Beyond Expression Similarity: Contrastive Learning Recovers Functional Gene Associations from Protein Interaction Structure

The Predictive Associative Memory (PAM) framework posits that useful relationships often connect items that co-occur in shared contexts rather than items that appear similar in embedding space. A contrastive MLP trained on co-occurrence annotations--Contrastive Association Learning (CAL)--has improved multi-hop passage retrieval and discovered narrative function at corpus scale in text. We test whether this principle transfers to molecular biology, where protein-protein interactions provide functional associations distinct from gene expression similarity. Four experiments across two biological domains map the operating envelope. On gene perturbation data (Replogle K562 CRISPRi, 2,285 gene...

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