Extended Data Fig. 3: Dynamics of BIONIC feature space through training.

Comparison of pairwise gene similarities (cosine similarity in the case of BIONIC, direct binary adjacency in the case of the network), as defined by IntAct Complexes for known co-complex relationships (positive pairs) and no co-complex relationships (negative pairs), between a yeast PPI network (as used in the Fig. 2 analyses) and the unsupervised BIONIC features produced from this network. The BIONIC similarities are shown throughout the training process (epochs), whereas the input network is constant so its pairwise similarities do not change. ‘Network’ denotes the input PPI network, ‘BIONIC’ denotes the features learned from this network using BIONIC.