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.Comment: 30 pages, 3 figures, 45 pages supplemen

Learning Joint Nonlinear Effects from Single-variable Interventions in the Presence of Hidden Confounders

We propose an approach to estimate the effect of multiple simultaneous interventions in the presence of hidden confounders. To overcome the problem of hidden confounding, we consider the setting where we have access to not only the observational data but also sets of single-variable interventions in which each of the treatment variables is intervened on separately. We prove identifiability under the assumption that the data is generated from a nonlinear continuous structural causal model with additive Gaussian noise. In addition, we propose a simple parameter estimation method by pooling all the data from different regimes and jointly maximizing the combined likelihood. We also conduct comprehensive experiments to verify the identifiability result as well as to compare the performance of our approach against a baseline on both synthetic and real-world data.Comment: Accepted to The Conference on Uncertainty in Artificial Intelligence (UAI) 202

Marginal integration for nonparametric causal inference

We consider the problem of inferring the total causal effect of a single variable intervention on a (response) variable of interest. We propose a certain marginal integration regression technique for a very general class of potentially nonlinear structural equation models (SEMs) with known structure, or at least known superset of adjustment variables: we call the procedure S-mint regression. We easily derive that it achieves the convergence rate as for nonparametric regression: for example, single variable intervention effects can be estimated with convergence rate $n^{-2/5}$ assuming smoothness with twice differentiable functions. Our result can also be seen as a major robustness property with respect to model misspecification which goes much beyond the notion of double robustness. Furthermore, when the structure of the SEM is not known, we can estimate (the equivalence class of) the directed acyclic graph corresponding to the SEM, and then proceed by using S-mint based on these estimates. We empirically compare the S-mint regression method with more classical approaches and argue that the former is indeed more robust, more reliable and substantially simpler.Comment: 40 pages, 14 figure

Learning Large-Scale Bayesian Networks with the sparsebn Package

Learning graphical models from data is an important problem with wide applications, ranging from genomics to the social sciences. Nowadays datasets often have upwards of thousands---sometimes tens or hundreds of thousands---of variables and far fewer samples. To meet this challenge, we have developed a new R package called sparsebn for learning the structure of large, sparse graphical models with a focus on Bayesian networks. While there are many existing software packages for this task, this package focuses on the unique setting of learning large networks from high-dimensional data, possibly with interventions. As such, the methods provided place a premium on scalability and consistency in a high-dimensional setting. Furthermore, in the presence of interventions, the methods implemented here achieve the goal of learning a causal network from data. Additionally, the sparsebn package is fully compatible with existing software packages for network analysis.Comment: To appear in the Journal of Statistical Software, 39 pages, 7 figure

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

Penalized Estimation of Directed Acyclic Graphs From Discrete Data

Bayesian networks, with structure given by a directed acyclic graph (DAG), are a popular class of graphical models. However, learning Bayesian networks from discrete or categorical data is particularly challenging, due to the large parameter space and the difficulty in searching for a sparse structure. In this article, we develop a maximum penalized likelihood method to tackle this problem. Instead of the commonly used multinomial distribution, we model the conditional distribution of a node given its parents by multi-logit regression, in which an edge is parameterized by a set of coefficient vectors with dummy variables encoding the levels of a node. To obtain a sparse DAG, a group norm penalty is employed, and a blockwise coordinate descent algorithm is developed to maximize the penalized likelihood subject to the acyclicity constraint of a DAG. When interventional data are available, our method constructs a causal network, in which a directed edge represents a causal relation. We apply our method to various simulated and real data sets. The results show that our method is very competitive, compared to many existing methods, in DAG estimation from both interventional and high-dimensional observational data.Comment: To appear in Statistics and Computin