Tracking Time-varying Graphical Structure

Neural Information Processing Systems

Structure learning algorithms for graphical models have focused almost exclusively on stable environments in which the underlying generative process does not change; that is, they assume that the generating model is globally stationary. In real-world environments, however, such changes often occur without warning or signal. Real-world data often come from generating models that are only locally stationary. In this paper, we present LoSST, a novel, heuristic structure learning algorithm that tracks changes in graphical model structure or parameters in a dynamic, real-time manner. We show by simulation that the algorithm performs comparably to batch-mode learning when the generating graphical structure is globally stationary, and significantly better when it is only locally stationary.

Comparative Benchmarking of Causal Discovery Techniques Machine Learning

In this paper we present a comprehensive view of prominent causal discovery algorithms, categorized into two main categories (1) assuming acyclic and no latent variables, and (2) allowing both cycles and latent variables, along with experimental results comparing them from three perspectives: (a) structural accuracy, (b) standard predictive accuracy, and (c) accuracy of counterfactual inference. For (b) and (c) we train causal Bayesian networks with structures as predicted by each causal discovery technique to carry out counterfactual or standard predictive inference. We compare causal algorithms on two pub- licly available and one simulated datasets having different sample sizes: small, medium and large. Experiments show that structural accuracy of a technique does not necessarily correlate with higher accuracy of inferencing tasks. Fur- ther, surveyed structure learning algorithms do not perform well in terms of structural accuracy in case of datasets having large number of variables.

Learning Functional Causal Models with Generative Neural Networks Machine Learning

We introduce a new approach to functional causal modeling from observational data. The approach, called Causal Generative Neural Networks (CGNN), leverages the power of neural networks to learn a generative model of the joint distribution of the observed variables, by minimizing the Maximum Mean Discrepancy between generated and observed data. An approximate learning criterion is proposed to scale the computational cost of the approach to linear complexity in the number of observations. The performance of CGNN is studied throughout three experiments. First, we apply CGNN to the problem of cause-effect inference, where two CGNNs model $P(Y|X,\textrm{noise})$ and $P(X|Y,\textrm{noise})$ identify the best causal hypothesis out of $X\rightarrow Y$ and $Y\rightarrow X$. Second, CGNN is applied to the problem of identifying v-structures and conditional independences. Third, we apply CGNN to problem of multivariate functional causal modeling: given a skeleton describing the dependences in a set of random variables $\{X_1, \ldots, X_d\}$, CGNN orients the edges in the skeleton to uncover the directed acyclic causal graph describing the causal structure of the random variables. On all three tasks, CGNN is extensively assessed on both artificial and real-world data, comparing favorably to the state-of-the-art. Finally, we extend CGNN to handle the case of confounders, where latent variables are involved in the overall causal model.

Mixed Graphical Models for Causal Analysis of Multi-modal Variables Machine Learning

Graphical causal models are an important tool for knowledge discovery because they can represent both the causal relations between variables and the multivariate probability distributions over the data. Once learned, causal graphs can be used for classification, feature selection and hypothesis generation, while revealing the underlying causal network structure and thus allowing for arbitrary likelihood queries over the data. However, current algorithms for learning sparse directed graphs are generally designed to handle only one type of data (continuous-only or discrete-only), which limits their applicability to a large class of multi-modal biological datasets that include mixed type variables. To address this issue, we developed new methods that modify and combine existing methods for finding undirected graphs with methods for finding directed graphs. These hybrid methods are not only faster, but also perform better than the directed graph estimation methods alone for a variety of parameter settings and data set sizes. Here, we describe a new conditional independence test for learning directed graphs over mixed data types and we compare performances of different graph learning strategies on synthetic data.

ParallelPC: an R package for efficient constraint based causal exploration Machine Learning

Discovering causal relationships from data is the ultimate goal of many research areas. Constraint based causal exploration algorithms, such as PC, FCI, RFCI, PC-simple, IDA and Joint-IDA have achieved significant progress and have many applications. A common problem with these methods is the high computational complexity, which hinders their applications in real world high dimensional datasets, e.g gene expression datasets. In this paper, we present an R package, ParallelPC, that includes the parallelised versions of these causal exploration algorithms. The parallelised algorithms help speed up the procedure of experimenting big datasets and reduce the memory used when running the algorithms. The package is not only suitable for super-computers or clusters, but also convenient for researchers using personal computers with multi core CPUs. Our experiment results on real world datasets show that using the parallelised algorithms it is now practical to explore causal relationships in high dimensional datasets with thousands of variables in a single multicore computer. ParallelPC is available in CRAN repository at