Encoding Higher Level Extensions of Petri Nets in Answer Set Programming
This work addresses the need for formalisms to model and reason about biological systems, but it is incremental as it builds on existing Petri Net and ASP methods with small extensions.
The paper tackles the problem of modeling biological pathways with higher-level constructs like colored tokens, which regular Petri Nets cannot represent succinctly, by encoding Petri Nets with colored tokens in Answer Set Programming (ASP) to enable simulation-based reasoning for answering realistic biological questions.
Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require simulation based reasoning. To answer such questions, we need formalisms to build pathway models, add extensions, simulate, and reason with them. We chose Petri Nets and Answer Set Programming (ASP) as suitable formalisms, since Petri Net models are similar to biological pathway diagrams; and ASP provides easy extension and strong reasoning abilities. We found that certain aspects of biological pathways, such as locations and substance types, cannot be represented succinctly using regular Petri Nets. As a result, we need higher level constructs like colored tokens. In this paper, we show how Petri Nets with colored tokens can be encoded in ASP in an intuitive manner, how additional Petri Net extensions can be added by making small code changes, and how this work furthers our long term research goals. Our approach can be adapted to other domains with similar modeling needs.