Parameter space abstraction and unfolding semantics of discrete
regulatory networks

J 2019

Parameter space abstraction and unfolding semantics of discrete regulatory networks

KOLČÁK, Juraj, David ŠAFRÁNEK, Stefan HAAR and Loïc PAULEVÉ

Basic information

Original name

Parameter space abstraction and unfolding semantics of discrete regulatory networks

Authors

KOLČÁK, Juraj (703 Slovakia, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution), Stefan HAAR (276 Germany) and Loïc PAULEVÉ (250 France)

Edition

Theoretical Computer Science, Elsevier, 2019, 0304-3975

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 0.747

RIV identification code

RIV/00216224:14330/19:00108116

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1016/j.tcs.2018.03.009

UT WoS

000473372600007

Keywords in English

Boolean networks; Thomas networks; Parametrised discrete dynamics; Asynchronous systems; Concurrency; Systems biology

Abstract

V originále

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.

Links

GA15-11089S, research and development project

Name: Získávání parametrů biologických modelů pomocí techniky ověřování modelů

Investor: Czech Science Foundation

Citovat

KOLČÁK, Juraj, David ŠAFRÁNEK, Stefan HAAR and Loïc PAULEVÉ. Parameter space abstraction and unfolding semantics of discrete regulatory networks. Theoretical Computer Science. Elsevier, 2019, vol. 765, April, p. 120-144. ISSN 0304-3975. Available from: https://dx.doi.org/10.1016/j.tcs.2018.03.009.

@article{1610817,
   author = {Kolčák, Juraj and Šafránek, David and Haar, Stefan and Paulevé, Loïc},
   article_number = {April},
   doi = {http://dx.doi.org/10.1016/j.tcs.2018.03.009},
   keywords = {Boolean networks; Thomas networks; Parametrised discrete dynamics; Asynchronous systems; Concurrency; Systems biology},
   language = {eng},
   issn = {0304-3975},
   journal = {Theoretical Computer Science},
   title = {Parameter space abstraction and unfolding semantics of discrete regulatory networks},
   url = {http://dx.doi.org/10.1016/j.tcs.2018.03.009},
   volume = {765},
   year = {2019}
}

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AU  - Kolčák, Juraj - Šafránek, David - Haar, Stefan - Paulevé, Loïc
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TI  - Parameter space abstraction and unfolding semantics of discrete regulatory networks
JF  - Theoretical Computer Science
VL  - 765
IS  - April
SP  - 120-144
EP  - 120-144
PB  - Elsevier
SN  - 03043975
KW  - Boolean networks
KW  - Thomas networks
KW  - Parametrised discrete dynamics
KW  - Asynchronous systems
KW  - Concurrency
KW  - Systems biology
UR  - http://dx.doi.org/10.1016/j.tcs.2018.03.009
L2  - http://dx.doi.org/10.1016/j.tcs.2018.03.009
N2  - 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.
ER  -

KOLČÁK, Juraj, David ŠAFRÁNEK, Stefan HAAR and Loïc PAULEVÉ. Parameter space abstraction and unfolding semantics of discrete regulatory networks. \textit{Theoretical Computer Science}. Elsevier, 2019, vol.~765, April, p.~120-144. ISSN~0304-3975. Available from: https://dx.doi.org/10.1016/j.tcs.2018.03.009.

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