J 2023

Trap spaces of multi-valued networks: definition, computation, and applications

TRINH, Van-Giang, Belaid BENHAMOU, Thomas HENZINGER and Samuel PASTVA

Basic information

Original name

Trap spaces of multi-valued networks: definition, computation, and applications

Authors

TRINH, Van-Giang, Belaid BENHAMOU, Thomas HENZINGER and Samuel PASTVA

Edition

Bioinformatics, Oxford (UK), Oxford University Press, 2023, 1367-4803

Other information

Language

English

Type of outcome

Article in a journal

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Organization

Fakulta informatiky – Repository – Repository

DOI

http://dx.doi.org/10.1093/bioinformatics/btad262

UT WoS

001027457000060

Keywords in English

Multivalued Network; Trap Space; Attractor; Petri net; Siphon
Changed: 26/3/2025 00:50, RNDr. Daniel Jakubík

Abstract

V originále

Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models.Source code and data are freely available at https://github.com/giang-trinh/trap-mvn.
Displayed: 15/6/2025 18:36