Parameter space abstraction and unfolding semantics of discrete regulatory networks

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Parameter space abstraction and unfolding semantics of discrete regulatory networks

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Parameter space abstraction and unfolding semantics of discrete regulatory networks

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

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

Projekt

<a href="/cs/project/GA15-11089S" target="_blank" >GA15-11089S: Získávání parametrů biologických modelů pomocí techniky ověřování modelů</a><br>

Návaznosti

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

Rok uplatnění

2019

Kód důvěrnosti údajů

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

Název periodika

Theoretical Computer Science

ISSN

0304-3975

e-ISSN

—

Svazek periodika

765

Číslo periodika v rámci svazku

April

Stát vydavatele periodika

CZ - Česká republika

Počet stran výsledku

25

Strana od-do

120-144

Kód UT WoS článku

000473372600007

EID výsledku v databázi Scopus

2-s2.0-85049004467