Searching for Bayesian Network Structures in the Space of Restricted Acyclic Partially Directed Graphs

Although many algorithms have been designed to construct Bayesian network structures using different approaches and principles, they all employ only two methods: those based on independence criteria, and those based on a scoring function and a search procedure (although some methods combine the two). Within the score+search paradigm, the dominant approach uses local search methods in the space of directed acyclic graphs (DAGs), where the usual choices for defining the elementary modifications (local changes) that can be applied are arc addition, arc deletion, and arc reversal. In this paper, we propose a new local search method that uses a different search space, and which takes account of the concept of equivalence between network structures: restricted acyclic partially directed graphs (RPDAGs). In this way, the number of different configurations of the search space is reduced, thus improving efficiency. Moreover, although the final result must necessarily be a local optimum given the nature of the search method, the topology of the new search space, which avoids making early decisions about the directions of the arcs, may help to find better local optima than those obtained by searching in the DAG space. Detailed results of the evaluation of the proposed search method on several test problems, including the well-known Alarm Monitoring System, are also presented

Causal Discovery with Continuous Additive Noise Models

We consider the problem of learning causal directed acyclic graphs from an observational joint distribution. One can use these graphs to predict the outcome of interventional experiments, from which data are often not available. We show that if the observational distribution follows a structural equation model with an additive noise structure, the directed acyclic graph becomes identifiable from the distribution under mild conditions. This constitutes an interesting alternative to traditional methods that assume faithfulness and identify only the Markov equivalence class of the graph, thus leaving some edges undirected. We provide practical algorithms for finitely many samples, RESIT (Regression with Subsequent Independence Test) and two methods based on an independence score. We prove that RESIT is correct in the population setting and provide an empirical evaluation

Application of new probabilistic graphical models in the genetic regulatory networks studies

This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian Network (GN) model with a novel greedy search method. The performances of both models were evaluated on four MAPK pathways in yeast and three simulated data sets. Generally, an IG model provides a sparse graph but a GN model produces a dense graph where more information about gene-gene interactions is preserved. Additionally, we found two key limitations in the prediction of genetic regulatory networks using DNA microarray data, the first is the sufficiency of sample size and the second is the complexity of network structures may not be captured without additional data at the protein level. Those limitations are present in all prediction methods which used only DNA microarray data.Comment: 38 pages, 3 figure

Structural Intervention Distance (SID) for Evaluating Causal Graphs

Causal inference relies on the structure of a graph, often a directed acyclic graph (DAG). Different graphs may result in different causal inference statements and different intervention distributions. To quantify such differences, we propose a (pre-) distance between DAGs, the structural intervention distance (SID). The SID is based on a graphical criterion only and quantifies the closeness between two DAGs in terms of their corresponding causal inference statements. It is therefore well-suited for evaluating graphs that are used for computing interventions. Instead of DAGs it is also possible to compare CPDAGs, completed partially directed acyclic graphs that represent Markov equivalence classes. Since it differs significantly from the popular Structural Hamming Distance (SHD), the SID constitutes a valuable additional measure. We discuss properties of this distance and provide an efficient implementation with software code available on the first author's homepage (an R package is under construction)