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Register a new userEoN (Epidemics on Networks): a fast, flexible Python package for simulation, analytic approximation, and analysis of epidemics on networks
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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.
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The exploration of epidemic dynamics on dynamically evolving (adaptive) networks poses nontrivial challenges to the modeler, such as the determination of a small number of informative statistics of the detailed network state (that is, a few good observables) that usefully summarize the overall (macroscopic, systems level) behavior. Trying to obtain reduced, small size, accurate models in terms of these few statistical observables - that is, coarse-graining the full network epidemic model to a small but useful macroscopic one - is even more daunting. Here we describe a data-based approach to solving the first challenge: the detection of a few informative collective observables of the detailed epidemic dynamics. This will be accomplished through Diffusion Maps, a recently developed data-mining technique. We illustrate the approach through simulations of a simple mathematical model of epidemics on a network: a model known to exhibit complex temporal dynamics. We will discuss potential extensions of the approach, as well as possible shortcomings.
We study several bayesian inference problems for irreversible stochastic epidemic models on networks from a statistical physics viewpoint. We derive equations which allow to accurately compute the posterior distribution of the time evolution of the state of each node given some observations. At difference with most existing methods, we allow very general observation models, including unobserved nodes, state observations made at different or unknown times, and observations of infection times, possibly mixed together. Our method, which is based on the Belief Propagation algorithm, is efficient, naturally distributed, and exact on trees. As a particular case, we consider the problem of finding the zero patient of a SIR or SI epidemic given a snapshot of the state of the network at a later unknown time. Numerical simulations show that our method outperforms previous ones on both synthetic and real networks, often by a very large margin.
Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling.
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 ${lambda_{2}}$ during SIS (susceptible-infected-susceptible) epidemic propagation to model perturbations (control state), whereas the infection rate is ${lambda_{1}}$ in the rest of time. Through simulations and theoretical analysis, we find that even for ${lambda_{2}<lambda_{c}}$, epidemics eventually could bounce back if control duration is below a threshold. This critical control time for epidemic resilience, i.e., ${cd_{max}}$ can be predicted by the diameter (${d}$) of the underlying network, with the quantitative relation ${cd_{max}sim d^{alpha}}$. Our findings can help to design a better mitigation strategy for epidemics.
Stochastic epidemic models on networks are inherently high-dimensional and the resulting exact models are intractable numerically even for modest network sizes. Mean-field models provide an alternative but can only capture average quantities, thus offering little or no information about variability in the outcome of the exact process. In this paper we conjecture and numerically prove that it is possible to construct PDE-limits of the exact stochastic SIS epidemics on regular and ErdH{o}s-Renyi networks. To do this we first approximate the exact stochastic process at population level by a Birth-and-Death process (BD) (with a state space of $O(N)$ rather than $O(2^N)$) whose coefficients are determined numerically from Gillespie simulations of the exact epidemic on explicit networks. We numerically demonstrate that the coefficients of the resulting BD process are density-dependent, a crucial condition for the existence of a PDE limit. Extensive numerical tests for Regular and ErdH{o}s-Renyi networks show excellent agreement between the outcome of simulations and the numerical solution of the Fokker-Planck equations. Apart from a significant reduction in dimensionality, the PDE also provides the means to derive the epidemic outbreak threshold linking network and disease dynamics parameters, albeit in an implicit way. Perhaps more importantly, it enables the formulation and numerical evaluation of likelihoods for epidemic and network inference as illustrated in a worked out example.
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