A Multimodal Representation Learning Framework for Molecular Graph and NMR Spectrum Alignment

Accurate matching between molecular structures and NMR spectra is an important task in automated structure elucidation. However, existing methods still face difficulties in jointly modeling multi-scale molecular topology and effectively exploiting the complementary information provided by paired 1H and 13C NMR spectra. To address these limitations, we propose SpecMol-MatchNet, a multimodal matching framework that integrates a hybrid molecular graph encoder, branch-specific spectral feature learning, and residual multimodal fusion. In the molecular branch, attention-based graph interaction is combined with multi-scale neighborhood aggregation to capture structural cues at different receptive fields. In the spectral branch, branch-specific attention enhancement and joint gating are introduced to better exploit the complementary characteristics of paired 1H and 13C spectra. The resulting molecular and spectral representations are integrated through a residual fusion module for final matching prediction. Experimental results on benchmark datasets demonstrate that SpecMol-MatchNet achieves consistently better overall performance than representative baseline methods.