Globally, the outbreaks of infectious diseases have exerted an extremely profound and severe influence on health security and the economy. During the critical phases of epidemics, devising effective intervention measures poses a significant challenge to both the academic and practical arenas. There is numerous research based on reinforcement learning to optimize intervention measures of infectious diseases. Nevertheless, most of these efforts have been confined within the differential equation based on infectious disease models. Although a limited number of studies have incorporated reinforcement learning methodologies into individual-based infectious disease models, the models employed therein have entailed simplifications and limitations, rendering it incapable of modeling the complexity and dynamics inherent in infectious disease transmission. We establish a decision-making framework based on an individual agent-based transmission model, utilizing reinforcement learning to continuously explore and develop a strategy function. The framework's validity is verified through both experimental and theoretical approaches. Covasim, a detailed and widely used agent-based disease transmission model, was modified to support reinforcement learning research. We conduct an exhaustive exploration of the application efficacy of multiple algorithms across diverse action spaces. Furthermore, we conduct an innovative preliminary theoretical analysis concerning the issue of "time coverage". The results of the experiment robustly validate the effectiveness and feasibility of the methodological framework of this study. The coping strategies gleaned therefrom prove highly efficacious in suppressing the expansion of the epidemic scale and safeguarding the stability of the economic system, thereby providing crucial reference perspectives for the formulation of global public health security strategies.

We employ an agent-based contact network model to study the relationship between vaccine uptake and disease dynamics in a hypothetical country town from New South Wales, Australia, undergoing a COVID-19 epidemic, over a period of three years. We model the contact network in this hypothetical township of N = 10000 people as a scale-free network, and simulate the spread of COVID-19 and vaccination program using disease and vaccination uptake parameters typically observed in such a NSW town. We simulate the spread of the ancestral variant of COVID-19 in this town, and study the disease dynamics while the town maintains limited but non-negligible contact with the rest of the country which is assumed to be undergoing a severe COVID-19 epidemic. We also simulate a maximum three doses of Pfizer Comirnaty vaccine being administered in this town, with limited vaccine supply at first which gradually increases, and analyse how the vaccination uptake affects the disease dynamics in this town, which is captured using an extended compartmental model with epidemic parameters typical for a COVID-19 epidemic in Australia. Our results show that, in such a township, three vaccination doses are sufficient to contain but not eradicate COVID-19, and the disease essentially becomes endemic. We also show that the average degree of infected nodes (the average number of contacts for infected people) predicts the proportion of infected people. Therefore, if the hubs (people with a relatively high number of contacts) are disproportionately infected, this indicates an oncoming peak of the infection, though the lag time thereof depends on the maximum number of vaccines administered to the populace. Overall, our analysis provides interesting insights in understanding the interplay between network topology, vaccination levels, and COVID-19 disease dynamics in a typical remote NSW country town.

We consider how human-centered causal theories and tools from the dynamical systems literature can be deployed to guide the representation of data when training neural networks for complex classification tasks. Specifically, we use simulated data to show that training a neural network with a data representation that makes explicit the invariant structural causal features of the data generating process of an epidemic system improves out-of-distribution (OOD) generalization performance on a classification task as compared to a more naive approach to data representation. We take these results to demonstrate that using human-generated causal knowledge to reduce the epistemic uncertainty of ML developers can lead to more well-specified ML pipelines. This, in turn, points to the utility of a dynamical systems approach to the broader effort aimed at improving the robustness and safety of machine learning systems via improved ML system development practices.

Classical epidemiological models assume homogeneous populations. There have been important extensions to model heterogeneous populations, when the identity of the sub-populations is known, such as age group or geographical location. Here, we propose two new methods to model the number of people infected with COVID-19 over time, each as a linear combination of latent sub-populations -- i.e., when we do not know which person is in which sub-population, and the only available observations are the aggregates across all sub-populations. Method #1 is a dictionary-based approach, which begins with a large number of pre-defined sub-population models (each with its own starting time, shape, etc), then determines the (positive) weight of small (learned) number of sub-populations. Method #2 is a mixture-of-$M$ fittable curves, where $M$, the number of sub-populations to use, is given by the user. Both methods are compatible with any parametric model; here we demonstrate their use with first (a)~Gaussian curves and then (b)~SIR trajectories. We empirically show the performance of the proposed methods, first in (i) modeling the observed data and then in (ii) forecasting the number of infected people 1 to 4 weeks in advance. Across 187 countries, we show that the dictionary approach had the lowest mean absolute percentage error and also the lowest variance when compared with classical SIR models and moreover, it was a strong baseline that outperforms many of the models developed for COVID-19 forecasting.

This paper describes an agent-based model of epidemics dynamics. This model is willingly simplified, as its goal is not to predict the evolution of the epidemics, but to explain the underlying mechanisms in an interactive way. This model allows to compare screening prioritisation strategies, as well as vaccination priority strategies, on a virtual population. The model is implemented in Netlogo in different simulators, published online to let people experiment with them. This paper reports on the model design, implementation, and experimentations. In particular we have compared screening strategies to evaluate the epidemics vs control it by quarantining infectious people; and we have compared vaccinating older people with more risk factors, vs younger people with more social contacts.

Simulating the spread of infectious diseases in human communities is critical for predicting the trajectory of an epidemic and verifying various policies to control the devastating impacts of the outbreak. Many existing simulators are based on compartment models that divide people into a few subsets and simulate the dynamics among those subsets using hypothesized differential equations. However, these models lack the requisite granularity to study the effect of intelligent policies that influence every individual in a particular way. In this work, we introduce a simulator software capable of modeling a population structure and controlling the disease's propagation at an individualistic level. In order to estimate the confidence of the conclusions drawn from the simulator, we employ a comprehensive probabilistic approach where the entire population is constructed as a hierarchical random variable. This approach makes the inferred conclusions more robust against sampling artifacts and gives confidence bounds for decisions based on the simulation results. To showcase potential applications, the simulator parameters are set based on the formal statistics of the COVID-19 pandemic, and the outcome of a wide range of control measures is investigated. Furthermore, the simulator is used as the environment of a reinforcement learning problem to find the optimal policies to control the pandemic. The obtained experimental results indicate the simulator's adaptability and capacity in making sound predictions and a successful policy derivation example based on real-world data. As an exemplary application, our results show that the proposed policy discovery method can lead to control measures that produce significantly fewer infected individuals in the population and protect the health system against saturation.

At least one out of every five people who get the coronavirus doesn't show symptoms and can unknowingly spread the virus to others. Those who don't feel sick and aren't notified of exposure can't know that they should get tested. But researchers at the Massachusetts Institute of Technology may have found a way to identify these silent coronavirus carriers without a test. A study published in September describes an artificial-intelligence model that can distinguish between the coughs of people with the coronavirus and those who are healthy. It can even tell from voluntary, forced coughs whether people were healthy or were asymptomatic carriers, based on sound variations too subtle for the human ear to discern.

If one good thing has come out of the COVID-19 pandemic, it's the vast amount of data we have acquired. In light of technological advancements, we have access to more information and computing power, which we can use to predict and curb the spread of the virus. One of the simplest ways to do this is through the SIR model. The SIR is a compartmental model that categorizes a constant population into three groups, namely the susceptible, infected, and recovered. These can all be expressed as functions that take time as an argument.

The global pandemic of the 2019-nCov requires the evaluation of policy interventions to mitigate future social and economic costs of quarantine measures worldwide. We propose an epidemiological model for forecasting and policy evaluation which incorporates new data in real-time through variational data assimilation. We analyze and discuss infection rates in China, the US and Italy. In particular, we develop a custom compartmental SIR model fit to variables related to the epidemic in Chinese cities, named SITR model. We compare and discuss model results which conducts updates as new observations become available. A hybrid data assimilation approach is applied to make results robust to initial conditions. We use the model to do inference on infection numbers as well as parameters such as the disease transmissibility rate or the rate of recovery. The parameterisation of the model is parsimonious and extendable, allowing for the incorporation of additional data and parameters of interest. This allows for scalability and the extension of the model to other locations or the adaption of novel data sources.

As the COVID-19 pandemic evolves, reliable prediction plays an important role for policy making. The classical infectious disease model SEIR (susceptible-exposed-infectious-recovered) is a compact yet simplistic temporal model. The data-driven machine learning models such as RNN (recurrent neural networks) can suffer in case of limited time series data such as COVID-19. In this paper, we combine SEIR and RNN on a graph structure to develop a hybrid spatio-temporal model to achieve both accuracy and efficiency in training and forecasting. We introduce two features on the graph structure: node feature (local temporal infection trend) and edge feature (geographic neighbor effect). For node feature, we derive a discrete recursion (called I-equation) from SEIR so that gradient descend method applies readily to its optimization. For edge feature, we design an RNN model to capture the neighboring effect and regularize the landscape of loss function so that local minima are effective and robust for prediction. The resulting hybrid model (called IeRNN) improves the prediction accuracy on state-level COVID-19 new case data from the US, out-performing standard temporal models (RNN, SEIR, and ARIMA) in 1-day and 7-day ahead forecasting. Our model accommodates various degrees of reopening and provides potential outcomes for policymakers.