Unlocking High-Fidelity Molecular Generation from Mass Spectra via Dual-Stream Line Graph Diffusion

ArXi:2605.07048v1 Announce Type: cross De novo molecular generation from tandem mass spectra is a challenging inverse problem whose core difficulty lies in the circular dependency between atom-level and bond-level reasoning: determining a bond's type requires knowing its endpoint atoms' chemical environment, yet an atom's environment is in turn defined by its incident bonds. Existing graph diffusion methods process atoms and bonds within a single computation stream, where atom-bond information synchronization can only occur implicitly across layers.