The article's structure is the following: section II provides a comprehensive breakdown of each step within the proposed graph-based symmetry search algorithm. In Section III, we present the results for the sGDML model trained for four organic molecules adsorbed on a graphene substrate, followed by an analysis of atomic force reconstruction heterogeneity based on TEA Challenge 2023 results for the Ac-Phe-Ala5-Lys molecule. Lastly, in the section, we explore the performance of the MACE model incorporating permutational symmetries, applied to a graphene system featuring a pyridinic-N defect and the CsPbI 3 perovskite slab. Section IV concludes our study.