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This work is the first to take advantage of recurrent neural networks to predict influenza-like illness (ILI) dynamics from various linguistic signals extracted from social media data. Unlike other approaches that rely on timeseries analysis of historical ILI data and the state-of-the-art machine learning models, we build and evaluate the predictive power of neural network architectures based on Long Short Term Memory (LSTMs) units capable of nowcasting (predicting in \"real-time\") and forecasting (predicting the future) ILI dynamics in the 2011 - 2014 influenza seasons. To build our models we integrate information people post in social media e.g., topics, embeddings, word ngrams, stylistic patterns, and communication behavior using hashtags and mentions. We then quantitatively evaluate the predictive power of different social media signals and contrast the performance of the-state-of-the-art regression models with neural networks using a diverse set of evaluation metrics. Finally, we combine ILI and social media signals to build a joint neural network model for ILI dynamics prediction. Unlike the majority of the existing work, we specifically focus on developing models for local rather than national ILI surveillance, specifically for military rather than general populations in 26 U.S. and six international locations., and analyze how model performance depends on the amount of social media data available per location. Our approach demonstrates several advantages: (a) Neural network architectures that rely on LSTM units trained on social media data yield the best performance compared to previously used regression models. (b) Previously under-explored language and communication behavior features are more predictive of ILI dynamics than stylistic and topic signals expressed in social media. (c) Neural network models learned exclusively from social media signals yield comparable or better performance to the models learned from ILI historical data, thus, signals from social media can be potentially used to accurately forecast ILI dynamics for the regions where ILI historical data is not available. (d) Neural network models learned from combined ILI and social media signals significantly outperform models that rely solely on ILI historical data, which adds to a great potential of alternative public sources for ILI dynamics prediction. (e) Location-specific models outperform previously used location-independent models e.g., U.S. only. (f) Prediction results significantly vary across geolocations depending on the amount of social media data available and ILI activity patterns. (g) Model performance improves with more tweets available per geo-location e.g., the error gets lower and the Pearson score gets higher for locations with more tweets.

Human mobility is a primary driver of infectious disease spread. However, existing data is limited in availability, coverage, granularity, and timeliness. Data-driven forecasts of disease dynamics are crucial for decision-making by health officials and private citizens alike. In this work, we focus on a machine-learned anonymized mobility map (hereon referred to as AMM) aggregated over hundreds of millions of smartphones and evaluate its utility in forecasting epidemics. We factor AMM into a metapopulation model to retrospectively forecast influenza in the USA and Australia. We show that the AMM model performs on-par with those based on commuter surveys, which are sparsely available and expensive. We also compare it with gravity and radiation based models of mobility, and find that the radiation model’s performance is quite similar to AMM and commuter flows. Additionally, we demonstrate our model’s ability to predict disease spread even across state boundaries. Our work contributes towards developing timely infectious disease forecasting at a global scale using human mobility datasets expanding their applications in the area of infectious disease epidemiology. Human mobility plays a central role in the spread of infectious diseases and can help in forecasting incidence. Here the authors show a comparison of multiple mobility benchmarks in forecasting influenza, and demonstrate the value of a machine-learned mobility map with global coverage at multiple spatial scales.

In China, dengue remains an important public health issue with expanded areas and increased incidence recently. Accurate and timely forecasts of dengue incidence in China are still lacking. We aimed to use the state-of-the-art machine learning algorithms to develop an accurate predictive model of dengue. Weekly dengue cases, Baidu search queries and climate factors (mean temperature, relative humidity and rainfall) during 2011-2014 in Guangdong were gathered. A dengue search index was constructed for developing the predictive models in combination with climate factors. The observed year and week were also included in the models to control for the long-term trend and seasonality. Several machine learning algorithms, including the support vector regression (SVR) algorithm, step-down linear regression model, gradient boosted regression tree algorithm (GBM), negative binomial regression model (NBM), least absolute shrinkage and selection operator (LASSO) linear regression model and generalized additive model (GAM), were used as candidate models to predict dengue incidence. Performance and goodness of fit of the models were assessed using the root-mean-square error (RMSE) and R-squared measures. The residuals of the models were examined using the autocorrelation and partial autocorrelation function analyses to check the validity of the models. The models were further validated using dengue surveillance data from five other provinces. The epidemics during the last 12 weeks and the peak of the 2014 large outbreak were accurately forecasted by the SVR model selected by a cross-validation technique. Moreover, the SVR model had the consistently smallest prediction error rates for tracking the dynamics of dengue and forecasting the outbreaks in other areas in China. The proposed SVR model achieved a superior performance in comparison with other forecasting techniques assessed in this study. The findings can help the government and community respond early to dengue epidemics.

Seasonal influenza continues to pose a substantial and recurrent public health challenge in Queensland, driven by annual variability in transmission and uncertainty in climatic, demographic, and behavioural determinants. Predictive modelling is constrained by data limitations and parameter uncertainty. In response, this study developed a Bayesian network (BN) model to estimate the probability of influenza epidemics in Queensland, Australia. The model integrated diverse inputs, including international and local influenza surveillance data, demographic health statistics, and expert and stakeholder insights to capture the complex multifactorial causal relationships underlying epidemic risk. Scenario-based simulations revealed that Southeast Asian viral origin, severe global influenza seasons, peak season timing, increasing international travel, absence of control measures, and low immunisation rates substantially elevate the likelihood of influenza epidemics. Southeast Queensland was identified as particularly vulnerable under high-risk conditions. Model evaluation demonstrated good discriminative performance (AUC = 0.6974, accuracy = 70%) with appropriate uncertainty quantification through credible intervals and sensitivity analysis. Its modular design and capacity for integrating various data sources make it a practical decision-making support tool for public health preparedness and responding to evolving climatic and epidemiological conditions.

Background Seasonal influenza annually creates a serious burden for people worldwide. The influenza surveillance system in China primarily indicates the intensity of the influenza epidemic trend, but it cannot provide accurate forecasts and early warnings. Meteorological conditions and antigenic variation rarely participated in optimizing the influenza model, which not only limits the simulation and prediction of influenza trends but also the development of reasonable preventive measures. Methods The weekly influenza-like illness percentage (ILI%) data from Baoji (BJ) and Qinhuangdao (QHD) were collected from the Chinese Center for Disease Control and Prevention. Data on meteorological factors were used from the China Meteorological Administration spanning from 1 January 2010 to 31 December 2019. The SIRS model, driven by temperature and relative humidity data, was employed to simulate and predict seasonal influenza over multiple years in two cities of Northern China: Baoji (Shaanxi Province) and Qinhuangdao (Hebei Province). Results Our model simulations indicated that both raw and smoothed meteorological data could be used to capture multi-year seasonal influenza trends. When antigenic variation was not incorporated, simulations based on raw data and those based on smoothed data yielded consistent performance within each city: in Baoji (RMSE_S = 1.59, =0.45) and Qinhuangdao (RMSE_S = 0.5, =0.56). Critically, incorporating antigenic variation was associated with a marked improvement in model performance. This improvement was evidenced by two key findings: in Baoji, this inclusion enabled a better representation of the 2016 peak and fitted the model more closely to the observed incidence in the following two seasons; in Qinhuangdao, it led to a more accurate prediction of the 2018 outbreak peak (raw data: RMSE_P: 0.55 < 0.67, : 0.48 > 0.24; smoothed data: RMSE_P: 0.47 < 0.67, : 0.62 > 0.24). Conclusions This study demonstrates that integrating antigenic variation data with meteorological drivers is critical for accurate influenza forecasting in temperate China. These findings provide a mechanistic basis for proactive surveillance. By combining real-time meteorological and genomic data, such systems would enhance early warning and help optimize the timing of interventions like targeted vaccination.

Background Accurate influenza activity forecasting helps public health officials prepare and allocate resources for unusual influenza activity. Traditional flu surveillance systems, such as the Centers for Disease Control and Prevention’s (CDC) influenza-like illnesses reports, lag behind real-time by one to 2 weeks, whereas information contained in cloud-based electronic health records (EHR) and in Internet users’ search activity is typically available in near real-time. We present a method that combines the information from these two data sources with historical flu activity to produce national flu forecasts for the United States up to 4 weeks ahead of the publication of CDC’s flu reports. Methods We extend a method originally designed to track flu using Google searches, named ARGO, to combine information from EHR and Internet searches with historical flu activities. Our regularized multivariate regression model dynamically selects the most appropriate variables for flu prediction every week. The model is assessed for the flu seasons within the time period 2013–2016 using multiple metrics including root mean squared error (RMSE). Results Our method reduces the RMSE of the publicly available alternative (Healthmap flutrends) method by 33, 20, 17 and 21%, for the four time horizons: real-time, one, two, and 3 weeks ahead, respectively. Such accuracy improvements are statistically significant at the 5% level. Our real-time estimates correctly identified the peak timing and magnitude of the studied flu seasons. Conclusions Our method significantly reduces the prediction error when compared to historical publicly available Internet-based prediction systems, demonstrating that: (1) the method to combine data sources is as important as data quality; (2) effectively extracting information from a cloud-based EHR and Internet search activity leads to accurate forecast of flu.

Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through time and the distribution of the sampling times depends on the effective population size, explicit statistical modeling of sampling times improves population size estimation. Previous work assumed that the genealogy relating sampled sequences is known and modeled sampling times as an inhomogeneous Poisson process with log-intensity equal to a linear function of the log-transformed effective population size. We improve this approach in two ways. First, we extend the method to allow for joint Bayesian estimation of the genealogy, effective population size trajectory, and other model parameters. Next, we improve the sampling time model by incorporating additional sources of information in the form of time-varying covariates. We validate our new modeling framework using a simulation study and apply our new methodology to analyses of population dynamics of seasonal influenza and to the recent Ebola virus outbreak in West Africa.

Infectious diseases impose considerable burden on society, despite significant advances in technology and medicine over the past century. Advanced warning can be helpful in mitigating and preparing for an impending or ongoing epidemic. Historically, such a capability has lagged for many reasons, including in particular the uncertainty in the current state of the system and in the understanding of the processes that drive epidemic trajectories. Presently we have access to data, models, and computational resources that enable the development of epidemiological forecasting systems. Indeed, several recent challenges hosted by the U.S. government have fostered an open and collaborative environment for the development of these technologies. The primary focus of these challenges has been to develop statistical and computational methods for epidemiological forecasting, but here we consider a serious alternative based on collective human judgment. We created the web-based \"Epicast\" forecasting system which collects and aggregates epidemic predictions made in real-time by human participants, and with these forecasts we ask two questions: how accurate is human judgment, and how do these forecasts compare to their more computational, data-driven alternatives? To address the former, we assess by a variety of metrics how accurately humans are able to predict influenza and chikungunya trajectories. As for the latter, we show that real-time, combined human predictions of the 2014-2015 and 2015-2016 U.S. flu seasons are often more accurate than the same predictions made by several statistical systems, especially for short-term targets. We conclude that there is valuable predictive power in collective human judgment, and we discuss the benefits and drawbacks of this approach.

In this work, we propose a data augmentation strategy aimed at improving the training phase of neural networks and, consequently, the accuracy of their predictions. Our approach relies on generating synthetic data through a suitable compartmental model combined with the incorporation of uncertainty. Available data are used to calibrate the model, which is further integrated with deep learning techniques to produce additional synthetic data for training. The results show that neural networks trained on these augmented datasets exhibit significantly improved predictive performances. In particular, we focus on two different neural network architectures: Physics-Informed Neural Networks (PINNs) and Nonlinear Autoregressive (NAR) models. The NAR approach proves especially effective for short-term forecasting, thereby providing accurate quantitative estimates by directly learning the dynamics from data and avoiding the additional computational cost of embedding physical constraints into the training. In contrast, PINNs yield less accurate quantitative predictions but capture the qualitative long-term behavior of the system, thus making them more suitable to explore broader dynamical trends. Numerical simulations of the second phase of the COVID-19 pandemic in the Lombardy region (Italy) validate the effectiveness of the proposed approach.

Process-based models have been used to simulate and forecast a number of nonlinear dynamical systems, including influenza and other infectious diseases. In this work, we evaluate the effects of model initial condition error and stochastic fluctuation on forecast accuracy in a compartmental model of influenza transmission. These two types of errors are found to have qualitatively similar growth patterns during model integration, indicating that dynamic error growth, regardless of source, is a dominant component of forecast inaccuracy. We therefore examine the nonlinear growth of model initial error and compute the fastest growing directions using singular vector analysis. Using this information, we generate perturbations in an ensemble forecast system of influenza to obtain more optimal ensemble spread. In retrospective forecasts of historical outbreaks for 95 US cities from 2003 to 2014, this approach improves short-term forecast of incidence over the next one to four weeks.