  Graph neural networks (GNNs), which are capable of learning representations
from graphical data, are naturally suitable for modeling molecular systems.
This review introduces GNNs and their various applications for small organic
molecules. GNNs rely on message-passing operations, a generic yet powerful
framework, to update node features iteratively. Many researches design GNN
architectures to effectively learn topological information of 2D molecule
graphs as well as geometric information of 3D molecular systems. GNNs have been
implemented in a wide variety of molecular applications, including molecular
property prediction, molecular scoring and docking, molecular optimization and
de novo generation, molecular dynamics simulation, etc. Besides, the review
also summarizes the recent development of self-supervised learning for
molecules with GNNs.
