DiffTMR: Diffusion-based Hierarchical Alignment for Text-Molecule Retrieval

Molecular retrieval is critical in drug discovery and molecular design. Traditional discriminative methods often model the conditional probability distribution of retrieving candidates, treating the query text as a deterministic input. However, these approaches have notable limitations: (1) They often overlook the statistical properties of the original data distributions of queries and candidates, preventing the recognition of out-of-distribution data. (2) They struggle to balance retrieval accuracy and diversity when processing open-ended semantic queries. To address these challenges, we introduce DiffTMR, a novel framework that reformulates text-molecule retrieval as a reverse denoising process, progressively generating the joint distribution of candidates and queries from noises. DiffTMR uniquely integrates hierarchical diffusion alignment with dynamic perturbation embedding mechanisms. By employing text-anchored perturbations, it enhances the diversity of molecular representations, and through global-local progressive denoising, it achieves cross-modal hierarchical alignment. This leads to significant improvements in retrieval accuracy and out-of-domain generalization. Evaluations on benchmark datasets ChEBI-20 and PCdes demonstrate that DiffTMR surpasses current leading baselines by 4.2%-5.4% in Hits@1 metrics and exhibits superior performance in out-of-domain retrieval tasks.