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Lumpability Abstractions of Rule-based Systems

Feret, J. and Henzinger, T. and Koeppl, H. and Petrov, T. (2012):
Lumpability Abstractions of Rule-based Systems.
In: Journal of Theoretical Comuter Science, pp. 137-164, 431, [Online-Edition: http://linkinghub.elsevier.com/retrieve/pii/S030439751101025...],
[Article]

Abstract

The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.

Item Type: Article
Erschienen: 2012
Creators: Feret, J. and Henzinger, T. and Koeppl, H. and Petrov, T.
Title: Lumpability Abstractions of Rule-based Systems
Language: English
Abstract:

The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.

Journal or Publication Title: Journal of Theoretical Comuter Science
Volume: 431
Place of Publication: Jena
Uncontrolled Keywords: Abstraction, Bisimulation, Lumpability, Markov chains
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Date Deposited: 04 Apr 2014 14:11
Official URL: http://linkinghub.elsevier.com/retrieve/pii/S030439751101025...
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