Abstract
Stochastic models in which agents interact with their neighborhood according to a network topology are a powerful modeling framework to study the emergence of complex dynamic patterns in real-world systems. Stochastic simulations are often the preferred—sometimes the only feasible—way to investigate such systems. Previous research focused primarily on Markovian models where the random time until an interaction happens follows an exponential distribution.
In this work, we study a general framework to model systems where each agent is in one of several states. Agents can change their state at random, influenced by their complete neighborhood, while the time to the next event can follow an arbitrary probability distribution. Classically, these simulations are hindered by high computational costs of updating the rates of interconnected agents and sampling the random residence times from arbitrary distributions.
We propose a rejection-based, event-driven simulation algorithm to overcome these limitations. Our method over-approximates the instantaneous rates corresponding to inter-event times while rejection events counter-balance these over-approximations. We demonstrate the effectiveness of our approach on models of epidemic and information spreading.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsNotes
- 1.
github.com/gerritgr/non-markovian-simulation.
References
Barabási, A.-L.: Network Science. Cambridge University Press, Cambridge (2016)
Goutsias, J., Jenkinson, G.: Markovian dynamics on complex reaction networks. Phys. Rep. 529(2), 199–264 (2013)
Pastor-Satorras, R., Castellano, C., Van Mieghem, P., Vespignani, A.: Epidemic processes in complex networks. Rev. Mod. Phys. 87(3), 925 (2015)
Kiss, I.Z., Miller, J.C., Simon, P.L.: Mathematics of Epidemics on Networks. Forthcoming in Springer TAM Series, Cham (2016)
Porter, M., Gleeson, J.: Dynamical Systems on Networks: A Tutorial, vol. 4. Springer, Cham (2016)
Rodrigues, H.S.: Application of SIR epidemiological model: new trends. arXiv preprint. arXiv:1611.02565 (2016)
Kitsak, M., Gallos, L.K., Havlin, S., Liljeros, F., Muchnik, L., Stanley, H.E., Makse, H.A.: Identification of influential spreaders in complex networks. Nat. Phys. 6(11), 888 (2010)
Zhao, L., Wang, J., Chen, Y., Wang, Q., Cheng, J., Cui, H.: SIHR rumor spreading model in social networks. Phys. A Stat. Mech. Appl. 391(7), 2444–2453 (2012)
Goltsev, A.V., De Abreu, F.V., Dorogovtsev, S.N., Mendes, J.F.F.: Stochastic cellular automata model of neural networks. Phys. Rev. E 81(6), 061921 (2010)
Meier, J., Zhou, X., Hillebrand, A., Tewarie, P., Stam, C.J., Van Mieghem, P.: The epidemic spreading model and the direction of information flow in brain networks. NeuroImage 152, 639–646 (2017)
Gan, C., Yang, X., Liu, W., Zhu, Q., Zhang, X.: Propagation of computer virus under human intervention: a dynamical model. Discret. Dyn. Nat. Soc. 2012 (2012)
May, R.M., Arinaminpathy, N.: Systemic risk: the dynamics of model banking systems. J. R. Soc. Interface 7(46), 823–838 (2009)
Peckham, R.: Contagion: epidemiological models and financial crises. J. Public Health 36(1), 13–17 (2013)
Masuda, N., Rocha, L.E.C.: A Gillespie algorithm for non-Markovian stochastic processes. SIAM Rev. 60(1), 95–115 (2018)
Lloyd, A.L.: Realistic distributions of infectious periods in epidemic models: changing patterns of persistence and dynamics. Theor. Popul. Biol. 60(1), 59–71 (2001)
Yang, G.L.: Empirical study of a non-Markovian epidemic model. Math. Biosci. 14(1–2), 65–84 (1972)
Blythe, S.P., Anderson, R.M.: Variable infectiousness in HFV transmission models. Math. Med. Biol. J. IMA 5(3), 181–200 (1988)
Hollingsworth, T.D., Anderson, R.M., Fraser, C.: HIV-1 transmission, by stage of infection. J. Infect. Dis. 198(5), 687–693 (2008)
Feng, Z., Thieme, H.R.: Endemic models for the spread of infectious diseases with arbitrarily distributed disease stages I: general theory. SIAM J. Appl. Math. 61(3), 803–833 (2000)
Barabasi, A.-L.: The origin of bursts and heavy tails in human dynamics. Nature 435(7039), 207 (2005)
Vázquez, A., Oliveira, J.G., Dezsö, Z., Goh, K.-I., Kondor, I., Barabási, A.-L.: Modeling bursts and heavy tails in human dynamics. Phys. Rev. E 73(3), 036127 (2006)
Softky, W.R., Koch, C.: The highly irregular firing of cortical cells is inconsistent with temporal integration of random EPSPs. J. Neurosci. 13(1), 334–350 (1993)
Boguná, M., Lafuerza, L.F., Toral, R., Serrano, M.A.: Simulating non-Markovian stochastic processes. Phys. Rev. E 90(4), 042108 (2014)
Cota, W., Ferreira, S.C.: Optimized Gillespie algorithms for the simulation of Markovian epidemic processes on large and heterogeneous networks. Comput. Phys. Commun. 219, 303–312 (2017)
St-Onge, G., Young, J.-G., Hébert-Dufresne, L., Dubé, L.J.: Efficient sampling of spreading processes on complex networks using a composition and rejection algorithm. arXiv preprint. arXiv:1808.05859 (2018)
Großmann, G., Wolf, V.: Rejection-based simulation of stochastic spreading processes on complex networks. In: International Workshop on Hybrid Systems Biology, pp. 63–79. Springer, Cham (2019)
Cox, D.R.: Renewal Theory (1962)
Pasupathy, R.: Generating Homogeneous Poisson Processes. Wiley Encyclopedia of Operations Research and Management Science, Hoboken (2010)
Kiss, I.Z., Röst, G., Vizi, Z.: Generalization of pairwise models to non-Markovian epidemics on networks. Phys. Rev. Lett. 115(7), 078701 (2015)
Pellis, L., House, T., Keeling, M.J.: Exact and approximate moment closures for non-Markovian network epidemics. J. Theor. Biol. 382, 160–177 (2015)
Jo, H.-H., Perotti, J.I., Kaski, K., Kertész, J.: Analytically solvable model of spreading dynamics with non-Poissonian processes. Phys. Rev. X 4(1), 011041 (2014)
Sherborne, N., Miller, J.C., Blyuss, K.B., Kiss, I.Z.: Mean-field models for non-Markovian epidemics on networks: from edge-based compartmental to pairwise models. arXiv preprint. arXiv:1611.04030 2016
Starnini, M., Gleeson, J.P., Boguñá, M.: Equivalence between non-Markovian and Markovian dynamics in epidemic spreading processes. Phys. Rev. Lett. 118(12), 128301 (2017)
Vestergaard, C.L., Génois, M.: Temporal Gillespie algorithm: fast simulation of contagion processes on time-varying networks. PLoS Comput. Biol. 11(10), e1004579 (2015)
Großmann, G., Bortolussi, L., Wolf, V.: Rejection-based simulation of non-Markovian agents on complex networks. arxiv.org/abs/1910.03964 (2019)
Ogata, Y.: On Lewis’ simulation method for point processes. IEEE Trans. Inf. Theor. 27(1), 23–31 (1981)
Dassios, A., Zhao, H., et al.: Exact simulation of Hawkes process with exponentially decaying intensity. Electron. Commun. 18 (2013)
Fosdick, B.K., Larremore, D.B., Nishimura, J., Ugander, J.: Configuring random graph models with fixed degree sequences. SIAM Rev. 60(2), 315–355 (2018)
Röst, G., Vizi, Z., Kiss, I.Z.: Impact of non-Markovian recovery on network epidemics. In: BIOMAT 2015: International Symposium on Mathematical and Computational Biology, pp. 40–53. World Scientific (2016)
Van Mieghem, P., Van de Bovenkamp, R.: Non-Markovian infection spread dramatically alters the susceptible-infected-susceptible epidemic threshold in networks. Phys. Rev. Lett. 110(10), 108701 (2013)
Jo, H.-H., Lee, B.-H., Hiraoka, T., Jung, W.-S.: Copula-based algorithm for generating bursty time series. arXiv preprint. arXiv:1904.08795 (2019)
Acknowledgements
We thank Guillaume St-Onge for helpful comments on non-Markovian dynamics. This research was been partially funded by the German Research Council (DFG) as part of the Collaborative Research Center “Methods and Tools for Understanding and Controlling Privacy”.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this paper
Cite this paper
Großmann, G., Bortolussi, L., Wolf, V. (2020). Rejection-Based Simulation of Non-Markovian Agents on Complex Networks. In: Cherifi, H., Gaito, S., Mendes, J., Moro, E., Rocha, L. (eds) Complex Networks and Their Applications VIII. COMPLEX NETWORKS 2019. Studies in Computational Intelligence, vol 881. Springer, Cham. https://doi.org/10.1007/978-3-030-36687-2_29
Download citation
DOI: https://doi.org/10.1007/978-3-030-36687-2_29
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-36686-5
Online ISBN: 978-3-030-36687-2
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)