Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval
arXiv:2512.08508v2 Announce Type: replace-cross Abstract: Identifying enzymes that catalyze target biochemical reactions is a key step in computational enzyme discovery and biocatalyst design. Recent representation-learning methods formulate this problem as enzyme--reaction matching, where paired enzymes and reactions are embedded into a shared space. However, most existing approaches primarily rely on pairwise enzyme--reaction supervision and make limited use of the relationships within reaction sets or enzyme families. This work introduces a multi-alignment contrastive learning framework for biochemical retrieval. The framework jointly models cross-domain compatibility between enzymes and reactions and within-domain relationships induced by functional annotations. In addition, a Gromov--Wasserstein-inspired regularization objective encourages geometric consistency between the learned enzyme and reaction representation spaces. By combining pairwise catalytic supervision with higher-or