Recent LLMs exhibit limited effectiveness on molecular property prediction task due to the semantic gap between molecular representations and natural language, as well as the lack of domain-specific knowledge. To address these challenges, we propose MolRAG, a Retrieval-Augmented Generation framework integrating Chain-of-Thought reasoning for molecular property prediction. MolRAG operates by retrieving structurally analogous molecules as contextual references to guide stepwise knowledge reasoning through chemical structure-property relationships. This dual mechanism synergizes molecular similarity analysis with structured inference, while generating human-interpretable rationales grounded in domain knowledge. Experimental results show MolRAG outperforms pre-trained LLMs on four datasets, and even matches supervised methods, achieving performance gains of 1.1%–45.7% over direct prediction approaches, demonstrating versatile effectiveness. Our code is available at https://github.com/AcaciaSin/MolRAG.

Large language models (LLMs) achieve strong performance on plain text tasks but underperform on structured data like tables and databases. Potential challenges arise from their underexposure during pre-training and rigid text-to-structure transfer mechanisms. Unlike humans who seamlessly apply learned patterns across data modalities, LLMs struggle to infer implicit relationships embedded in tabular formats, especially in the absence of explicit structural guidance. To bridge this cognitive gap, we introduce Contrastive Retrieval-Augmented Generation on Experience (CoRE), a framework that builds experience memory representations and enhances generalization through contrastive In-Context Learning (ICL) to simulate human-like knowledge transfer. Experiments on Text-to-SQL and TableQA show CoRE significantly improves performance, achieving average gains of 3.44% and 4.24%, with up to 17.2% on challenging tasks. Our Monte Carlo Tree Search (MCTS)-generated Experience Memory expands training data 8-9×, enhancing diversity and domain coverage. This training-free and continual method propels LLMs toward structured knowledge expertise.