Fig. 1.

Example graph representation for acetic acid. a Graph representation of acetic acid with nodes numbered from one to four. b Example adjacency matrix, A, for an acetic acid graph with the corresponding node ordering on the left. c Example node features matrix, X, which one-hot encodes a few selected properties. d Example edge features matrix, E, where each edge feature vector is a one-hot encoding of single, double, or triple bonds. “Implicit Hs” stands for the number of implicit hydrogens on a given node