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Combining Model Reductions

Camporesi, F. and Feret, J. and Koeppl, H. and Petrov, T. (2010):
Combining Model Reductions.
In: Electronic Notes in Theoretical Computer Science, pp. 73-96, 265, [Online-Edition: http://linkinghub.elsevier.com/retrieve/pii/S157106611000085...],
[Article]

Abstract

Molecular biological models usually suffer from a large combinatorial explosion. Indeed, proteins form complexes and modify each others, which leads to the formation of a huge number of distinct chemical species (i.e. non-isomorphic connected components of proteins). Thus we cannot generate explicitly the quantitative semantics of these models, and even less compute their properties. Model reduction aims at reducing this complexity by providing another grain of observation. In this paper, we propose two unifying frameworks for combining model reductions: we propose a symmetric product operator for combining model reductions for stochastic semantics and we show how to abstract further existing reduced differential systems by the means of linear projections. We apply both frameworks so as to abstract further existing reduced quantitative semantics of the models that are written in Kappa, by taking into account symmetries among binding sites in proteins. © 2010 Elsevier B.V. All rights reserved.

Item Type: Article
Erschienen: 2010
Creators: Camporesi, F. and Feret, J. and Koeppl, H. and Petrov, T.
Title: Combining Model Reductions
Language: English
Abstract:

Molecular biological models usually suffer from a large combinatorial explosion. Indeed, proteins form complexes and modify each others, which leads to the formation of a huge number of distinct chemical species (i.e. non-isomorphic connected components of proteins). Thus we cannot generate explicitly the quantitative semantics of these models, and even less compute their properties. Model reduction aims at reducing this complexity by providing another grain of observation. In this paper, we propose two unifying frameworks for combining model reductions: we propose a symmetric product operator for combining model reductions for stochastic semantics and we show how to abstract further existing reduced differential systems by the means of linear projections. We apply both frameworks so as to abstract further existing reduced quantitative semantics of the models that are written in Kappa, by taking into account symmetries among binding sites in proteins. © 2010 Elsevier B.V. All rights reserved.

Journal or Publication Title: Electronic Notes in Theoretical Computer Science
Volume: 265
Uncontrolled Keywords: abstract interpretation,model reduction,rules-based modeling,symmetries
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 14:18
Official URL: http://linkinghub.elsevier.com/retrieve/pii/S157106611000085...
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