For example, the most-used text representation of molecules, SMILES, are a string-encoding of the depth-first tree traversal of the molecular graph retaining all topological information and, in the case of isomeric SMILES, geometrical information pertaining to stereochemistry . The same applies to molecular fingerprints, which often even explicitly encode topological features . Meanwhile, the molecular graph introduces implicit constraints on the molecular 3D geometry, as topology and atom types induce structure. Conversely, representing a molecule as a graph often only encapsulates an approximation of molecular topology and geometry, as only a subset of chemical bonds, the covalent Molecular Set Representation Learning bonds, can be represented in this static data structure. However, in addition to covalent bonds, molecules and substances used as drugs or materials also contain ionic and metallic bonds generally not well represented in molecular graphs.