Abstract
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-order relational alignment, the model captures both direct enzyme--reaction associations and broader functional organization. We evaluate the approach on enzyme virtual screening and bidirectional enzyme--reaction retrieval tasks. Experiments on EnzymeMap show improved early-recognition performance under BEDROC and enrichment-factor metrics compared with strong contrastive baselines. On ReactZyme, the method achieves consistent gains across time-based, enzyme-similarity, and reaction-similarity splits, demonstrating robustness to unseen enzymes and unseen reactions. Ablation studies further indicate that within-domain alignment, functional supervision, and the geometric regularization term each contribute to the observed improvements. These results suggest that modeling multiple forms of alignment can improve contrastive retrieval models for enzyme discovery, reaction annotation, and related computational biology applications.