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Life sciences · Preprint
arXiv · October 21, 2026
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While Chain-of-Thought (CoT) prompting improves the reasoning performance of large language models (LLMs), recent studies have shown that final answers do not always depend on the generated rationales. In particular, LLMs may rely on query-specific shortcuts rather than the information provided by their reasoning steps. In this paper, we investigate whether context-aware decoding (CAD), an existing contrastive decoding method, can mitigate such shortcut behavior when applied to CoT reasoning. We study this application as Rationale Contrastive Decoding (RCD), which contrasts the next-token distributions conditioned on the query with and without its rationale, amplifying tokens whose likelihood increases due to the rationale. We provide a theoretical interpretation of this decoding rule via a KL-regularized reward-maximization objective. Experiments across five reasoning benchmarks demonstrate that RCD improves answer accuracy over standard CoT. Furthermore, intervention analyses using ground-truth and random rationales reveal that RCD increases the behavioral dependence of final answers on the rationale content. Our findings suggest that contrastive decoding offers a simple, training-free approach to mitigating query shortcuts.