When applied to chemistry, atoms can be defined as vertices and chemical bonds can be defined as edges. First, all the atoms and chemical bonds will be embedded as real valued vectors with d-dimensions based on their different types. Since the diversity of atoms (eg: C, N, O, etc.) and bonds (eg: single bonds, double bonds, triple bonds, etc.) in a small molecule is limited, the number of learning parameters are limited. Therefore, a strategy called r-radius sub-graphs was used to avoid this limitation.