Chapter 11. Junction Tree Variational Autoencoder for Molecular Graph Generation

We seek to develop computational methods to accelerate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generative modeling to molecular translation with the goal of discovering new compounds with desired properties. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.