The Molecular Structure of Thought: Mapping the Topology of Long Chain-of-Thought Reasoning

Qiguang Chen, Yantao Du, Ziniu Li, Jinhao Liu, Songyao Duan, Jiarui Guo, minghao, Jiaheng Liu, Tong Yang, Ge Zhang, Libo Qin, Wanxiang Che, Wenhao Huang

The Molecular Structure of Thought: Mapping the Topology of Long Chain-of-Thought Reasoning: 49 upvotes on Hugging Face Daily Papers, #4 of 31 papers on 2026-01-12. Day-by-day upvote history. It lost 11 votes when the Hub removed votes in bulk.

Large language models (LLMs) often fail to learn effective long chain-of-thought (Long CoT) reasoning from human or non-Long-CoT LLMs imitation. To understand this, we propose that effective and learnable Long CoT trajectories feature stable molecular-like structures in unified view, which are formed by three interaction types: Deep-Reasoning (covalent-like), Self-Reflection (hydrogen-bond-like), and Self-Exploration (van der Waals-like). Analysis of distilled trajectories reveals these structures emerge from Long CoT fine-tuning, not keyword imitation. We introduce Effective Semantic Isomers and show that only bonds promoting fast entropy convergence support stable Long CoT learning, while structural competition impairs training. Drawing on these findings, we present Mole-Syn, a distribution-transfer-graph method that guides synthesis of effective Long CoT structures, boosting performance and RL stability across benchmarks.

Paper page on Hugging Face · arXiv

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