Figure shows the ATC values for each atom in Y6, EH-IDTBR and ITIC, as obtained from the GNN and DFT. Green, grey, and pink correspond to positive, neutral, and negative ATC values, respectively. We can see that the GNN is able to capture the magnitude of the transition density along the rigid π-backbone of these molecules, particularly the large transition density magnitudes at the centre of these molecules. We can also see that both the GNN and DFT do not predict any significant transition density at the other conjugated sites in these molecules. This can be seen in the thiophene groups in Y6 and EH-IDTBR (Figure directly in the π-backbone of these molecules. Another feature that is captured by our GNN is the neutral transition density of the benzyl side-groups that are not involved in the πbackbone of ITIC-2Cl, which can be seen in Figure . This suggests that the graph embedding of the GNN discriminates correctly between the various types of conjugation that appear in these molecules.