Univariate zero-inflated models are increasingly being used to account for excess zeros in spatio-temporal infectious disease counts. However, the multivariate case is challenging due to the need to account for correlations across space, time and disease in both the count and zero-inflated components of the model. We are interested in comparing the transmission dynamics of several co-circulating infectious diseases across space and time, where some of the diseases can be absent for long periods. We first assume there is a baseline disease that is well-established and always present in the region. The other diseases switch between periods of presence and absence in each area through a series of coupled Markov chains, which account for long periods of disease absence, disease interactions and disease spread from neighboring areas. Since we are mainly interested in comparing the diseases, we assume the cases of the present diseases in an area jointly follow an autoregressive multinomial model. We use the multinomial model to investigate whether there are associations between certain factors, such as temperature, and differences in the transmission intensity of the diseases. Inference
Infectious diseases, either emerging or long-lasting, place numerous people at risk and bring heavy public health burdens worldwide. In the process against infectious diseases, predicting the epidemic risk by modeling the disease transmission plays an essential role in assisting with preventing and controlling disease transmission in a more effective way. In this paper, we systematically describe how machine learning can play an essential role in quantitatively characterizing disease transmission patterns and accurately predicting infectious disease risks. First, we introduce the background and motivation of using machine learning for infectious disease risk prediction. Next, we describe the development and components of various machine learning models for infectious disease risk prediction. Specifically, existing models fall into three categories: Statistical prediction, data-driven machine learning, and epidemiology-inspired machine learning. Subsequently, we discuss challenges encountered when dealing with model inputs, designing task-oriented objectives, and conducting performance evaluation. Finally, we conclude with a discussion of open questions and future directions.
Reinforcement learning (RL), owing to its adaptability to various dynamic systems in many real-world scenarios and the capability of maximizing long-term outcomes under different constraints, has been used in infectious disease control to optimize the intervention strategies for controlling infectious disease spread and responding to outbreaks in recent years. The potential of RL for assisting public health sectors in preventing and controlling infectious diseases is gradually emerging and being explored by rapidly increasing publications relevant to COVID-19 and other infectious diseases. However, few surveys exclusively discuss this topic, that is, the development and application of RL approaches for optimizing strategies of non-pharmaceutical and pharmaceutical interventions of public health. Therefore, this paper aims to provide a concise review and discussion of the latest literature on how RL approaches have been used to assist in controlling the spread and outbreaks of infectious diseases, covering several critical topics addressing public health demands: resource allocation, balancing between lives and livelihoods, mixed policy of multiple interventions, and inter-regional
Interaction patterns among individuals play vital roles in spreading infectious diseases. Understanding these patterns and integrating their impact in modeling diffusion dynamics of infectious diseases are important for epidemiological studies. Current network-based diffusion models assume that diseases transmit through interactions where both infected and susceptible individuals are co-located at the same time. However, there are several infectious diseases that can transmit when a susceptible individual visits a location after an infected individual has left. Recently, we introduced a diffusion model called same place different time (SPDT) transmission to capture the indirect transmissions that happen when an infected individual leaves before a susceptible individual's arrival along with direct transmissions. In this paper, we demonstrate how these indirect transmission links significantly enhance the emergence of infectious diseases simulating airborne disease spreading on a synthetic social contact network. We denote individuals having indirect links but no direct links during their infectious periods as hidden spreaders. Our simulation shows that indirect links play similar ro
Infectious disease forecasting is of great interest to the public health community and policymakers, since forecasts can provide insight into disease dynamics in the near future and inform interventions. Due to delays in case reporting, however, forecasting models may often underestimate the current and future disease burden. In this paper, we propose a general framework for addressing reporting delay in disease forecasting efforts with the goal of improving forecasts. We propose strategies for leveraging either historical data on case reporting or external internet-based data to estimate the amount of reporting error. We then describe several approaches for adapting general forecasting pipelines to account for under- or over-reporting of cases. We apply these methods to address reporting delay in data on dengue fever cases in Puerto Rico from 1990 to 2009 and to reports of influenza-like illness (ILI) in the United States between 2010 and 2019. Through a simulation study, we compare method performance and evaluate robustness to assumption violations. Our results show that forecasting accuracy and prediction coverage almost always increase when correction methods are implemented to
This study embarks on a comprehensive exploration of the decadal trends and future trajectories of twenty distinct infectious diseases in China from 1998 to 2021. A refined Hybrid Bayesian Structural Time Series (BSTS)-Markov Chain Monte Carlo (MCMC) model is employed, intertwining with Long Short-Term Memory (LSTM) networks to dissect intricate relationships amidst population demographics, economic indices, and the evolution of infectious diseases. The findings reveal the persistent prevalence of high incidence diseases in future 10 years, like AIDS, Gonorrhea, and Syphilis, and stable occurrences of middle incidence rate diseases such as Brucellosis and Scarlet Fever, while also foretelling the potential disappearance of lower incidence rate diseases like Cholera, Encephalitis B, and Measles. The study particularly underscores the transformative impact of the COVID-19 pandemic, showcasing its extensive implications on the incidences and management of a plethora of diseases, urging a deeper probe into the nuanced alterations in disease transmission, testing, and reporting modalities amidst global health crises. This research accentuates the critical role of advanced predictive ana
This paper conducts research on the established model and presents the main conclusions . Firstly, by separately considering the infectivity of each of the two infectious diseases and the infectivity of the population simultaneously infected with the two infectious diseases, the existence of three types of boundary equilibrium points is determined, as well as the existence of the interior equilibrium point when the parameters are under specific conditions. Then, the stability of the equilibrium points is analyzed. It is concluded that under different parameter conditions, the stability of the disease free equilibrium point can exhibit various scenarios, such as a stable node or a saddle-node, etc. For the boundary equilibrium points, the situation is more intricate,and a cusp may occur. The stability of the interior equilibrium point under specific conditions is also presented. Finally,the degeneracy of the equilibrium points is studied through the bifurcation theory.Mainly, the saddle-node bifurcation occurring at the interior equilibrium point is obtained, and when the infection rate of the first infectious disease, the infection rate of the second infectious disease, and the inf
The global public health landscape is perpetually challenged by the looming threat of infectious diseases. Central to addressing this concern is the imperative to prevent and manage disease transmission during pandemics, particularly in unique settings. This study addresses the transmission dynamics of infectious diseases within conference venues, presenting a computational model designed to simulate transmission processes within a condensed timeframe (one day), beginning with sporadic cases. Our model intricately captures the activities of individual attendees within the conference venue, encompassing meetings, rest intervals, and meal breaks. While meetings entail proximity seating, rest and lunch periods allow attendees to interact with diverse individuals. Moreover, the restroom environment poses an additional avenue for potential infection transmission. Employing an individual-based model, we meticulously replicated the transmission dynamics of infectious diseases, with a specific emphasis on close-contact interactions between infected and susceptible individuals. Through comprehensive analysis of model simulations, we elucidated the intricacies of disease transmission dynamic
Mathematical models of infectious diseases are frequently used as a tool to support public health policy and decisions around implementation of interventions such as school closures. However, most publications on policy-relevant modelling lack an ethical framework and do not explicitly consider the ethical implications of the work. This creates a risk that unintended consequences of interventions are overlooked or that models are used to justify decisions that are inconsistent with public health ethics. In this article, we focus on the case study of school closures as a commonly modelled intervention against pandemic influenza, COVID-19, and other infectious disease threats. We briefly review some of the key concepts in public health ethics and describe approaches to modelling the effects of school closures. We then identify a series of ethical considerations involved in modelling school closures. These include accounting for population heterogeneity and inequalities; including a diversity of viewpoints and expertise in model design; considering the distribution of benefits and harms; and model transparency and contextualisation. We conclude with some recommendations to ensure that
Understanding dynamics of an infectious disease helps in designing appropriate strategies for containing its spread in a population. Recent mathematical models are aimed at studying dynamics of some specific types of infectious diseases. In this paper we propose a new model for infectious diseases spread having susceptible, infected, and recovered populations and study its dynamics in presence of incubation delays and relapse of the disease. The influence of treatment and vaccination efforts on the spread of infection in presence of time delays are studied. Sufficient conditions for local stability of the equilibria and change of stability are derived in various cases. The problem of global stability is studied for an important special case of the model. Simulations carried out in this study brought out the importance of treatment rate in controlling the disease spread. It is observed that incubation delays have influence on the system even under enhanced vaccination. The present study has clearly brought out the fact that treatment rate in presence of time delays would contain the disease as compared to popular belief that eradication can only be done through vaccination.
Supervised machine learning models and public surveillance data has been employed for infectious disease forecasting in many settings. These models leverage various data sources capturing drivers of disease spread, such as climate conditions or human behavior. However, few models have incorporated the organizational structure of different geographic locations for forecasting. Traveling waves of seasonal outbreaks have been reported for dengue, influenza, and other infectious diseases, and many of the drivers of infectious disease dynamics may be shared across different cities, either due to their geographic or socioeconomic proximity. In this study, we developed a machine learning model to predict case counts of four infectious diseases across Brazilian cities one week ahead by incorporating information from related cities. We compared selecting related cities using both geographic distance and GDP per capita. Incorporating information from geographically proximate cities improved predictive performance for two of the four diseases, specifically COVID-19 and Zika. We also discuss the impact on forecasts in the presence of anomalous contagion patterns and the limitations of the prop
The main aim to build models capable of simulating the spreading of infectious diseases is to control them. And along this way, the key to find the optimal strategy for disease control is to obtain a large number of simulations of disease transitions under different scenarios. Therefore, the models that can simulate the spreading of diseases under scenarios closer to the reality and are with high efficiency are preferred. In the realistic social networks, the random contact, including contacts between people in the public places and the public transits, becomes the important access for the spreading of infectious diseases. In this paper, a model can efficiently simulate the spreading of infectious diseases under random contacts is proposed. In this approach, the random contact between people is characterized by the random matrix with elements randomly generated and the spread of the diseases is simulated by the Markov process. We report an interesting property of the proposed model: the main indicators of the spreading of the diseases such as the death rate are invariant of the size of the population. Therefore, representative simulations can be conducted on models consist of small
Infectious disease models can be of great use for understanding the underlying mechanisms that influence the spread of diseases and predicting future disease progression. Modeling has been increasingly used to evaluate the potential impact of different control measures and to guide public health policy decisions. In recent years, there has been rapid progress in developing spatio-temporal modeling of infectious diseases and an example of such recent developments is the discrete time individual-level models (ILMs). These models are well developed and provide a common framework for modeling many disease systems, however, they assume the probability of disease transmission between two individuals depends only on their spatial separation and not on their spatial locations. In cases where spatial location itself is important for understanding the spread of emerging infectious diseases and identifying their causes, it would be beneficial to incorporate the effect of spatial location in the model. In this study, we thus generalize the ILMs to a new class of geographically-dependent ILMs (GD-ILMs), to allow for the evaluation of the effect of spatially varying risk factors (e.g., education
Prion diseases are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. By now there have not been some effective therapeutic approaches to treat all these prion diseases. In 2008, canine mammals including dogs (canis familials) were the first time academically reported to be resistant to prion diseases (Vaccine 26: 2601--2614 (2008)). Rabbits are the mammalian species known to be resistant to infection from prion diseases from other species (Journal of Virology 77: 2003--2009 (2003)). Horses were reported to be resistant to prion diseases too (Proceedings of the National Academy of Sciences USA 107: 19808--19813 (2010)). By now all the NMR structures of dog, rabbit and horse prion proteins had been released into protein data bank respectively in 2005, 2007 and 2010 (Proceedings of the National Academy of Sciences USA 102: 640--645 (2005), Journal of Biomolecular NMR 38:181 (2007), Journal of Molecular Biology 400: 121--128 (2010)). Thus, at this moment it is very worth studying the NMR molecular structures of horse, dog and rabbit prion proteins to obtain insights into their immunity prion diseases. This article reports the findings of th
Background: National or local laws, norms or regulations (sometimes and in some countries) require medical providers to report notifiable diseases to public health authorities. Reporting, however, is almost always incomplete. This is due to a variety of reasons, ranging from not recognizing the diseased to failures in the technical or administrative steps leading to the final official register in the disease notification system. The reported fraction varies from 9% to 99% and is strongly associated with the disease being reported. Methods: In this paper we propose a method to approximately estimate the full prevalence (and any other variable or parameter related to transmission intensity) of infectious diseases. The model assumes incomplete notification of incidence and allows the estimation of the non-notified number of infections and it is illustrated by the case of hepatitis C in Brazil. The method has the advantage that it can be corrected iteratively by comparing its findings with empirical results. Results: The application of the model for the case of hepatitis C in Brazil resulted in a prevalence of notified cases that varied between 163,902 and 169,382 cases; a prevalence o
Networks of person-person contacts form the substrate along which infectious diseases spread. Most network-based studies of the spread focus on the impact of variations in degree (the number of contacts an individual has). However, other effects such as clustering, variations in infectiousness or susceptibility, or variations in closeness of contacts may play a significant role. We develop analytic techniques to predict how these effects alter the growth rate, probability, and size of epidemics and validate the predictions with a realistic social network. We find that (for given degree distribution and average transmissibility) clustering is the dominant factor controlling the growth rate, heterogeneity in infectiousness is the dominant factor controlling the probability of an epidemic, and heterogeneity in susceptibility is the dominant factor controlling the size of an epidemic. Edge weights (measuring closeness or duration of contacts) have impact only if correlations exist between different edges. Combined, these effects can play a minor role in reinforcing one another, with the impact of clustering largest when the population is maximally heterogeneous or if the closer contact
In retrospective assessments, internet news reports have been shown to capture early reports of unknown infectious disease transmission prior to official laboratory confirmation. In general, media interest and reporting peaks and wanes during the course of an outbreak. In this study, we quantify the extent to which media interest during infectious disease outbreaks is indicative of trends of reported incidence. We introduce an approach that uses supervised temporal topic models to transform large corpora of news articles into temporal topic trends. The key advantages of this approach include, applicability to a wide range of diseases, and ability to capture disease dynamics - including seasonality, abrupt peaks and troughs. We evaluated the method using data from multiple infectious disease outbreaks reported in the United States of America (U.S.), China and India. We noted that temporal topic trends extracted from disease-related news reports successfully captured the dynamics of multiple outbreaks such as whooping cough in U.S. (2012), dengue outbreaks in India (2013) and China (2014). Our observations also suggest that efficient modeling of temporal topic trends using time-serie
During an infectious disease pandemic, it is critical to share electronic medical records or models (learned from these records) across regions. Applying one region's data/model to another region often have distribution shift issues that violate the assumptions of traditional machine learning techniques. Transfer learning can be a solution. To explore the potential of deep transfer learning algorithms, we applied two data-based algorithms (domain adversarial neural networks and maximum classifier discrepancy) and model-based transfer learning algorithms to infectious disease detection tasks. We further studied well-defined synthetic scenarios where the data distribution differences between two regions are known. Our experiments show that, in the context of infectious disease classification, transfer learning may be useful when (1) the source and target are similar and the target training data is insufficient and (2) the target training data does not have labels. Model-based transfer learning works well in the first situation, in which case the performance closely matched that of the data-based transfer learning models. Still, further investigation of the domain shift in real world
In this work, we present an approach called Disease Informed Neural Networks (DINNs) that can be employed to effectively predict the spread of infectious diseases. This approach builds on a successful physics informed neural network approaches that have been applied to a variety of applications that can be modeled by linear and non-linear ordinary and partial differential equations. Specifically, we build on the application of PINNs to SIR compartmental models and expand it a scaffolded family of mathematical models describing various infectious diseases. We show how the neural networks are capable of learning how diseases spread, forecasting their progression, and finding their unique parameters (e.g. death rate). To demonstrate the robustness and efficacy of DINNs, we apply the approach to eleven highly infectious diseases that have been modeled in increasing levels of complexity. Our computational experiments suggest that DINNs is a reliable candidate for effectively learn about the dynamics of spread and forecast its progression into the future from available real-world data.
Infectious diseases spread through human networks. Susceptible-Infected-Removed (SIR) model is one of the epidemic models to describe infection dynamics on a complex network connecting individuals. In the metapopulation SIR model, each node represents a population (group) which has many individuals. In this paper, we propose a modified metapopulation SIR model in which a latent period is taken into account. We call it SIIR model. We divide the infection period into two stages: an infected stage, which is the same as the previous model, and a seriously ill stage, in which individuals are infected and cannot move to the other populations. The two infectious stages in our modified metapopulation SIR model produce a discontinuous final size distribution. Individuals in the infected stage spread the disease like individuals in the seriously ill stage and never recover directly, which makes an effective recovery rate smaller than the given recovery rate.