arXiv — cs.AI preprintsInternational19 October 2026
GEMS: Molecular Structure Elucidation as Learned Search over Isomer Graphs
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arXiv:2610.23617v1 Announce Type: new Abstract: Identifying small-molecule structures from molecular formulas and tandem mass spectra remains a bottleneck in untargeted metabolomics and natural-product discovery. Even when database retrieval or de novo prediction misses the exact structure, the resulting candidates can provide starting points for exploring nearby structures through a few bond edits. We introduce GEMS (Guided Editing of Molecular Structures), which refines candidates through learned 2-switch bond edits that preserve the molecular formula and each atom's total valence. GEMS uses
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