Disease spread in most biological populations requires the proximity of agents. In populations where the individuals have spatial mobility, the contact graph is generated by the "collision dynamics" of the agents, and thus the evolution of epidemics couples directly to the spatial dynamics of the population. We first briefly review the properties and the methodology of an agent-based simulation (EPISIMS) to model disease spread in realistic urban dynamic contact networks. Using the data generated by this simulation, we introduce the notion of dynamic proximity networks which takes into account the relevant time scales for disease spread: contact duration, infectivity period and rate of contact creation. This approach promises to be a good candidate for a unified treatment of epidemic types that are driven by agent collision dynamics. In particular, using a simple model, we show that it can can account for the observed qualitative differences between the degree distributions of contact graphs of diseases with short infectivity period (such as air-transmitted diseases) or long infectivity periods (such as HIV).
Recently developed techniques to acquire high-quality human mobility data allow large-scale simulations of the spread of infectious diseases with high spatial and temporal resolution.Analysis of such data has revealed the oversimplification of existing theoretical frameworks to infer the final epidemic size or influential nodes from the network topology. Here we propose a spectral decomposition-based framework for the quantitative analysis of epidemic processes on realistic networks of human proximity derived from urban mobility data. Common wisdom suggests that modes with larger eigenvalues c…
A key characteristic of the spread of infectious diseases is their ability to use efficient transmission paths within contact graphs. This enables the pathogen to maximise infection rates and spread within a target population. In this work, we devise techniques to localise infections and decrease infection rates based on a principled analysis of disease transmission paths within human-contact networks (proximity graphs). Experimental results of disease spreading shows that that at low visibility rates contact tracing slows disease spreading. However to stop disease spreading, contact tracing r…
We introduce a theoretical framework that highlights the impact of physical distancing variables such as human mobility and physical proximity on the evolution of epidemics and, crucially, on the reproduction number. In particular, in response to the coronavirus disease (CoViD-19) pandemic, countries have introduced various levels of 'lockdown' to reduce the number of new infections. Specifically we use a collisional approach to an infection-age structured model described by a renewal equation for the time homogeneous evolution of epidemics. As a result, we show how various contributions of th…
Human proximity networks are temporal networks representing the close-range proximity among humans in a physical space. They have been extensively studied in the past 15 years as they are critical for understanding the spreading of diseases and information among humans. Here we address the problem of mapping human proximity networks into hyperbolic spaces. Each snapshot of these networks is often very sparse, consisting of a small number of interacting (i.e., non-zero degree) nodes. Yet, we show that the time-aggregated representation of such systems over sufficiently large periods can be mean…
Mexico, like the rest of the world, is currently facing the The COVID-19 pandemic. Given the size of its territory, the efforts to contain the disease have involved both national and regional measures. For this work, the curves of daily new cases of each municipality reported by the federal government were compared. We found that 114 municipalities form a large network of statistically dependent epidemic phenomena. Based on the network's modular structure, these 114 municipalities can be split into four distinct communities of coordinated epidemic phenomena. These clusters are not limited by g…
Since roughly a decade ago, network science has focused among others on the problem of how the spreading of diseases depends on structural patterns. Here, we contribute to further advance our understanding of epidemic spreading processes by proposing a non-perturbative formulation of the heterogeneous mean field approach that has been commonly used in the physics literature to deal with this kind of spreading phenomena. The non-perturbative equations we propose have no assumption about the proximity of the system to the epidemic threshold, nor any linear approximation of the dynamics. In parti…
Epidemic propagation on complex networks has been widely investigated, mostly with invariant parameters. However, the process of epidemic propagation is not always constant. Epidemics can be affected by various perturbations, and may bounce back to its original state, which is considered resilient. Here, we study the resilience of epidemics on networks, by introducing a different infection rate ${λ_{2}}$ during SIS (susceptible-infected-susceptible) epidemic propagation to model perturbations (control state), whereas the infection rate is ${λ_{1}}$ in the rest of time. Through simulations and …
Many complex networks exhibit vulnerability to spreading of epidemics, and such vulnerability relates to the viral strain as well as to the network characteristics. For instance, the structure of the network plays an important role in spreading of epidemics. Additionally, properties of previous epidemic models require prior knowledge of the complex network structure, which means the models are limited to only well-known network structures. In this paper, we propose a new epidemiological SIR model based on the continuous time Markov chain, which is generalized to any type of network. The new mo…
Weight distribution largely impacts the epidemic spreading taking place on top of networks. This paper studies a susceptible-infected-susceptible model on regular random networks with different kinds of weight distributions. Simulation results show that the more homogeneous weight distribution leads to higher epidemic prevalence, which, unfortunately, could not be captured by the traditional mean-field approximation. This paper gives an edge-based mean-field solution for general weight distribution, which can quantitatively reproduce the simulation results. This method could find its applicati…
The dynamics of contact networks and epidemics of infectious diseases often occur on comparable time scales. Ignoring one of these time scales may provide an incomplete understanding of the population dynamics of the infection process. We develop an individual-based approximation for the susceptible-infected-recovered epidemic model applicable to arbitrary dynamic networks. Our framework provides, at the individual-level, the probability flow over time associated with the infection dynamics. This computationally efficient framework discards the correlation between the states of different nodes…
Recently, motivated by the pioneer works that reveal the small-world effect and scale-free property of various real-life networks, many scientists devote themselves into studying complex networks. One of the ultimate goals is to understand how the topological structures of networks affect the dynamics upon them. In this paper, we give a brief review on the studies of epidemic dynamics on complex networks, including the description of classical epidemic models, the epidemic spread on small-world and scale-free networks, and network immunization. Finally, a prospect is addressed and some interes…
Bipartite networks are composed of two types of nodes and there are no links between nodes of the same type. Thus the study of epidemic spread and control on such networks is relevant to sexually transmitted diseases (STDs). When entire populations of two types cannot be immunized and the effect of immunization is not perfect, we have to consider the targeted immunization with immunization rates. We derive the epidemic thresholds of SIR and SIS models with immunization and illustrate the results with STDs on heterosexual contact networks.
We provide a description of the Epidemics on Networks (EoN) python package designed for studying disease spread in static networks. The package consists of over $100$ methods available for users to perform stochastic simulation of a range of different processes including SIS and SIR disease, and generic simple or comlex contagions.
We study the traffic-driven epidemic spreading on scale-free networks with tunable degree distribution. The heterogeneity of networks is controlled by the exponent $γ$ of power-law degree distribution. It is found that the epidemic threshold is minimized at about $γ=2.2$. Moreover, we find that nodes with larger algorithmic betweenness are more likely to be infected. We expect our work to provide new insights into the effect of network structures on traffic-driven epidemic spreading.
In this paper, we analyze dynamic switching networks, wherein the networks switch arbitrarily among a set of topologies. For this class of dynamic networks, we derive an epidemic threshold, considering the SIS epidemic model. First, an epidemic probabilistic model is developed assuming independence between states of nodes. We identify the conditions under which the epidemic dies out by linearizing the underlying dynamical system and analyzing its asymptotic stability around the origin. The concept of joint spectral radius is then used to derive the epidemic threshold, which is later validated …
We study geographical effects on the spread of diseases in lattice-embedded scale-free networks. The geographical structure is represented by the connecting probability of two nodes that is related to the Euclidean distance between them in the lattice. By studying the standard Susceptible-Infected model, we found that the geographical structure has great influences on the temporal behavior of epidemic outbreaks and the propagation in the underlying network: the more geographically constrained the network is, the more smoothly the epidemic spreads.
Epidemics on complex networks is a widely investigated topic in the last few years, mainly due to the last pandemic events. Usually, real contact networks are dynamic, hence much effort has been invested in studying epidemics on evolving networks. Here we propose and study a model for evolving networks based on varying degrees, where at each time step a node might get, with probability $r$, a new degree and new neighbors according to a given degree distribution, instead of its former neighbors. We find analytically, using the generating functions framework, the epidemic threshold and the proba…
This letter investigates the multiple routes transmitted epidemic process on multiplex networks. We propose detailed theoretical analysis that allows us to accurately calculate the epidemic threshold and outbreak size. It is found that the epidemic can spread across the multiplex network even if all the network layers are well below their respective epidemic thresholds. Strong positive degree-degree correlation of nodes in multiplex network could lead to a much lower epidemic threshold and a relatively smaller outbreak size. However, the average similarity of neighbors from different layers of…
It is often useful to represent the infectious dynamics of mobile agents by metapopulation models. In such a model, metapopulations form a static network, and individuals migrate from one metapopulation to another. It is known that heterogeneous degree distributions of metapopulation networks decrease the epidemic threshold above which epidemic spreads can occur. We investigate the combined effect of heterogeneous degree distributions and diffusion on epidemics in metapopulation networks. We show that for arbitrary heterogeneous networks, diffusion suppresses epidemics in the sense of an incre…
Changs in individual behavior often entangles with the dynamic interaction of individuals, which complicates the epidemic process and brings great challenges for the understanding and control of the epidemic. In this work, we consider three kinds of typical behavioral changes in epidemic process that is, self-quarantine of infected individuals, self-protection of susceptible individuals, and social distancing between them. We connect the behavioral changes with individual's social attributes by the activity-driven network with attractiveness. A mean-field theory is established to derive an ana…
The role of waning immunity in basic epidemic models on networks has been undervalued while being noticeable fundamental for real epidemic outbreaks. One central question is which mean-field approach is more accurate in describing the epidemic dynamics. We tackled this problem considering the susceptible-infected-recovered-susceptible (SIRS) epidemic model on networks. Two pairwise mean-field theories, one based on recurrent dynamical message-passing (rDMP) and the other on the pair quenched mean-field theory (PQMF), are compared with extensive stochastic simulations on large networks of diffe…
Models of epidemic spreading on complex networks have attracted great attention among researchers in physics, mathematics, and epidemiology due to their success in predicting and controlling scenarios of epidemic spreading in real-world scenarios. To understand the interplay between epidemic spreading and the topology of a contact network, several outstanding theoretical approaches have been developed. An accurate theoretical approach describing the spreading dynamics must take both the network topology and dynamical correlations into consideration at the expense of increasing the complexity o…
Epidemic spread on networks is one of the most studied dynamics in network science and has important implications in real epidemic scenarios. Nonetheless, the dynamics of real epidemics and how it is affected by the underline structure of the infection channels are still not fully understood. Here we apply the SIR model and study analytically and numerically the epidemic spread on a recently developed spatial modular model imitating the structure of cities in a country. The model assumes that inside a city the infection channels connect many different locations, while the infection channels be…
This letter investigates the epidemic spreading in two-vectors propagation network (TPN). We propose detailed theoretical analysis that allows us to accurately calculate the epidemic threshold and outbreak size. It is found that the epidemics can spread across the TPN even if two sub-single-vector propagation networks (SPNs) of TPN are well below their respective epidemic thresholds. Strong positive degree-degree correlation of nodes in TPN could lead to a much lower epidemic threshold and a relatively smaller outbreak size. However, the average similarity between the neighbors from different …
We investigate the effects of modular and temporal connectivity patterns on epidemic spreading. To this end, we introduce and analytically characterise a model of time-varying networks with tunable modularity. Within this framework, we study the epidemic size of Susceptible-Infected-Recovered, SIR, models and the epidemic threshold of Susceptible-Infected-Susceptible, SIS, models. Interestingly, we find that while the presence of tightly connected clusters inhibit SIR processes, it speeds up SIS diseases. In this case, we observe that heterogeneous temporal connectivity patterns and modular st…
The dynamic nature of system gives rise to dynamical features of epidemic spreading, such as oscillation and bistability. In this paper, by studying the epidemic spreading in growing networks, in which susceptible nodes may adaptively break the connections with infected ones yet avoid getting isolated, we reveal a new phenomenon - \emph{epidemic reemergence}, where the number of infected nodes is incubated at a low level for a long time and then bursts up for a short time. The process may repeat several times before the infection finally vanishes. Simulation results show that all the three fac…
Social contact networks underlying epidemic processes in humans and animals are highly dynamic. The spreading of infections on such temporal networks can differ dramatically from spreading on static networks. We theoretically investigate the effects of concurrency, the number of neighbors that a node has at a given time point, on the epidemic threshold in the stochastic susceptible-infected-susceptible dynamics on temporal network models. We show that network dynamics can suppress epidemics (i.e., yield a higher epidemic threshold) when the nodes' concurrency is low, but can also enhance epide…
This study is concerned with the dynamical behaviors of epidemic spreading over a two-layered interconnected network. Three models in different levels are proposed to describe cooperative spreading processes over the interconnected network, wherein the disease in one network can spread to the other. Theoretical analysis is provided for each model to reveal that the global epidemic threshold in the interconnected network is not larger than the epidemic thresholds for the two isolated layered networks. In particular, in an interconnected homogenous network, detailed theoretical analysis is prese…
We develop a theory for the susceptible-infected-susceptible (SIS) epidemic model on networks that incorporate both network structure and dynamic correlations. This theory can account for the multistage onset of the epidemic phase in scale-free networks. This phenomenon is characterized by multiple peaks in the susceptibility as a function of the infection rate. It can be explained by that, even under the global epidemic threshold, a hub can sustain the epidemics for an extended period. Moreover, our approach improves theoretical calculations of prevalence close to the threshold in heterogeneo…
We consider a standard \textit{susceptible-infected-susceptible} (SIS) model to study behaviors of steady states of epidemic spreading in small-world networks. Using analytical methods and large scale simulations, we recover the usual epidemic behavior with a critical threshold $λ_{c}$ below which infectious diseases die out. Whereas for the spreading rate $λ$ far above $λ_{c}$, it was found that the density of infected individuals $ρ$ as a function of $λ$ has the property $ρ\approx F(K)(\ln λ- \ln λ_{c})$.
We present a modified \emph{susceptible-infected-susceptible} (SIS) model on complex networks, small-world and scale-free, to study epidemic spreading with the effect of time delay which is introduced to the infected phase. Considering the topology of the network, both uniform and degree-dependent delays are studied during the contagion process. We find that the existence of time delay will enhance both outbreaks and prevalence of infectious diseases in the network.
The adoption of prophylaxis attitudes, such as social isolation and use of face masks, to mitigate epidemic outbreaks strongly depends on the support of the population. In this work, we investigate a susceptible-infected-recovered (SIR) epidemic model, in which the epidemiological perception of the environment can adapt the behavior of susceptible individuals towards preventive behavior. {Two compartments of susceptible individuals are considered, to distinguish those that adopt or not prophylaxis attitudes.} Two rules, depending on local and global epidemic prevalence, for the spread of the e…
It has been known that epidemic outbreaks in the SIR model on networks are described by phase transitions. Despite the similarity with percolation transitions, whether an epidemic outbreak occurs or not cannot be predicted with probability one in the thermodynamic limit. We elucidate its mechanism by deriving a simple Langevin equation that captures an essential aspect of the phenomenon. We also calculate the probability of epidemic outbreaks near the transition point.
The effects of local and global connectivity on the spread of synergistic susceptible-infected-removed epidemics were studied in lattice models with infinite- and finite-range rewiring (small-world and small-world-like models). Several effects were found numerically and supported analytically within a simple model: (i) rewiring enhanced resilience to epidemics with strong constructive synergy on networks with high local connectivity; (ii) rewiring enhanced spread of epidemics with destructive or weak constructive synergy on networks with arbitrary local connectivity; (iii) rewiring enhanced sp…
Epidemic threshold is one of the most important features of the epidemic dynamics. Through a lot of numerical simulations in classic Susceptible-Infected-Recovered (SIR) and Susceptible-Infected-Susceptible (SIS) models on various types of networks, we study the simulated identification of epidemic thresholds on finite-size networks. We confirm that the susceptibility measure goes awry for the SIR model due to the bimodal distribution of outbreak sizes near the critical point, while the simulated thresholds of the SIS and SIR models can be accurately determined by analyzing the peak of the epi…
We propose a novel SIR epidemic model which is driven by the transmission of infection packets in networks. Specifically, infected nodes generate and deliver infection packets causing the spread of the epidemic, while recovered nodes block the delivery of infection packets, and this inhibits the epidemic spreading. The efficient routing protocol governed by a control parameter $α$ is used in the packet transmission. We obtain the maximum instantaneous population of infected nodes, the maximum population of ever infected nodes, as well as the corresponding optimal $α$ through simulation. We fin…
Realistic human contact networks capable of spreading infectious disease, for example studied in social contact surveys, exhibit both significant degree heterogeneity and clustering, both of which greatly affect epidemic dynamics. To understand the joint effects of these two network properties on epidemic dynamics, the effective degree model of Lindquist et al. is reformulated with a new moment closure to apply to highly clustered networks. A simulation study comparing alternative ODE models and stochastic simulations is performed for SIR (Susceptible-Infected-Removed) epidemic dynamics, inclu…
Nowadays, the emergence of online services provides various multi-relation information to support the comprehensive understanding of the epidemic spreading process. In this Letter, we consider the edge weights to represent such multi-role relations. In addition, we perform detailed analysis of two representative metrics, outbreak threshold and epidemic prevalence, on SIS and SIR models. Both theoretical and simulation results find good agreements with each other. Furthermore, experiments show that, on fully mixed networks, the weight distribution on edges would not affect the epidemic results …
We investigate the spread of diseases, computer viruses or information on complex networks and also immunization strategies to prevent or control the spread. When an entire population cannot be immunized and the effect of immunization is not perfect, we need the targeted immunization with immunization rate. Under such a circumstance we calculate epidemic thresholds for the SIR and SIS epidemic models. It is shown that, in scale-free networks, the targeted immunization is effective only if the immunization rate is equal to one. We analyze here epidemic spreading on directed complex networks, bu…
Just like the degrees of human and animal interaction networks, the distribution of the times between interactions is known to often be right-skewed and fat-tailed. Both these distributions affect epidemic dynamics strongly, but, as we show in this Letter, for very different reasons. Whereas the high degrees of the tail are critical for facilitating epidemics, it is the small interevent times that control the dynamics of epidemics. We investigate this effect both analytically and numerically for different versions of the Susceptible-Infected-Recovered model on different types of networks.
The availability of new data sources on human mobility is opening new avenues for investigating the interplay of social networks, human mobility and dynamical processes such as epidemic spreading. Here we analyze data on the time-resolved face-to-face proximity of individuals in large-scale real-world scenarios. We compare two settings with very different properties, a scientific conference and a long-running museum exhibition. We track the behavioral networks of face-to-face proximity, and characterize them from both a static and a dynamic point of view, exposing important differences as well…
In spite of the extensive previous efforts on traffic dynamics and epidemic spreading in complex networks, the problem of traffic-driven epidemic spreading on {\em correlated} networks has not been addressed. Interestingly, we find that the epidemic threshold, a fundamental quantity underlying the spreading dynamics, exhibits a non-monotonic behavior in that it can be minimized for some critical value of the assortativity coefficient, a parameter characterizing the network correlation. To understand this phenomenon, we use the degree-based mean-field theory to calculate the traffic-driven epid…
Most infectious diseases spread on a dynamic network of human interactions. Recent studies of social dynamics have provided evidence that spreading patterns may depend strongly on detailed micro-dynamics of the social system. We have recorded every single interaction within a large population, mapping out---for the first time at scale---the complete proximity network for a densely-connected system. Here we show the striking impact of interaction-distance on the network structure and dynamics of spreading processes. We create networks supporting close (intimate network, up to ~1m) and longer di…
In this paper, we investigate the epidemic spreading for SIR model in weighted scale-free networks with nonlinear infectivity, where the transmission rate in our analytical model is weighted. Concretely, we introduce the infectivity exponent $α$ and the weight exponent $β$ into the analytical SIR model, then examine the combination effects of $α$ and $β$ on the epidemic threshold and phase transition. We show that one can adjust the values of $α$ and $β$ to rebuild the epidemic threshold to a finite value, and it is observed that the steady epidemic prevalence $R$ grows in an exponential form …
Epidemic spreading and cascading failure are two important dynamical processes over complex networks. They have been investigated separately for a long history. But in the real world, these two dynamics sometimes may interact with each other. In this paper, we explore a model combined with SIR epidemic spreading model and local loads sharing cascading failure model. There exists a critical value of tolerance parameter that whether the epidemic with high infection probability can spread out and infect a fraction of the network in this model. When the tolerance parameter is smaller than the crit…
In this paper we investigate a susceptible-infected-susceptible (SIS) epidemic model describing data dissemination in opportunistic networks with heterogeneous setting of transmission parameters. We obtained the estimation of the final epidemic size assuming that amount of data transferred between network nodes possesses a Pareto distribution, implying scale-free properties. In this context, more heterogeneity in susceptibility means the less severe epidemic progression, and, on the contrary, more heterogeneity in infectivity leads to more severe epidemics -- assuming that the other parameter …
Data of physical contacts and face-to-face communications suggest temporally varying networks as the media on which infections take place among humans and animals. Epidemic processes on temporal networks are complicated by complexity of both network structure and temporal dimensions. Theoretical approaches are much needed for identifying key factors that affect dynamics of epidemics. In particular, what factors make some temporal networks stronger media of infection than other temporal networks is under debate. We develop a theory to understand the susceptible-infected-susceptible epidemic mod…
Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality of epidemics and has allowed the modelling community to focus on the complexity of other factors such as population structure and interventions. However, there is an increasing amount of evidence that the strain diversity of pathogens, and their interplay with the host immune system, can play a large role in shaping the dynamics of epidemics. Here, we introd…
Several systems can be modeled as sets of interdependent networks where each network contains distinct nodes. Diffusion processes like the spreading of a disease or the propagation of information constitute fundamental phenomena occurring over such coupled networks. In this paper we propose a new concept of multidimensional epidemic threshold characterizing diffusion processes over interdependent networks, allowing different diffusion rates on the different networks and arbitrary degree distributions. We analytically derive and numerically illustrate the conditions for multilayer epidemics, i.…
Understanding spreading dynamics will benefit society as a whole in better preventing and controlling diseases, as well as facilitating the socially responsible information while depressing destructive rumors. In network-based spreading dynamics, edges with different weights may play far different roles: a friend from afar usually brings novel stories, and an intimate relationship is highly risky for a flu epidemic. In this article, we propose a weighted susceptible-infected-susceptible model on complex networks, where the weight of an edge is defined by the topological proximity of the two as…
