Systematic design of program analysis frameworks
POPL '79 Proceedings of the 6th ACM SIGACT-SIGPLAN symposium on Principles of programming languages
Theoretical Computer Science - Special issue: Computational systems biology
Bisimulation relations for weighted automata
Theoretical Computer Science
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction
LICS '10 Proceedings of the 2010 25th Annual IEEE Symposium on Logic in Computer Science
Formal Reduction for Rule-based Models
Electronic Notes in Theoretical Computer Science (ENTCS)
Lumpability abstractions of rule-based systems
Theoretical Computer Science
Reconstructing species-based dynamics from reduced stochastic rule-based models
Proceedings of the Winter Simulation Conference
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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.