SafeMol: Dual-Modality Safety Alignment for Molecular Multimodal Models

Xinmiao Wang, Ruijie Wang, Menghui Wang, Jiawei Chen, Haoyue Deng +3

Molecular multimodal models support diverse understanding and generation tasks but may introduce safety vulnerabilities when handling hazardous molecules. In this work, We reveal substantial jailbreak vulnerabilities under both text-only and graph-conditioned settings. Our analysis further shows that safety robustness must hold across input modalities while balancing safety, over-refusal, and utility. To address these challenges, we construct SafeMolBench, a molecular multimodal safety-alignment benchmark with 3702 samples covering 618 unique hazardous molecules and safe molecular tasks, organized into hazardous-harmful, hazardous-allowed, and utility-replay subsets to support unified training and evaluation of safety, over-refusal, and utility. Based on SafeMolBench, we propose SafeMol, a parameter-efficient safety alignment framework that jointly optimizes lightweight modules across text-only and graph-conditioned inputs, uses MMD for distribution-level representation alignment to reduce modality-induced discrepancies, and explicitly models molecular hazardousness and harmful operational intent. Experiments on SafeMolBench show that SafeMol reduces attack success by several…