$\text{GSF-}\chi$: Global Stereochemical Fields for Chiral Graph Transformers

Abstract:Enantiomers share atoms, bonds, and pairwise distances yet can behave differently in chiral environments, so molecular encoders must respect atom relabelings and proper rotations without becoming blind to reflection. We introduce GSF-$\chi$, a graph transformer in which stereogenic units modulate all pairwise interactions rather than single out one atom as special. Each central or axial stereogenic unit creates a reflection-even phase field over all atoms, a handedness pseudoscalar $\chi$ sets the direction of a relative rotation on latent query--key blocks, giving a \textbf{Chiral-RoPE} that reflection inverts rather than leaves fixed. A $C_2$ projection separates mirror-even ECD peak counts and positions from mirror-odd peak signs. We prove the operator's even--odd decomposition and its annotation-inversion, permutation, and unit-order identities under explicit canonical-role conditions; property tests and a coordinate-reflection audit verify the laws end to end. GSF-$\chi$ leads every central-ECD output and improves axial Rotation and Symbol by $12.6\%$ and $7.9\%$ over the strongest baseline. Equal-budget controls attribute the Rotation advantage to global signed support rather than parameter or edge count; the $C_2$ projection yields exact enantiomer-pair consistency at a small raw-accuracy cost under complete supervision and becomes predictive when mirror supervision is scarce.

Machine Learning (cs.LG)

arXiv:2609.12532 [cs.LG]

(or arXiv:2609.12532v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2609.12532 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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