Lumpability abstractions of rule-based systems

DOI10.1016/j.tcs.2011.12.059zbMath1267.68153arXiv1011.0496OpenAlexW2122360082MaRDI QIDQ418843

Jerome Feret, Tatjana Petrov, Thomas A. Henzinger, Heinz Koeppl

Publication date: 30 May 2012

Published in: Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1011.0496

zbMATH Keywords

Markov chainsbisimulationmolecular biologylumpabilityweighed labelled transition system

Mathematics Subject Classification ID

Specification and verification (program logics, model checking, etc.) (68Q60) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Systems biology, networks (92C42) Probability in computer science (algorithm analysis, random structures, phase transitions, etc.) (68Q87)

Related Items (18)

Lumping Reductions for Multispread in Multi-Layer Networks ⋮ Unnamed Item ⋮ Markov chain aggregation and its applications to combinatorial reaction networks ⋮ Comparing chemical reaction networks: a categorical and algorithmic perspective ⋮ Exact hierarchical reductions of dynamical models via linear transformations ⋮ Tropical abstraction of biochemical reaction networks with guarantees ⋮ Long lived transients in gene regulation ⋮ Model Decomposition and Stochastic Fragments ⋮ Stochastic Semantics of Signaling as a Composition of Agent-view Automata ⋮ Free Energy of Petri Nets ⋮ Formal Reduction for Rule-based Models ⋮ Rigid geometric constraints for Kappa models ⋮ An algebraic approach for inferring and using symmetries in rule-based models ⋮ Automated deep abstractions for stochastic chemical reaction networks ⋮ Symbolic computation of differential equivalences ⋮ Quantitative Abstractions for Collective Adaptive Systems ⋮ Approximate lumpability for Markovian agent-based models using local symmetries ⋮ Unwinding biological systems

Uses Software

• gnuplot
• BioNetGen

Cites Work

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