The surrogate model is trained to predict two atom-level descriptors (atomic Mulliken charges and spin densities), as well as three molecule-level descriptors (relaxed BDFEs, frozen BDEs, and V bur of the radical sites). Based on a hyperparameter grid search, the depth was set to 5 for the D-MPNN and 4 for the FFNN. For the hidden size, 1200 neurons were selected for the D-MPNN and 900 for the FFNN (cf. Section S2.1 in the Supporting Information).