Optimized Gillespie algorithms for the simulation of Markovian epidemic processes on large and heterogeneous networks

Numerical simulation of continuous-time Markovian processes is an essential and widely applied tool in the investigation of epidemic spreading on complex networks. Due to the high heterogeneity of the connectivity structure through which epidemics is transmitted, efficient and accurate implementations of generic epidemic processes are not trivial and deviations from statistically exact prescriptions can lead to uncontrolled biases. Based on the Gillespie algorithm (GA), in which only steps that change the state are considered, we develop numerical recipes and describe their computer implementations for statistically exact and computationally efficient simulations of generic Markovian epidemic processes aiming at highly heterogeneous and large networks. The central point of the recipes investigated here is to include phantom processes, that do not change the states but do count for time increments. We compare the efficiencies for the susceptible-infected-susceptible, contact process and susceptible-infected-recovered models, that are particular cases of a generic model considered here. We numerically confirm that the simulation outcomes of the optimized algorithms are statistically indistinguishable from the original GA and can be several orders of magnitude more efficient.Comment: 12 pages, 9 figure

Griffiths effects of the susceptible-infected-susceptible epidemic model on random power-law networks

We provide numerical evidence for slow dynamics of the susceptible-infected-susceptible model evolving on finite-size random networks with power-law degree distributions. Extensive simulations were done by averaging the activity density over many realizations of networks. We investigated the effects of outliers in both highly fluctuating (natural cutoff) and non-fluctuating (hard cutoff) most connected vertices. Logarithmic and power-law decays in time were found for natural and hard cutoffs, respectively. This happens in extended regions of the control parameter space $\lambda_1<\lambda<\lambda_2$, suggesting Griffiths effects, induced by the topological inhomogeneities. Optimal fluctuation theory considering sample-to-sample fluctuations of the pseudo thresholds is presented to explain the observed slow dynamics. A quasistationary analysis shows that response functions remain bounded at $\lambda_2$. We argue these to be signals of a smeared transition. However, in the thermodynamic limit the Griffiths effects loose their relevancy and have a conventional critical point at $\lambda_c=0$. Since many real networks are composed by heterogeneous and weakly connected modules, the slow dynamics found in our analysis of independent and finite networks can play an important role for the deeper understanding of such systems.Comment: 10 pages, 8 figure

Griffiths phases in infinite-dimensional, non-hierarchical modular networks

Griffiths phases (GPs), generated by the heterogeneities on modular networks, have recently been suggested to provide a mechanism, rid of fine parameter tuning, to explain the critical behavior of complex systems. One conjectured requirement for systems with modular structures was that the network of modules must be hierarchically organized and possess finite dimension. We investigate the dynamical behavior of an activity spreading model, evolving on heterogeneous random networks with highly modular structure and organized non-hierarchically. We observe that loosely coupled modules act as effective rare-regions, slowing down the extinction of activation. As a consequence, we find extended control parameter regions with continuously changing dynamical exponents for single network realizations, preserved after finite size analyses, as in a real GP. The avalanche size distributions of spreading events exhibit robust power-law tails. Our findings relax the requirement of hierarchical organization of the modular structure, which can help to rationalize the criticality of modular systems in the framework of GPs.Comment: 14 pages, 8 figure

Quantifying echo chamber effects in information spreading over political communication networks

Echo chambers in online social networks, in which users prefer to interact only with ideologically-aligned peers, are believed to facilitate misinformation spreading and contribute to radicalize political discourse. In this paper, we gauge the effects of echo chambers in information spreading phenomena over political communication networks. Mining 12 million Twitter messages, we reconstruct a network in which users interchange opinions related to the impeachment of the former Brazilian President Dilma Rousseff. We define a continuous {political position} parameter, independent of the network's structure, that allows to quantify the presence of echo chambers in the strongly connected component of the network, reflected in two well-separated communities of similar sizes with opposite views of the impeachment process. By means of simple spreading models, we show that the capability of users in propagating the content they produce, measured by the associated spreadability, strongly depends on their attitude. Users expressing pro-impeachment sentiments are capable to transmit information, on average, to a larger audience than users expressing anti-impeachment sentiments. Furthermore, the users' spreadability is correlated to the diversity, in terms of political position, of the audience reached. Our method can be exploited to identify the presence of echo chambers and their effects across different contexts and shed light upon the mechanisms allowing to break echo chambers.Comment: 9 pages, 4 figures. Supplementary Information available as ancillary fil

Griffiths phases in infinite-dimensional, non-hierarchical modular networks

Griffiths phases (GPs), generated by the heterogeneities on modular networks, have recently been suggested to provide a mechanism, rid of fine parameter tuning, to explain the critical behavior of complex systems. One conjectured requirement for systems with modular structures was that the network of modules must be hierarchically organized and possess finite dimension. We investigate the dynamical behavior of an activity spreading model, evolving on heterogeneous random networks with highly modular structure and organized non-hierarchically. We observe that loosely coupled modules act as effective rare-regions, slowing down the extinction of activation. As a consequence, we find extended control parameter regions with continuously changing dynamical exponents for single network realizations, preserved after finite size analyses, as in a real GP. The avalanche size distributions of spreading events exhibit robust power-law tails. Our findings relax the requirement of hierarchical organization of the modular structure, which can help to rationalize the criticality of modular systems in the framework of GPs

Robustness and fragility of the susceptible-infected-susceptible epidemic models on complex networks

We analyze two alterations of the standard susceptible-infected-susceptible (SIS) dynamics that preserve the central properties of spontaneous healing and infection capacity of a vertex increasing unlimitedly with its degree. All models have the same epidemic thresholds in mean-field theories but depending on the network properties, simulations yield a dual scenario, in which the epidemic thresholds of the modified SIS models can be either dramatically altered or remain unchanged in comparison with the standard dynamics. For uncorrelated synthetic networks having a power-law degree distribution with exponent $\gamma<5/2$, the SIS dynamics are robust exhibiting essentially the same outcomes for all investigated models. A threshold in better agreement with the heterogeneous rather than quenched mean-field theory is observed in the modified dynamics for exponent $\gamma>5/2$. Differences are more remarkable for $\gamma>3$ where a finite threshold is found in the modified models in contrast with the vanishing threshold of the original one. This duality is elucidated in terms of epidemic lifespan on star graphs. We verify that the activation of the modified SIS models is triggered in the innermost component of the network given by a $k$-core decomposition for $\gamma<3$ while it happens only for $\gamma3$, the activation in the modified dynamics is collective involving essentially the whole network while it is triggered by hubs in the standard SIS. The duality also appears in the finite-size scaling of the critical quantities where mean-field behaviors are observed for the modified, but not for the original dynamics. Our results feed the discussions about the most proper conceptions of epidemic models to describe real systems and the choices of the most suitable theoretical approaches to deal with these models.Comment: 13 pages, 8 figure

Modeling communicable diseases, human mobility, and epidemics: a review

The spatiotemporal propagation patterns of recent infectious diseases, originated as localized epidemic outbreaks and eventually becoming global pandemics, are highly influenced by human mobility. Case exportation from endemic areas to the rest of the countries has become unavoidable because of the striking growth of the global mobility network, helping to overcome the physical distance existing between faraway regions. In this context, understanding the features driving contagions upon the arrival of an index case in local environments constitutes an essential task to devise policies aimed at avoiding the community transmission of these diseases and the subsequent case exportation to other unaffected areas. In this review, an overview of the different models addressing this topic is given, focusing on the movement–interaction–return model and different subsequent frameworks introduced to explain the complex interplay between the recurrent movements and contagion dynamics

Monitorando o número de casos e óbitos por COVID-19 no Brasil em nível munipal e de unidades federativas

We present a dataset containing the reported number of COVID-19 cases and deaths at municipal and federative units level in Brazil. Data is aggregated daily from official sources with the most updated numbers, providing a reliable, free and simple resource for researchers, health authorities and general public. Interactive pages in English and Portuguese are available, containing maps, graphs and tables with all the data. Data about recovered, suspected and tests made are also available for most federative units.Apresentamos um banco de dados contendo o número de casos e óbitos reportados por COVID-19 no Brasil em nível municipal e de unidades federativas. Os dados são agregados diariamente a partir de fontes oficiais com os números mais atualizados, disponibilizando um recurso confiável, livre e simples para pesquisadores, autoridades desaúde e o público geral. Páginas interativas em inglês e português estão disponíveis, contendo mapa, gráficos e tabelas com todos os dados. Dados sobre recuperados, suspeitos e testes realizados também estão disponíveis para a maioria das unidades federativas