Graph Algorithms and Deepchem

Deepchem is a module written on top of Rdkit. We’ve built our toolkit with rdkit and tensorflow using 2D SMILES to represent chemical structures. The SMILES can then be fed into machine learning models.

Recently, some groups have found that it is more accurate to represent a molecule as a graph rather than as a 2D SMILES string. Some of the features are lost when you use SMILES strings. When you use graphs, with atoms represented as nodes and bonds represented as edges, there is more information, more features, which translates into more accuracy.