Graphlets in comparison of Petri net‑based models of biological systems
[ 1 ] Instytut Informatyki, Wydział Informatyki i Telekomunikacji, Politechnika Poznańska | [ P ] employee
2022
scientific article
english
EN Capability to compare biological models is a crucial step needed in an analysis of complex organisms. Petri nets as a popular modelling technique, needs a possibility to determine the degree of structural similarities (e.g., comparison of metabolic or signaling pathways). However, existing comparison methods use matching invariants approach for establishing a degree of similarity, and because of that are vulnerable to the state explosion problem which may appear during calculation of a minimal invariants set. Its occurrence will block usage of existing methods. To find an alternative for this situation, we decided to adapt and tests in a Petri net environment a method based on finding a distribution of graphlets. First, we focused on adapting the original graphlets for notation of bipartite, directed graphs. As a result, 151 new graphlets with 592 orbits were created. The next step focused on evaluating a performance of the popular Graphlet Degree Distribution Agreement (GDDA) metric in the new environment. To do that, we decided to use randomly generated networks that share typical characteristics of biological models represented in Petri nets. Our results confirmed the usefulness of graphlets and GDDA in Petri net comparison and discovered its limitations.
04.12.2022
20942-1 - 20942-13
Article Number: 20942
CC BY (attribution alone)
open journal
final published version
at the time of publication
140
4,6