title: Molecular graph convolutions: moving beyond fingerprints.
abstract: Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph-atoms, bonds, distances, etc.-which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.
authors: Stanford University, 318 Campus Dr. S296, Stanford, CA, 94305, USA. kearnes@stanford.edu.
authors: Steven
authors: 0000-0003-4579-4388
authors: S
authors: Kearnes
authors: Google Inc., 1600 Amphitheatre Pkwy, Mountain View, CA, 94043, USA.
authors: Kevin
authors: K
authors: McCloskey
authors: Google Inc., 1600 Amphitheatre Pkwy, Mountain View, CA, 94043, USA.
authors: Marc
authors: M
authors: Berndl
authors: Stanford University, 318 Campus Dr. S296, Stanford, CA, 94305, USA.
authors: Vijay
authors: V
authors: Pande
authors: Google Inc., 1600 Amphitheatre Pkwy, Mountain View, CA, 94043, USA.
authors: Patrick
authors: P
authors: Riley
mesh_terms: D003196:Computer Graphics; D017076:Computer-Aided Design; D015195:Drug Design; D008024:Ligands; D000069550:Machine Learning; D015394:Molecular Structure; D016571:Neural Networks, Computer; D004364:Pharmaceutical Preparations / Q000737:chemistry
chemical_list: D008024:Ligands; D004364:Pharmaceutical Preparations
keywords: Artificial neural networks; Deep learning; Machine learning; Molecular descriptors; Virtual screening