publications-journals

Journal articles

B. P. Evans, M. Prokopenko, Bounded rationality for relaxing best response and mutual consistency: the Quantal Hierarchy model of decision making, Theory and Decision, 10.1007/s11238-023-09941-z, 2023.
S. L. Chang, Q. D. Nguyen, A. Martiniuk, V. Sintchenko, T. C. Sorrell, M. Prokopenko, Persistence of the Omicron variant of SARS-CoV-2 in Australia: The impact of fluctuating social distancing, PLOS Global Public Health, 3(4): e0001427, 2023.
A. J. Svahn, C. J. E. Suster, S. L. Chang, R. J. Rockett, E. M. Sim, O. M. Cliff, Q. Wang, A. Arnott, M. Ramsperger, T. C. Sorrell, V. Sintchenko, M. Prokopenko, Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene gogB, Microbiology Spectrum, 11(2): e02791-22, 2023.
B. P. Evans, M. Prokopenko, Bounded strategic reasoning explains crisis emergence in multi-agent market games, Royal Society Open Science, 10(2): 221164, 2023.
Q. D. Nguyen, M. Prokopenko, A general framework for optimising cost-effectiveness of pandemic response under partial intervention measures, Scientific Reports, 12: 19482, 2022.
J. Thompson, R. McClure, N. Scott, M. Hellard, R. Abeysuriya, R. Vidinaarachichi, J. Thwaites, J. Lazarus, S. Michie, C. Bullen, M. Prokopenko, S. Chang, O. Cliff, C. Zachreson, T. Blakely, T. Wilson, D. Ait Oakrim, V. Sundararajan, A framework for communicating the utility of models when facing tough decisions in public health, Health Research Policy and Systems, 20, 107, 2022.
A. Malik, M. Li, M. Lenzen, J. Fry, N. Liyanapathirana, K. Beyer, S. Boylan, A. Lee, D. Raubenheimer, A. Geschke, M. Prokopenko, Impacts of climate change and extreme weather on food supply chains cascade across sectors and regions in Australia, Nature Food, 3: 631-643, 2022.
C. Zachreson, S. L. Chang, N. Harding, M. Prokopenko, The effects of local homogeneity assumptions in metapopulation models of infectious disease, Royal Society Open Science, 9, 211919, 2022.
S. L. Chang, O. M. Cliff, C. Zachreson, M. Prokopenko, Simulating Transmission Scenarios of the Delta Variant of SARS-CoV-2 in Australia, Frontiers in Public Health, 10, 10.3389/fpubh.2022.823043, 2022.
A. J. Svahn, S. L. Chang, R. J. Rockett, O. M. Cliff, Q. Wang, A. Arnott, M. Ramsperger, T. C. Sorrell, V. Sintchenko, M. Prokopenko, Genome-wide networks reveal emergence of epidemic strains of Salmonella Enteritidis, International Journal of Infectious Diseases, 117: P65-73, 2022.
C. Zachreson, S. L. Chang, O. M. Cliff, M. Prokopenko, How will mass-vaccination change COVID-19 lockdown requirements in Australia?, The Lancet Regional Health – Western Pacific, 14: 100224, 2021.
R. Nigmatullin, M. Prokopenko, Thermodynamic efficiency of interactions in self-organizing systems, Entropy, 23(6): 757, 2021.
B. Slavko, K. Glavatskiy, M. Prokopenko, Revealing configurational attractors in the evolution of modern Australian and US cities, Chaos, Solitons & Fractals, 148: 111079, 2021.
B. P. Evans, M. Prokopenko, A maximum entropy model of bounded rational decision-making with prior beliefs and market feedback, Entropy, 23(6): 669, 2021.
B. P. Evans, K. Glavatskiy, M. Harré, M. Prokopenko, The impact of social influence in Australian real-estate: market forecasting with a spatial agent-based model, Journal of Economic Interaction and Coordination, DOI: 10.1007/s11403-021-00324-7, 2021 (also on arXiv).
K. Glavatskiy, M. Prokopenko, A. Carro, P. Ormerod, M. Harré, Explaining herding and volatility in the cyclical price dynamics of urban housing markets using a large‑scale agent‑based model, Business and Economics, 1:76, DOI: 10.1007/s43546-021-00077-2, 2021.
E. Crosato, M. Prokopenko, M. Harré, The polycentric dynamics of Melbourne and Sydney: Suburb attractiveness divides a city at the home ownership level, Proceedings of Royal Society A, 477: 20200514, 2021.
B. Slavko, M. Prokopenko, K. Glavatskiy, Diffusive resettlement: irreversible urban transitions in closed systems, Entropy, 23 (1): 66, 2021.
J. Bell, G. Bianconi, D. Butler, J. Crowcroft, P. C. W. Davies, C. Hicks, H. Kim, I. Kiss, F. Di Lauro, C. Maple, A. Paul, M. Prokopenko, P. Tee, S. I. Walker, Beyond COVID-19: Network science and sustainable exit strategies, Journal of Physics: Complexity, 2(2): 021001, 2021.
S. L. Chang, N. Harding, C. Zachreson, O. M. Cliff, M. Prokopenko, Modelling transmission and control of the COVID-19 pandemic in Australia, Nature Communications, 11, 5710, 2020.
O. M. Cliff, N. McLean, V. Sintchenko, K. M. Fair, T. C. Sorrell, S. Kauffman, M. Prokopenko, Inferring evolutionary pathways and directed genotype networks of foodborne pathogens, PLoS Computational Biology, 16(10): e1008401, 2020.
Q. D. Nguyen, M. Prokopenko, Structure-preserving imitation learning with delayed reward: an evaluation within the RoboCup Soccer 2D Simulation environment, Frontiers in Robotics and AI, 7: 123, 2020.
R. J. Rockett, A. Arnott, C. Lam, R. Sadsad, V. Timms, K.-A. Gray, J.-S. Eden, S. L. Chang, M. Gall, J. Draper, E. Sim, N. L. Bachmann, I. Carter, K. Basile, R. Byun, M. V. O. Sullivan, S. C. A. Chen, S. Maddocks, T. C. Sorrell, D. E. Dwyer, E. C. Holmes, J. Kok, M. Prokopenko, V. Sintchenko, Revealing COVID-19 transmission by SARS-CoV-2 genome sequencing and agent based modelling, Nature Medicine, 26: 1398–1404, 2020.
S. L. Chang, M. Piraveenan, M. Prokopenko, Impact of network assortativity on epidemic and vaccination behaviour, Chaos, Solitons & Fractals, 140: 110143, 2020.
M. Lenzen, M. Li, A. Malik, F. Pomponi, Y.-Y. Sun, T. Wiedmann, F. Faturay, J. Fry, B. Gallego, A. Geschke, J. Gómez-Paredes, K. Kanemoto, S. Kenway, K. Nansai, M. Prokopenko, T. Wakiyama, Y. Wang, M. Yousefzadeh, Global socio-economic losses and environmental gains from the Coronavirus pandemic, PLoS ONE, 15(7): e0235654, 2020.
B. Slavko, K. Glavatskiy, M. Prokopenko, City structure shapes directional resettlement flows in Australia, Scientific Reports, 10: 8235, 2020.
N. Harding, R. E. Spinney, M. Prokopenko, Population mobility induced phase separation in SIS epidemic and social dynamics, Scientific Reports, 10: 7646, 2020.
C. Zachreson, K. M. Fair, N. Harding, M. Prokopenko, Interfering with influenza: nonlinear coupling of reactive and static mitigation strategies, Journal of Royal Society Interface, 17(165): 20190728, 2020.
N. Harding, R. E. Spinney, M. Prokopenko, Phase transitions in spatial connectivity during influenza pandemics, Entropy, 22(2), 133, 2020.
S. Chang, M. Piraveenan, P. Pattison, M. Prokopenko, Game theoretic modelling of infectious disease dynamics and intervention methods: a review, Journal of Biological Dynamics, 14(1): 57-89, 2020.
M. Prokopenko, M. Harré, J. Lizier, F. Boschetti, P. Peppas, S. Kauffman, Self-referential basis of undecidable dynamics: from The Liar Paradox and the halting Problem to the edge of chaos, Physics of Life Reviews, 31, 134-156, 2019 (also on arXiv).
E. Crosato, M. Prokopenko, R. E. Spinney, Irreversibility and emergent structure in active matter, Physical Review E, 100, 042613, 2019.
K. M. Fair, C. Zachreson, M. Prokopenko, Creating a surrogate commuter network from Australian Bureau of Statistics census data, Scientific Data, 6, 150, 2019.
S. L. Chang, M. Piraveenan, M. Prokopenko, The Effects of Imitation Dynamics on Vaccination Behaviours in SIR-Network Model, International Journal of Environmental Research and Public Health, 16(14), 2477, 2019.
O. M. Cliff, V. Sintchenko, T. C. Sorrell, K. Vadlamudi, N. McLean, M. Prokopenko, Network properties of Salmonella epidemics, Scientific Reports, 9, 6159, 2019; see also: Supplementary Information.
B. Slavko, K. Glavatskiy, M. Prokopenko, Dynamic resettlement as a mechanism of phase transitions in urban configurations, Physical Review E, 99, 042143, 2019.
A. D. M. Wilson, A. L. J Burns, E. Crosato, J. Lizier, M. Prokopenko, T. M. Schaerf, A. J. W. Ward, Conformity in the collective: differences in hunger affect individual and group behavior in a shoaling fish, Behavioral Ecology, arz036, 2019.
C. Zachreson, K. M. Fair, O. M. Cliff, N. Harding, M. Piraveenan, M. Prokopenko, Urbanization affects peak timing, prevalence, and bimodality of influenza pandemics in Australia: Results of a census-calibrated model, Science Advances, 4(12), eaau5294, 2018.
A. J. W. Ward, T. M. Schaerf, A. L. J. Burns, J. T. Lizier, E. Crosato, M. Prokopenko and M. M. Webster, Cohesion, order and information flow in the collective motion of mixed-species shoals, Royal Society Open Science, 5: 181132, 2018.
D. Penny, C. Zachreson, R. Fletcher, D. Lau, J. T. Lizier, N. Fischer, D. Evans, C. Pottier, M. Prokopenko, The demise of Angkor: Systemic vulnerability of urban infrastructure to climatic variations, Science Advances, 4(10), eaau4029, 2018.
E. Crosato, R. Nigmatullin, M. Prokopenko, On critical dynamics and thermodynamic efficiency of urban transformations, Royal Society Open Science, 5: 180863, 2018.
D. Chu, M. Prokopenko, J. C. J. Ray, Computation by natural systems, Interface Focus, 8, 20180058, 2018.
N. Harding, R. Nigmatullin, M. Prokopenko, Thermodynamic efficiency of contagions: a statistical mechanical analysis of the SIS epidemic model, Interface Focus, 8 20180036, 2018.
R. E. Spinney, J. T. Lizier, M. Prokopenko, Entropy balance and information processing in bipartite and non-bipartite composite systems, Physical Review E, 98 (3), 032141, 2018.
R. E. Spinney, M. Prokopenko, D. Chu, Information ratchets exploiting spatially structured information reservoirs, Physical Review E, 98 (2), 022124, 2018.
A. C. Kalloniatis, M. L. Zuparic, M. Prokopenko, Fisher information and criticality in the Kuramoto model of nonidentical oscillators, Physical Review E, 98 (2), 022302, 2018.
O. M. Cliff, N. Harding, M. Piraveenan, E. Y. Erten, M. Gambhir, M. Prokopenko, Investigating Spatiotemporal Dynamics and Synchrony of Influenza Epidemics in Australia: An Agent-Based Modelling Approach, Simulation Modelling Practice and Theory, 87, 412-431, 2018 (also on arXiv).
O. M. Cliff, M. Prokopenko, R. Fitch, Minimising the Kullback–Leibler Divergence for Model Selection in Distributed Nonlinear Systems, Entropy 20 (2), 51, 2018.
E. Crosato, R. E. Spinney, R. Nigmatullin, J. T. Lizier, M. Prokopenko, Thermodynamics and computation during collective motion near criticality, Physical Review E, 97 (1), 012120, 2018.
E. Crosato, L. Jiang, V. Lecheval, J. T. Lizier, X. R. Wang, P. Tichit, G. Theraulaz, M. Prokopenko, Informative and misinformative interactions in a school of fish, Swarm Intelligence, 12(4): 283-305, 2018 (also on arXiv).
S. L. Chang, M. Prokopenko, Instability of mixed Nash equilibria in generalised Hawk-Dove game: A project conflict management scenario, Games, 8 (4), 42, 2017.
M. Zuparic, V. Jauregui, M. Prokopenko, Y. Yue, Quantifying the impact of communication on performance in multi-agent teams, Artificial Life and Robotics, 22 (3), 357-373, 2017.
M. Prokopenko, Complexity, Criticality and Computation, Entropy, 19 (8), 403, 2017.
M. Prokopenko, Modelling complex systems and guided self-organisation, Journal and Proceedings of the Royal Society of New South Wales, 150, 463/464, 104-109, 2017.
E. Y. Erten, J. T. Lizier, M. Piraveenan, M. Prokopenko, Criticality and Information dynamics in epidemiological models, Entropy, 19 (5), 194, 2017.
R. E. Spinney, M. Prokopenko, J. T. Lizier, Transfer entropy in continuous time, with applications to jump and neural spiking processes, Physical Review E, 95 (3), 032319, 2017.
O. M. Cliff, J. T. Lizier, X. R. Wang, P. Wang, O. Obst, M. Prokopenko, Quantifying long-range interactions and coherent structure in multi-agent dynamics, Artificial life, 23 (1), 34-57, 2017.
O. M. Cliff, M. Prokopenko, R. Fitch, An information criterion for inferring coupling in distributed dynamical systems, Frontiers of Robotics and AI, 3, 71, 2016.
R. E. Spinney, J. T. Lizier, M. Prokopenko, Transfer entropy in physical systems and the arrow of time, Physical Review E, 94, 022135, 2016.
M. Harré, M. Prokopenko, The social brain: scale-invariant layering of Erdős–Rényi networks in small-scale human societies, Journal of The Royal Society Interface, vol. 13(118), 20160044, 2016.
M. Prokopenko, L. Barnett, M. Harré, J. T. Lizier, O. Obst, X. R. Wang, Fisher Transfer Entropy: Quantifying the gain in transient sensitivity, Proceedings of The Royal Society A, vol. 471(2184), 20150610, 2015.
C. Salge, N. Ay, D. Polani, M. Prokopenko. Zipf's Law: Balancing Signal Usage Cost and Communication Efficiency, PLOS ONE, 10(10): e0139475, 2015.
M. Prokopenko, I. Einav, Information thermodynamics of near-equilibrium computation, Physical Review E, 91(6), 1-8, 2015.
D. Budden, P. Wang, O. Obst, M. Prokopenko, RoboCup Simulation Leagues: Enabling Replicable and Robust Investigation of Complex Robotic Systems, IEEE Robotics and Automation Magazine, 22(3), 140-146, 2015.
M. Prokopenko and C. Gershenson, Entropy Methods in Guided Self-Organisation, Entropy, 16(10), 5232-5241, 2014.
M. Prokopenko, J. T. Lizier, Transfer Entropy and Transient Limits of Computation, Scientific Reports, 4:5394, 2014.
M. Prokopenko, Grand challenges for Computational Intelligence, Frontiers of Robotics and AI, 1:2, 1-3, 2014.
X. R. Wang, J. T. Lizier, T. Nowotny, A. Z. Berna, M. Prokopenko, S. C. Trowell, Feature Selection for Chemical Sensor Arrays Using Mutual Information, PLoS ONE, 9(3): e89840, 2014.
M. Prokopenko, J. T. Lizier, D. C. Price, On thermodynamic interpretation of transfer entropy, Entropy, 15(2): 524-543, 2013.
M. Piraveenan, M. Prokopenko, L. Hossein, Percolation Centrality: Quantifying Graph-Theoretic Impact of Nodes during Percolation in Networks, PLoS ONE, 8(1): e53095, 2013.
V. Cupac, J. T. Lizier, M. Prokopenko, Comparing dynamics of cascading failures between network-centric and power flow models, International Journal of Electrical Power and Energy Systems, 49: 369-379, 2013.
D. Polani, M. Prokopenko, L. S. Yaeger, Information and Self-Organization of Behavior, Advances in Complex Systems, topical issue on Guided Self-Organisation, 16(2): 1303001-1-1303001-12, 2013.
A. Adamatzky, S. Akl, R. Alonso-Sanz, W. van Dessel, Z. Ibrahim, A. Ilachinski, J. Jones, A. V. D. M. Kayem, G. J. Martinez, P. de Oliveira, M. Prokopenko, T. Schubert, P. Sloot, E. Strano, X.-S. Yang, Are motorways rational from slime mould's point of view?, International Journal of Parallel, Emergent and Distributed Systems, 28(3): 230-248, 2013.
X. R. Wang, J. M. Miller, J. T. Lizier, M. Prokopenko, L. F. Rossi, Quantifying and Tracing Information Cascades in Swarms, PLoS ONE, 7(7): e40084, 2012.
J. T. Lizier, M. Prokopenko, and A. Y. Zomaya, Coherent information structure in complex computation, Theory in Biosciences, special issue on Guided Self-Organisation (GSO-2010), 131: 193–203, 2012.
N. Ay, H. Bernigau, R. Der, M. Prokopenko, Information driven self-organization: The dynamical system approach to autonomous robot behavior, Theory in Biosciences, special issue on Guided Self-Organisation (GSO-2010), 131: 161–179, 2012.
N. Ay, R. Der, M. Prokopenko, Guided Self-Organization: Perception-Action Loops of Embodied Systems, Theory in Biosciences, special issue on Guided Self-Organisation (GSO-2010), 131: 125–127, 2012.
M. Piraveenan, M. Prokopenko, A. Y. Zomaya, On congruity of nodes and assortative information content in complex networks, Networks and Heterogeneous Media, 7(3): 441–461, September, 2012.
J. T. Lizier, M. Prokopenko, and A. Y. Zomaya, Local measures of information storage in complex distributed computation, Information Sciences, 208: 39–54, DOI: 10.1016/j.ins.2012.04.016, 2012.
A. Adamatzky, M. Prokopenko, Slime mould evaluation of Australian motorways, International Journal of Parallel, Emergent and Distributed Systems, 27(4): 275–295, 2012.
M. Piraveenan, M. Prokopenko, A. Y. Zomaya. Assortative mixing in directed biological networks, IEEE Transactions on Computational Biology and Bioinformatics, 9(1): 66-78, 2012.
M. Prokopenko, J. T. Lizier, O. Obst, and X. R. Wang, Relating Fisher information to order parameters, Physical Review E, 84, 041116, 2011.
C. Gershenson, M. Prokopenko, Complex networks, Artificial Life, special issue on Complex Networks, 17(4), 1-3, 2011.
J. T. Lizier, S. Pritam, M. Prokopenko, Information dynamics in small-world Boolean networks, Artificial Life, special issue on Complex Networks, 17(4), 293-314, 2011.
X. R. Wang, J. T. Lizier, M. Prokopenko, Fisher Information at the Edge of Chaos in Random Boolean Networks, Artificial Life, special issue on Complex Networks, 17(4), 315-329, 2011.
J. T. Lizier, J. Heinzle, C. S Soon, J.-D. Haynes, M. Prokopenko, Spatiotemporal information transfer pattern differences in motor selection, BMC Neuroscience, 12(Suppl 1):P261, doi:10.1186/1471-2202-12-S1-P261, 2011.
M. Rubinov, J. T. Lizier, M. Prokopenko, M. Breakspear, Maximized directed information transfer in critical neuronal networks, BMC Neuroscience, 12(Suppl 1):P18, doi:10.1186/1471-2202-12-S1-P18, 2011.
J. T. Lizier, J. Heinzle, A. Horstmann, J.-D. Haynes, M. Prokopenko, Multivariate information-theoretic measures reveal directed information structure and task relevant changes in fMRI connectivity, Journal of Computational Neuroscience, 30:85–107, 2011.
M. Prokopenko, N. Ay, O. Obst and D. Polani, Phase Transitions in Least-Effort Communications, Journal of Statistical Mechanics: Theory and Experiment, 2010(11): P11025, 2010.
J. T. Lizier, M. Prokopenko, and A. Y. Zomaya, Information modification and particle collisions in distributed computation, Chaos, 20(3): 037109, 2010.
M. Piraveenan, M. Prokopenko, A. Y. Zomaya. Local assortativeness in scale-free networks – Addendum, Europhysics Letters, 89, 49901, 2010.
J. T. Lizier, M. Prokopenko. Differentiating information transfer and causal effect, European Physical Journal B, 73(4), 605-615, 2010 (also on arXiv).
M. Prokopenko, Guided Self-organization, HFSP Journal, 3(5), 287-289, DOI: 10.2976/1.3233933, 2009.
M. Prokopenko, F. Boschetti, A. Ryan. An information-theoretic primer on complexity, self-organisation and emergence, Complexity, 15(1), 11-28, Wiley, 2009.
M. Prokopenko, D. Polani, M. Chadwick. Stigmergic gene transfer and emergence of universal coding, HFSP Journal, 3(5), 317-327, DOI: 10.2976/1.3175813, 2009.
M. Piraveenan, M. Prokopenko, A. Y. Zomaya, Local Assortativity and Growth of Internet, European Physical Journal B, 70, 275–285, 2009.
J. T. Lizier, J.-D. Haynes, J. Heinzle, M. Prokopenko. Directed information structure in inter-regional cortical interactions in a visuomotor tracking task, BMC Neuroscience, 10(Suppl 1):P117, DOI: 10.1186/1471-2202-10-S1-P117, 2009.
M. Prokopenko. Book review: Information and Self-Organization: A Macroscopic Approach to Complex Systems (H. Haken), Artificial Life, 15(3), 377-383, 2009.
M. Piraveenan, M. Prokopenko, A. Y. Zomaya. Assortativeness and information in scale-free networks, European Physical Journal B, 67, 291–300, 2009.
G. Mathews, H. F. Durrant-Whyte, M. Prokopenko. Decentralised decision making in heterogeneous teams using anonymous optimisation, Robotics and Autonomous Systems, 57(3): 310-320, 2009.
M. Piraveenan, M. Prokopenko, A. Y. Zomaya. Local assortativeness in scale-free networks, Europhysics Letters, 84, 28002, 2008.
J. T. Lizier, M. Prokopenko, and A. Y. Zomaya. Local information transfer as a spatiotemporal filter for complex systems. Physical Review E, 77, 026110, 2008 .
Prokopenko, M., Polani, D., Wang, P. Optimizing Associative Information Transfer within Content-addressable Memory, International Journal of Unconventional Computation, Vol. 4(3), Special issue "Towards Theory of Unconventional Computing", 273-296, 2008.
Prokopenko, M. A Preferential Semantics for Causal Reasoning about Action, Annals of Mathematics and Artificial Intelligence, Vol. 46(4), 375-413, April, 2006.
M. Prokopenko, P. Wang, D. C. Price, P. Valencia, M. Foreman, A. J. Farmer. Self-organizing Hierarchies in Sensor and Communication Networks. Artificial Life, Special Issue on Dynamic Hierarchies, Vol. 11(4), 407-426, 2005.
M. Prokopenko, P. Wang, M. Foreman, P. Valencia, D. C. Price, G. T. Poulton. On Connectivity of Reconfigurable Impact Networks in Ageless Aerospace Vehicles. Robotics and Autonomous Systems, Vol. 53(1), 36-58, 2005.
D.A. Scott, A. Batten, G.C. Edwards, A.J. Farmer, M. Hedley, N. Hoschke, P. Isaacs, M.E. Johnson, A. Murdoch, C.J. Lewis, D.C. Price, M. Prokopenko, P. Valencia and P. Wang, An Intelligent Sensor System for Detection and Evaluation of Particle Impact Damage, Review of Progress in Quantitative Nondestructive Evaluation, Vol. 24, pp. 1825-32 (eds. D.O. Thompson and D.E. Chimenti), American Institute of Physics Conference Proceedings Vol. 760, 2005.
D. Abbott, B. Doyle, J.B. Dunlop, A.J. Farmer, M. Hedley, J. Herrmann, G.C. James, M.E. Johnson, B. Joshi, G.T. Poulton, D.C. Price, M. Prokopenko, T. Reda, D.E. Rees, D.A. Scott, P. Valencia, D. Ward and J.G. Winter, Concepts for an Integrated Vehicle Health Monitoring System, Review of Progress in Quantitative Nondestructive Evaluation, Vol. 22, pp. 1606-14 (eds. D.O. Thompson and D.E. Chimenti), American Institute of Physics Conference Proceedings Vol. 657, 2003.