Tiered Latent Representations and Latent Spaces for Molecular Graphs

Abstract

Molecular graphs generally contain subgraphs (known as groups) that are identifiable and significant in composition, functionality, geometry, etc. Flat latent representations (node embeddings or graph embeddings) fail to represent, and support the use of, groups. Fully hierarchical latent representations, on the other hand, are difficult to learn and, even if learned, may be too complex to use or interpret. We propose tiered latent representations and latent spaces for molecular graphs as a simple way to explicitly represent and utilize groups, which consist of the atom (node) tier, the group tier and the molecule (graph) tier. Specifically, we propose an architecture for learning tiered latent representations and latent spaces using graph autoencoders, graph neural networks, differentiable group pooling and the membership matrix. We discuss its various components, major challenges and related work, for both a deterministic and a probabilistic model. We also briefly discuss the usage and exploration of tiered latent spaces. The tiered approach is applicable to other types of structured graphs similar in nature to molecular graphs.

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Cited by in corpus (3)

• Bayesian Hyperparameter Optimization with BoTorch, GPyTorch and Ax
• Tiered Graph Autoencoders with PyTorch Geometric for Molecular Graphs
• An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design