Numerical Analysis of Superposed GSPNs
IEEE Transactions on Software Engineering - Special issue: best papers of the sixth international workshop on Petri nets and performance models (PNPM'95)
The ubiquitous Kronecker product
Journal of Computational and Applied Mathematics - Special issue on numerical analysis 2000 Vol. III: linear algebra
Model-Checking Algorithms for Continuous-Time Markov Chains
IEEE Transactions on Software Engineering
Theoretical Computer Science - Special issue: Computational systems biology
Abstract interpretation of cellular signalling networks
VMCAI'08 Proceedings of the 9th international conference on Verification, model checking, and abstract interpretation
Model Decomposition and Stochastic Fragments
Electronic Notes in Theoretical Computer Science (ENTCS)
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In this paper we present a formalism based on stochastic automata to describe the stochastic dynamics of signal transduction networks that are specified by rule-sets. Our formalism gives a modular description of the underlying stochastic process, in the sense that it is a composition of smaller units, agent-views. The view of an agent is an automaton that identifies all local modification changes of that agent (internal state modifications, binding and unbinding), but also those of interacting agents, which are tested within the same rule. We show how to represent the generator matrix of the underlying Markov process of the whole rule-set as Kronecker sums of the rate matrices belonging to individual view-automata. In the absence of birth the automata are finite, since the number of different contexts in which one agent can appear in a