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@article{caiComputerScienceMethodsFor2023,
 author = {Wentong Cai and  Philipp Andelfinger and  Luca Bortolussi and  Christopher Carothers and  Dong Kevin Jin and  Till Köster and  Michael Lees and  Jason Liu and  Margaret Loper and  Alessandro Pellegrini and  Wen Jun Tan and Verena Wolf},
 journal = {Dagstuhl Reports},
 month = {5},
 number = {10},
 pages = {1-44},
 publisher = {Dagstuhl Reports},
 title = {Computer Science Methods for Effective and Sustainable Simulation Studies},
 volume = {12},
 year = {2023}
}

@inproceedings{caiIntelligentModelingAndSimulation2023,
 author = {Wentong Cai and Philipp Andelfinger and Luca Bortolussi and Christopher Carothers and Dong Kevin Jin and Till Köster and Michael Lees and Jason Liu and Margaret Loper and Alessandro Pellegrini and Wen Jun Tan and Verena Wolf},
 booktitle = {Dagstuhl-Seminar Report 22401. Dagstuhl Seminare/Workshops, Computer Science Methods for Effective and Sustainable Simulation Studies, October 3-7, Schloß Dagstuhl, Germany},
 doi = {10.4230/DagRep.12.10.1},
 pages = {44-46},
 publisher = {Schloss Dagstuhl-Leibniz-Zentrum für Informatik},
 series = {Dagstuhl Seminar Report},
 title = {Intelligent Modeling and Simulation Lifecycle},
 url = {https://www.dfki.de/fileadmin/user_upload/import/13355_dagrep_v012_i010_p001_22401.pdf},
 volume = {22401},
 year = {2023}
}

@inproceedings{backenkohlerAnalysisOfMarkovJump2021,
 author = {Michael Backenköhler and Luca Bortolussi and Gerrit Großmann and Verena Wolf},
 booktitle = {Tools and Algorithms for the Construction and Analysis of Systems. International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS-2021), 27th International Conference, TACAS 2021, Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2021, March 27 - April 1, Luxembourg City, Luxembourg},
 doi = {10.1007/978-3-030-72016-2_12},
 edition = {1st},
 editor = {Jan Friso Groote and Kim Guldstrand Larsen and },
 isbn = {978-3-030-72016-2},
 month = {3},
 pages = {210-229},
 publisher = {Springer, Switzerland},
 title = {Analysis of Markov jump processes under terminal constraints},
 volume = {12651},
 year = {2021}
}

@inproceedings{backenkohlerAbstractionGuidedTruncationsForStationary2021,
 address = {Cham},
 author = {Backenköhler, Michael and Bortolussi, Luca and Großmann, Gerrit and Wolf, Verena},
 booktitle = {Quantitative Evaluation of Systems},
 editor = {Abate, Alessandro and Marin, Andrea},
 isbn = {978-3-030-85172-9},
 pages = {351--371},
 publisher = {Springer International Publishing},
 title = {Abstraction-Guided Truncations for Stationary Distributions of Markov Population Models},
 year = {2021}
}

@article{grossmannEfficientSimulationOfNonMarkovian2020,
 author = {Gerrit Großmann and Luca Bortolussi and Verena Wolf},
 doi = {10.1371/journal.pone.0241394},
 editor = {Hocine Cherifi},
 journal = {PLOS ONE},
 month = {10},
 number = {10},
 pages = {1-18},
 publisher = {PLOS ONE},
 title = {Efficient simulation of non-Markovian dynamics on complex networks},
 volume = {15},
 year = {2020}
}

@inproceedings{backenkohlerBoundingMeanFirstPassage2020,
 author = {Michael Backenköhler and Luca Bortolussi and Verena Wolf},
 booktitle = {Quantitative Evaluation of Systems. International Conference on Quantitative Evaluation of Systems (QEST), Cham},
 doi = {10.1007/978-3-030-59854-9_13},
 editor = {Marco Gribaudo and David N. Jansen and Anne Remke},
 isbn = {9783030598549},
 pages = {155-174},
 publisher = {Springer International Publishing},
 title = {Bounding Mean First Passage Times in Population Continuous-Time Markov Chains},
 url = {https://link.springer.com/chapter/10.1007/978-3-030-59854-9_13},
 year = {2020}
}

@inproceedings{grossmannRejectionBasedSimulationOfNonMarkovian2020,
 address = {Cham},
 author = {Großmann, Gerrit and Bortolussi, Luca and Wolf, Verena},
 booktitle = {Complex Networks and Their Applications VIII},
 editor = {Cherifi, Hocine and Gaito, Sabrina and Mendes, José Fernendo and Moro, Esteban and Rocha, Luis Mateus},
 isbn = {978-3-030-36687-2},
 pages = {349--361},
 publisher = {Springer International Publishing},
 title = {Rejection-Based Simulation of Non-Markovian Agents on Complex Networks},
 year = {2020}
}

@inproceedings{backenkohlerBoundingFirstPassageTimes2019,
 author = {Michael Backenköhler and Luca Bortolussi and Verena Wolf},
 booktitle = {Computational Methods in Systems Biology - 17th International Conference - Proceedings. International Conference on Computational Methods in Systems Biology (CMSB-2019), September 18-20, Trieste, Italy},
 doi = {10.1007/978-3-030-31304-3_31},
 editor = {Luca Bortolussi and Guido Sanguinetti},
 isbn = {9783030313043},
 pages = {379-382},
 publisher = {Springer International Publishing},
 series = {Lecture Notes in Computer Science, LNBI},
 title = {Bounding First Passage Times in Chemical Reaction Networks},
 url = {https://link.springer.com/chapter/10.1007/978-3-030-31304-3_31},
 volume = {11773},
 year = {2019}
}

@inproceedings{backenkohlerControlVariatesForStochastic2019,
 address = {Cham},
 author = {Backenköhler, Michael and Bortolussi, Luca and Wolf, Verena},
 booktitle = {Computational Methods in Systems Biology},
 editor = {Bortolussi, Luca and Sanguinetti, Guido},
 isbn = {978-3-030-31304-3},
 pages = {42--59},
 publisher = {Springer International Publishing},
 title = {Control Variates for Stochastic Simulation of Chemical Reaction Networks},
 year = {2019}
}

@inproceedings{grossmannReducingSpreadingProcessesOn2019,
 address = {Cham},
 author = {Großmann, Gerrit and Bortolussi, Luca},
 booktitle = {Quantitative Evaluation of Systems},
 editor = {Parker, David and Wolf, Verena},
 isbn = {978-3-030-30281-8},
 pages = {292--309},
 publisher = {Springer International Publishing},
 title = {Reducing Spreading Processes on Networks to Markov Population Models},
 year = {2019}
}

@article{kyriakopoulosLumpingOfDegreeBasedMeanField2018,
$ of the network, which is much smaller than the size of the master equation of the underlying stochastic model, yet numerically solving these equations can still be problematic for large $k_{\max}$. In this paper, we consider AME and PA, extended to cope with multiple local states, and we provide an aggregation procedure that clusters together nodes having similar degrees, treating those in the same cluster as indistinguishable, thus reducing the number of equations while preserving an accurate description of global observables of interest. We also provide an automatic way to build such equations and to identify a small number of degree clusters that give accurate results. The method is tested on several case studies, where it shows a high level of compression and a reduction of computational time of several orders of magnitude for large networks, with minimal loss in accuracy},
 author = {Kyriakopoulos, Charalampos and Grossmann, Gerrit and Wolf, Verena and Bortolussi, Luca},
 doi = {10.1103/PhysRevE.97.012301},
 issue = {1},
 journal = {Phys. Rev. E},
 month = {Jan},
 numpages = {15},
 pages = {012301},
 publisher = {American Physical Society},
 title = {Lumping of degree-based mean-field and pair-approximation equations for multistate contact processes},
 url = {https://link.aps.org/doi/10.1103/PhysRevE.97.012301},
 volume = {97},
 year = {2018}
}

@inproceedings{grossmannLumpingTheApproximateMaster2018,
 address = {Cham},
 author = {Großmann, Gerrit and Kyriakopoulos, Charalampos and Bortolussi, Luca and Wolf, Verena},
 booktitle = {Quantitative Evaluation of Systems},
 editor = {McIver, Annabelle and Horvath, Andras},
 isbn = {978-3-319-99154-2},
 pages = {157--172},
 publisher = {Springer International Publishing},
 title = {Lumping the Approximate Master Equation for Multistate Processes on Complex Networks},
 year = {2018}
}

@article{backenkohlerMomentBasedParameterEstimationFor2017,
 author = {Michael Backenköhler and Luca Bortolussi and Verena Wolf},
 doi = {10.1109/TCBB.2017.2775219},
 journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)},
 month = {11},
 number = {4},
 pages = {1180-1192},
 publisher = {IEEE},
 title = {Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium},
 volume = {15},
 year = {2017}
}

@inproceedings{backenkohlerGeneralizedMethodOfMoments2016,
 author = {Michael Backenköhler and Luca Bortolussi and Verena Wolf},
 booktitle = {Computational Methods in Systems Biology. International Conference on Computational Methods in Systems Biology (CMSB-2016), 14th International Conference, CMSB 2016, September 21-23, Cambridge, United Kingdom},
 doi = {10.1007/978-3-319-45177-0_2},
 editor = {Ezio Bartocci and Pietro Lio and Nicola Paoletti},
 isbn = {9783319451770},
 month = {9},
 pages = {15-29},
 publisher = {Springer International Publishing},
 title = {Generalized Method of Moments for Stochastic Reaction Networks in Equilibrium},
 year = {2016}
}

@inproceedings{bockModelBasedWholeGenomeAnalysisOf2015,
 author = {Christoph Bock and Luca Bortolussi and Thilo Krüger and Linar Mikeev and Verena Wolf},
 booktitle = {Hybrid Systems Biology - Fourth International Workshop. Revised Selected Papers. International Conference on Hybrid Systems Biology (HSB-2015), September 4-5, Madrid, Spain},
 doi = {10.1007/978-3-319-26916-0_8},
 editor = {Alessandro Abate and David Šafránek},
 isbn = {9783319269160},
 month = {9},
 pages = {141-155},
 publisher = {Springer International Publishing, Switzerland},
 series = {Lecture Notes in Computer Science, LNCS},
 title = {Model-Based Whole-Genome Analysis of DNA Methylation Fidelity},
 volume = {9271},
 year = {2015}
}

@incollection{bortolussiRuleBasedModellingAndSimulation2015,
 author = {Luca Bortolussi and Thilo Krüger and Thorsten Lehr and Verena Wolf},
 booktitle = {MSM '15: Proceedings of the Symposium on Modeling and Simulation in Medicine},
 editor = {Nicht bekannt},
 isbn = {978-1-5108-0102-8},
 month = {4},
 pages = {53-60},
 publisher = {ACM},
 title = {Rule-based modelling and simulation of drug-administration policies},
 year = {2015}
}