Variational Quantum Attention for Molecular Graph Learning

Yu-Cheng Lin, Yu-Chao Hsu, Tai-Yue Li, Nan-Yow Chen, Samuel Yen-Chi Chen

Molecular property prediction is central to computational drug discovery, where graph neural networks learn to weight neighboring atomic environments during message passing. Yet it remains unclear how variational quantum circuits alter learned attention behavior in molecular graphs. We introduce an edge-aware variational quantum attention mechanism for molecular graph learning, in which the receiving atom, neighboring atom, and connecting bond jointly determine the quantum attention state. Across five molecular property and bioactivity prediction tasks, QGAT achieves competitive performance relative to GATv2, with a consistent improvement on BBBP across all six evaluated circuit ansatzes. We further compare how the quantum and classical attention scores weight molecular structure beyond accuracy. In the Verubecestat BACE1 inhibitor series, QGAT achieves a higher Spearman correlation than GATv2 and assigns positive attributions to several structural changes consistent with reported structure-activity relationships (SARs). This case study shows that the two attention mechanisms can exhibit different prediction and attribution behavior across structurally related BACE1 analogues,…