Higher-Order Molecular Grammars for Generative and Foundation Models in Chemistry

Original description

Molecular learning models are strongly shaped by their underlying representations. Yet standard sequential and graph formalisms struggle to explicitly encode higher-order topology, such as ring systems and recurring motifs. Existing higher-order representations can capture these structures directly, but they are often computationally demanding and difficult to decode into valid molecules. Here, we introduce Higher-order Grammar Representation (HGR), a principled, topology-aware framework that lifts molecules to combinatorial complexes and parses each complex into a compact sequence of producti...