Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad

Abstract:Chemical reasoning language models are expected to derive molecular answers through faithful chain-of-thought (CoT). However, across four reasoning model families and twelve chemistry tasks, hallucination is widespread and largely decoupled from answer correctness: correct answers often coexist with fabricated structural claims absent from the relevant molecules. Yet this does not make the reasoning trace computationally irrelevant. Attribution analyses suggest a shared scratchpad function expressed in model-specific forms: Chem-R and ether-0 rely on fragmented SMILES drafts, whereas ChemDFM-R emphasizes scaffold, positional, and naming cues. Notably, perturbing Chem-R's SMILES sketches degrades generation, showing that structural drafts can be causally load-bearing even when verbal structural claims are largely inert. Together, these results show that chemical CoT is neither a faithful explanation nor merely a post-hoc rationalization, but a hallucination-prone molecular scratchpad. This finding cautions against treating CoT as direct evidence of faithful reasoning and motivates process-level supervision beyond answer-only evaluation.

Computational Engineering, Finance, and Science (cs.CE); Computation and Language (cs.CL)

arXiv:2607.20935 [cs.CE]

(or arXiv:2607.20935v1 [cs.CE] for this version)

https://doi.org/10.48550/arXiv.2607.20935 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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