This supplementary material is divided as follows: Section 1 has a description about how to simulate Genetic Regulatory Networks and Section 2 explains how to perform these simulations using Netbuilder. Section 3 presents details about the Graphical Gaussian Models and Section 4 presents details about Bayesian Networks. In Section 5 we discuss how the data was pre-processed for our analysis. Section 6 presents the v-structure network, which was used to create simulated data to give some idea of how the network topology influences the different inference methods. In Section 7 we present an overview of all the results. Sections 8 and 9 present tables for comparing the performance between methods. These sections present comparisons for AUC scores and TP scores respectively. Sections 10 and 11 present tables for comparing the performanc
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