Dissemin is shutting down on January 1st, 2025

Published in

2008 47th IEEE Conference on Decision and Control

DOI: 10.1109/cdc.2008.4739364

Links

Tools

Export citation

Search in Google Scholar

Dynamical structure analysis of sparsity and minimality heuristics for reconstruction of biochemical networks

Proceedings article published in 2008 by Russell Howes, Lee J. Eccleston, Jorge Goncalves, Guy-Bart Stan ORCID, Sean Warnick
This paper is available in a repository.
This paper is available in a repository.

Full text: Download

Green circle
Preprint: archiving allowed
Green circle
Postprint: archiving allowed
Red circle
Published version: archiving forbidden
Data provided by SHERPA/RoMEO

Abstract

Network reconstruction, i.e. obtaining network structure from input-output information, is a central theme in systems biology. A variety of approaches aim to obtaining structural information from available data. Previous work has introduced dynamical structure functions as a tool for posing and solving the network reconstruction problem. Even for linear time invariant systems, reconstruction requires specific additional information not generated in the typical system identification process. This paper demonstrates that such extra information can be obtained through a limited sequence of system identification experiments on structurally modified systems, analogous to gene silencing and overexpression experiments. In the absence of such extra information, we discuss whether combined assumptions of network sparsity and minimality contribute to the recovery of the network dynamical structure. We provide sufficient conditions for a transfer function to have a completely decoupled minimal realization, and demonstrate that every transfer function is arbitrarily close to one that admits a perfectly decoupled minimal realization. This indicates that the assumptions of sparsity and minimality alone do not lend insight into the network structure.