Name
Title | ||
|---|---|---|
Dynamical structure analysis of sparsity and minimality heuristics for reconstruction of biochemical networks |
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 sys- tem 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. I. INTRODUCTION |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1109/CDC.2008.4739364 | CDC |
Keywords | Field | DocType |
biochemistry,biocomputing,linear systems,transfer functions,biochemical network reconstruction,decoupled minimal realization,dynamical structure analysis,input-output information,linear time invariant systems,sparsity-minimality heuristics,systems biology,transfer function | Structure analysis,LTI system theory,Mathematical optimization,Linear system,Control theory,Computer science,Systems biology,Heuristics,Transfer function,System identification,Minimal realization | Conference |
ISSN | Citations | PageRank |
0743-1546 | 5 | 1.07 |
References | Authors | |
7 | 5 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Russell Howes | 1 | 30 | 4.15 |
| Lee John Eccleston | 2 | 5 | 1.07 |
| Jorge M. Goncalves | 3 | 32 | 4.61 |
| Guy-bart Stan | 4 | 281 | 26.54 |
| Sean Warnick | 5 | 198 | 25.76 |