Fig. 3

Visualization of atom-pair matching performed by the Graph Aligner module. The red-highlighted atoms within each molecule represent those that match atoms in the reference molecule. Five molecules in a series from the structural similarity benchmark are positioned horizontally, where the first molecule serves as the reference and the next four are ordered on the basis of their similarity to this reference. The values labeled “G” and “E” below each molecule denote the similarity scores calculated by GESim and the Tanimoto similarity using ECFP, respectively, in relation to the reference molecule. The rankings in descending order based on these scores are also indicated, along with Spearman’s rank correlation coefficient (\(\rho\)) computed from these rankings