Towards Atoms of Large Language Models

The fundamental representational units (FRUs) of large language models (LLMs) remain undefined, limiting further understanding of their underlying mechanisms. In this paper, we introduce ***Atom Theory*** to systematically define, evaluate, and identify such FRUs, which we term atoms. Building on the atomic inner product (AIP), a non-Euclidean metric that captures the underlying geometry of LLM representations, we formally define atoms and propose two key criteria for ideal atoms: faithfulness ( $ R^2 $ ) and stability ( $ q^{\star} $ ). We further prove that atoms are identifiable under threshold-activated sparse autoencoders (TSAEs). Empirically, we uncover a pervasive representation shift in LLMs and demonstrate that the AIP corrects this shift to capture the underlying representational geometry, thereby grounding Atom Theory. We find that two widely used units, neurons and features, fail to qualify as ideal atoms: neurons are faithful ( $ R^2=1 $ ) but unstable ( $ q^{\star}=0.5 $% ), while features are more stable ( $ q^{\star}=68.2 $% ) but unfaithful ( $ R^2=48.8 $% ). To find atoms of LLMs, leveraging atom identifiability under TSAEs, we show via large-scale experiments that reliable atom identification occurs only when the TSAE capacity matches the data scale. Guided by this insight, we identify FRUs with near-perfect faithfulness ( $ R^2=99.9 $% ) and stability ( $ q^{\star}=99.8 $% ) across layers of Gemma2-2B, Gemma2-9B, and Llama3.1-8B, satisfying the criteria of ideal atoms statistically. Further analysis confirms that these atoms align with theoretical expectations and exhibit substantially higher monosemanticity. Overall, we propose and validate Atom Theory as a foundation for understanding the internal representations of LLMs.

Large language models are powerful, but we still do not know what their basic “pieces of meaning” are. This makes it hard to understand how they store ideas, facts, or concepts inside the model. We propose Atom Theory, a way to find these basic pieces, which we call atoms. A good atom should do two things: it should accurately explain the model’s internal activity, and it should stay clear when the model sees different text. We show that commonly studied units, such as neurons and learned features, do not fully satisfy both requirements. We then develop a method to find better atoms in Gemma and Llama models. These atoms are much more accurate, stable, and easier to connect to single human-understandable ideas. This work gives a clearer way to look inside large language models and may help make them easier to understand, analyze, and trust.