Towards Knowledge‑and‑Data‑Driven Organic Reaction Prediction: RAG‑Enhanced and Reasoning‑Powered Hybrid System with LLMs

Abstract

In organic reaction prediction, many recent approaches ranging from traditional task-specific models to Large Language Models (LLMs), have demonstrated notable success. However, these methods are inherently data-driven, exhibit constrained interpretability, and have hit fundamental performance bottlenecks. To overcome these limitations, we present Reaction-Thinker, a hybrid, knowledge‑and-data‑driven system that is enhanced by Retrieval‑Augmented Generation (RAG) and powered by advanced reasoning, improving both the interpretability of prediction process and the explainability of results. We develop similar-case retrieval database and train a RAG‑based LLM through supervised fine-tuning (SFT) to apply both reaction types and similar reaction cases as knowledge. We also construct a reaction reasoning chain-of-thought (CoT) dataset and train a reasoning-based LLM through SFT, then further optimize it using Group Relative Policy Optimization (GRPO). Experimental results show that our method outperforms all compared LLMs and task-specific models, achieving the highest accuracy (Exact Match) and fingerprint similarity (FTS). Ablation study indicates improvements in relative accuracy of 7.5% and 13.9% for RAG and GRPO, respectively. Further analysis of mispredictions reveals limitations in conventional evaluation metrics, which motivates our proposed benchmarking refinement.