Our two-step algorithm first uses invariance tests between regression coefficients of the two data sets to estimate the skeleton of the difference graph and then orients some of the edges using invariance tests between regression residual variances. We demonstrate the properties of our method through a simulation study and apply it to the analysis of gene expression data from ovarian cancer and during T-cell activation.

For many computer vision applications, the ideal image feature would be invariant to multiple confounding image properties, such as illumination and viewing angle. Recently, deep architectures trained in an unsupervised manner have been proposed as an automatic method for extracting useful features. However, outside of using these learning algorithms in a classifier, they can be sometimes difficult to evaluate. In this paper, we propose a number of empirical tests that directly measure the degree to which these learned features are invariant to different image transforms. We find that deep autoencoders become invariant to increasingly complex image transformations with depth. This further justifies the use of “deep” vs. “shallower” representations. Our performance metrics agree with existing measures of invariance. Our evaluation metrics can also be used to evaluate future work in unsupervised deep learning, and thus help the development of future algorithms.