arXiv subjects

Mikhail Prokopenko

Publications and source records attributed to Mikhail Prokopenko.

At least 37 records · Page 2Linked to original sources

arXiv2022

Genome-wide networks reveal emergence of epidemic strains of Salmonella Enteritidis

Objectives: To enhance monitoring of high-burden foodborne pathogens, there is opportunity to combine pangenome data with network analysis. Methods: Salmonella enterica subspecies Enterica serovar Enteritidis isolates were referred to the New South Wales (NSW) Enteric Reference Laboratory between August 2015 and December 2019 (1033 isolates in total), inclusive of a confirmed outbreak. All isolates underwent whole genome sequencing. Distances between genomes were quantified by in silico MLVA as well as core SNPs, which informed construction of undirected networks. Prevalence-centrality spaces were generated from the undirected networks. Components on the undirected SNP network were considered alongside a phylogenetic tree representation. Results: Outbreak isolates were identifiable as distinct components on the MLVA and SNP networks. The MLVA network based centrality/prevalence space did not delineate the outbreak, whereas the outbreak was clearly delineated in the SNP network based centrality/prevalence space. Components on the undirected SNP network showed a high concordance to the SNP clusters based on phylogenetic analysis. Conclusions: Bacterial whole genome data in network based analysis can improve the resolution of population analysis. High concordance of network components and SNP clusters is promising for rapid population analyses of foodborne Salmonella spp. due to the low overhead of network analysis.

q-bio.QM↗

arXiv2021

The effects of local homogeneity assumptions in metapopulation models of infectious disease

Computational models of infectious disease can be broadly categorized into two types: individual-based (Agent-based), or compartmental models. While compartmental models can be structured to separate distinct sectors of a population, they are conceptually distinct from individual-based models in which population structure emerges from micro-scale interactions. While the conceptual distinction is straightforward, a fair comparison of the approaches is difficult to achieve. Here, we carry out such a comparison by building a set of compartmental metapopulation models from an agent-based representation of a real population. By adjusting the compartmental model to approximately match the dynamics of the Agent-based model, we identify two key qualitative properties of the individual-based dynamics which are lost upon aggregation into metapopulations. These are (1) the local depletion of susceptibility to infection, and (2) decoupling of different regional groups due to correlation between commuting behaviors and contact rates. The first of these effects is a general consequence of aggregating small, closely connected groups (i.e., families) into larger homogeneous metapopulations. The second can be interpreted as a consequence of aggregating two distinct types of individuals: school children, who travel short distances but have many potentially infectious contacts, and adults, who travel further but tend to have fewer contacts capable of transmitting infection. Our results could be generalised to other types of correlations between the characteristics of individuals and the behaviors that distinguish them.

q-bio.PE↗

arXiv2021

How will mass-vaccination change COVID-19 lockdown requirements in Australia?

Background: To prevent future outbreaks of COVID-19, Australia is pursuing a mass-vaccination approach in which a targeted group of the population comprising healthcare workers, aged-care residents and other individuals at increased risk of exposure will receive a highly effective priority vaccine. The rest of the population will instead have access to a less effective vaccine. Methods: We apply a large-scale agent-based model of COVID-19 in Australia to investigate the possible implications of this hybrid approach to mass-vaccination. The model is calibrated to recent epidemiological and demographic data available in Australia, and accounts for several components of vaccine efficacy. Findings: Within a feasible range of vaccine efficacy values, our model supports the assertion that complete herd immunity due to vaccination is not likely in the Australian context. For realistic scenarios in which herd immunity is not achieved, we simulate the effects of mass-vaccination on epidemic growth rate, and investigate the requirements of lockdown measures applied to curb subsequent outbreaks. In our simulations, Australia's vaccination strategy can feasibly reduce required lockdown intensity and initial epidemic growth rate by 43% and 52%, respectively. The severity of epidemics, as measured by the peak number of daily new cases, decreases by up to two orders of magnitude under plausible mass-vaccination and lockdown strategies. Interpretation: The study presents a strong argument for a large-scale vaccination campaign in Australia, which would substantially reduce both the intensity of future outbreaks and the stringency of non-pharmaceutical interventions required for their suppression.

q-bio.PE↗

arXiv2021

A maximum entropy model of bounded rational decision-making with prior beliefs and market feedback

Bounded rationality is an important consideration stemming from the fact that agents often have limits on their processing abilities, making the assumption of perfect rationality inapplicable to many real tasks. We propose an information-theoretic approach to the inference of agent decisions under Smithian competition. The model explicitly captures the boundedness of agents (limited in their information-processing capacity) as the cost of information acquisition for expanding their prior beliefs. The expansion is measured as the Kullblack-Leibler divergence between posterior decisions and prior beliefs. When information acquisition is free, the homo economicus agent is recovered, while in cases when information acquisition becomes costly, agents instead revert to their prior beliefs. The maximum entropy principle is used to infer least-biased decisions based upon the notion of Smithian competition formalised within the Quantal Response Statistical Equilibrium framework. The incorporation of prior beliefs into such a framework allowed us to systematically explore the effects of prior beliefs on decision-making in the presence of market feedback, as well as importantly adding a temporal interpretation to the framework. We verified the proposed model using Australian housing market data, showing how the incorporation of prior knowledge alters the resulting agent decisions. Specifically, it allowed for the separation of past beliefs and utility maximisation behaviour of the agent as well as the analysis into the evolution of agent beliefs.

cs.IT↗

arXiv2021

The impact of social influence in Australian real-estate: market forecasting with a spatial agent-based model

Housing markets are inherently spatial, yet many existing models fail to capture this spatial dimension. Here we introduce a new graph-based approach for incorporating a spatial component in a large-scale urban housing agent-based model (ABM). The model explicitly captures several social and economic factors that influence the agents' decision-making behaviour (such as fear of missing out, their trend following aptitude, and the strength of their submarket outreach), and interprets these factors in spatial terms. The proposed model is calibrated and validated with the housing market data for the Greater Sydney region. The ABM simulation results not only include predictions for the overall market, but also produce area-specific forecasting at the level of local government areas within Sydney as arising from individual buy and sell decisions. In addition, the simulation results elucidate agent preferences in submarkets, highlighting differences in agent behaviour, for example, between first-time home buyers and investors, and between both local and overseas investors.

q-fin.CP↗

arXiv2021

Diffusive resettlement: irreversible urban transitions in closed systems

We propose a phenomenological non-equilibrium framework for modelling the evolution of cities which describes the intra-urban resettlement as an irreversible diffusive process. We validate this framework using the actual migration data for the Australian capital cities. With respect to the residential relocation, the population is shown to be composed of two distinct groups, exhibiting different relocation frequencies. In the context of the developed framework, these groups can be interpreted as two components of a binary mixture, each with its own diffusive relaxation time. Using this approach, we obtain long-term predictions of the cities' spatial structure, which defines their equilibrium population distribution.

physics.soc-ph↗

arXiv2020

Revealing configurational attractors in the evolution of modern Australian and US cities

The spatial structure of modern cities exhibits highly diverse patterns and keeps evolving under numerous constraints. Two key dimensions have recently achieved prominence in characterizing this diversity: heterogeneity and spreading. However, modern settlements do not fill the entire heterogeneity--spreading space. Yet, the dynamic mechanisms leading to emergence of the observed layouts are unclear. Here, we assess the heterogeneity and spreading of population density in 25 Australian and 175 US cities. We observe that larger cities tend to form a cluster with a low degree of spreading and a high degree of heterogeneity, and relate this observation to the dynamic properties of intra-urban migration in these cities. In doing so, we introduce a model consistent with the relocation data which predicts such highly compact and heterogeneous structure for the majority of cities, in concordance with the actual layout data. In addition, we analyze the stability of the long-term dynamics of urban configurations with respect to changes in the mobility characteristics, such as social disposition and relocation impedance near their equilibrium states. As a result, we report three qualitatively distinct feasible phases of urban structures: uniform, monocentric, and polycentric. These phases are shown to be separated by either smooth or sharp transitions, observed in the space of suitably chosen configurational parameters. Finally, this analysis reveals that the set of all possible equilibrium configurations ("configurational attractors") form a narrow region in the heterogeneity--spreading space, thus explaining the emergence of clustering patterns.

physics.soc-ph↗

arXiv2020

Modelling transmission and control of the COVID-19 pandemic in Australia

There is a continuing debate on relative benefits of various mitigation and suppression strategies aimed to control the spread of COVID-19. Here we report the results of agent-based modelling using a fine-grained computational simulation of the ongoing COVID-19 pandemic in Australia. This model is calibrated to match key characteristics of COVID-19 transmission. An important calibration outcome is the age-dependent fraction of symptomatic cases, with this fraction for children found to be one-fifth of such fraction for adults. We apply the model to compare several intervention strategies, including restrictions on international air travel, case isolation, home quarantine, social distancing with varying levels of compliance, and school closures. School closures are not found to bring decisive benefits, unless coupled with high level of social distancing compliance. We report several trade-offs, and an important transition across the levels of social distancing compliance, in the range between 70% and 80% levels, with compliance at the 90% level found to control the disease within 13--14 weeks, when coupled with effective case isolation and international travel restrictions.

q-bio.PE↗

arXiv2020

Thermodynamic efficiency of interactions in self-organizing systems

The emergence of global order in complex systems with locally interacting components is most striking at criticality, where small changes in control parameters result in a sudden global re-organization. We introduce a measure of thermodynamic efficiency of interactions in self-organizing systems, which quantifies the change in the system's order per unit work carried out on (or extracted from) the system. We analytically derive the thermodynamic efficiency of interactions for the case of quasi-static variations of control parameters in the exactly solvable Curie-Weiss (fully connected) Ising model, and demonstrate that this quantity diverges at the critical point of a second order phase transition. This divergence is shown for quasi-static perturbations in both control parameters, the external field and the coupling strength. Our analysis formalizes an intuitive understanding of thermodynamic efficiency across diverse self-organizing dynamics in physical, biological and social domains.

cond-mat.stat-mech↗

arXiv2020

Beyond COVID-19: Network science and sustainable exit strategies

On May $28^{th}$ and $29^{th}$, a two day workshop was held virtually, facilitated by the Beyond Center at ASU and Moogsoft Inc. The aim was to bring together leading scientists with an interest in Network Science and Epidemiology to attempt to inform public policy in response to the COVID-19 pandemic. Epidemics are at their core a process that progresses dynamically upon a network, and are a key area of study in Network Science. In the course of the workshop a wide survey of the state of the subject was conducted. We summarize in this paper a series of perspectives of the subject, and where the authors believe fruitful areas for future research are to be found.

physics.soc-ph↗

arXiv2020

The Polycentric Dynamics of Melbourne and Sydney: Suburb attractiveness divides a city at the home ownership level

Urban dynamics in large metropolitan areas result from complex interactions across social, economic, and political factors, including population distribution, flows of wealth, and infrastructure requirements. We develop a Census-calibrated model of urban dynamics for the Greater Sydney and Melbourne areas for 2011 and 2016, highlighting the evolution of population distributions and the housing market structure in these two cities in terms of their mortgage and rent distributions. We show that there is a tendency to homophily between renters and mortgage holders: renters tend to cluster nearer commercial centres, whereas mortgagors tend to populate the outskirts of these centres. We also identify a critical threshold at which the long-term evolution of these two cities will bifurcate between a `sprawling' and a `polycentric' configuration, showing that both cities lie on the polycentric side of the critical point in the long-run. Importantly, there is a divergence of these centric tendencies between the renters and mortgage holders. The polycentric patterns characterising the mortgagors are focused around commercial centres, and we show that the emergent housing patterns follow the major transport routes through the cities.

physics.soc-ph↗

arXiv2020

Impact of network assortativity on epidemic and vaccination behaviour

The resurgence of measles is largely attributed to the decline in vaccine adoption and the increase in mobility. Although the vaccine for measles is readily available and highly successful, its current adoption is not adequate to prevent epidemics. Vaccine adoption is directly affected by individual vaccination decisions, and has a complex interplay with the spatial spread of disease shaped by an underlying mobility (travelling) network. In this paper, we model the travelling connectivity as a scale-free network, and investigate dependencies between the network's assortativity and the resultant epidemic and vaccination dynamics. In doing so we extend an SIR-network model with game-theoretic components, capturing the imitation dynamics under a voluntary vaccination scheme. Our results show a correlation between the epidemic dynamics and the network's assortativity, highlighting that networks with high assortativity tend to suppress epidemics under certain conditions. In highly assortative networks, the suppression is sustained producing an early convergence to equilibrium. In highly disassortative networks, however, the suppression effect diminishes over time due to scattering of non-vaccinating nodes, and frequent switching between the predominantly vaccinating and non-vaccinating phases of the dynamics.

q-bio.PE↗

arXiv2020

Explaining herding and volatility in the cyclical price dynamics of urban housing markets using a large scale agent-based model

Urban housing markets, along with markets of other assets, universally exhibit periods of strong price increases followed by sharp corrections. The mechanisms generating such non-linearities are not yet well understood. We develop an agent-based model populated by a large number of heterogeneous households. The agents' behavior is compatible with economic rationality, with the trend-following behavior found to be essential in replicating market dynamics. The model is calibrated using several large and distributed datasets of the Greater Sydney region (demographic, economic and financial) across three specific and diverse periods since 2006. The model is not only capable of explaining price dynamics during these periods, but also reproduces the novel behavior actually observed immediately prior to the market peak in 2017, namely a sharp increase in the variability of prices. This novel behavior is related to a combination of trend-following aptitude of the household agents (rational herding) and their propensity to borrow.

q-fin.CP↗

arXiv2019

Fractals2019: Combinatorial Optimisation with Dynamic Constraint Annealing

Fractals2019 started as a new experimental entry in the RoboCup Soccer 2D Simulation League, based on Gliders2d code base, and advanced to become a RoboCup-2019 champion. We employ combinatorial optimisation methods, within the framework of Guided Self-Organisation, with the search guided by local constraints. We present examples of several tactical tasks based on the Gliders2d code (version v2), including the search for an optimal assignment of heterogeneous player types, as well as blocking behaviours, offside trap, and attacking formations. We propose a new method, Dynamic Constraint Annealing, for solving dynamic constraint satisfaction problems, and apply it to optimise thermodynamic potential of collective behaviours, under dynamically induced constraints.

cs.AI↗

arXiv2019

The effects of imitation dynamics on vaccination behaviours in SIR-network model

We present a series of SIR-network models, extended with a game-theoretic treatment of imitation dynamics which result from regular population mobility across residential and work areas and the ensuing interactions. Each considered SIR-network model captures a class of vaccination behaviours influenced by epidemic characteristics, interaction topology, and imitation dynamics. Our focus is the eventual vaccination coverage, produced under voluntary vaccination schemes, in response to these varying factors. Using the next generation matrix method, we analytically derive and compare expressions for the basic reproduction number $R_0$ for the proposed SIR-network models. Furthermore, we simulate the epidemic dynamics over time for the considered models, and show that if individuals are sufficiently responsive towards the changes in the disease prevalence, then the more expansive travelling patterns encourage convergence to the endemic, mixed equilibria. On the contrary, if individuals are insensitive to changes in the disease prevalence, we find that they tend to remain unvaccinated in all the studied models. Our results concur with earlier studies in showing that residents from highly connected residential areas are more likely to get vaccinated. We also show that the existence of the individuals committed to receiving vaccination reduces $R_0$ and delays the disease prevalence, and thus is essential to containing epidemics.

q-bio.PE↗

arXiv2019

Thermodynamics of emergent structure in active matter

Active matter is rapidly becoming a key paradigm of out-of-equilibrium soft matter exhibiting complex collective phenomena, yet the thermodynamics of such systems remain poorly understood. In this letter we study the nonequilbrium thermodynamics of large scale active systems capable of mobility-induced phase separation and polar alignment, using a fully under-damped model which exhibits hidden entropy productions not previously reported in the literature. We quantify steady state entropy production at each point in the phase diagram, revealing characteristic dissipation rates associated with the distinct phases and configurational structure. This reveals sharp discontinuities in the entropy production at phase transitions and facilitates identification of the thermodynamics of micro-features, such as defects in the emergent structure. The interpretation of the time reversal symmetry in the dynamics of the particles is found to be crucial.

cond-mat.stat-mech↗

arXiv2019

Urbanization affects peak timing, prevalence, and bimodality of influenza pandemics in Australia: results of a census-calibrated model

We examine salient trends of influenza pandemics in Australia, a rapidly urbanizing nation. To do so, we implement state-of-the-art influenza transmission and progression models within a large-scale stochastic computer simulation, generated using comprehensive Australian census datasets from 2006, 2011, and 2016. Our results offer a simulation-based investigation of a population's sensitivity to pandemics across multiple historical time points, and highlight three significant trends in pandemic patterns over the years: increased peak prevalence, faster spreading rates, and decreasing spatiotemporal bimodality. We attribute these pandemic trends to increases in two key quantities indicative of urbanization: population fraction residing in major cities, and international air traffic. In addition, we identify features of the pandemic's geographic spread that we attribute to changes in the commuter mobility network. The generic nature of our model and the ubiquity of urbanization trends around the world make it likely for our results to be applicable in other rapidly urbanizing nations.

physics.soc-ph↗

arXiv2019

Self-referential basis of undecidable dynamics: from The Liar Paradox and The Halting Problem to The Edge of Chaos

In this paper we explore several fundamental relations between formal systems, algorithms, and dynamical systems, focussing on the roles of undecidability, universality, diagonalization, and self-reference in each of these computational frameworks. Some of these interconnections are well-known, while some are clarified in this study as a result of a fine-grained comparison between recursive formal systems, Turing machines, and Cellular Automata (CAs). In particular, we elaborate on the diagonalization argument applied to distributed computation carried out by CAs, illustrating the key elements of Gödel's proof for CAs. The comparative analysis emphasizes three factors which underlie the capacity to generate undecidable dynamics within the examined computational frameworks: (i) the program-data duality; (ii) the potential to access an infinite computational medium; and (iii) the ability to implement negation. The considered adaptations of Gödel's proof distinguish between computational universality and undecidability, and show how the diagonalization argument exploits, on several levels, the self-referential basis of undecidability.

cs.LO↗