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Inferring quantities of interest from fluorescence microscopy time-lapse measurements of cells is a key step in parameterizing models of biomolecular reaction networks, and also in comparing different models. In this article, we propose a method which performs inference in continuous-time Markov chain models and thus takes into account the discrete nature of molecule counts. It targets the important...
Due to missing IP multicast support on an Internet scale, over-the-top media streams are delivered with the help of overlays as used by content delivery networks and their peer-to-peer (P2P) extensions. In this context, mesh/pull-based swarming plays an important role either as a pure streaming approach or in combination with tree/push mechanisms. The crucial impact of today's variety of client systems...
In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback–Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with...
The paper considers a model reduction technique that is well-suited for biochemical reaction systems giving rise to the assembly of a large number of different molecular species. The reduction is performed by grouping species with common properties, directly from the model specification in terms of a rule-based language. In recent works, general algorithms for the exact reductions of rule-based models...
Many bio-molecular reactions inside the cell are characterized by complex-formation and mutual modification of a few constituent molecules that give rise to a combinatorial number of reachable complexes or species. For such cases rule-based models (or site-graph-rewrite rules), offer a compact model description, by enumerating only the necessary context of interacting molecules. Such a model specification...
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