Deep Learning for Molecular Graphs with Tiered Graph Autoencoders and Graph Prediction
This work addresses the need for interpretable and efficient deep learning methods in computational chemistry, though it appears incremental as it builds on existing graph autoencoder and prediction techniques.
The paper tackles the problem of learning hierarchical representations for molecular graphs by introducing tiered graph autoencoders that capture atom, group, and molecule tiers, and applies them with graph prediction for tasks like property prediction on the QM9 dataset, showing that functional and ring groups effectively represent chemical structures.
Tiered graph autoencoders provide the architecture and mechanisms for learning tiered latent representations and latent spaces for molecular graphs that explicitly represent and utilize groups (e.g., functional groups). This enables the utilization and exploration of tiered molecular latent spaces, either individually - the node (atom) tier, the group tier, or the graph (molecule) tier - or jointly, as well as navigation across the tiers. In this paper, we discuss the use of tiered graph autoencoders together with graph prediction for molecular graphs. We show features of molecular graphs used, and groups in molecular graphs identified for some sample molecules. We briefly review graph prediction and the QM9 dataset for background information, and discuss the use of tiered graph embeddings for graph prediction, particularly weighted group pooling. We find that functional groups and ring groups effectively capture and represent the chemical essence of molecular graphs (structures). Further, tiered graph autoencoders and graph prediction together provide effective, efficient and interpretable deep learning for molecular graphs, with the former providing unsupervised, transferable learning and the latter providing supervised, task-optimized learning.