Encoding Higher Level Extensions of Petri Nets in Answer Set Programming

TL;DR

This paper demonstrates how to encode higher-level Petri Net extensions, including colored tokens, in Answer Set Programming to enhance biological pathway modeling and reasoning capabilities.

Contribution

It introduces an ASP encoding for Petri Nets with colored tokens and extensions, facilitating more expressive biological pathway simulations.

Findings

ASP encoding of colored Petri Nets is intuitive

Extensions can be added with minimal code changes

Approach is adaptable to other domains

Abstract

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.