Collaborative Drug Discovery, Inc. (CDD) is a cheminformatics company that has been developing an automated drug discovery application to identify molecules predicted to be safe and effective drugs. CDD’s existing approach represents molecules as a sequence of characters. This character string representation contains artifacts that do not reflect chemical properties of the molecule, thereby obfuscating the real chemical properties that the model must learn. The team has investigated, prototyped, and tested two molecule generation models that represent the molecule as a graph rather than as a character string. With these models, the team has been able to generate chemically valid novel molecules.