Discrete dynamic models are a powerful tool for the understanding and modeling of large biological networks. Although a lot of progress has been made in developing analysis tools for these models, there is still a need to find approaches that can directly relate the network structure to its dynamics. Of special interest is identifying the stable patterns of activity, i.e., the attractors of the system. This is a problem for large networks, because the state space of the system increases exponentially with network size. In this work, we present a novel network reduction approach that is based on finding network motifs that stabilize in a fixed state. Notably, we use a topological criterion to identify these motifs. Specifically, we find certain types of strongly connected components in a suitably expanded representation of the network. To test our method, we apply it to a dynamic network model for a type of cytotoxic T cell cancer and to an ensemble of random Boolean networks of size up to 200. Our results show that our method goes beyond reducing the network and in most cases can actually predict the dynamical repertoire of the nodes (fixed states or oscillations) in the attractors of the system.
Skip Nav Destination
,
Article navigation
June 2013
Research Article|
June 13 2013
An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks Available to Purchase
Jorge G. T. Zañudo;
Jorge G. T. Zañudo
a)
1
Department of Physics, The Pennsylvania State University, University Park
, Pennsylvania 16802-6300, USA
Search for other works by this author on:
Réka Albert
Réka Albert
b)
1
Department of Physics, The Pennsylvania State University, University Park
, Pennsylvania 16802-6300, USA
2
Department of Biology, The Pennsylvania State University, University Park
, Pennsylvania 16802-5301, USA
Search for other works by this author on:
Jorge G. T. Zañudo
1,a)
Réka Albert
1,2,b)
1
Department of Physics, The Pennsylvania State University, University Park
, Pennsylvania 16802-6300, USA
2
Department of Biology, The Pennsylvania State University, University Park
, Pennsylvania 16802-5301, USA
Chaos 23, 025111 (2013)
Article history
Received:
December 31 2012
Accepted:
May 22 2013
Citation
Jorge G. T. Zañudo, Réka Albert; An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks. Chaos 1 June 2013; 23 (2): 025111. https://doi.org/10.1063/1.4809777
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Citing articles via
Reservoir computing with the minimum description length principle
Antony Mizzi, Michael Small, et al.
Recent achievements in nonlinear dynamics, synchronization, and networks
Dibakar Ghosh, Norbert Marwan, et al.
Data-driven nonlinear model reduction to spectral submanifolds via oblique projection
Leonardo Bettini, Bálint Kaszás, et al.
Related Content
Dynamical modeling and analysis of large cellular regulatory networks
Chaos (June 2013)
An optimal control approach for enhancing natural killer cells' secretion of cytolytic molecules
APL Bioeng. (December 2020)
Structure-based approach to identifying small sets of driver nodes in biological networks
Chaos (June 2022)
Phenotypic deconstruction of gene circuitry
Chaos (June 2013)
Protein array processing software for automated semiquantitative analysis of serum antibody repertoires
Biomicrofluidics (September 2023)