MolSpecFlow: Mass-Constrained Hybrid Flow Matching for Joint Molecular-Spectral Analysis

Abstract Identifying the “dark matter” of the chemical universe requires bridging the fundamental gap between molecules and mass spectra. Existing approaches struggle to accurately map between these distinct data formats, often yielding results that are either chemically implausible or inconsistent with the physical evidence. We introduce MolSpecFlow, a unified foundation model pretrained on 100 million molecules and 42 million spectra, which leverages a hybrid flow matching framework to orchestrate optimal transport paths for spectral peaks and discrete probability flows for molecular tokens. Furthermore, to guarantee the physicochemical validity of the generated structures, we incorporate explicit rule-based constraints into the generative process, utilizing a token-level mass control mechanism that strictly enforces alignment with the precursor molecular weight. MolSpecFlow establishes a new state-of-the-art on the MassSpecGym benchmark, surpassing diffusion and retrieval baselines in de novo generation (Top-1 accuracy +35%), spectral simulation, and molecular retrieval, demonstrating the power of physics-grounded unified modeling. Competing Interest Statement The authors have declared no competing interest.