Figure reports per-molecule, temperature-reduced entropy differences between low and high-temperature ensembles of the same systems, based on the estimates from the three methods (PGM models: H (panel A) and C (panel B), and the ground truth method: ECM (all panels)). These estimates are plotted as a function of training progress. Also, in this case, the agreements between the PGM-based and the ground truth (ECMbased) estimates of the temperature-dependent entropy difference in the three system sizes are significant. As for the comparison between polymorphs, estimates obtained from model H are associated with significantly smaller error bars than the estimates from model C, once again underscoring the importance of adopting a physically motivated representation in constructing flowbased maps for targeted FE calculations.