Learning Adjustment Sets from Observational and Limited Experimental Data

Estimating causal effects from observational data is not always possible due to confounding. Identifying a set of appropriate covariates (adjustment set) and adjusting for their influence can remove confounding bias; however, such a set is typically not identifiable from observational data alone. Experimental data do not have confounding bias, but are typically limited in sample size and can therefore yield imprecise estimates. Furthermore, experimental data often include a limited set of covariates, and therefore provide limited insight into the causal structure of the underlying system. In this work we introduce a method that combines large observational and limited experimental data to identify adjustment sets and improve the estimation of causal effects. The method identifies an adjustment set (if possible) by calculating the marginal likelihood for the experimental data given observationally-derived prior probabilities of potential adjustmen sets. In this way, the method can make inferences that are not possible using only the conditional dependencies and independencies in all the observational and experimental data. We show that the method successfully identifies adjustment sets and improves causal effect estimation in simulated data, and it can sometimes make additional inferences when compared to state-of-the-art methods for combining experimental and observational data.Comment: 10 pages, 5 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

Model selection and local geometry

We consider problems in model selection caused by the geometry of models close to their points of intersection. In some cases---including common classes of causal or graphical models, as well as time series models---distinct models may nevertheless have identical tangent spaces. This has two immediate consequences: first, in order to obtain constant power to reject one model in favour of another we need local alternative hypotheses that decrease to the null at a slower rate than the usual parametric $n^{-1/2}$ (typically we will require $n^{-1/4}$ or slower); in other words, to distinguish between the models we need large effect sizes or very large sample sizes. Second, we show that under even weaker conditions on their tangent cones, models in these classes cannot be made simultaneously convex by a reparameterization. This shows that Bayesian network models, amongst others, cannot be learned directly with a convex method similar to the graphical lasso. However, we are able to use our results to suggest methods for model selection that learn the tangent space directly, rather than the model itself. In particular, we give a generic algorithm for learning Bayesian network models

A Complete Generalized Adjustment Criterion

Covariate adjustment is a widely used approach to estimate total causal effects from observational data. Several graphical criteria have been developed in recent years to identify valid covariates for adjustment from graphical causal models. These criteria can handle multiple causes, latent confounding, or partial knowledge of the causal structure; however, their diversity is confusing and some of them are only sufficient, but not necessary. In this paper, we present a criterion that is necessary and sufficient for four different classes of graphical causal models: directed acyclic graphs (DAGs), maximum ancestral graphs (MAGs), completed partially directed acyclic graphs (CPDAGs), and partial ancestral graphs (PAGs). Our criterion subsumes the existing ones and in this way unifies adjustment set construction for a large set of graph classes.Comment: 10 pages, 6 figures, To appear in Proceedings of the 31st Conference on Uncertainty in Artificial Intelligence (UAI2015

Learning high-dimensional directed acyclic graphs with latent and selection variables

We consider the problem of learning causal information between random variables in directed acyclic graphs (DAGs) when allowing arbitrarily many latent and selection variables. The FCI (Fast Causal Inference) algorithm has been explicitly designed to infer conditional independence and causal information in such settings. However, FCI is computationally infeasible for large graphs. We therefore propose the new RFCI algorithm, which is much faster than FCI. In some situations the output of RFCI is slightly less informative, in particular with respect to conditional independence information. However, we prove that any causal information in the output of RFCI is correct in the asymptotic limit. We also define a class of graphs on which the outputs of FCI and RFCI are identical. We prove consistency of FCI and RFCI in sparse high-dimensional settings, and demonstrate in simulations that the estimation performances of the algorithms are very similar. All software is implemented in the R-package pcalg.Comment: Published in at http://dx.doi.org/10.1214/11-AOS940 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Interpreting and using CPDAGs with background knowledge

We develop terminology and methods for working with maximally oriented partially directed acyclic graphs (maximal PDAGs). Maximal PDAGs arise from imposing restrictions on a Markov equivalence class of directed acyclic graphs, or equivalently on its graphical representation as a completed partially directed acyclic graph (CPDAG), for example when adding background knowledge about certain edge orientations. Although maximal PDAGs often arise in practice, causal methods have been mostly developed for CPDAGs. In this paper, we extend such methodology to maximal PDAGs. In particular, we develop methodology to read off possible ancestral relationships, we introduce a graphical criterion for covariate adjustment to estimate total causal effects, and we adapt the IDA and joint-IDA frameworks to estimate multi-sets of possible causal effects. We also present a simulation study that illustrates the gain in identifiability of total causal effects as the background knowledge increases. All methods are implemented in the R package pcalg.Comment: 17 pages, 6 figures, UAI 201