On Robustness Computation and Optimization in BIOCHAM-4

Abstract : BIOCHAM-4 is a tool for modeling, analyzing and synthesizing biochemical reaction networks with respect to some formal, yet possibly imprecise, specification of their behavior. We focus here on one new capability of this tool to optimize the robustness of a parametric model with respect to a specification of its dynamics in quantitative temporal logic. More precisely, we present two complementary notions of robustness: the statistical notion of model robustness to parameter perturbations, defined as its mean functionality, and a metric notion of formula satisfaction robustness, defined as the penetration depth in the validity domain of the temporal logic constraints. We show how the formula robustness can be used in BIOCHAM-4 with no extra cost as an objective function in the parameter optimization procedure, to actually improve the model robustness. We illustrate these unique features with a classical example of the hybrid systems community and provide some performance figures on a model of MAPK signalling with 37 parameters.
Document type :
Conference papers
Complete list of metadatas

Cited literature [34 references]  Display  Hide  Download

https://hal.inria.fr/hal-01814854
Contributor : François Fages <>
Submitted on : Wednesday, June 13, 2018 - 3:51:53 PM
Last modification on : Thursday, December 13, 2018 - 4:57:05 PM
Long-term archiving on : Friday, September 14, 2018 - 2:35:13 PM

File

FS18cmsbhal.pdf
Files produced by the author(s)

Identifiers

Collections

Citation

François Fages, Sylvain Soliman. On Robustness Computation and Optimization in BIOCHAM-4. 16th Int. Conf. on Computational Methods in Systems Biology, Sep 2018, Brno, Czech Republic. ⟨10.1007/978-3-319-99429-1_18⟩. ⟨hal-01814854⟩

Share

Metrics

Record views

214

Files downloads

226