Title :

Computing Difference Abstractions of Linear Equation Systems

Author(s) :

Allart, Emilie [Auteur]
BioComputing
Niehren, Joachim [Auteur]
BioComputing
Linking Dynamic Data [LINKS]
Versari, Cristian [Auteur]
BioComputing

Journal title :

Theoretical Computer Science

Publisher :

Elsevier

Publication date :

2021

ISSN :

0304-3975

English keyword(s) :

boolean abstraction
metabolic networks
synthetic biology
systems biology
reaction networks
gene knockout prediction
first-order definitions
constraint programming
abstract interpretation

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]/Calcul formel [cs.SC]
Mathématiques [math]/Logique [math.LO]

English abstract : [en]

Abstract interpretation was proposed for predicting changes of reaction networks with partial kinetic information in systems biology. This requires to compute the set of difference abstractions of a system of linear equations ...
Show more >Abstract interpretation was proposed for predicting changes of reaction networks with partial kinetic information in systems biology. This requires to compute the set of difference abstractions of a system of linear equations under nonlinear constraints. We present the first practical algorithm that can compute the difference abstractions of linear equation systems exactly. We also present a new heuristics based on minimal support consequences for overapproximating the set of difference abstractions. Our algorithms rely on elementary modes, first-order definitions, and finite domain constraint programming. We implemented our algorithms and applied them to change prediction in systems biology. It turns out experimentally that the new heuristics is often exact in practice, while outperforming the exact algorithm.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Comment :

This is an extension of a previous publication, see hal-02302463v1.

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL