Encoding Higher Level Extensions of Petri Nets in Answer Set Programming

DOI10.1007/978-3-642-40564-8_12zbMATH Open1405.68040arXiv1306.3548OpenAlexW1517819683MaRDI QIDQ2851238FDOQ2851238

Saadat Anwar, Katsumi Inoue, Chitta Baral

Publication date: 10 October 2013

Published in: Logic Programming and Nonmonotonic Reasoning (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1306.3548

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Mathematics Subject Classification ID

Logic programming (68N17) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Student assessment, achievement control, and rating (aspects of mathematics education) (97D60)

Cited In (2)

• Encoding reversing Petri nets in answer set programming
• Modeling delayed dynamics in biological regulatory networks from time series data

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