Preprint—not peer reviewed
Physics-Based Molecular Fingerprints from Spectral Graph Theory Provide Efficient Geometry-Aware Measures of Chemical Similarity
The authors construct fixed-length molecular fingerprints from spectral graph theory using three-dimensional interaction-weighted graphs. The authors report strong benchmark performance across organic, inorganic, biological, reticular, and reaction-chemistry datasets while distinguishing structures with identical two-dimensional connectivity. This matters because an interpretable representation of three-dimensional similarity could scale beyond pairwise descriptors without depending on learned embedding coverage.
AI–chemistryAI–materials Materials representationMolecular representation