During the third step, we sum the adjacency matrices of the constructed graphs, obtaining the frequencies of edge formations. Only the edges whose frequencies are above some predefined threshold become a part of the candidate for the final graph, as illustrated in Figure . This eliminates the edges that are not characteristic of most configurations. The eliminating threshold value varies from system to system and depends on both the softness of the system and the presence of transient states and should be set manually. A good choice is between 70 -90%. After the threshold is applied, the candidate for the final graph is constructed.