Critical Mass: Structure-Disjoint Splits Drift With the Libraries They Are Built On
Molecular machine learning evaluates out-of-distribution performance with structure disjoint splits, a construction rule fixed once at the scale its library happened to have: threshold a pairwise distance, then assign whole connected components to folds. For predicting structures from mass spectra, the field has converged on single-linkage clustering under the myopic Maximum Common Edge Subgraph (MCES) distance at a threshold of 10. This convention was set on 29,000 molecules but public libraries now hold 227,690 molecules. MCES is NP-hard per pair over a quadratically growing set, and so the criterion has never been evaluated at that scale. We propose an optimized version of this criteri...
| Authors | Tomo Oga, Devesh Shah, Cailum M. K. Stienstra et al. |
|---|---|
| Primary category | cs.LG |
| Published | 8 October 2026 |
| Last updated at source | 8 October 2026 |
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