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arXiv · 2606.23443

What Does a Chemical Language Model Know About Molecules?

Christian Kenneth·Etowah Adams·Liam Bai·Gerard JP van Westen
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Abstract

Chemical language models (cLMs) are widely assumed to learn surface-level syntactic patterns rather than learning meaningful molecular semantics. Here, we apply sparse autoencoders (SAEs) to MolFormer, an encoder-only cLM, to mechanistically examine how molecular representations are built across layers. We discover that early layers rely on position-tracking latents to parse molecular grammar, while later layers encode atom-in-substructure and pharmacologically relevant features. Additionally, we show that non-canonical SMILES produce more disruptive representation shifts than invalid SMILES, driven by position-latent disruption propagating across layers. To support further exploration, we develop InterMol, an interactive visualizer for SAE activations on molecular strings and structures.

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Christian Kenneth, Etowah Adams, Liam Bai, Gerard JP van Westen. 2026-06-22. What Does a Chemical Language Model Know About Molecules?. https://arxiv.org/abs/2606.23443

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