arXiv subjects

Mikhail Prokopenko

Publications and source records attributed to Mikhail Prokopenko.

At least 19 recordsLinked to original sources

arXiv2026

Algorithmic bottlenecks in evolution: Genetic code, symbolic language, and the Great Filter hypothesis

The Great Filter hypothesis proposes that the emergence of technological societies capable of interstellar travel depends on a small number of exceptionally hard and highly improbable steps. Traditional versions of this hypothesis enumerate such "hard steps" along the trajectory from inanimate matter to complex technological societies but diverge in their explanations for why these particular steps should be so improbable. The theory of Major Evolutionary Transitions also faces challenges in identifying which steps should be considered universally "hard" across different evolutionary pathways. In contrast, we argue that two deeply structural obstacles dominate the evolutionary landscape: the coding threshold associated with the origin of genetic code, and the language threshold associated with the emergence of symbolic communication. We examine the developmental precursors of both transitions and analyze the underlying algorithmic bottlenecks: points at which evolving systems separate code from function, while entangling them within information hierarchies. Using a game-theoretic analysis of coupled signaling and coordination dynamics, we then argue that the corresponding multichannel games may exhibit saddle-type equilibria whose stable manifolds define narrow evolutionary paths, making the transitions intrinsically difficult to traverse. We conjecture that the so-called Great Filter is best understood not as a sequence of isolated improbable events, but as a nested structure of tangled information hierarchies. Under this conjecture, the rarity of advanced societies follows from the difficulty of crossing these coding thresholds in a competitive noisy environment. This hypothesis reframes the Great Filter as an algorithmic property of evolving systems, suggesting that only a small fraction of life may ever traverse the path toward technological societies capable of interstellar travel.

q-bio.PE↗

arXiv2026

Thermodynamic efficiency of self-organisation in nonequilibrium steady states

Active matter generates order or patterns through nonequilibrium dynamics. An open research challenge is to determine how efficiently a nonequilibrium self-organising system can convert consumed energy into macroscopic order. We study an information-theoretic quantity that directly addresses this challenge by estimating the entropy reduction induced by a small control-parameter perturbation, relative to the generalised work required for the perturbation. This quantity has previously been considered mainly in an equilibrium or near-equilibrium context, and here we extend this framework and apply it to two nonequilibrium self-organising systems: persistent and active Ising models. We observe that the thermodynamic efficiency of nonequilibrium systems maximises at phase transitions, as in equilibrium systems. Furthermore, we compare thermodynamic efficiency and inferential efficiency across control parameters. While these two quantities are equal in equilibrium as a consequence of the fluctuation-dissipation theorem, we report that they diverge out of equilibrium, and the gap serves as a phenomenological signature of broken detailed balance.

nlin.AO↗

arXiv2026

The Non-Orientable Topology of Condorcet's Paradox

Preference cycles are prevalent in problems of decision-making, and are contradictory when preferences are assumed to be transitive. This contradiction underlies Condorcet's Paradox, a pioneering result of social choice theory, wherein intuitive and seemingly desirable constraints on decision-making necessarily lead to contradictory preference cycles. Topological methods have since broadened social choice theory and elucidated existing results. However, characterisations of preference cycles in topological social choice theory are lacking. In this paper, we address this gap by introducing a framework for topologically modelling preference cycles that generalises Baryshnikov's existing topological model of strict, ordinal preferences on 3 alternatives. In our framework, the contradiction underlying Condorcet's Paradox topologically corresponds to the non-orientability of a surface homeomorphic to either the Klein bottle or real projective plane, depending on how preference cycles are represented. These findings allow us to reformulate Arrow's Impossibility Theorem in terms of the orientability of a surface as well.

math.AT↗

arXiv2025

Arrow's Impossibility Theorem as a Generalisation of Condorcet's Paradox

Arrow's Impossibility Theorem is a seminal result of Social Choice Theory that demonstrates the impossibility of ranked-choice decision-making processes to jointly satisfy a number of intuitive and seemingly desirable constraints. The theorem is often described as a generalisation of Condorcet's Paradox, wherein pairwise majority voting may fail to jointly satisfy the same constraints due to the occurrence of elections that result in contradictory preference cycles. However, a formal proof of this relationship has been limited to D'Antoni's work, which applies only to the strict preference case, i.e., where indifference between alternatives is not allowed. In this paper, we generalise D'Antoni's methodology to prove in full (i.e., accounting for weak preferences) that Arrow's Impossibility Theorem can be equivalently stated in terms of contradictory preference cycles. This methodology involves explicitly constructing profiles that lead to preference cycles. Using this framework, we also prove a number of additional facts regarding social welfare functions. As a result, this methodology may yield further insights into the nature of preference cycles in other domains e.g., Money Pumps, Dutch Books, Intransitive Games, etc.

econ.TH↗

arXiv2025

Generalising thermodynamic efficiency of interactions: inferential, information-geometric and computational perspectives

Self-organizing systems consume energy to generate internal order. The concept of thermodynamic efficiency, drawing from statistical physics and information theory, has previously been proposed to characterise a change in control parameter by relating the resulting predictability gain to the required amount of work. However, previous studies have taken a system-centric perspective and considered only single control parameters. Here, we generalise thermodynamic efficiency to multiple control parameters and extend the definition of thermodynamic efficiency to protocols in arbitrary directions, by introducing directional efficiency. Taking an observer-centric perspective, we derive two novel formulations. The first, an inferential form, relates efficiency to fluctuations of macroscopic observables, interpreting thermodynamic efficiency in terms of how well the system parameters can be inferred from observable macroscopic behaviour. The second, an information-geometric form, expresses efficiency in terms of the Fisher information matrix, interpreting it with respect to how difficult it is to navigate the statistical manifold defined by the control protocol. This observer-centric perspective is contrasted with the existing system-centric view, where efficiency is considered an intrinsic property of the system.

nlin.AO↗

arXiv2025

Comparing and Contrasting Arrow's Impossibility Theorem and G\"odel's Incompleteness Theorem

Incomputability results in Formal Logic and the Theory of Computation (i.e., incompleteness and undecidability) have deep implications for the foundations of mathematics and computer science. Likewise, Social Choice Theory, a branch of Welfare Economics, contains various impossibility results that place limits on the potential fairness, rationality and consistency of social decision-making processes. However, a relationship between the fields' most seminal results: G\"odel's First Incompleteness Theorem of Formal Logic, and Arrow's Impossibility Theorem in Social Choice Theory is lacking. In this paper, we address this gap by introducing a general mathematical object called a Self-Reference System. Correspondences between the two theorems are formalised by abstracting well-known diagonalisation and fixed-point arguments, and consistency and completeness properties of provability predicates in the language of Self-Reference Systems. Nevertheless, we show that the mechanisms generating Arrovian impossibility and G\"odelian incompleteness have subtle differences.

math.LO↗

arXiv2024

Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution

Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the rapid emergence of new variants, (2) human interactions within a heterogeneous population, and (3) public health responses which constrain individual actions to control the disease transmission. We then present a pandemic modelling framework satisfying these requirements and capable of simulating feedback loops between dynamics unfolding at these different scales. The developed framework comprises a stochastic agent-based model of pandemic spread, coupled with a phylodynamic model that incorporates within-host pathogen evolution. It is validated with a case study, modelling the punctuated evolution of SARS-CoV-2, based on global and contemporary genomic surveillance data, which captures a large heterogeneous population. We demonstrate that the model replicates the essential features of the COVID-19 pandemic and virus evolution, while retaining computational tractability and scalability.

q-bio.PE↗

arXiv2024

Why collective behaviours self-organise to criticality: A primer on information-theoretic and thermodynamic utility measures

Collective behaviours are frequently observed to self-organise to criticality. Existing proposals to explain these phenomena are fragmented across disciplines and only partially answer the question. This primer compares the underlying, intrinsic, utilities that may explain the self-organisation of collective behaviours near criticality. We focus on information-driven approaches (predictive information, empowerment, and active inference), as well as an approach incorporating both information theory and thermodynamics (thermodynamic efficiency). By interpreting the Ising model as a perception-action loop, we compare how different intrinsic utilities shape collective behaviour and analyse the distinct characteristics that arise when each is optimised. In particular, we highlight that thermodynamic efficiency -- measuring the ratio of predictability gained by the system to its energy costs -- reaches its maximum at the critical regime. Finally, we propose the Principle of Super-efficiency, suggesting that collective behaviours self-organise to the critical regime where optimal efficiency is achieved with respect to the entropy reduction relative to the thermodynamic costs.

nlin.AO↗

arXiv2024

Biological arrow of time: Emergence of tangled information hierarchies and self-modelling dynamics

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.

q-bio.PE↗

arXiv2024

Impact of opinion dynamics on recurrent pandemic waves: balancing risk aversion and peer pressure

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.

q-bio.QM↗

arXiv2023

Measuring unequal distribution of pandemic severity across census years, variants of concern and interventions

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.

q-bio.PE↗

arXiv2022

Persistence of the Omicron variant of SARS-CoV-2 in Australia: The impact of fluctuating social distancing

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.

q-bio.PE↗

arXiv2022

Bounded strategic reasoning explains crisis emergence in multi-agent market games

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.

cs.MA↗

arXiv2022

A general framework for optimising cost-effectiveness of pandemic response under partial intervention measures

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.

cs.MA↗

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

Simulating transmission scenarios of the Delta variant of SARS-CoV-2 in Australia

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.

q-bio.PE↗

arXiv2021

Bounded rationality for relaxing best response and mutual consistency: The Quantal Hierarchy model of decision-making

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.

cs.GT↗