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Predicting Collision Cross Sections with GRACE: Geometric Residual Adduct Conditioning via Early-fusion

arXiv · AI, language, vision and robotics · article · Sep 10, 2026 · UTC

Collision cross section (CCS), derived from ion mobility mass spectrometry, is a common descriptor for molecular annotation. Prediction is challenging for machine learning models because it reflects the size, shape, and ionization state of a gas-phase molecular ion. Most predictors either ignore explicit 3D structure or treat adduct identity as a late categorical feature, which limits their ability to capture adduct-dependent geometric effects. We present GRACE (Geometric Residual Adduct Conditioning via Early-fusion), a 3D CCS predictor that adapts a pretrained molecular geometry encoder usin

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