Extended Data Fig. 2: Visualization of XPert’s learned atomic attention for EGFR and HDAC inhibitors.
For each drug, the figure displays three panels: (left) the chemical structure with atoms colored by their mean attention score, highlighting key pharmacophoric groups; (middle) a heatmap showing the attention weight distribution for each atom across different cell line samples; and (right) a scatter plot of mean attention scores across five random seeds, used to quantify pattern similarity (Mean Cosine Similarity) and variance (Mean CV). (a) For EGFR inhibitors Gefitinib and Erlotinib, attention is consistently concentrated on the quinazoline ring scaffold, which is crucial for their binding activity. (b) For HDAC inhibitors Belinostat and Vorinostat, the model places higher attention on the Zinc-Binding Group (ZBG), the moiety responsible for chelating the catalytic zinc ion in the enzyme’s active site.
