Parameter space abstraction and unfolding semantics of discrete regulatory networks

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F19%3A00108116" target="_blank" >RIV/00216224:14330/19:00108116 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1016/j.tcs.2018.03.009" target="_blank" >http://dx.doi.org/10.1016/j.tcs.2018.03.009</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.tcs.2018.03.009" target="_blank" >10.1016/j.tcs.2018.03.009</a>

Result language

angličtina

Original language name

Parameter space abstraction and unfolding semantics of discrete regulatory networks

Original language description

The modelling of discrete regulatory networks combines a graph specifying the pairwise influences between the variables of the system, and a parametrisation from which can be derived a discrete transition system. Given the influence graph only, the exploration of admissible parametrisations and the behaviours they enable is computationally demanding due to the combinatorial explosions of both parametrisation and reachable state space. This article introduces an abstraction of the parametrisation space and its refinement to account for the existence of given transitions, and for constraints on the sign and observability of influences. The abstraction uses a convex sublattice containing the concrete parametrisation space specified by its infimum and supremum parametrisations. It is shown that the computed abstractions are optimal, i.e., no smaller convex sublattice exists. Although the abstraction may introduce over-approximation, it has been proven to be conservative with respect to reachability of states. Then, an unfolding semantics for Parametric Regulatory Networks is defined, taking advantage of concurrency between transitions to provide a compact representation of reachable transitions. A prototype implementation is provided: it has been applied to several examples of Boolean and multi-valued networks, showing its tractability for networks with numerous components.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/GA15-11089S" target="_blank" >GA15-11089S: Parameter Discovery for Biological Models Using Model Checking</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Theoretical Computer Science

ISSN

0304-3975

e-ISSN

—

Volume of the periodical

765

Issue of the periodical within the volume

April

Country of publishing house

CZ - CZECH REPUBLIC

Number of pages

25

Pages from-to

120-144

UT code for WoS article

000473372600007

EID of the result in the Scopus database

2-s2.0-85049004467