Graphlet Degree Distribution Sensibility in Petri Net-Based Models of Biological Systems

Graphlet Degree Distribution Agreement (GDDA) is a comparison metric created for graphlets. Unfortunately, it has been reported and confirmed that it has an issue with the stability of result values in low-density graphs. Recently, graphlets have been modified for comparison of Petri net-based models of biological systems. It is crucial to find out if those problems reaper in the case of the modified graphlets, establish a scale of the instability impact on the GDDA value, and find out if it is a common problem for models of biological systems represented by Petri nets. Our results confirmed that the GDDA metric when used for the new graphlets is also unstable for part of the searched density spectrum. Because of that, some biological networks represented by Petri nets are vulnerable to this problem. While instability occurs in the Petri net environment, its characteristics have changed. The scale of an instability impact on the GDDA value is around half of its original size. The localization of vulnerable density areas is different from that in the case of undirected Protein-Protein Interaction (PPI) models. In contrast to the latter, the existence of a high stability area for very sparse models has been observed.