  Networks are ubiquitous in biology and computational approaches have been
largely investigated for their inference. In particular, supervised machine
learning methods can be used to complete a partially known network by
integrating various measurements. Two main supervised frameworks have been
proposed: the local approach, which trains a separate model for each network
node, and the global approach, which trains a single model over pairs of nodes.
Here, we systematically investigate, theoretically and empirically, the
exploitation of tree-based ensemble methods in the context of these two
approaches for biological network inference. We first formalize the problem of
network inference as classification of pairs, unifying in the process
homogeneous and bipartite graphs and discussing two main sampling schemes. We
then present the global and the local approaches, extending the later for the
prediction of interactions between two unseen network nodes, and discuss their
specializations to tree-based ensemble methods, highlighting their
interpretability and drawing links with clustering techniques. Extensive
computational experiments are carried out with these methods on various
biological networks that clearly highlight that these methods are competitive
with existing methods.
