SMolLM: Small Language Models Learn Small Molecular Grammar

Language models for molecular design have scaled to hundreds of millions of parameters, yet how they learn chemical grammar is poorly understood. We train SMolLM, a 53K-parameter weight-shared transformer, to generate novel SMILES with 95% validity on the ZINC-250K drug-like-molecule benchmark, outperforming a standard GPT with 10 times more parameters. Mechanistically, the same block resolves SMILES constraints across passes in a fixed order: brackets first, rings second, and valence last, as shown by error classification, linear probing, and sparse autoencoders. A systematic ablation across attention heads and passes further localizes the first bracket-matching step to a single attention head. Together, these results yield a compact, mechanistically interpretable molecular generator and a testbed for studying iterative computation in formal-language domains.

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