Bayesian spatio-temporal modeling of the Brazilian fire spots between 2011 and 2022.

Wildfires are among the most common natural disasters in many world regions and actively impact life quality. These events have become frequent due to climate change, other local policies, and human behavior. Fire spots are areas where the temperature is significantly higher than in the surrounding areas and are often used to identify wildfires. This study considers the historical data with the geographical locations of all the "fire spots" detected by the reference satellites covering the Brazilian territory between January 2011 and December 2022, comprising more than 2.2 million fire spots. This data was modeled with a spatio-temporal generalized linear mixed model for areal unit data, whose inferences about its parameters are made in a Bayesian framework and use meteorological variables (precipitation, air temperature, humidity, and wind speed) and a human variable (land-use transition and occupation) as covariates. The meteorological variables humidity and air temperature showed the most significant impact on the number of fire spots for each of the six Brazilian biomes.

Bayesian Spatio-Temporal Modeling of the Dynamics of COVID-19 Deaths in Peru.

Amid the COVID-19 pandemic, understanding the spatial and temporal dynamics of the disease is crucial for effective public health interventions. This study aims to analyze COVID-19 data in Peru using a Bayesian spatio-temporal generalized linear model to elucidate mortality patterns and assess the impact of vaccination efforts. Leveraging data from 194 provinces over 651 days, our analysis reveals heterogeneous spatial and temporal patterns in COVID-19 mortality rates. Higher vaccination coverage is associated with reduced mortality rates, emphasizing the importance of vaccination in mitigating the pandemic's impact. The findings underscore the value of spatio-temporal data analysis in understanding disease dynamics and guiding targeted public health interventions.

Improving the spatial and temporal resolution of burden of disease measures with Bayesian models.

This paper contributes to the field by addressing the critical issue of enhancing the spatial and temporal resolution of health data. Although Bayesian methods are frequently employed to address this challenge in various disciplines, the application of Bayesian spatio-temporal models to burden of disease (BOD) studies remains limited. Our novelty lies in the exploration of two existing Bayesian models that we show to be applicable to a wide range of BOD data, including mortality and prevalence, thereby providing evidence to support the adoption of Bayesian modeling in full BOD studies in the future. We illustrate the benefits of Bayesian modeling with an Australian case study involving asthma and coronary heart disease. Our results showcase the effectiveness of Bayesian approaches in increasing the number of small areas for which results are available and improving the reliability and stability of the results compared to using data directly from surveys or administrative sources.

A multi-resolution ensemble model of three decision-tree-based algorithms to predict daily NO2 concentration in France 2005-2022.

Understanding and managing the health effects of Nitrogen Dioxide (NO2) requires high resolution spatiotemporal exposure maps. Here, we developed a multi-stage multi-resolution ensemble model that predicts daily NO2 concentration across continental France from 2005 to 2022. Innovations of this work include the computation of daily predictions at a 200 m resolution in large urban areas and the use of a spatio-temporal blocking procedure to avoid data leakage and ensure fair performance estimation. Predictions were obtained after three cascading stages of modeling: (1) predicting NO2 total column density from Ozone Monitoring Instrument satellite; (2) predicting daily NO2 concentrations at a 1 km spatial resolution using a large set of potential predictors such as predictions obtained from stage 1, land-cover and road traffic data; and (3) predicting residuals from stage 2 models at a 200 m resolution in large urban areas. The latter two stages used a generalized additive model to ensemble predictions of three decision-tree algorithms (random forest, extreme gradient boosting and categorical boosting). Cross-validated performances of our ensemble models were overall very good, with a ten-fold cross-validated R2 for the 1 km model of 0.83, and of 0.69 for the 200 m model. All three basis learners participated in the ensemble predictions to various degrees depending on time and space. In sum, our multi-stage approach was able to predict daily NO2 concentrations with a relatively low error. Ensembling the predictions maximizes the chance of obtaining accurate values if one basis learner fails in a specific area or at a particular time, by relying on the other learners. To the best of our knowledge, this is the first study aiming to predict NO2 concentrations in France with such a high spatiotemporal resolution, large spatial extent, and long temporal coverage. Exposure estimates are available to investigate NO2 health effects in epidemiological studies.

Spatio-temporal characterization of phenotypic resistance in malaria vector species.

BACKGROUND: Malaria, a deadly disease caused by Plasmodium protozoa parasite and transmitted through bites of infected female Anopheles mosquitoes, remains a significant public health challenge in sub-Saharan Africa. Efforts to eliminate malaria have increasingly focused on vector control using insecticides. However, the emergence of insecticide resistance (IR) in malaria vectors pose a formidable obstacle, and the current IR mapping models remain static, relying on fixed coefficients. This study introduces a dynamic spatio-temporal approach to characterize phenotypic resistance in Anopheles gambiae complex and Anopheles arabiensis. We developed a cellular automata (CA) model and applied it to data collected from Ethiopia, Nigeria, Cameroon, Chad, and Burkina Faso. The data encompasses georeferenced records detailing IR levels in mosquito vector populations across various classes of insecticides. In characterizing the dynamic patterns of confirmed resistance, we identified key driving factors through correlation analysis, chi-square tests, and extensive literature review. RESULTS: The CA model demonstrated robustness in capturing the spatio-temporal dynamics of confirmed IR states in the vector populations. In our model, the key driving factors included insecticide usage, agricultural activities, human population density, Land Use and Land Cover (LULC) characteristics, and environmental variables. CONCLUSIONS: The CA model developed offers a robust tool for countries that have limited data on confirmed IR in malaria vectors. The embrace of a dynamical modeling approach and accounting for evolving conditions and influences, contribute to deeper understanding of IR dynamics, and can inform effective strategies for malaria vector control, and prevention in regions facing this critical health challenge.

Predicting COVID-19 hospitalizations: The importance of healthcare hotlines, test positivity rates and vaccination coverage.

In this study, we developed a negative binomial regression model for one-week ahead spatio-temporal predictions of the number of COVID-19 hospitalizations in Uppsala County, Sweden. Our model utilized weekly aggregated data on testing, vaccination, and calls to the national healthcare hotline. Variable importance analysis revealed that calls to the national healthcare hotline were the most important contributor to prediction performance when predicting COVID-19 hospitalizations. Our results support the importance of early testing, systematic registration of test results, and the value of healthcare hotline data in predicting hospitalizations. The proposed models may be applied to studies modeling hospitalizations of other viral respiratory infections in space and time assuming count data are overdispersed. Our suggested variable importance analysis enables the calculation of the effects on the predictive performance of each covariate. This can inform decisions about which types of data should be prioritized, thereby facilitating the allocation of healthcare resources.

Spatio-temporal interpolation and delineation of extreme heat events in California between 2017 and 2021.

Robust spatio-temporal delineation of extreme climate events and accurate identification of areas that are impacted by an event is a prerequisite for identifying population-level and health-related risks. In prior research, attributes such as temperature and humidity have often been linearly assigned to the population of the study unit from the closest weather station. This could result in inaccurate event delineation and biased assessment of extreme heat exposure. We have developed a spatio-temporal model to dynamically delineate boundaries for Extreme Heat Events (EHE) across space and over time, using a relative measure of Apparent Temperature (AT). Our surface interpolation approach offers a higher spatio-temporal resolution compared to the standard nearest-station (NS) assignment method. We show that the proposed approach can provide at least 80.8 percent improvement in identification of areas and populations impacted by EHEs. This improvement in average adjusts the misclassification of about one million Californians per day of an extreme event, who would be either unidentified or misidentified under EHEs between 2017 and 2021.

Malaria Risk Drivers in the Brazilian Amazon: Land Use-Land Cover Interactions and Biological Diversity.

Malaria is a prevalent disease in several tropical and subtropical regions, including Brazil, where it remains a significant public health concern. Even though there have been substantial efforts to decrease the number of cases, the reoccurrence of epidemics in regions that have been free of cases for many years presents a significant challenge. Due to the multifaceted factors that influence the spread of malaria, influencing malaria risk factors were analyzed through regional outbreak cluster analysis and spatio-temporal models in the Brazilian Amazon, incorporating climate, land use/cover interactions, species richness, and number of endemic birds and amphibians. Results showed that high amphibian and bird richness and endemism correlated with a reduction in malaria risk. The presence of forest had a risk-increasing effect, but it depended on its juxtaposition with anthropic land uses. Biodiversity and landscape composition, rather than forest formation presence alone, modulated malaria risk in the period. Areas with low endemic species diversity and high human activity, predominantly anthropogenic landscapes, posed high malaria risk. This study underscores the importance of considering the broader ecological context in malaria control efforts.

A Bayesian multistage spatio-temporally dependent model for spatial clustering and variable selection.

In spatio-temporal epidemiological analysis, it is of critical importance to identify the significant covariates and estimate the associated time-varying effects on the health outcome. Due to the heterogeneity of spatio-temporal data, the subsets of important covariates may vary across space and the temporal trends of covariate effects could be locally different. However, many spatial models neglected the potential local variation patterns, leading to inappropriate inference. Thus, this article proposes a flexible Bayesian hierarchical model to simultaneously identify spatial clusters of regression coefficients with common temporal trends, select significant covariates for each spatial group by introducing binary entry parameters and estimate spatio-temporally varying disease risks. A multistage strategy is employed to reduce the confounding bias caused by spatially structured random components. A simulation study demonstrates the outperformance of the proposed method, compared with several alternatives based on different assessment criteria. The methodology is motivated by two important case studies. The first concerns the low birth weight incidence data in 159 counties of Georgia, USA, for the years 2007 to 2018 and investigates the time-varying effects of potential contributing covariates in different cluster regions. The second concerns the circulatory disease risks across 323 local authorities in England over 10 years and explores the underlying spatial clusters and associated important risk factors.

A multivariate spatio-temporal model for the incidence of imported COVID-19 cases and COVID-19 deaths in Cuba.

To monitor the COVID-19 epidemic in Cuba, data on several epidemiological indicators have been collected on a daily basis for each municipality. Studying the spatio-temporal dynamics in these indicators, and how they behave similarly, can help us better understand how COVID-19 spread across Cuba. Therefore, spatio-temporal models can be used to analyze these indicators. Univariate spatio-temporal models have been thoroughly studied, but when interest lies in studying the association between multiple outcomes, a joint model that allows for association between the spatial and temporal patterns is necessary. The purpose of our study was to develop a multivariate spatio-temporal model to study the association between the weekly number of COVID-19 deaths and the weekly number of imported COVID-19 cases in Cuba during 2021. To allow for correlation between the spatial patterns, a multivariate conditional autoregressive prior (MCAR) was used. Correlation between the temporal patterns was taken into account by using two approaches; either a multivariate random walk prior was used or a multivariate conditional autoregressive prior (MCAR) was used. All models were fitted within a Bayesian framework.

Beta-negative binomial nonlinear spatio-temporal random effects modeling of COVID-19 case counts in Japan.

Coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 virus has spread seriously throughout the world. Predicting the spread, or the number of cases, in the future can facilitate preparation for, and prevention of, a worst-case scenario. To achieve these purposes, statistical modeling using past data is one feasible approach. This paper describes spatio-temporal modeling of COVID-19 case counts in 47 prefectures of Japan using a nonlinear random effects model, where random effects are introduced to capture the heterogeneity of a number of model parameters associated with the prefectures. The negative binomial distribution is frequently used with the Paul-Held random effects model to account for overdispersion in count data; however, the negative binomial distribution is known to be incapable of accommodating extreme observations such as those found in the COVID-19 case count data. We therefore propose use of the beta-negative binomial distribution with the Paul-Held model. This distribution is a generalization of the negative binomial distribution that has attracted much attention in recent years because it can model extreme observations with analytical tractability. The proposed beta-negative binomial model was applied to multivariate count time series data of COVID-19 cases in the 47 prefectures of Japan. Evaluation by one-step-ahead prediction showed that the proposed model can accommodate extreme observations without sacrificing predictive performance.

Spatiotemporal trends in neonatal, infant, and child mortality (1990-2019) based on Bayesian spatiotemporal modeling.

Background: Neonatal mortality rate (NMR), infant mortality rate (IMR), and child mortality rate (CMR) show a huge difference across countries, which has been posing challenges for public health policies and medical resource allocation. Methods: Bayesian spatiotemporal model is applied to assess the detailed spatiotemporal evolution of NMR, IMR, and CMR from a global perspective. Panel data from 185 countries from 1990 to 2019 are collected. Results: The continuously decreasing trend of NMR, IMR, and CMR indicated a great improvement in neonatal, infant, and child mortality worldwide. Further, huge differences in the NMR, IMR, and CMR still exist across countries. In addition, the gap of NMR, IMR, and CMR across the countries presented a widening trend from the perspective of dispersion degree and kernel densities. The spatiotemporal heterogeneities demonstrated that the decline degree among these three indicators could be observed as CMR > IMR > NMR. Countries such as Brazil, Sweden, Libya, Myanmar, Thailand, Uzbekistan, Greece, and Zimbabwe showed the highest values of b1i , indicating a weaker downward trend compared to the overall downward trend in the world. Conclusions: This study revealed the spatiotemporal patterns and trends in the levels and improvement of NMR, IMR, and CMR across countries. Further, NMR, IMR, and CMR show a continuously decreasing trend, but the differences in improvement degree present a widening trend across countries. This study provides further implications for policy in newborns, infants, and children's health to reduce health inequality worldwide.

BrainTGL: A dynamic graph representation learning model for brain network analysis.

Modeling the dynamics characteristics in functional brain networks (FBNs) is important for understanding the functional mechanism of the human brain. However, the current works do not fully consider the potential complex spatial and temporal correlations in human brain. To solve this problem, we propose a temporal graph representation learning framework for brain networks (BrainTGL). The framework involves a temporal graph pooling for eliminating the noisy edges as well as data inconsistency, and a dual temporal graph learning for capturing the spatio-temporal features of the temporal graphs. The proposed method has been evaluated in both tasks of brain disease (ASD, MDD and BD) diagnosis/gender classification (classification task) and subtype identification (clustering task) on the four datasets: Human Connectome Project (HCP), Autism Brain Imaging Data Exchange (ABIDE), NMU-MDD and NMU-BD. A large improvement is achieved for the ASD diagnosis. Specifically, our model outperforms the GroupINN and ST-GCN by an average increase of 4.2% and 8.6% on accuracy, respectively, demonstrating its advantages in comparison to the state-of-the-art methods based on functional connectivity features or learned spatio-temporal features. The results demonstrate that learning the spatial-temporal brain network representation for modeling dynamics characteristics in FBNs can improve the model's performance on both disease diagnosis and subtype identification tasks for multiple disorders. Apart from performance, the improvements of computational efficiency and convergence speed reduce training costs.

Spatio-temporal modeling of infectious diseases by integrating compartment and point process models.

Infectious disease modeling plays an important role in understanding disease spreading dynamics and can be used for prevention and control. The well-known SIR (Susceptible, Infected, and Recovered) compartment model and spatial and spatio-temporal statistical models are common choices for studying problems of this kind. This paper proposes a spatio-temporal modeling framework to characterize infectious disease dynamics by integrating the SIR compartment and log-Gaussian Cox process (LGCP) models. The method's performance is assessed via simulation using a combination of real and synthetic data for a region in São Paulo, Brazil. We also apply our modeling approach to analyze COVID-19 dynamics in Cali, Colombia. The results show that our modified LGCP model, which takes advantage of information obtained from the previous SIR modeling step, leads to a better forecasting performance than equivalent models that do not do that. Finally, the proposed method also allows the incorporation of age-stratified contact information, which provides valuable decision-making insights. Supplementary Information: The online version contains supplementary material available at 10.1007/s00477-022-02354-4.

Simulation and forecasting models of COVID-19 taking into account spatio-temporal dynamic characteristics: A review.

The COVID-19 epidemic has caused more than 6.4 million deaths to date and has become a hot topic of interest in different disciplines. According to bibliometric analysis, more than 340,000 articles have been published on the COVID-19 epidemic from the beginning of the epidemic until recently. Modeling infectious diseases can provide critical planning and analytical tools for outbreak control and public health research, especially from a spatio-temporal perspective. However, there has not been a comprehensive review of the developing process of spatio-temporal dynamic models. Therefore, the aim of this study is to provide a comprehensive review of these spatio-temporal dynamic models for dealing with COVID-19, focusing on the different model scales. We first summarized several data used in the spatio-temporal modeling of the COVID-19, and then, through literature review and summary, we found that the existing COVID-19 spatio-temporal models can be divided into two categories: macro-dynamic models and micro-dynamic models. Typical representatives of these two types of models are compartmental and metapopulation models, cellular automata (CA), and agent-based models (ABM). Our results show that the modeling results are not accurate enough due to the unavailability of the fine-grained dataset of COVID-19. Furthermore, although many models have been developed, many of them focus on short-term prediction of disease outbreaks and lack medium- and long-term predictions. Therefore, future research needs to integrate macroscopic and microscopic models to build adaptive spatio-temporal dynamic simulation models for the medium and long term (from months to years) and to make sound inferences and recommendations about epidemic development in the context of medical discoveries, which will be the next phase of new challenges and trends to be addressed. In addition, there is still a gap in research on collecting fine-grained spatial-temporal big data based on cloud platforms and crowdsourcing technologies to establishing world model to battle the epidemic.

Modeling infectious disease dynamics: Integrating contact tracing-based stochastic compartment and spatio-temporal risk models.

Major infectious diseases such as COVID-19 have a significant impact on population lives and put enormous pressure on healthcare systems globally. Strong interventions, such as lockdowns and social distancing measures, imposed to prevent these diseases from spreading, may also negatively impact society, leading to jobs losses, mental health problems, and increased inequalities, making crucial the prioritization of riskier areas when applying these protocols. The modeling of mobility data derived from contact-tracing data can be used to forecast infectious trajectories and help design strategies for prevention and control. In this work, we propose a new spatial-stochastic model that allows us to characterize the temporally varying spatial risk better than existing methods. We demonstrate the use of the proposed model by simulating an epidemic in the city of Valencia, Spain, and comparing it with a contact tracing-based stochastic compartment reference model. The results show that, by accounting for the spatial risk values in the model, the peak of infected individuals, as well as the overall number of infected cases, are reduced. Therefore, adding a spatial risk component into compartment models may give finer control over the epidemic dynamics, which might help the people in charge to make better decisions.

Toward Benchmarking of Long-Term Spatio-Temporal Maps of Pedestrian Flows for Human-Aware Navigation.

Despite the advances in mobile robotics, the introduction of autonomous robots in human-populated environments is rather slow. One of the fundamental reasons is the acceptance of robots by people directly affected by a robot's presence. Understanding human behavior and dynamics is essential for planning when and how robots should traverse busy environments without disrupting people's natural motion and causing irritation. Research has exploited various techniques to build spatio-temporal representations of people's presence and flows and compared their applicability to plan optimal paths in the future. Many comparisons of how dynamic map-building techniques show how one method compares on a dataset versus another, but without consistent datasets and high-quality comparison metrics, it is difficult to assess how these various methods compare as a whole and in specific tasks. This article proposes a methodology for creating high-quality criteria with interpretable results for comparing long-term spatio-temporal representations for human-aware path planning and human-aware navigation scheduling. Two criteria derived from the methodology are then applied to compare the representations built by the techniques found in the literature. The approaches are compared on a real-world, long-term dataset, and the conception is validated in a field experiment on a robotic platform deployed in a human-populated environment. Our results indicate that continuous spatio-temporal methods independently modeling spatial and temporal phenomena outperformed other modeling approaches. Our results provide a baseline for future work to compare a wide range of methods employed for long-term navigation and provide researchers with an understanding of how these various methods compare in various scenarios.

Modeling the dynamic brain network representation for autism spectrum disorder diagnosis.

The dynamic functional connectivity analysis provides valuable information for understanding functional brain activity underlying different cognitive processes. Modeling spatio-temporal dynamics in functional brain networks is critical for underlying the functional mechanism of autism spectrum disorder (ASD). In our study, we propose a machine learning approach for the classification of neurological disorders while providing an interpretable framework, which thoroughly captures spatio-temporal features in resting-state functional magnetic resonance imaging (rs-fMRI) data. Specifically, we first transform rs-fMRI time-series into temporal multi-graph using the sliding window technique. A temporal multi-graph clustering is then designed to eliminate the inconsistency of the temporal multi-graph series. Then, a graph structure-aware LSTM (GSA-LSTM) is further proposed to capture the spatio-temporal embedding for temporal graphs. Furthermore, The proposed GSA-LSTM can not only capture discriminative features for prediction but also impute the incomplete graphs for the temporal multi-graph series. Extensive experiments on the autism brain imaging data exchange (ABIDE) dataset demonstrate that the proposed dynamic brain network embedding learning outperforms the state-of-the-art brain network classification models. Furthermore, the obtained clustering results are consistent with the previous neuroimaging-derived evidence of biomarkers for autism spectrum disorder (ASD).

Estimation of the Covariance Matrix in Hierarchical Bayesian Spatio-Temporal Modeling via Dimension Expansion.

Ozone concentrations are key indicators of air quality. Modeling ozone concentrations is challenging because they change both spatially and temporally with complicated structures. Missing data bring even more difficulties. One of our interests in this paper is to model ozone concentrations in a region in the presence of missing data. We propose a method without any assumptions on the correlation structure to estimate the covariance matrix through a dimension expansion method for modeling the semivariograms in nonstationary fields based on the estimations from the hierarchical Bayesian spatio-temporal modeling technique (Le and Zidek). Further, we apply an entropy criterion (Jin et al.) based on a predictive model to decide if new stations need to be added. This entropy criterion helps to solve the environmental network design problem. For demonstration, we apply the method to the ozone concentrations at 25 stations in the Pittsburgh region studied. The comparison of the proposed method and the one is provided through leave-one-out cross-validation, which shows that the proposed method is more general and applicable.

Shape-restricted estimation and spatial clustering of COVID-19 infection rate curves.

The study of regional COVID-19 daily reported cases is used to understand pattern of spread and disease progression over time. These data are challenging to model due to noise that is present, which arises from failures in reporting, false positive tests, etc., and the spatial dependence between regions. In this work, we extend a recently developed Bayesian modeling framework for inference of functional data to jointly estimate and cluster daily reported cases data from US states, while accounting for spatial dependence between US states. Shape-restriction allows us to directly infer the number of extrema of a smooth infection rate curve that underlies noisy data. Other parameters in the model account for the relative timing of extrema, and the magnitude and severity of infection rates. We incorporate mobility behavior of each US state's population into an informative prior model to account for the spatial dependence between US states. Our model corroborates past work that shows that different US states have indeed experienced COVID-19 differently, but that there are regional patterns within the US. The modeling results can be used to assess severity of infection in individual US states and trends of neighboring US states to aid pandemic planning. Retrospectively, this model can be used to see which factors (governmental, behavioral, etc.) are associated with the varying shapes of infection rate curves, which is left as future work.