We consider the problem of learning a causal graph in the presence of measurement error. This setting is for example common in genomics, where gene expression is corrupted through the measurement process. We develop a provably consistent procedure for estimating the causal structure in a linear Gaussian structural equation model from corrupted observations on its nodes, under a variety of measurement error models. We provide an estimator based on the method-of-moments, which can be used in conjunction with constraint-based causal structure discovery algorithms. We prove asymptotic consistency of the procedure and also discuss finite-sample considerations. We demonstrate our method's performance through simulations and on real data, where we recover the underlying gene regulatory network from zero-inflated single-cell RNA-seq data.
In the presence of latent variables, identifiability is further weakened (only the so-called PAG is identifiable) and various algorithms have been developed for learning a PAG @cite_13 @cite_22 @cite_4 @cite_19 . However, these algorithms cannot estimate causal relations among the latent variables, which is our problem of interest. @cite_28 study identifiability of directed Gaussian graphical models in the presence of a single latent variable. @cite_6 , @cite_21 , @cite_26 and @cite_23 all consider the problem of learning causal edges among latent variables from the observed variables, i.e. models as in Figure a or generalizations thereof, but under assumptions that may not hold for our applications of interest, namely that the measurement error is independent of the latent variables @cite_6 , that the observed variables are a linear function of the latent variables @cite_21 , that the observed variables are binary @cite_26 , or that each latent variable is non-Gaussian with sufficient outgoing edges to guarantee identifiability @cite_23 .
@cite_26 @cite_4 @cite_22 @cite_28 @cite_21 @cite_6 @cite_19 @cite_23 @cite_13
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We present a semi-supervised learning algorithm for learning discrete factor analysis models with arbitrary structure on the latent variables. Our algorithm assumes that every latent variable has an "anchor", an observed variable with only that latent variable as its parent. Given such anchors, we show that it is possible to consistently recover moments of the latent variables and use these moments to learn complete models. We also introduce a new technique for improving the robustness of method-of-moment algorithms by optimizing over the marginal polytope or its relaxations. We evaluate our algorithm using two real-world tasks, tag prediction on questions from the Stack Overflow website and medical diagnosis in an emergency department. We study parameter identifiability of directed Gaussian graphical models with one latent variable. In the scenario we consider, the latent vari- able is a confounder that forms a source node of the graph and is a parent to all other nodes, which correspond to the observed variables. We give a graphical condition that is sufficient for the Jacobian matrix of the parametrization map to be full rank, which entails that the parametrization is generically finite-to- one, a fact that is sometimes also referred to as local identifiability. We also derive a graphical condition that is necessary for such identifiability. Finally, we give a condition under which generic parameter identifiability can be deter- mined from identifiability of a model associated with a subgraph. The power of these criteria is assessed via an exhaustive algebraic computational study on models with 4, 5, and 6 observable variables. We describe anytime search procedures that (1) find disjoint subsets of recorded variables for which the members of each subset are d-separated by a single common unrecorded cause, if such exists; (2) return information about the causal relations among the latent factors so identified. We prove the procedure is point-wise consistent assuming (a) the causal relations can be represented by a directed acyclic graph (DAG) satisfying the Markov Assumption and the Faithfulness Assumption; (b) unrecorded variables are not caused by recorded variables; and (c) dependencies are linear. We compare the procedure with standard approaches over a variety of simulated structures and sample sizes, and illustrate its practical value with brief studies of social science data sets. Finally, we consider generalizations for non-linear systems. Measurement error in the observed values of the variables can greatly change the output of various causal discovery methods. This problem has received much attention in multiple fields, but it is not clear to what extent the causal model for the measurement-error-free variables can be identified in the presence of measurement error with unknown variance. In this paper, we study precise sufficient identifiability conditions for the measurement-error-free causal model and show what information of the causal model can be recovered from observed data. In particular, we present two different sets of identifiability conditions, based on the second-order statistics and higher-order statistics of the data, respectively. The former was inspired by the relationship between the generating model of the measurement-error-contaminated data and the factor analysis model, and the latter makes use of the identifiability result of the over-complete independent component analysis problem. Causal discovery becomes especially challenging when the possibility of latent confounding and or selection bias is not assumed away. For this task, ancestral graph models are particularly useful in that they can represent the presence of latent confounding and selection effect, without explicitly invoking unobserved variables. Based on the machinery of ancestral graphs, there is a provably sound causal discovery algorithm, known as the FCI algorithm, that allows the possibility of latent confounders and selection bias. However, the orientation rules used in the algorithm are not complete. In this paper, we provide additional orientation rules, augmented by which the FCI algorithm is shown to be complete, in the sense that it can, under standard assumptions, discover all aspects of the causal structure that are uniquely determined by facts of probabilistic dependence and independence. The result is useful for developing any causal discovery and reasoning system based on ancestral graph models. This work considers the problem of learning linear Bayesian networks when some of the variables are unobserved. Identifiability and efficient recovery from low-order observable moments are established under a novel graphical constraint. The constraint concerns the expansion properties of the underlying directed acyclic graph (DAG) between observed and unobserved variables in the network, and it is satisfied by many natural families of DAGs that include multi-level DAGs, DAGs with effective depth one, as well as certain families of polytrees. 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.