A Comparison of Public Causal Search Packages on Linear, Gaussian Data with No Latent Variables

We compare Tetrad (Java) algorithms to the other public software packages BNT (Bayes Net Toolbox, Matlab), pcalg (R), bnlearn (R) on the \vanilla" task of recovering DAG structure to the extent possible from data generated recursively from linear, Gaussian structure equation models (SEMs) with no latent variables, for random graphs, with no additional knowledge of variable order or adjacency structure, and without additional specification of intervention information. Each one of the above packages offers at least one implementation suitable to this purpose. We compare them on adjacency and orientation accuracy as well as time performance, for fixed datasets. We vary the number of variables, the number of samples, and the density of graph, for a total of 27 combinations, averaging all statistics over 10 runs, for a total of 270 datasets. All runs are carried out on the same machine and on their native platforms. An interactive visualization tool is provided for the reader who wishes to know more than can be documented explicitly in this report.