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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.
Belief propagation is a widely used message passing method for the solution of probabilistic models on networks such as epidemic models, spin models, and Bayesian graphical models, but it suffers from the serious shortcoming that it works poorly in t
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 differen
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 obse
Learned neural solvers have successfully been used to solve combinatorial optimization and decision problems. More general counting variants of these problems, however, are still largely solved with hand-crafted solvers. To bridge this gap, we introd
Attention-based neural networks have achieved state-of-the-art results on a wide range of tasks. Most such models use deterministic attention while stochastic attention is less explored due to the optimization difficulties or complicated model design