In a molecular graph, atoms are nodes and bonds are edges. Edges carry spatial-distance information, while three-dimensional orientation is encoded through pairwise relationships. Message-passing neural networks use edges to pass learned messages between connected atoms. section 7.3.2
Physical and virtual edges
A bond links atoms that are connected in the molecule. To help information travel farther in fewer message-passing rounds, a model can add virtual edges between originally unconnected atoms. Distinct labels or weights mark these added connections as different from physical bonds. section 7.3.2
