Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery

Jiatong LI, Weida Wang, Qinggang Zhang, Junxian Li, Di Zhang, Changmeng Zheng, Shufei Zhang, Xiaoyong Wei, Li Qing

Keywords: Long CoT Reasoning, Large Language Models, Text-based Molecule Discovery

Abstract:

Large language models (LLMs), especially Explicit Long Chain-of-Thought (CoT) reasoning models like DeepSeek-R1 and QWQ, have demonstrated powerful reasoning capabilities, achieving impressive performance in commonsense reasoning and mathematical inference. Despite their effectiveness, Long-CoT reasoning models are often criticized for their limited ability and low efficiency in knowledge-intensive domains such as molecule discovery. Success in this field requires a precise understanding of domain knowledge, including molecular structures and chemical principles, which is challenging due to the inherent complexity of molecular data and the scarcity of high-quality expert annotations. To bridge this gap, we introduce **Mol-R1**, a novel framework designed to improve explainability and reasoning performance of R1-like Explicit Long-CoT reasoning LLMs in text-based molecule generation.
Our approach begins with a high-quality reasoning dataset curated through **P**rior **R**egulation via **I**n-context **D**istillation (**PRID**), a dedicated distillation strategy to effectively generate paired reasoning traces guided by prior regulations. Building upon this, we introduce **MoIA**, **Mo**lecular **I**terative **A**daptation, a sophisticated training strategy that iteratively combines Supervised Fine-tuning (SFT) with Reinforced Policy Optimization (RPO), tailored to boost the reasoning performance of R1-like reasoning models for molecule discovery.
Finally, we examine the performance of Mol-R1 in the text-based molecule reasoning generation task, showing superior performance against existing baselines.

Primary Area: generative models

Submission Number: 6123