Multi-Modal Constrastive Learning for Chemical Structure Elucidation with VibraCLIP

Abstract

Identifying molecular structures from vibrational spectra is central to chemical analysis but remains challenging due to spectral ambiguity and the limitations of single-modality methods. While deep learning has advanced various spectroscopic characterization techniques, leveraging the complementary nature of infrared (IR) and Raman spectroscopies remains largely underexplored. We introduce VibraCLIP, a contrastive learning framework that embeds molecular graphs, IR and Raman spectra into a shared latent space. A lightweight fine-tuning protocol ensures generalization from theoretical to experimental datasets. VibraCLIP enables accurate, scalable, and data-efficient molecular identification, linking vibrational spectroscopy with structural interpretation. This tri-modal design captures rich structure–spectra relationships, achieving Top-1 retrieval accuracy of 81.7% and reaching 98.9% Top-25 accuracy with molecular mass integration. By integrating complementary vibrational spectroscopic signals with molecular representations, VibraCLIP provides a practical framework for automated spectral analysis, with potential applications in fields such as synthesis monitoring, drug development, and astrochemical detection.