Learning Molecular Chirality via Chiral Determinant Kernels

arXiv:2602.07415v2 Announce Type: replace Abstract: Chirality is a fundamental molecular property that governs stereospecific behavior in chemistry and biology. Capturing chirality in machine learning models remains challenging due to the geometric complexity of stereochemical relationships and the limitations of traditional molecular representations that often lack explicit stereochemical encoding. Existing approaches to chiral molecular representation primarily focus on central chirality, relying on handcrafted stereochemical tags or limited 3D encodings, and thus fail to generalize to more complex forms such as axial chirality. In this work, we introduce ChiDeK (Chiral Determinant Kernels), a framework that systematically integrates stereogenic information into molecular representation learning. We propose the chiral determinant kernel to encode the SE(3)-invariant chirality product and employ cross-attention to integrate stereochemical information from local chiral centers into the global molecular representation. This design enables explicit modeling of chiral-related features within a unified architecture, capable of jointly encoding central and axial chirality. To support the evaluation of axial chirality, we construct a new benchmark for electronic circular dichroism (ECD) and optical rotation (OR) prediction. Across four tasks, including R/S configuration classification, enantiomer ranking, ECD spectrum prediction, and OR prediction, ChiDeK achieves substantial improvements over state-of-the-art baselines, most notably yielding over 7% higher accuracy on axially chiral tasks on average.

Abstract:Chirality is a fundamental molecular property that governs stereospecific behavior in chemistry and biology. Capturing chirality in machine learning models remains challenging due to the geometric complexity of stereochemical relationships and the limitations of traditional molecular representations that often lack explicit stereochemical encoding. Existing approaches to chiral molecular representation primarily focus on central chirality, relying on handcrafted stereochemical tags or limited 3D encodings, and thus fail to generalize to more complex forms such as axial chirality. In this work, we introduce ChiDeK (Chiral Determinant Kernels), a framework that systematically integrates stereogenic information into molecular representation learning. We propose the chiral determinant kernel to encode the SE(3)-invariant chirality product and employ cross-attention to integrate stereochemical information from local chiral centers into the global molecular representation. This design enables explicit modeling of chiral-related features within a unified architecture, capable of jointly encoding central and axial chirality. To support the evaluation of axial chirality, we construct a new benchmark for electronic circular dichroism (ECD) and optical rotation (OR) prediction. Across four tasks, including R/S configuration classification, enantiomer ranking, ECD spectrum prediction, and OR prediction, ChiDeK achieves substantial improvements over state-of-the-art baselines, most notably yielding over 7% higher accuracy on axially chiral tasks on average.

Machine Learning (cs.LG); Artificial Intelligence (cs.AI)

arXiv:2602.07415 [cs.LG]

(or arXiv:2602.07415v2 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2602.07415 Focus to learn more arXiv-issued DOI via DataCite

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Learning Molecular Chirality via Chiral Determinant Kernels

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