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We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate regularities in their phase-spaces through interactions with their environment. These emergent information patterns can then be encoded within the organism's components, leading to self-modelling "tangled hierarchies". Our main conjecture is that when macro-scale patterns are encoded within micro-scale components, it creates fundamental tensions (computational inconsistencies) between what is encodable at a particular evolutionary stage and what is potentially realisable in the environment. A resolution of these tensions triggers an evolutionary transition which expands the problem-space, at the cost of generating new tensions in the expanded space, in a continual process. We argue that biological complexification can be interpreted computation-theoretically, within the G\"odel--Turing--Post recursion-theoretic framework, as open-ended generation of computational novelty. In general, this process can be viewed as a meta-simulation performed by higher-order systems that successively simulate the computation carried out by lower-order systems. This computation-theoretic argument provides a basis for hypothesising the biological arrow of time., Comment: 30 pages, 13 figures

Recurrent waves which are often observed during long pandemics typically form as a result of several interrelated dynamics including public health interventions, population mobility and behaviour, varying disease transmissibility due to pathogen mutations, and changes in host immunity due to recency of vaccination or previous infections. Complex nonlinear dependencies among these dynamics, including feedback between disease incidence and the opinion-driven adoption of social distancing behaviour, remain poorly understood, particularly in scenarios involving heterogeneous population, partial and waning immunity, and rapidly changing public opinions. This study addressed this challenge by proposing an opinion dynamics model that accounts for changes in social distancing behaviour (i.e., whether to adopt social distancing) by modelling both individual risk perception and peer pressure. The opinion dynamics model was integrated and validated within a large-scale agent-based COVID-19 pandemic simulation that modelled the spread of the Omicron variant of SARS-CoV-2 between December 2021 and June 2022 in Australia. Our study revealed that the fluctuating adoption of social distancing, shaped by individual risk aversion and social peer pressure from both household and workplace environments, may explain the observed pattern of recurrent waves of infections., Comment: 18 pages, 7 figures

Diverse and complex intervention policies deployed over the last years have shown varied effectiveness in controlling the COVID-19 pandemic. However, a systematic analysis and modelling of the combined effects of different viral lineages and complex intervention policies remains a challenge. Using large-scale agent-based modelling and a high-resolution computational simulation matching census-based demographics of Australia, we carried out a systematic comparative analysis of several COVID-19 pandemic scenarios. The scenarios covered two most recent Australian census years (2016 and 2021), three variants of concern (ancestral, Delta and Omicron), and five representative intervention policies. In addition, we introduced pandemic Lorenz curves measuring an unequal distribution of the pandemic severity across local areas. We quantified nonlinear effects of population heterogeneity on the pandemic severity, highlighting that (i) the population growth amplifies pandemic peaks, (ii) the changes in population size amplify the peak incidence more than the changes in density, and (iii) the pandemic severity is distributed unequally across local areas. We also examined and delineated the effects of urbanisation on the incidence bimodality, distinguishing between urban and regional pandemic waves. Finally, we quantified and examined the impact of school closures, complemented by partial interventions, and identified the conditions when inclusion of school closures may decisively control the transmission. Our results suggest that (a) public health response to long-lasting pandemics must be frequently reviewed and adapted to demographic changes, (b) in order to control recurrent waves, mass-vaccination rollouts need to be complemented by partial NPIs, and (c) healthcare and vaccination resources need to be prioritised towards the localities and regions with high population growth and/or high density., Comment: 43 pages, 25 figures, source code: https://zenodo.org/record/5778218

We modelled emergence and spread of the Omicron variant of SARS-CoV-2 in Australia between December 2021 and June 2022. This pandemic stage exhibited a diverse epidemiological profile with emergence of co-circulating sub-lineages of Omicron, further complicated by differences in social distancing behaviour which varied over time. Our study delineated distinct phases of the Omicron-associated pandemic stage, and retrospectively quantified the adoption of social distancing measures, fluctuating over different time periods in response to the observable incidence dynamics. We also modelled the corresponding disease burden, in terms of hospitalisations, intensive care unit occupancy, and mortality. Supported by good agreement between simulated and actual health data, our study revealed that the nonlinear dynamics observed in the daily incidence and disease burden were determined not only by introduction of sub-lineages of Omicron, but also by the fluctuating adoption of social distancing measures. Our high-resolution model can be used in design and evaluation of public health interventions during future crises., Comment: 30 pages, 12 figures, source code: https://doi.org/10.5281/zenodo.7325675

The efficient market hypothesis (EMH), based on rational expectations and market equilibrium, is the dominant perspective for modelling economic markets. However, the most notable critique of the EMH is the inability to model periods of out-of-equilibrium behaviour in the absence of any significant external news. When such dynamics emerge endogenously, the traditional economic frameworks provide no explanation for such behaviour and the deviation from equilibrium. This work offers an alternate perspective explaining the endogenous emergence of punctuated out-of-equilibrium dynamics based on bounded rational agents. In a concise market entrance game, we show how boundedly rational strategic reasoning can lead to endogenously emerging crises, exhibiting fat tails in "returns". We also show how other common stylised facts of economic markets, such as clustered volatility, can be explained due to agent diversity (or lack thereof) and the varying learning updates across the agents. This work explains various stylised facts and crisis emergence in economic markets, in the absence of any external news, based purely on agent interactions and bounded rational reasoning., Comment: 10 pages + 7 page appendix, 7 figures

The COVID-19 pandemic created enormous public health and socioeconomic challenges. The health effects of vaccination and non-pharmaceutical interventions (NPIs) were often contrasted with significant social and economic costs. We describe a general framework aimed to derive adaptive cost-effective interventions, adequate for both recent and emerging pandemic threats. We also quantify the net health benefits and propose a reinforcement learning approach to optimise adaptive NPIs. The approach utilises an agent-based model simulating pandemic responses in Australia, and accounts for a heterogeneous population with variable levels of compliance fluctuating over time and across individuals. Our analysis shows that a significant net health benefit may be attained by adaptive NPIs formed by partial social distancing measures, coupled with moderate levels of the society's willingness to pay for health gains (health losses averted). We demonstrate that a socially acceptable balance between health effects and incurred economic costs is achievable over a long term, despite possible early setbacks.

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.

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.

An outbreak of the Delta (B.1.617.2) variant of SARS-CoV-2 that began around mid-June 2021 in Sydney, Australia, quickly developed into a nation-wide epidemic. The ongoing epidemic is of major concern as the Delta variant is more infectious than previous variants that circulated in Australia in 2020. Using a re-calibrated agent-based model, we explored a feasible range of non-pharmaceutical interventions, including case isolation, home quarantine, school closures, and stay-at-home restrictions (i.e., "social distancing"). Our modelling indicated that the levels of reduced interactions in workplaces and across communities attained in Sydney and other parts of the nation were inadequate for controlling the outbreak. A counter-factual analysis suggested that if 70% of the population followed tight stay-at-home restrictions, then at least 45 days would have been needed for new daily cases to fall from their peak to below ten per day. Our model predicted that, under a progressive vaccination rollout, if 40-50% of the Australian population follow stay-at-home restrictions, the incidence will peak by mid-October 2021: the peak in incidence across the nation was indeed observed in mid-October. We also quantified an expected burden on the healthcare system and potential fatalities across Australia., Comment: 36 pages, 15 figures, published in "Frontiers in Public Health", 24 February 2022

While game theory has been transformative for decision-making, the assumptions made can be overly restrictive in certain instances. In this work, we investigate some of the underlying assumptions of rationality, such as mutual consistency and best response, and consider ways to relax these assumptions using concepts from level-$k$ reasoning and quantal response equilibrium (QRE) respectively. Specifically, we propose an information-theoretic two-parameter model called the Quantal Hierarchy model, which can relax both mutual consistency and best response while still approximating level-$k$, QRE, or typical Nash equilibrium behaviour in the limiting cases. The model is based on a recursive form of the variational free energy principle, representing higher-order reasoning as (pseudo) sequential decision-making in extensive-form game tree. This representation enables us to treat simultaneous games in a similar manner to sequential games, where reasoning resources deplete throughout the game-tree. Bounds in player processing abilities are captured as information costs, where future branches of reasoning are discounted, implying a hierarchy of players where lower-level players have fewer processing resources. We demonstrate the effectiveness of the Quantal Hierarchy model in several canonical economic games, {both simultaneous and sequential}, using out-of-sample modelling., Comment: 31 pages, 20 figures

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.

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., Comment: 39 pages, 15 figures

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., Comment: 18 pages, 7 figures, 1 table

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., Comment: Ayan Paul references preprints (DESY 20-142, HU-EP-20/23)

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., Comment: 25 pages + 31 page appendix

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., Comment: 35 pages, 13 figures

In this Ansatz we consider theoretical constructions of RNA polymers into automata, a form of computational structure. The basis for transitions in our automata are plausible RNA enzymes that may perform ligation or cleavage. Limited to these operations, we construct RNA automata of increasing complexity; from the Finite Automaton (RNA-FA) to the Turing Machine equivalent 2-stack PDA (RNA-2PDA) and the universal RNA-UPDA. For each automaton we show how the enzymatic reactions match the logical operations of the RNA automaton. A critical theme of the Ansatz is the self-reference in RNA automata configurations which exploits the program-data duality but results in computational undecidability. We describe how computational undecidability is exemplified in the self-referential Liar paradox that places a boundary on a logical system, and by construction, any RNA automata. We argue that an expansion of the evolutionary space for RNA-2PDA automata can be interpreted as a hierarchical resolution of computational undecidability by a meta-system (akin to Turing's oracle), in a continual process analogous to Turing's ordinal logics and Post's extensible recursively generated logics. On this basis, we put forward the hypothesis that the resolution of undecidable configurations in RNA automata represent a novelty generation mechanism and propose avenues for future investigation of biological automata.

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.

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., Comment: 18 pages, 3 figures, plus supplementary materials

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., Comment: 45 pages, 19 figures

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., Comment: 17 pages, 13 figures

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., Comment: 9 pages, 3 figures

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., Comment: 12 pages, 1 figure, RoboCup-2019, champion paper

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., Comment: 23 pages, 11 figures

We review research papers which use game theory to model the decision making of individuals during an epidemic, attempting to classify the literature and identify the emerging trends in this field. We show that the literature can be classified based on (i) type of population modelling (compartmental or network-based), (ii) frequency of the game (non-iterative or iterative), and (iii) type of strategy adoption (self-evaluation or imitation). We highlight that the choice of model depends on many factors such as the type of immunity the disease confers, the type of immunity the vaccine confers, and size of population and level of mixing therein. We show that while early studies used compartmental modelling with self-evaluation based strategy adoption, the recent trend is to use network-based modelling with imitation-based strategy adoption. Our review indicates that game theory continues to be an effective tool to model intervention (vaccination or social distancing) decision-making by individuals., Comment: 24 pages, 10 figures

We describe Gliders2d, a base code release for Gliders, a soccer simulation team which won the RoboCup Soccer 2D Simulation League in 2016. We trace six evolutionary steps, each of which is encapsulated in a sequential change of the released code, from v1.1 to v1.6, starting from agent2d-3.1.1 (set as the baseline v1.0). These changes improve performance by adjusting the agents' stamina management, their pressing behaviour and the action-selection mechanism, as well as their positional choice in both attack and defense, and enabling riskier passes. The resultant behaviour, which is sufficiently generic to be applicable to physical robot teams, increases the players' mobility and achieves a better control of the field. The last presented version, Gliders2d-v1.6, approaches the strength of Gliders2013, and outperforms agent2d-3.1.1 by four goals per game on average. The sequential improvements demonstrate how the methodology of human-based evolutionary computation can markedly boost the overall performance with even a small number of controlled steps., Comment: 12 pages, 1 figure, Gliders2d code release

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.

Between the 2011 and 2016 national censuses, the Australian Bureau of Statistics changed its anonymity policy compliance system for the distribution of census data. The new method has resulted in dramatic inconsistencies when comparing low-resolution data to aggregated high-resolution data. Hence, aggregated totals do not match true totals, and the mismatch gets worse as the data resolution gets finer. Here, we address several aspects of this inconsistency with respect to the 2016 usual-residence to place-of-work travel data. We introduce a re-sampling system that rectifies many of the artifacts introduced by the new ABS protocol, ensuring a higher level of consistency across partition sizes. We offer a surrogate high-resolution 2016 commuter dataset that reduces the difference between aggregated and true commuter totals from ~34% to only ~7%, which is on the order of the discrepancy across partition resolutions in data from earlier years.

We present a novel approach to the study of epidemics on networks as thermodynamic phenomena, considering the thermodynamic efficiency of contagions, considered as distributed computational processes. Modelling SIS dynamics on a contact network statistical-mechanically, we follow the Maximum Entropy principle to obtain steady state distributions and derive, under certain assumptions, relevant thermodynamic quantities both analytically and numerically. In particular, we obtain closed form solutions for some cases, while interpreting key epidemic variables, such as the reproductive ratio $R_0$ of a SIS model, in a statistical mechanical setting. On the other hand, we consider configuration and free entropy, as well as the Fisher Information, in the epidemiological context. This allowed us to identify criticality and distinct phases of epidemic processes. For each of the considered thermodynamic quantities, we compare the analytical solutions informed by the Maximum Entropy principle with the numerical estimates for SIS epidemics simulated on Watts-Strogatz random graphs.

Urban transformations within large and growing metropolitan areas often generate critical dynamics affecting social interactions, transport connectivity and income flow distribution. We develop a statistical-mechanical model of urban transformations, exemplified for Greater Sydney, and derive a thermodynamic description highlighting critical regimes. We consider urban dynamics at two time scales: fast dynamics for the distribution of population and income, modelled via the maximum entropy principle, and slower dynamics evolving the urban structure under spatially distributed competition. We identify phase transitions between dispersed and polycentric phases, induced by varying the social disposition---a factor balancing the suburbs' attractiveness---in contrast with the travel impedance. Using the Fisher information we identify critical thresholds and quantify the thermodynamic cost of urban transformation, as the minimal work required to vary the underlying parameter. Finally, we introduce the notion of thermodynamic efficiency of urban transformation, as the ratio of the order gained during a change to the amount of required work, showing that this measure is maximised at criticality.

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., Comment: 31 pages, 8 figures, 1 table, 3 supplemental movies

In this paper we present ACEMod, an agent-based modelling framework for studying influenza epidemics in Australia. The simulator is designed to analyse the spatiotemporal spread of contagion and influenza spatial synchrony across the nation. The individual-based epidemiological model accounts for mobility (worker and student commuting) patterns and human interactions derived from the 2006 Australian census and other national data sources. The high-precision simulation comprises 19.8 million stochastically generated software agents and traces the dynamics of influenza viral infection and transmission at several scales. Using this approach, we are able to synthesise epidemics in Australia with varying outbreak locations and severity. For each scenario, we investigate the spatiotemporal profiles of these epidemics, both qualitatively and quantitatively, via incidence curves, prevalence choropleths, and epidemic synchrony. This analysis exemplifies the nature of influenza pandemics within Australia and facilitates future planning of effective intervention, mitigation and crisis management strategies., Comment: 24 pages, 11 figures, under review (Simulation Modelling Practice and Theory)

Information dynamics is an emerging description of information processing in complex systems which describes systems in terms of intrinsic computation, identifying computational primitives of information storage and transfer. In this paper we make a formal analogy between information dynamics and stochastic thermodynamics which describes the thermal behaviour of small irreversible systems. As stochastic dynamics is increasingly being utilized to quantify the thermodynamics associated with the processing of information we suggest such an analogy is instructive, highlighting that existing thermodynamic quantities can be described solely in terms of extant information theoretic measures related to information processing. In this contribution we construct irreversibility measures in terms of these quantities and relate them to the physical entropy productions that characterise the behaviour of single and composite systems in stochastic thermodynamics illustrating them with simple examples. Moreover, we can apply such a formalism to systems which do not have a bipartite structure. In particular we demonstrate that, given suitable non-bipartite processes, the heat flow in a subsystem can still be identified and one requires the present formalism to recover generalizations of the second law. In these systems residual irreversibility is associated with neither subsystem and this must be included in the these generalised second laws. This opens up the possibility of describing all physical systems in terms of computation allowing us to propose a framework for discussing the reversibility of systems traditionally out of scope of stochastic thermodynamics., Comment: 28 pages, 4 figures

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 G\"odel'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 G\"odel's proof distinguish between computational universality and undecidability, and show how the diagonalization argument exploits, on several levels, the self-referential basis of undecidability., Comment: 25 pages

Information ratchets extract work from heat baths using low entropy information reservoirs. We find that the structure of the reservoirs affects both their performance and phase diagram. By deriving exact probabilities of recurrence in d-dimensional reservoirs we calculate the net extraction of work. Performance is characterised by two critical dimensions (i) For d < 3 driven exploration of the reservoir is essential to extract work (ii) For d > 4 purely diffusive exploration is optimal. This has important consequences for computation where sequential operations constitute a 1D path.

We study self-organisation of collective motion as a thermodynamic phenomenon, in the context of the first law of thermodynamics. It is expected that the coherent ordered motion typically self-organises in the presence of changes in the (generalised) internal energy and of (generalised) work done on, or extracted from, the system. We aim to explicitly quantify changes in these two quantities in a system of simulated self-propelled particles, and contrast them with changes in the system's configuration entropy. In doing so, we adapt a thermodynamic formulation of the curvatures of the internal energy and the work, with respect to two parameters that control the particles' alignment. This allows us to systematically investigate the behaviour of the system by varying the two control parameters to drive the system across a kinetic phase transition. Our results identify critical regimes and show that during the phase transition, where the configuration entropy of the system decreases, the rates of change of the work and of the internal energy also decrease, while their curvatures diverge. Importantly, the reduction of entropy achieved through expenditure of work is shown to peak at criticality. We relate this both to a thermodynamic efficiency and the significance of the increased order with respect to a computational path. Additionally, this study provides an information-geometric interpretation of the curvature of the internal energy as the difference between two curvatures: the curvature of the free entropy, captured by the Fisher information, and the curvature of the configuration entropy.

We summarise the results of RoboCup 2D Soccer Simulation League in 2016 (Leipzig), including the main competition and the evaluation round. The evaluation round held in Leipzig confirmed the strength of RoboCup-2015 champion (WrightEagle, i.e. WE2015) in the League, with only eventual finalists of 2016 competition capable of defeating WE2015. An extended, post-Leipzig, round-robin tournament which included the top 8 teams of 2016, as well as WE2015, with over 1000 games played for each pair, placed WE2015 third behind the champion team (Gliders2016) and the runner-up (HELIOS2016). This establishes WE2015 as a stable benchmark for the 2D Simulation League. We then contrast two ranking methods and suggest two options for future evaluation challenges. The first one, "The Champions Simulation League", is proposed to include 6 previous champions, directly competing against each other in a round-robin tournament, with the view to systematically trace the advancements in the League. The second proposal, "The Global Challenge", is aimed to increase the realism of the environmental conditions during the simulated games, by simulating specific features of different participating countries., Comment: 12 pages, RoboCup-2017, Nagoya, Japan, July 2017

It is generally accepted that, when moving in groups, animals process information to coordinate their motion. Recent studies have begun to apply rigorous methods based on Information Theory to quantify such distributed computation. Following this perspective, we use transfer entropy to quantify dynamic information flows locally in space and time across a school of fish during directional changes around a circular tank, i.e. U-turns. This analysis reveals peaks in information flows during collective U-turns and identifies two different flows: an informative flow (positive transfer entropy) based on fish that have already turned about fish that are turning, and a misinformative flow (negative transfer entropy) based on fish that have not turned yet about fish that are turning. We also reveal that the information flows are related to relative position and alignment between fish, and identify spatial patterns of information and misinformation cascades. This study offers several methodological contributions and we expect further application of these methodologies to reveal intricacies of self-organisation in other animal groups and active matter in general.

We review disruptive innovations introduced in the RoboCup 2D Soccer Simulation League over the twenty years since its inception, and trace the progress of our champion team (Gliders). We conjecture that the League has been developing as an ecosystem shaped by diverse approaches taken by participating teams, increasing in its overall complexity. A common feature is that different champion teams succeeded in finding a way to decompose the enormous search-space of possible single- and multi-agent behaviours, by automating the exploration of the problem space with various techniques which accelerated the software development efforts. These methods included interactive debugging, machine learning, automated planning, and opponent modelling. The winning approach developed by Gliders is centred on human-based evolutionary computation which optimised several components such as an action-dependent evaluation function, dynamic tactics with Voronoi diagrams, information dynamics, and bio-inspired collective behaviour., Comment: 12 pages, RoboCup-2016, Leipzig, Germany, July 2016

In this work, we are interested in structure learning for a set of spatially distributed dynamical systems, where individual subsystems are coupled via latent variables and observed through a filter. We represent this model as a directed acyclic graph (DAG) that characterises the unidirectional coupling between subsystems. Standard approaches to structure learning are not applicable in this framework due to the hidden variables, however we can exploit the properties of certain dynamical systems to formulate exact methods based on state space reconstruction. We approach the problem by using reconstruction theorems to analytically derive a tractable expression for the KL-divergence of a candidate DAG from the observed dataset. We show this measure can be decomposed as a function of two information-theoretic measures, transfer entropy and stochastic interaction. We then present two mathematically robust scoring functions based on transfer entropy and statistical independence tests. These results support the previously held conjecture that transfer entropy can be used to infer effective connectivity in complex networks.

Transfer entropy has been used to quantify the directed flow of information between source and target variables in many complex systems. While transfer entropy was originally formulated in discrete time, in this paper we provide a framework for considering transfer entropy in continuous time systems, based on Radon-Nikodym derivatives between measures of complete path realizations. To describe the information dynamics of individual path realizations, we introduce the pathwise transfer entropy, the expectation of which is the transfer entropy accumulated over a finite time interval. We demonstrate that this formalism permits an instantaneous transfer entropy rate. These properties are analogous to the behavior of physical quantities defined along paths such as work and heat. We use this approach to produce an explicit form for the transfer entropy for pure jump processes, and highlight the simplified form in the specific case of point processes (frequently used in neuroscience to model neural spike trains). Finally, we present two synthetic spiking neuron model examples to exhibit the pertinent features of our formalism, namely, that the information flow for point processes consists of discontinuous jump contributions (at spikes in the target) interrupting a continuously varying contribution (relating to waiting times between target spikes). Numerical schemes based on our formalism promise significant benefits over existing strategies based on discrete time formalisms., Comment: 24 pages, 2 figures

The behaviour of many real-world phenomena can be modelled by nonlinear dynamical systems whereby a latent system state is observed through a filter. We are interested in interacting subsystems of this form, which we model by a set of coupled maps as a synchronous update graph dynamical systems. Specifically, we study the structure learning problem for spatially distributed dynamical systems coupled via a directed acyclic graph. Unlike established structure learning procedures that find locally maximum posterior probabilities of a network structure containing latent variables, our work exploits the properties of dynamical systems to compute globally optimal approximations of these distributions. We arrive at this result by the use of time delay embedding theorems. Taking an information-theoretic perspective, we show that the log-likelihood has an intuitive interpretation in terms of information transfer.

Physically-realistic simulated environments are powerful platforms for enabling measurable, replicable and statistically-robust investigation of complex robotic systems. Such environments are epitomised by the RoboCup simulation leagues, which have been successfully utilised to conduct massively-parallel experiments in topics including: optimisation of bipedal locomotion, self-localisation from noisy perception data and planning complex multi-agent strategies without direct agent-to-agent communication. Many of these systems are later transferred to physical robots, making the simulation leagues invaluable well-beyond the scope of simulated soccer matches. In this study, we provide an overview of the RoboCup simulation leagues and describe their properties as they pertain to replicable and robust robotics research. To demonstrate their utility directly, we leverage the ability to run parallelised experiments to evaluate different competition formats (e.g. round robin) for the RoboCup 2D simulation league. Our results demonstrate that a previously-proposed hybrid format minimises fluctuations from 'true' (statistically-significant) team performance rankings within the time constraints of the RoboCup world finals. Our experimental analysis would be impossible with physical robots alone, and we encourage other researchers to explore the potential for enriching their experimental pipelines with simulated components, both to minimise experimental costsand enable others to replicate and expand upon their results in a hardware-independent manner., Comment: 9 pages, 4 figures. arXiv admin note: text overlap with arXiv:1403.4023