Parameter Synthesis and Robustness Analysis of Rule-Based
Models

D 2020

Parameter Synthesis and Robustness Analysis of Rule-Based Models

TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM

Basic information

Original name

Parameter Synthesis and Robustness Analysis of Rule-Based Models

Authors

TROJÁK, Matej (703 Slovakia, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, belonging to the institution), Lukrécia MERTOVÁ (703 Slovakia, belonging to the institution) and Luboš BRIM (203 Czech Republic, belonging to the institution)

Edition

LNCS 12229. Moffett Field, CA, USA, 12th International Symposium on NASA Formal Methods, NFM 2020, p. 41-59, 19 pp. 2020

Publisher

Springer

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

URL

Impact factor

Impact factor: 0.402 in 2005

RIV identification code

RIV/00216224:14330/20:00114280

Organization unit

Faculty of Informatics

ISBN

978-3-030-55753-9

ISSN

DOI

http://dx.doi.org/10.1007/978-3-030-55754-6_3

UT WoS

000890074700003

Keywords in English

rule-based modelling; probabilistic models; parameter synthesis; robustness analysis

Abstract

V originále

We introduce the Quantitative Biochemical Space Language, a rule-based language for a compact modelling of probabilistic behaviour of complex parameter-dependent biological systems. Application of rules is governed by an associated parametrised rate function, expressing partially known information about the behaviour of the modelled system. The parameter values influence the behaviour of the model. We propose a formal verification-based method for the synthesis of parameter values (parameter synthesis) which ensure the behaviour of the modelled system satisfies a given PCTL property. In addition, we demonstrate how this method can be used for robustness analysis.

Links

GA18-00178S, research and development project

Name: Diskrétní bifurkační analýza reaktivních systémů

Investor: Czech Science Foundation

MUNI/A/1050/2019, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace IX (Acronym: SV-FI MAV IX)

Investor: Masaryk University, Category A

Citovat

TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM. Parameter Synthesis and Robustness Analysis of Rule-Based Models. In Ritchie Lee, Susmit Jha, Anastasia Mavridou. 12th International Symposium on NASA Formal Methods, NFM 2020. LNCS 12229. Moffett Field, CA, USA: Springer, 2020, p. 41-59. ISBN 978-3-030-55753-9. Available from: https://dx.doi.org/10.1007/978-3-030-55754-6_3.

@inproceedings{1675379,
   author = {Troják, Matej and Šafránek, David and Mertová, Lukrécia and Brim, Luboš},
   address = {Moffett Field, CA, USA},
   booktitle = {12th International Symposium on NASA Formal Methods, NFM 2020},
   doi = {http://dx.doi.org/10.1007/978-3-030-55754-6_3},
   edition = {LNCS 12229},
   editor = {Ritchie Lee, Susmit Jha, Anastasia Mavridou},
   keywords = {rule-based modelling; probabilistic models; parameter synthesis; robustness analysis},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Moffett Field, CA, USA},
   isbn = {978-3-030-55753-9},
   pages = {41-59},
   publisher = {Springer},
   title = {Parameter Synthesis and Robustness Analysis of Rule-Based Models},
   url = {https://link.springer.com/chapter/10.1007/978-3-030-55754-6_3},
   year = {2020}
}

TY  - JOUR
ID  - 1675379
AU  - Troják, Matej - Šafránek, David - Mertová, Lukrécia - Brim, Luboš
PY  - 2020
TI  - Parameter Synthesis and Robustness Analysis of Rule-Based Models
PB  - Springer
CY  - Moffett Field, CA, USA
SN  - 9783030557539
KW  - rule-based modelling
KW  - probabilistic models
KW  - parameter synthesis
KW  - robustness analysis
UR  - https://link.springer.com/chapter/10.1007/978-3-030-55754-6_3
L2  - https://link.springer.com/chapter/10.1007/978-3-030-55754-6_3
N2  - We introduce the Quantitative Biochemical Space Language, a rule-based language for a compact modelling of probabilistic behaviour of complex parameter-dependent biological systems. Application of rules is governed by an associated parametrised rate function, expressing partially known information about the behaviour of the modelled system. The parameter values influence the behaviour of the model. We propose a formal verification-based method for the synthesis of parameter values (parameter synthesis) which ensure the behaviour of the modelled system satisfies a given PCTL property. In addition, we demonstrate how this method can be used for robustness analysis.
ER  -

TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM. Parameter Synthesis and Robustness Analysis of Rule-Based Models. In Ritchie Lee, Susmit Jha, Anastasia Mavridou. \textit{12th International Symposium on NASA Formal Methods, NFM 2020}. LNCS 12229. Moffett Field, CA, USA: Springer, 2020, p.~41-59. ISBN~978-3-030-55753-9. Available from: https://dx.doi.org/10.1007/978-3-030-55754-6\_{}3.

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