Susceptible-infected-susceptible model: a comparison of N-intertwined and heterogeneous mean-field approximations

Deciphering population-level response under spatial drug heterogeneity on microhabitat structures

Bacteria and cancer cells live in a spatially heterogeneous environment, where migration shapes the microhabitat structures critical for colonization and metastasis. The interplay between growth, migration, and microhabitat structure complicates the prediction of population responses to drugs, such as clearance or sustained growth, posing a longstanding challenge. Here, we disentangle growth-migration dynamics and identify that population decline is determined by two decoupled terms: a spatial growth variation term and a microhabitat structure term. Notably, the microhabitat structure term can be interpreted as a dynamic-related centrality measure. For fixed spatial drug arrangements, we show that interpreting these centralities reveals how different network structures, even with identical edge densities, microhabitat numbers, and spatial heterogeneity, can lead to distinct population-level responses. Increasing edge density shifts the population response from growth to clearance, supporting an inversed centrality-connectivity relationship, and mirroring the effects of higher migration rates. Furthermore, we derive a sufficient condition for robust population decline across various spatial growth rate arrangements, regardless of spatial-temporal fluctuations induced by drugs. Additionally, we demonstrate that varying the maximum growth-to-death ratio, determined by drug-bacteria interactions, can lead to distinct population decline profiles and a minimal decline phase emerges. These findings address key challenges in predicting population-level responses and provide insights into divergent clinical outcomes under identical drug dosages. This work may offer a new method of interpreting treatment dynamics and potential approaches for optimizing spatially explicit drug dosing strategies.

Predicting epidemic threshold in complex networks by graph neural network

To achieve precision in predicting an epidemic threshold in complex networks, we have developed a novel threshold graph neural network (TGNN) that takes into account both the network topology and the spreading dynamical process, which together contribute to the epidemic threshold. The proposed TGNN could effectively and accurately predict the epidemic threshold in homogeneous networks, characterized by a small variance in the degree distribution, such as Erdős-Rényi random networks. Usability has also been validated when the range of the effective spreading rate is altered. Furthermore, extensive experiments in ER networks and scale-free networks validate the adaptability of the TGNN to different network topologies without the necessity for retaining. The adaptability of the TGNN is further validated in real-world networks.

Validity of annealed approximation in a high-dimensional system

This study investigates the suitability of the annealed approximation in high-dimensional systems characterized by dense networks with quenched link disorder, employing models of coupled oscillators. We demonstrate that dynamic equations governing dense-network systems converge to those of the complete-graph version in the thermodynamic limit, where link disorder fluctuations vanish entirely. Consequently, the annealed-network systems, where fluctuations are attenuated, also exhibit the same dynamic behavior in the thermodynamic limit. However, a significant discrepancy arises in the incoherent (disordered) phase wherein the finite-size behavior becomes critical in determining the steady-state pattern. To explicitly elucidate this discrepancy, we focus on identical oscillators subject to competitive attractive and repulsive couplings. In the incoherent phase of dense networks, we observe the manifestation of random irregular states. In contrast, the annealed approximation yields a symmetric (regular) incoherent state where two oppositely coherent clusters of oscillators coexist, accompanied by the vanishing order parameter. Our findings imply that the annealed approximation should be employed with caution even in dense-network systems, particularly in the disordered phase.

Transition from time-variant to static networks: Timescale separation in N-intertwined mean-field approximation of susceptible-infectious-susceptible epidemics

We extend the N-intertwined mean-field approximation (NIMFA) for the susceptible-infectious-susceptible (SIS) epidemiological process to time-varying networks. Processes on time-varying networks are often analyzed under the assumption that the process and network evolution happen on different timescales. This approximation is called timescale separation. We investigate timescale separation between disease spreading and topology updates of the network. We introduce the transition times [under T]̲(r) and T[over ¯](r) as the boundaries between the intermediate regime and the annealed (fast changing network) and quenched (static network) regimes, respectively, for a fixed accuracy tolerance r. By analyzing the convergence of static NIMFA processes, we analytically derive upper and lower bounds for T[over ¯](r). Our results provide insights and bounds on the time of convergence to the steady state of the static NIMFA SIS process. We show that, under our assumptions, the upper-transition time T[over ¯](r) is almost entirely determined by the basic reproduction number R_{0} of the network. The value of the upper-transition time T[over ¯](r) around the epidemic threshold is large, which agrees with the current understanding that some real-world epidemics cannot be approximated with the aforementioned timescale separation.

Scalable parallel and distributed simulation of an epidemic on a graph

We propose an algorithm to simulate Markovian SIS epidemics with homogeneous rates and pairwise interactions on a fixed undirected graph, assuming a distributed memory model of parallel programming and limited bandwidth. This setup can represent a broad class of simulation tasks with compartmental models. Existing solutions for such tasks are sequential by nature. We provide an innovative solution that makes trade-offs between statistical faithfulness and parallelism possible. We offer an implementation of the algorithm in the form of pseudocode in the Appendix. Also, we analyze its algorithmic complexity and its induced dynamical system. Finally, we design experiments to show its scalability and faithfulness. In our experiments, we discover that graph structures that admit good partitioning schemes, such as the ones with clear community structures, together with the correct application of a graph partitioning method, can lead to better scalability and faithfulness. We believe this algorithm offers a way of scaling out, allowing researchers to run simulation tasks at a scale that was not accessible before. Furthermore, we believe this algorithm lays a solid foundation for extensions to more advanced epidemic simulations and graph dynamics in other fields.

Moment closure approximations of susceptible-infected-susceptible epidemics on adaptive networks

The influence of people's individual responses to the spread of contagious phenomena, like the COVID-19 pandemic, is still not well understood. We investigate the Markovian Generalized Adaptive Susceptible-Infected-Susceptible (G-ASIS) epidemic model. The G-ASIS model comprises many contagious phenomena on networks, ranging from epidemics and information diffusion to innovation spread and human brain interactions. The connections between nodes in the G-ASIS model change adaptively over time, because nodes make decisions to create or break links based on the health state of their neighbors. Our contribution is fourfold. First, we rigorously derive the first-order and second-order mean-field approximations from the continuous-time Markov chain. Second, we illustrate that the first-order mean-field approximation fails to approximate the epidemic threshold of the Markovian G-ASIS model accurately. Third, we show that the second-order mean-field approximation is a qualitative good approximation of the Markovian G-ASIS model. Finally, we discuss the Adaptive Information Diffusion (AID) model in detail, which is contained in the G-ASIS model. We show that, similar to most other instances of the G-ASIS model, the AID model possesses a unique steady state, but that in the AID model, the convergence time toward the steady state is very large. Our theoretical results are supported by numerical simulations.

The impact of information dissemination on vaccination in multiplex networks

The impact of information dissemination on epidemic control is essentially subject to individual behaviors. Vaccination is one of the most effective strategies against the epidemic spread, whose correlation with the information dissemination should be better understood. To this end, we propose an evolutionary vaccination game model in multiplex networks by integrating an information-epidemic spreading process into the vaccination dynamics, and explore how information dissemination influences vaccination. The spreading process is described by a two-layer coupled susceptible-alert-infected-susceptible (SAIS) model, where the strength coefficient between two layers characterizes the tendency and intensity of information dissemination. We find that the impact of information dissemination on vaccination decision-making depends on not only the vaccination cost and network topology, but also the stage of the system evolution. For instance, in a two-layer BA scale-free network, information dissemination helps to improve vaccination density only at the early stage of the system evolution, as well as when the vaccination cost is smaller. A counter-intuitive conclusion that more information transmission cannot promote vaccination is obtained when the vaccination cost is larger. Moreover, we study the impact of the strength coefficient and individual sensitivity on the fraction of infected individuals and social cost, and unveil the role of information dissemination in controlling the epidemic.

Brain Connectivity Studies on Structure-Function Relationships: A Short Survey with an Emphasis on Machine Learning

This short survey reviews the recent literature on the relationship between the brain structure and its functional dynamics. Imaging techniques such as diffusion tensor imaging (DTI) make it possible to reconstruct axonal fiber tracks and describe the structural connectivity (SC) between brain regions. By measuring fluctuations in neuronal activity, functional magnetic resonance imaging (fMRI) provides insights into the dynamics within this structural network. One key for a better understanding of brain mechanisms is to investigate how these fast dynamics emerge on a relatively stable structural backbone. So far, computational simulations and methods from graph theory have been mainly used for modeling this relationship. Machine learning techniques have already been established in neuroimaging for identifying functionally independent brain networks and classifying pathological brain states. This survey focuses on methods from machine learning, which contribute to our understanding of functional interactions between brain regions and their relation to the underlying anatomical substrate.

Modeling airport congestion contagion by heterogeneous SIS epidemic spreading on airline networks

In this work, we explore the possibility of using a heterogeneous Susceptible- Infected-Susceptible SIS spreading process on an airline network to model airport congestion contagion with the objective to reproduce airport vulnerability. We derive the vulnerability of each airport from the US Airport Network data as the congestion probability of each airport. In order to capture diverse flight features between airports, e.g. frequency and duration, we construct three types of airline networks. The infection rate of each link in the SIS spreading process is proportional to its corresponding weight in the underlying airline network constructed. The recovery rate of each node is also heterogeneous, dependent on its node strength in the underlying airline network, which is the total weight of the links incident to the node. Such heterogeneous recovery rate is motivated by the fact that large airports may recover fast from congestion due to their well-equipped infrastructures. The nodal infection probability in the meta-stable state is used as a prediction of the vulnerability of the corresponding airport. We illustrate that our model could reproduce the distribution of nodal vulnerability and rank the airports in vulnerability evidently better than the SIS model whose recovery rate is homogeneous. The vulnerability is the largest at airports whose strength in the airline network is neither too large nor too small. This phenomenon can be captured by our heterogeneous model, but not the homogeneous model where a node with a larger strength has a higher infection probability. This explains partially the out-performance of the heterogeneous model. This proposed congestion contagion model may shed lights on the development of strategies to identify vulnerable airports and to mitigate global congestion by e.g. congestion reduction at selected airports.

Effect of heterogeneous risk perception on information diffusion, behavior change, and disease transmission

Motivated by the importance of individual differences in risk perception and behavior change in people's responses to infectious disease outbreaks (particularly the ongoing COVID-19 pandemic), we propose a heterogeneous disease-behavior-information transmission model, in which people's risk of getting infected is influenced by information diffusion, behavior change, and disease transmission. We use both a mean-field approximation and Monte Carlo simulations to analyze the dynamics of the model. Information diffusion influences behavior change by allowing people to be aware of the disease and adopt self-protection and subsequently affects disease transmission by changing the actual infection rate. Results show that (a) awareness plays a central role in epidemic prevention, (b) a reasonable fraction of overreacting nodes are needed in epidemic prevention (c) the basic reproduction number R_{0} has different effects on epidemic outbreak for cases with and without asymptomatic infection, and (d) social influence on behavior change can remarkably decrease the epidemic outbreak size. This research indicates that the media and opinion leaders should not understate the transmissibility and severity of diseases to ensure that people become aware of the disease and adopt self-protection to protect themselves and the whole population.

Classification of link-breaking and link-creation updating rules in susceptible-infected-susceptible epidemics on adaptive networks

In the classical susceptible-infected-susceptible (SIS) model, a disease or infection spreads over a given, mostly fixed graph. However, in many real complex networks, the topology of the underlying graph can change due to the influence of the dynamical process. In this paper, besides the spreading process, the network adaptively changes its topology based on the states of the nodes in the network. An entire class of link-breaking and link-creation mechanisms, which we name Generalized Adaptive SIS (G-ASIS), is presented and analyzed. For each instance of G-ASIS using the complete graph as initial network, the relation between the epidemic threshold and the effective link-breaking rate is determined to be linear, constant, or unknown. Additionally, we show that there exist link-breaking and link-creation mechanisms for which the metastable state does not exist. We confirm our theoretical results with several numerical simulations.

Time dependence of susceptible-infected-susceptible epidemics on networks with nodal self-infections

The average fraction of infected nodes, in short the prevalence, of the Markovian ɛ-SIS (susceptible-infected-susceptible) process with small self-infection rate ɛ>0 exhibits, as a function of time, a typical "two-plateau" behavior, which was first discovered in the complete graph K_{N}. Although the complete graph is often dismissed as an unacceptably simplistic approximation, its analytic tractability allows to unravel deeper details, that are surprisingly also observed in other graphs as demonstrated by simulations. The time-dependent mean-field approximation for K_{N} performs only reasonably well for relatively large self-infection rates, but completely fails to mimic the typical Markovian ɛ-SIS process with small self-infection rates. While self-infections, particularly when their rate is small, are usually ignored, the interplay of nodal self-infection and spread over links may explain why absorbing processes are hardly observed in reality, even over long time intervals.

Explosive phase transition in susceptible-infected-susceptible epidemics with arbitrary small but nonzero self-infection rate

The ɛ-susceptible-infected-susceptible (SIS) epidemic model on a graph adds an independent, Poisson self-infection process with rate ɛ to the "classical" Markovian SIS process. The steady state in the classical SIS process (with ɛ=0) on any finite graph is the absorbing or overall-healthy state, in which the virus is eradicated from the network. We report that there always exists a phase transition around τ_{c}^{ɛ}=O(ɛ^{-1/N-1}) in the ɛ-SIS process on the complete graph K_{N} with N nodes, above which the effective infection rate τ>τ_{c}^{ɛ} causes the average steady-state fraction of infected nodes to approach that of the mean-field approximation, no matter how small, but not zero, the self-infection rate ɛ is. For τ<τ_{c}^{ɛ} and small ɛ, the network is almost overall healthy. The observation was found by mathematical analysis on the complete graph K_{N}, but we claim that the phase transition of explosive type may also occur in any other finite graph. We thus conclude that the overall-healthy state of the classical Markovian SIS model is unstable in the ɛ-SIS process and, hence, unlikely to exist in reality, where "background" infection ɛ>0 is imminent.

Autocorrelation of the susceptible-infected-susceptible process on networks

In this paper, we focus on the autocorrelation of the susceptible-infected-susceptible (SIS) process on networks. The N-intertwined mean-field approximation (NIMFA) is applied to calculate the autocorrelation properties of the exact SIS process. We derive the autocorrelation of the infection state of each node and the fraction of infected nodes both in the steady and transient states as functions of the infection probabilities of nodes. Moreover, we show that the autocorrelation can be used to estimate the infection and curing rates of the SIS process. The theoretical results are compared with the simulation of the exact SIS process. Our work fully utilizes the potential of the mean-field method and shows that NIMFA can indeed capture the autocorrelation properties of the exact SIS process.

Unified mean-field framework for susceptible-infected-susceptible epidemics on networks, based on graph partitioning and the isoperimetric inequality

We propose an approximation framework that unifies and generalizes a number of existing mean-field approximation methods for the susceptible-infected-susceptible (SIS) epidemic model on complex networks. We derive the framework, which we call the unified mean-field framework (UMFF), as a set of approximations of the exact Markovian SIS equations. Our main novelty is that we describe the mean-field approximations from the perspective of the isoperimetric problem, which results in bounds on the UMFF approximation error. These new bounds provide insight in the accuracy of existing mean-field methods, such as the N-intertwined mean-field approximation and heterogeneous mean-field method, which are contained by UMFF. Additionally, the isoperimetric inequality relates the UMFF approximation accuracy to the regularity notions of Szemerédi's regularity lemma.

Ranking of Nodal Infection Probability in Susceptible-Infected-Susceptible Epidemic

The prevalence, which is the average fraction of infected nodes, has been studied to evaluate the robustness of a network subject to the spread of epidemics. We explore the vulnerability (infection probability) of each node in the metastable state with a given effective infection rate τ. Specifically, we investigate the ranking of the nodal vulnerability subject to a susceptible-infected-susceptible epidemic, motivated by the fact that the ranking can be crucial for a network operator to assess which nodes are more vulnerable. Via both theoretical and numerical approaches, we unveil that the ranking of nodal vulnerability tends to change more significantly as τ varies when τ is smaller or in Barabási-Albert than Erdős-Rényi random graphs.

Unification of theoretical approaches for epidemic spreading on complex networks

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 of the equations. In this short survey we unify the most widely used theoretical approaches for epidemic spreading on complex networks in terms of increasing complexity, including the mean-field, the heterogeneous mean-field, the quench mean-field, dynamical message-passing, link percolation, and pairwise approximation. We build connections among these approaches to provide new insights into developing an accurate theoretical approach to spreading dynamics on complex networks.

Web malware spread modelling and optimal control strategies

The popularity of the Web improves the growth of web threats. Formulating mathematical models for accurate prediction of malicious propagation over networks is of great importance. The aim of this paper is to understand the propagation mechanisms of web malware and the impact of human intervention on the spread of malicious hyperlinks. Considering the characteristics of web malware, a new differential epidemic model which extends the traditional SIR model by adding another delitescent compartment is proposed to address the spreading behavior of malicious links over networks. The spreading threshold of the model system is calculated, and the dynamics of the model is theoretically analyzed. Moreover, the optimal control theory is employed to study malware immunization strategies, aiming to keep the total economic loss of security investment and infection loss as low as possible. The existence and uniqueness of the results concerning the optimality system are confirmed. Finally, numerical simulations show that the spread of malware links can be controlled effectively with proper control strategy of specific parameter choice.

The Accuracy of Mean-Field Approximation for Susceptible-Infected-Susceptible Epidemic Spreading with Heterogeneous Infection Rates

The epidemic spreading over a network has been studied for years by applying the mean-field approach in both homogeneous case, where each node may get infected by an infected neighbor with the same rate, and heterogeneous case, where the infection rates between different pairs of nodes are also different. Researchers have discussed whether the mean-field approaches could accurately describe the epidemic spreading for the homogeneous cases but not for the heterogeneous cases. In this paper, we explore if and under what conditions the mean-field approach could perform well when the infection rates are heterogeneous. In particular, we employ the Susceptible-Infected-Susceptible (SIS) model and compare the average fraction of infected nodes in the metastable state, where the fraction of infected nodes remains stable for a long time, obtained by the continuous-time simulation and the mean-field approximation. We concentrate on an individual-based mean-field approximation called the N-intertwined Mean Field Approximation (NIMFA), which is an advanced approach considered the underlying network topology. Moreover, for the heterogeneity of the infection rates, we consider not only the independent and identically distributed (i.i.d.) infection rate but also the infection rate correlated with the degree of the two end nodes. We conclude that NIMFA is generally more accurate when the prevalence of the epidemic is higher. Given the same effective infection rate, NIMFA is less accurate when the variance of the i.i.d. infection rate or the correlation between the infection rate and the nodal degree leads to a lower prevalence. Moreover, given the same actual prevalence, NIMFA performs better in the cases: 1) when the variance of the i.i.d. infection rates is smaller (while the average is unchanged); 2) when the correlation between the infection rate and the nodal degree is positive. Our work suggests the conditions when the mean-field approach, in particular NIMFA, is more accurate in the approximation of the SIS epidemic with heterogeneous infection rates.

The Rationality of Four Metrics of Network Robustness: A Viewpoint of Robust Growth of Generalized Meshes

There are quite a number of different metrics of network robustness. This paper addresses the rationality of four metrics of network robustness (the algebraic connectivity, the effective resistance, the average edge betweenness, and the efficiency) by investigating the robust growth of generalized meshes (GMs). First, a heuristic growth algorithm (the Proximity-Growth algorithm) is proposed. The resulting proximity-optimal GMs are intuitively robust and hence are adopted as the benchmark. Then, a generalized mesh (GM) is grown up by stepwise optimizing a given measure of network robustness. The following findings are presented: (1) The algebraic connectivity-optimal GMs deviate quickly from the proximity-optimal GMs, yielding a number of less robust GMs. This hints that the rationality of the algebraic connectivity as a measure of network robustness is still in doubt. (2) The effective resistace-optimal GMs and the average edge betweenness-optimal GMs are in line with the proximity-optimal GMs. This partly justifies the two quantities as metrics of network robustness. (3) The efficiency-optimal GMs deviate gradually from the proximity-optimal GMs, yielding some less robust GMs. This suggests the limited utility of the efficiency as a measure of network robustness.

Epidemic outbreak for an SIS model in multiplex networks with immunization

With the aim of understanding epidemic spreading in a general multiplex network and designing optimal immunization strategies, a mathematical model based on multiple degree is built to analyze the threshold condition for epidemic outbreak. Two kinds of strategies, the multiplex node-based immunization and the layer node-based immunization, are examined. Theoretical results show that the general framework proposed here can illustrate the effect of diverse correlations and immunizations on the outbreak condition in multiplex networks. Under a set of conditions on uncorrelated coefficients, the specific epidemic thresholds are shown to be only dependent on the respective degree distribution in each layer.

Predicting the epidemic threshold of the susceptible-infected-recovered model

Researchers have developed several theoretical methods for predicting epidemic thresholds, including the mean-field like (MFL) method, the quenched mean-field (QMF) method, and the dynamical message passing (DMP) method. When these methods are applied to predict epidemic threshold they often produce differing results and their relative levels of accuracy are still unknown. We systematically analyze these two issues-relationships among differing results and levels of accuracy-by studying the susceptible-infected-recovered (SIR) model on uncorrelated configuration networks and a group of 56 real-world networks. In uncorrelated configuration networks the MFL and DMP methods yield identical predictions that are larger and more accurate than the prediction generated by the QMF method. As for the 56 real-world networks, the epidemic threshold obtained by the DMP method is more likely to reach the accurate epidemic threshold because it incorporates full network topology information and some dynamical correlations. We find that in most of the networks with positive degree-degree correlations, an eigenvector localized on the high k-core nodes, or a high level of clustering, the epidemic threshold predicted by the MFL method, which uses the degree distribution as the only input information, performs better than the other two methods.

Accuracy criterion for the mean-field approximation in susceptible-infected-susceptible epidemics on networks

Mean-field approximations (MFAs) are frequently used in physics. When a process (such as an epidemic or a synchronization) on a network is approximated by MFA, a major hurdle is the determination of those graphs for which MFA is reasonably accurate. Here, we present an accuracy criterion for Markovian susceptible-infected-susceptible (SIS) epidemics on any network, based on the spectrum of the adjacency and SIS covariance matrix. We evaluate the MFA criterion for the complete and star graphs analytically, and numerically for connected Erdős-Rényi random graphs for small size N≤14. The accuracy of MFA increases with average degree and with N. Precise simulations (up to network sizes N=100) of the MFA accuracy criterion versus N for the complete graph, star, square lattice, and path graphs lead us to conjecture that the worst MFA accuracy decreases, for large N, proportionally to the inverse of the spectral radius of the adjacency matrix of the graph.

Network impact on persistence in a finite population dynamic diffusion model: application to an emergent seed exchange network

Dynamic extinction colonisation models (also called contact processes) are widely studied in epidemiology and in metapopulation theory. Contacts are usually assumed to be possible only through a network of connected patches. This network accounts for a spatial landscape or a social organization of interactions. Thanks to social network literature, heterogeneous networks of contacts can be considered. A major issue is to assess the influence of the network in the dynamic model. Most work with this common purpose uses deterministic models or an approximation of a stochastic Extinction-Colonisation model (sEC) which are relevant only for large networks. When working with a limited size network, the induced stochasticity is essential and has to be taken into account in the conclusions. Here, a rigorous framework is proposed for limited size networks and the limitations of the deterministic approximation are exhibited. This framework allows exact computations when the number of patches is small. Otherwise, simulations are used and enhanced by adapted simulation techniques when necessary. A sensitivity analysis was conducted to compare four main topologies of networks in contrasting settings to determine the role of the network. A challenging case was studied in this context: seed exchange of crop species in the Réseau Semences Paysannes (RSP), an emergent French farmers׳ organisation. A stochastic Extinction-Colonisation model was used to characterize the consequences of substantial changes in terms of RSP׳s social organization on the ability of the system to maintain crop varieties.

Epidemic outbreaks in two-scale community networks

We consider a model for the diffusion of epidemics in a population that is partitioned into local communities. In particular, assuming a mean-field approximation, we analyze a continuous-time susceptible-infected-susceptible (SIS) model that has appeared recently in the literature. The probability by which an individual infects individuals in its own community is different from the probability of infecting individuals in other communities. The aim of the model, compared to the standard, nonclustered one, is to provide a compact description for the presence of communities of local infection where the epidemic process is faster compared to the rate at which it spreads across communities. Ultimately, it provides a tool to express the probability of epidemic outbreaks in the form of a metastable infection probability. In the proposed model, the spatial structure of the network is encoded by the adjacency matrix of clusters, i.e., the connections between local communities, and by the vector of the sizes of local communities. Thus, the existence of a nontrivial metastable occupancy probability is determined by an epidemic threshold which depends on the clusters' size and on the intercommunity network structure.

Domination-time dynamics in susceptible-infected-susceptible virus competition on networks

When two viruses compete for healthy nodes in a simple network and both spreading rates are above the epidemic threshold, only one virus will survive. However, if we prevent the viruses from dying out, rich dynamics emerge. When both viruses are identical, one virus always dominates the other, but the dominating and dominated virus alternate. We show in the complete graph that the domination time depends on the total number of infected nodes at the beginning of the domination period and, moreover, that the distribution of the domination time decays exponentially yet slowly. When the viruses differ moderately in strength and/or speed the weaker and/or slower virus can still dominate the other but for a short time. Interestingly, depending on the number of infected nodes at the start of a domination period, being quicker can be a disadvantage.

Epidemic spread on weighted networks

The contact structure between hosts shapes disease spread. Most network-based models used in epidemiology tend to ignore heterogeneity in the weighting of contacts between two individuals. However, this assumption is known to be at odds with the data for many networks (e.g. sexual contact networks) and to have a critical influence on epidemics' behavior. One of the reasons why models usually ignore heterogeneity in transmission is that we currently lack tools to analyze weighted networks, such that most studies rely on numerical simulations. Here, we present a novel framework to estimate key epidemiological variables, such as the rate of early epidemic expansion () and the basic reproductive ratio (), from joint probability distributions of number of partners (contacts) and number of interaction events through which contacts are weighted. These distributions are much easier to infer than the exact shape of the network, which makes the approach widely applicable. The framework also allows for a derivation of the full time course of epidemic prevalence and contact behaviour, which we validate with numerical simulations on networks. Overall, incorporating more realistic contact networks into epidemiological models can improve our understanding of the emergence and spread of infectious diseases.

Understanding how infectious diseases spread has public health and ecological implications. The contact structure between hosts strongly affects this spread. However, most studies assume that all types of contacts are identical, when in reality some individuals interact more strongly than others. This is particularly striking for sexual-contact networks, where the number of sex acts is not identical for all partnerships. This heterogeneity in activity can either speed up or slow down epidemic spread depending on how strongly the individuals' number of contacts coincides with their activity. There are two limitations to current frameworks that can explain the lack of studies on weighted networks. First, analytical results are difficult to obtain, which requires numerical simulations. Second, inferring weighted networks from survey data is extremely difficult. Here, we present a novel framework that allows to alleviate these two limitations. Building on configuration type network epidemic approaches, we manage to capture disease spread on weighted networks from the distribution of the number of contacts and distribution of the number of interaction events (e.g. sex acts). This allows us to derive analytical estimates for the epidemic threshold and the rate of spread of the disease. It also allows us to readily incorporate survey data, as illustrated in this study with data from the National Survey of Sexual Attitudes and Lifestyles (NATSAL) carried out in the UK.

Epidemic threshold and topological structure of susceptible-infectious-susceptible epidemics in adaptive networks

The interplay between disease dynamics on a network and the dynamics of the structure of that network characterizes many real-world systems of contacts. A continuous-time adaptive susceptible-infectious-susceptible (ASIS) model is introduced in order to investigate this interaction, where a susceptible node avoids infections by breaking its links to its infected neighbors while it enhances the connections with other susceptible nodes by creating links to them. When the initial topology of the network is a complete graph, an exact solution to the average metastable-state fraction of infected nodes is derived without resorting to any mean-field approximation. A linear scaling law of the epidemic threshold τ(c) as a function of the effective link-breaking rate ω is found. Furthermore, the bifurcation nature of the metastable fraction of infected nodes of the ASIS model is explained. The metastable-state topology shows high connectivity and low modularity in two regions of the τ,ω plane for any effective infection rate τ>τ(c): (i) a "strongly adaptive" region with very high ω and (ii) a "weakly adaptive" region with very low ω. These two regions are separated from the other half-open elliptical-like regions of low connectivity and high modularity in a contour-line-like way. Our results indicate that the adaptation of the topology in response to disease dynamics suppresses the infection, while it promotes the network evolution towards a topology that exhibits assortative mixing, modularity, and a binomial-like degree distribution.

Effect of the interconnected network structure on the epidemic threshold

Most real-world networks are not isolated. In order to function fully, they are interconnected with other networks, and this interconnection influences their dynamic processes. For example, when the spread of a disease involves two species, the dynamics of the spread within each species (the contact network) differs from that of the spread between the two species (the interconnected network). We model two generic interconnected networks using two adjacency matrices, A and B, in which A is a 2N×2N matrix that depicts the connectivity within each of two networks of size N, and B a 2N×2N matrix that depicts the interconnections between the two. Using an N-intertwined mean-field approximation, we determine that a critical susceptible-infected-susceptible (SIS) epidemic threshold in two interconnected networks is 1/λ(1)(A+αB), where the infection rate is β within each of the two individual networks and αβ in the interconnected links between the two networks and λ(1)(A+αB) is the largest eigenvalue of the matrix A+αB. In order to determine how the epidemic threshold is dependent upon the structure of interconnected networks, we analytically derive λ(1)(A+αB) using a perturbation approximation for small and large α, the lower and upper bound for any α as a function of the adjacency matrix of the two individual networks, and the interconnections between the two and their largest eigenvalues and eigenvectors. We verify these approximation and boundary values for λ(1)(A+αB) using numerical simulations, and determine how component network features affect λ(1)(A+αB). We note that, given two isolated networks G(1) and G(2) with principal eigenvectors x and y, respectively, λ(1)(A+αB) tends to be higher when nodes i and j with a higher eigenvector component product x(i)y(j) are interconnected. This finding suggests essential insights into ways of designing interconnected networks to be robust against epidemics.

Non-Markovian infection spread dramatically alters the susceptible-infected-susceptible epidemic threshold in networks

Most studies on susceptible-infected-susceptible epidemics in networks implicitly assume Markovian behavior: the time to infect a direct neighbor is exponentially distributed. Much effort so far has been devoted to characterize and precisely compute the epidemic threshold in susceptible-infected-susceptible Markovian epidemics on networks. Here, we report the rather dramatic effect of a nonexponential infection time (while still assuming an exponential curing time) on the epidemic threshold by considering Weibullean infection times with the same mean, but different power exponent α. For three basic classes of graphs, the Erdős-Rényi random graph, scale-free graphs and lattices, the average steady-state fraction of infected nodes is simulated from which the epidemic threshold is deduced. For all graph classes, the epidemic threshold significantly increases with the power exponents α. Hence, real epidemics that violate the exponential or Markovian assumption can behave seriously differently than anticipated based on Markov theory.

Epidemic spreading in annealed directed networks: susceptible-infected-susceptible model and contact process

We investigate epidemic spreading in annealed directed scale-free networks with the in-degree (k) distribution P(in)(k)~k(-γ(in)) and the out-degree (ℓ) distribution, P(out)(ℓ)~ℓ(-γ(out)). The correlation <kl> of each node on the networks is controlled by the probability r(0≤r≤1) in two different algorithms, the so-called k and ℓ algorithms. For r=1, the k algorithm gives <kl>=<k(2)>, whereas the ℓ algorithm gives <kl>=<ℓ(2)>. For r=0, <kl>=<k><ℓ> for both algorithms. As the prototype of epidemic spreading, the susceptible-infected-susceptible model and contact process on the networks are analyzed using the heterogeneous mean-field theory and Monte Carlo simulations. The directedness of links and the correlation of the network are found to play important roles in the spreading, so that critical behaviors of both models are distinct from those on undirected scale-free networks.

Susceptible-infected-susceptible epidemics on the complete graph and the star graph: exact analysis

Since mean-field approximations for susceptible-infected-susceptible (SIS) epidemics do not always predict the correct scaling of the epidemic threshold of the SIS metastable regime, we propose two novel approaches: (a) an ε-SIS generalized model and (b) a modified SIS model that prevents the epidemic from dying out (i.e., without the complicating absorbing SIS state). Both adaptations of the SIS model feature a precisely defined steady state (that corresponds to the SIS metastable state) and allow an exact analysis in the complete and star graph consisting of a central node and N leaves. The N-intertwined mean-field approximation (NIMFA) is shown to be nearly exact for the complete graph but less accurate to predict the correct scaling of the epidemic threshold τ(c) in the star graph, which is found as τ(c)=ατ(c)((1)), where α=√[1/2 logN + 3/2 log logN] and where τ(c)((1))=1/√[N]<τ(c) is the first-order epidemic threshold for the star in NIMFA and equal to the inverse of the spectral radius of the star's adjacency matrix.

Epidemic thresholds of the susceptible-infected-susceptible model on networks: a comparison of numerical and theoretical results

Recent work has shown that different theoretical approaches to the dynamics of the susceptible-infected-susceptible (SIS) model for epidemics lead to qualitatively different estimates for the position of the epidemic threshold in networks. Here we present large-scale numerical simulations of the SIS dynamics on various types of networks, allowing the precise determination of the effective threshold for systems of finite size N. We compare quantitatively the numerical thresholds with theoretical predictions of the heterogeneous mean-field theory and of the quenched mean-field theory. We show that the latter is in general more accurate, scaling with N with the correct exponent, but often failing to capture the correct prefactor.