Article

September 30, 2026

Prediction of dengue cases based on climatic variables by machine learning

Prediction of Dengue Cases Based on Climatic Variables by Machine Learning

Anna Beatriz Pereira Lima; Brayan Dias Dauria

DOI: 10.22167/2675-6528-202602684

Article derived from a Course Conclusion Work (TCC), with content based on the student’s original work and adapted to the editorial format of the E&S Magazine with the support of the ResumeAI tool, an artificial intelligence solution developed by Instituto Pecege for textual synthesis and organization.

Summary

Dengue has characterized itself as an important public health problem in Brazil, with its occurrence influenced by climatic, environmental, and temporal factors. The study aimed to develop and evaluate predictive models to estimate the number of dengue cases in the state of São Paulo by integrating epidemiological data from the Information System for Notifiable Diseases (SINAN) and meteorological variables from the National Institute of Meteorology (INMET). The investigation was conducted as a case study, based on a temporal structure at the municipality-month level, built from the processing, standardization, and integration of databases. The methodological process included the selection and aggregation of confirmed notifications, the spatial association between municipalities and meteorological stations, the creation of lagged and moving average variables, as well as the temporal division of data into training, validation, and testing sets. The Random Forest, Support Vector Regression, XGBoost, and Long Short-Term Memory models were applied, evaluated using MAE, RMSE, and coefficient of determination (R²) metrics. The results showed that the models captured relevant patterns from the historical series, especially the seasonality of the disease and the influence of the recent history of cases and climatic variables. Among the evaluated algorithms, Random Forest presented the best overall performance, demonstrating potential to support epidemiological surveillance, monitoring, and outbreak anticipation actions.

Keywords: Dengue; Epidemiological forecasting; Public health; Time series; Climate variables.

1. Introduction

Dengue is an arbovirus disease caused by the DENV virus, transmitted to humans by the bite of an infected Aedes aegypti mosquito (World Health Organization, 2025). The virus belongs to the Flaviviridae family and the Orthoflavivirus genus, presenting four known serotypes: DENV-1, DENV-2, DENV-3, and DENV-4, which differ by genetic variations and specific lineages (Cardoso et al., 2024). Widely disseminated in tropical and subtropical regions, the disease represents a serious public health problem in Brazil, one of the countries with the highest number of cases and recurrence of epidemics (Felix, 2024).

The spread of dengue is directly related to environmental and climatic conditions that favor the mosquito’s life cycle and the virus’s dissemination. Aedes aegypti, the main transmitter of the disease, finds ideal conditions for reproduction in urban areas, especially in places with stagnant water accumulation and precarious sanitation (Carvalho Da Silva et al., 2024). Variations in temperature, humidity, and precipitation directly influence the mosquito’s life cycle and viral replication, making climate a determining element in the disease’s dynamics (Gui et al., 2021). Thus, the interaction between biological, environmental, and social factors contributes to the maintenance and intensification of dengue cases in the country.

Faced with a large, dense, and heterogeneous population, Brazil faces significant challenges related to the increase in dengue cases, the occurrence of which is strongly influenced by socioeconomic and seasonal factors. The severity of this problem becomes even more evident, with the registration of more than a thousand deaths from dengue in 2025, according to data from the Ministry of Health (Coelho, 2025). Social inequality contributes to precarious housing, sanitation, and waste management conditions, creating environments conducive to the proliferation of the mosquito (Bezerra, T.; Matos, C. 2023).

In this context, hybrid models based on machine learning and deep learning show promise in predicting dengue cases, using climatic and epidemiological data (Lanlan, F., 2024). Studies in the field have applied machine learning algorithms such as Random Forest, Extreme Gradient Boosting, and Support Vector Machine/Regression, recognized for their ability to capture complex relationships between multiple climatic factors and the dynamics of dengue case variation (Ong et al., 2023). Within the scope of deep learning, recurrent neural networks of the Long Short-Term Memory type have also shown expressive results in predicting dengue based on climatic variables (Xiang, C.; Morgan, P., 2025; Lanlan, F. et al., 2024).

Although the main focus of this study is the prediction of dengue cases, the proposed methodological approach has the potential for extension to other infectious diseases influenced by environmental and climatic factors, such as chikungunya and zika. The integrated use of epidemiological data and climatic variables, combined with machine learning techniques, allows for the construction of predictive models applicable to different public health contexts. This versatility expands the potential application of the solution, enabling its use in various geographical regions and contributing to the development of national-scale monitoring and alert systems. Thus, the objective of this work was to develop and compare machine learning and deep learning models applied to the prediction of dengue cases from climatic variables and historical epidemiological data, evaluating the performance of different algorithms in capturing temporal patterns and nonlinear relationships associated with the disease dynamics, as well as investigating their potential as a tool to support epidemiological surveillance, contributing to the anticipation of outbreaks and to public health decision-making.

2. Material and Methods

The research developed was characterized as a study of an applied and descriptive nature. The applied approach aimed at solving a practical problem, focused on predicting dengue cases from climatic variables and epidemiological data, with potential to support public health surveillance. Regarding the objectives, the research was descriptive, seeking to identify and organize temporal patterns, as well as relationships between environmental variables and the incidence of the disease, without establishing direct causal relationships.

The methodological procedure consisted of a case study, in which different machine learning and deep learning models were applied to the same dataset to compare their performances. The study steps were organized into five main phases, which included data acquisition, database processing, information integration, algorithm modeling and implementation, and analysis of the obtained results.

For the analysis, epidemiological data of dengue cases that occurred in Brazil and associated meteorological information were used. The epidemiological data were obtained from the Information System for Notifiable Diseases (SINAN), made available by the Informatics Department of the Unified Health System (DATASUS), covering the period from 2014 to 2025. The meteorological data came from the National Institute of Meteorology (INMET), referring to the municipalities of the state of São Paulo.

The collection of epidemiological data from SINAN was carried out through a connection via File Transfer Protocol (FTP), using FileZilla software. The databases, originally in DataBase Compressed (DBC) format, were converted to DataBase File (DBF) with TabWin software and, subsequently, to Comma-separated values (CSV) via Python language. The columns DT_NOTIFIC, ID_MUNICIP, FEBRE, CEFALEIA, VOMITO, RESUL_SORO, RESUL_NS1, RESUL_PCR_, HOSPITALIZ, CLASSI_FIN, and CRITERIO were selected, converting the notification date to temporal format and standardizing municipal codes.

SINAN data were filtered to include only cases from the state of São Paulo, selecting notifications with a final dengue classification (codes 10, 11, or 12). Subsequently, the data were aggregated monthly by municipality, using the IBGE code as an identifier. A complete temporal structure was created for all municipality, year, and month combinations, filling months with no confirmed cases with zero.

INMET meteorological data were obtained through automated email submission, generating an individual file for each station. Climate information, collected on a monthly scale, included variables such as accumulated precipitation, average air temperature, and average wind speed. The consolidation of these databases was carried out by an automated process implemented in Python.

To associate the climatic data with the municipalities, it was considered that the state of São Paulo has 645 municipalities and the INMET network has 43 meteorological stations. Each municipality was associated with the nearest meteorological station. The municipal grid of IBGE in shapefile format was used, representing the stations as geographic points and the municipalities by their centroids. The linkage was carried out based on the spatial proximity between the municipal centroids and the meteorological station points, a procedure similar to that adopted by Aune et al. (2023) and Gómez-Barroso et al. (2017).

After data processing, epidemiological and meteorological data were joined by municipality, year, and month. Lagged variables, known as “lags”, were created to represent the influence of values observed in previous periods on the number of dengue cases. For the target variable confirmed_cases, lags of one, two, three, six, and twelve months were used. Lags were also created for climatic variables, and moving averages with temporal displacement were calculated to avoid data leakage.

The consolidated dataset was divided into training, validation, and test sets, temporally, without random shuffling of records, in order to preserve the chronological order of observations. The year 2025 was reserved as the final test set, while the preceding years were used in the training and validation stages. The month variable was transformed into cyclic sine and cosine components to incorporate the seasonal nature of the calendar.

In the training base, temporal validation was applied using the “TimeSeriesSplit” method, with five divisions. This procedure partitioned the data into successive divisions over time, keeping the older observations for training and the later ones for validation. In each iteration, the model was trained with a historical period and validated on a subsequent period, simulating a realistic forecasting scenario.

For the definition of the models’ hyperparameters, the grid search technique was used through the “GridSearchCV” method. This procedure systematically evaluated different combinations of hyperparameters, using the temporal splits defined by “TimeSeriesSplit”. The selection of the best configurations was carried out exclusively on the training and validation data, considering the performance on the R², MAE, and RMSE metrics.

In the predictive modeling stage, the Random Forest (RF), Support Vector Regression (SVR), XGBoost, and Long Short-Term Memory (LSTM) models were applied. Random Forest, a supervised learning method, combined multiple decision trees to estimate continuous values, using the bagging technique (Rahman et al., 2025). XGBoost, based on boosting, trained decision trees sequentially to correct previous errors (Ribeiro et al., 2021).

Support Vector Regression (SVR), implemented through the LinearSVR algorithm, sought to estimate a continuous function with error limited by a tolerance margin (Leão, 2025). The Long Short-Term Memory (LSTM) neural network was used as a recurrent neural network architecture, designed to capture short- and long-term temporal dependencies in time series (Chen et al., 2025). For the XGBoost and LSTM models, the log1p transformation was applied to the target variable to reduce the asymmetry of the distribution and mitigate the influence of extreme values.

The research development was carried out in a computational environment configured for data treatment, integration, analysis, and modeling. The programming language used was Python, due to its versatility and the wide availability of libraries. Libraries such as Pandas for data manipulation, NumPy for numerical operations, Scikit-learn for preprocessing and evaluation, XGBoost and TensorFlow/Keras for model implementation, Matplotlib for visualization, and GeoPandas for spatial data manipulation were employed.

The evaluation of the models constituted a fundamental step, carried out based on the predictive performance obtained on the final test set, corresponding to the year 2025. For this comparison, the metrics Mean Absolute Error (MAE), Root Mean Squared Error (RMSE), and Coefficient of Determination (R²) were used. The MAE measured the average of the absolute differences between the actual and predicted values, while the RMSE quantified the model’s accuracy relative to the actual values, calculating the square root of the average of the squared errors. The R² represented the percentage of the data variance explained by the model.

3. Results and Discussion

This section details the results obtained from applying the previously described methodological steps, covering data collection, processing, analysis, and merging of databases, as well as predictive modeling and algorithm evaluation. The main objective was to demonstrate the progress achieved in predicting dengue cases in the state of São Paulo, identify the particularities observed during the process, and discuss the implications of these findings for epidemiological surveillance. The systematic approach allowed for an in-depth understanding of the disease dynamics and the models’ capacity to capture complex patterns.

Database and Pre-processing

The construction of the database for this study involved the integration of epidemiological and meteorological information, fundamental for the predictive modeling of dengue. Dengue case data were extracted from the Notifiable Diseases Information System (SINAN), covering the period from 2014 to 2025. Initially, this data, available in DBC format, was converted to DBF and subsequently to CSV, using tools such as FileZilla, TabWin, and the Python language, ensuring compatibility for analysis. This conversion step was crucial for standardizing the information and enabling its manipulation in the computational environment.

For the treatment of epidemiological data, a rigorous filtering was performed to include only confirmed dengue cases in the state of São Paulo, identified by final classification codes (CLASSI_FIN) 10, 11, or 12. Notifications, originally daily, were aggregated monthly by municipality, using the IBGE code as an identifier. Clinical and laboratory variables, such as fever, headache, vomiting, and examination results (NS1, RT-PCR, serology), were also aggregated, providing a detailed overview of the cases. The standardization of municipal codes and the filling of months with no records with zero cases were essential to create a balanced and complete time series, ready for integration.

The meteorological data were obtained from the National Institute of Meteorology (INMET), referring to stations located in the state of São Paulo. The variables included accumulated precipitation, average air temperature, and average wind speed, collected on a monthly scale. A significant challenge was the disparity between the number of municipalities (645) and meteorological stations (43) in the state. To address this issue, each municipality was associated with the nearest meteorological station, using the municipal grid from IBGE in “shapefile” format and calculating the spatial proximity between municipal centroids and station points, following approaches by Aune et al. (2023) and Gómez-Barroso et al. (2017).

The spatial association resulted in a mapping table that linked the 645 municipalities to the 43 INMET stations, with an average distance of 33.01 km and a maximum distance of 152.75 km between municipal centroids and stations. This step was fundamental to incorporate climatic variables into the epidemiological database, allowing for a joint analysis. The final consolidated database totaled 92,880 records, covering 645 municipalities over 12 years, from 2014 to 2025. The month variable was transformed into cyclic sine and cosine components to capture annual seasonality more precisely, recognizing the circular nature of the calendar.

The exploratory analysis of the aggregated time series of dengue cases in the state of São Paulo revealed significant oscillations and recurrent epidemic peaks. Among the years evaluated, 2024 stood out as the period with the highest volume of cases, configuring the main peak in the historical series. In contrast, years like 2017 and 2018 presented considerably reduced totals, characterizing periods of lower disease circulation. Meanwhile, 2025, although remaining at a high level, presented a total lower than that observed in 2024. The seasonality of the disease was clearly observed, with the highest concentration of cases in the first months of the year, especially in March, April, and May, a pattern that aligns with the vector’s life cycle and favorable climatic conditions.

The climatic variables also exhibited a pronounced seasonal behavior, compatible with the dynamics of dengue. The average monthly precipitation was higher in the first and last months of the year, with a notable reduction between June and August. The average temperature, in turn, remained higher between October and March, decreasing in the central months. This seasonal correlation between climatic patterns and disease incidence reinforced the importance of these variables for predictive modeling, as discussed by Gui et al. (2021) on the influence of climate on the spread of dengue.

However, the analysis of INMET meteorological data also revealed the presence of missing values, with greater incompleteness between 2020 and 2022. Precipitation was the variable with the highest percentages of absence, while average temperature showed a lower proportion of missing data. These limitations in the temporal coverage of the climate database were considered in the subsequent stages of the study, influencing the robustness of the models. The management of this missing data was a critical aspect for maintaining the integrity of the time series and the validity of the forecasts.

To capture the temporal dependence of the series, lagged variables, or “lags”, were created for both the number of confirmed cases and the climatic variables. For the target variable, lags of 1, 2, 3, 6, and 12 months were used, reflecting the influence of previous periods. For the climatic variables, in addition to lags, moving averages with temporal displacement were calculated, ensuring that only past information was used in the forecast, avoiding data leakage and preserving the chronological order of records, an essential procedure in time series (Sacay et al., 2025; Chen et al., 2025).

The autocorrelation analysis of the confirmed cases series showed a strong temporal dependence, with a lag of 1 month presenting the highest correlation (0.822), followed by a gradual decrease. Lags of 11, 12, and 24 months also showed relevant values (0.363, 0.349, and 0.349, respectively), confirming the annual seasonality of the disease. The lagged climatic variables also presented significant correlations, with average temperature at lags of 3 (0.615) and 2 (0.571), and precipitation at lags of 3 (0.514) and 2 (0.488), indicating that the relationship between climate and dengue is not immediate, but time-lagged.

The database was then organized for the predictive modeling stage, with the year 2025 reserved as the final test set, and the preceding years for training and validation. Temporal validation was performed using the “TimeSeriesSplit” method, with five divisions, ensuring that the chronological sequence of the data was maintained. This method simulates a situation closer to the real use of the model, where only past information is available at the time of prediction. Hyperparameter selection was carried out using “GridSearchCV”, optimizing performance based on the R², MAE, and RMSE metrics.

Predictive Modeling and Algorithm Configuration

In the predictive modeling stage, four distinct algorithms were applied: Random Forest (RF), Support Vector Regression (SVR), Extreme Gradient Boosting (XGBoost), and Long Short-Term Memory (LSTM). Each model was configured with hyperparameters optimized through the “GridSearchCV” technique, which sought the best combinations to maximize predictive performance in the context of the dengue cases time series. The choice of these algorithms reflects the diversity of approaches in machine learning and deep learning for time series regression problems.

The Random Forest model, as described by Rahman et al. (2025), was configured with 200 trees, a minimum size of 3 samples per terminal leaf, and 10 minimum samples for splitting nodes, using all available variables in each partition. This architecture, based on the “bagging” technique, is known for its ability to reduce variance and the risk of overfitting, combining multiple decision trees to generate robust predictions. The optimized configuration aimed to enhance the model’s generalization to unseen data.

For Support Vector Regression (SVR), implemented via the “LinearSVR” algorithm, the selected hyperparameters were C=3.0, epsilon=0.05, random_state=42, max_iter=30000, and dual=auto. According to Leão (2025), SVR seeks to estimate a continuous function with limited error, being effective in modeling linear and non-linear relationships, even in high-dimensional scenarios. The optimization of these parameters was fundamental for the model to find a representation that preserved generalization capability and adequately fit the data patterns.

In the XGBoost and LSTM models, a logarithmic transformation (log1p) was applied to the target variable, the number of confirmed dengue cases. The main objective of this procedure was to reduce the asymmetry of the data distribution and mitigate the influence of extreme values, contributing to greater stability in training, especially in a time series characterized by high variability and epidemic peaks. After prediction, the values were converted back to the original scale, allowing for direct interpretation of the results in terms of the actual number of cases.

The XGBoost model, based on “boosting” and described by Ribeiro et al. (2021), was configured with 800 estimators, a learning rate of 0.03, a maximum depth of 4, a minimum child weight of 5, a subsample of 0.85, and a colsample_bytree of 0.85, with reg_lambda of 5.0 and a quadratic error regression objective. This configuration aims to progressively enhance predictive performance by correcting errors from previous trees and incorporating regularization terms to mitigate overfitting, representing a robust approach for regression problems.

For the Long Short-Term Memory (LSTM) neural network, a deep learning architecture suitable for time series, the defined hyperparameters included a window size of 12, 32 units, 0.2 dropout, 16 dense units, Adam optimizer, MSE loss function, 30 epochs, batch size of 64, shuffle FALSE, and an early stopping patience of 5. The LSTM, as per Chen et al. (2025), is designed to capture short- and long-term temporal dependencies, being particularly effective in modeling complex patterns such as trend and seasonality in epidemiological time series.

Performance Evaluation of Models

The performance evaluation of the models was carried out on the final test set, corresponding to the 2025 data, using the Mean Absolute Error (MAE), Root Mean Squared Error (RMSE), and Coefficient of Determination (R²) metrics. The results obtained by the Random Forest, SVR with LinearSVR, XGBoost, and LSTM models, considering the best selected configuration, were: Random Forest (MAE 63.94, RMSE 324.92, R² 0.77); SVR (MAE 55.64, RMSE 360.02, R² 0.72); XGBoost (MAE 86.63, RMSE 551.45, R² 0.34); and LSTM (MAE 51.75, RMSE 435.26, R² 0.59). These metrics allowed for a comprehensive analysis of the accuracy of the predictions and the models’ ability to fit the observed values.

The Random Forest model demonstrated the best overall performance, with an RMSE of 324.93 and an R² of 0.77. Although it did not present the lowest MAE, its balance between predictive accuracy and ability to explain data variability was superior to the others. This result suggests that Random Forest effectively captured the complex relationships between climatic and epidemiological variables and the occurrence of dengue, offering more consistent and reliable predictions for the analyzed period, as observed in similar studies (Rahman et al., 2025).

Support Vector Regression (SVR), using the LinearSVR algorithm, presented the second best performance, with MAE of 55.64, RMSE of 360.03, and R² of 0.72. These values indicate consistent results and relatively close to those of Random Forest, confirming SVR’s ability to model complex relationships and generalize well, even with the presence of noise in the data. The robust performance of SVR positions it as a viable alternative for predicting dengue cases, corroborating findings by Leão (2025).

The Long Short-Term Memory (LSTM) neural network obtained the lowest Mean Absolute Error (MAE) of 51.76, indicating that, on average, its predictions were closest to the actual values in terms of absolute deviation. However, the RMSE of 435.27 and R² of 0.59 suggest lower model stability in the face of more significant errors in certain periods, and a slightly lower capacity to explain data variance compared to Random Forest and SVR. This can be attributed to LSTM’s sensitivity to peaks and abrupt variations in the time series, despite its ability to capture long-term dependencies (Chen et al., 2025).

On the other hand, the XGBoost model presented the least satisfactory performance among the evaluated algorithms, with an MAE of 86.63, RMSE of 551.46, and R² of 0.34. These results indicate a lower capacity to adjust to the observed dynamics of the time series in the test period, suggesting that XGBoost had greater difficulty in handling the complexity and variability of dengue data in the state of São Paulo, especially when compared to the Random Forest and SVR-based approaches, which proved more suitable for this dataset.

The visual analysis of the comparison between the real cases and the monthly forecasts for 2025 revealed that all models were able to capture the general seasonality of the series, characterized by higher values in the first months of the year and a significant reduction in the second half. However, the Random Forest stood out for presenting a behavior closer to the observed trajectory, consistently following the trends of growth and reduction in cases throughout the year. The SVR also reproduced the general shape of the curve, but with a more evident underestimation in the months of highest incidence.

Despite the low MAE, the LSTM exhibited oscillations that distanced it from the observed values in some months of the epidemic period, while XGBoost tended to overestimate cases in peak months, diverging more intensely from the actual series. This visual observation complements the quantitative metrics, reinforcing that Random Forest demonstrated the best ability to reproduce the temporal behavior of the disease. The monthly comparison between actual cases and the values predicted by Random Forest for 2025 indicated that the largest differences were concentrated in the first months of the year, a period of higher disease incidence, while in subsequent months, the predictions came closer to the observed values.

The spatial analysis, through heat maps comparing the actual and predicted cases by Random Forest, indicated a relevant correspondence in the spatial distribution of the disease. Areas with higher intensity of actual cases also showed higher intensity in the model’s predictions, and regions with lower occurrence maintained a similar behavior. This finding suggests that Random Forest was able to adequately represent the spatial heterogeneity of dengue cases in the state of São Paulo, generally preserving the distribution observed among municipalities, which is crucial for epidemiological surveillance.

In summary, the results demonstrate that machine learning and deep learning models are promising tools for predicting dengue cases, with Random Forest standing out as the algorithm with the best overall performance. The models’ ability to capture the seasonality of the disease, the influence of recent case history and climatic variables, as well as spatial heterogeneity, validates the proposed methodological approach. Although limitations related to data availability and quality have been identified, the research offers a significant advancement in understanding dengue dynamics and in developing public health support tools.

4. Conclusion

This study sought to develop and compare machine learning and deep learning models for predicting dengue cases in the state of São Paulo, integrating epidemiological data from SINAN and meteorological variables from INMET. It was found that the models were capable of capturing relevant patterns from the historical series, including the seasonality of the disease and the influence of recent case history and climatic variables. Among the evaluated algorithms, Random Forest demonstrated the best overall performance, with a superior balance between predictive accuracy and the ability to explain data variability, followed by Support Vector Regression. The Long Short-Term Memory neural network presented the lowest mean absolute error, but with less stability regarding more significant errors. Random Forest’s predictions satisfactorily reproduced the temporal and spatial behavior of cases in the analyzed period, highlighting its capacity to represent the heterogeneity of the disease among municipalities.

This approach represents a significant contribution to epidemiological surveillance, offering a potential tool for monitoring and anticipating dengue outbreaks, thereby supporting public health decision-making. However, the study faced limitations related to the difficulty of accessing and standardizing epidemiological databases, the presence of missing values in meteorological data, and the need to associate municipalities with the nearest weather stations. As future perspectives, it is suggested to incorporate new variables, expand the analysis to other geographical regions, and evaluate different forecasting horizons in order to improve the robustness and applicability of the predictive models.

Bibliographic References

Cardoso, R. L.; Corioletti, N. S. D.; Costa, L. F.; Taveira, J. H. da S.; Bueno, C. P.; Corioletti, S.; Giongo, P. R.; Silva, R. T. da. Dengue no Brasil: uma revisão sistemática. Revista Foco, v. 17, n. 3, p. e4640, 2024. DOI: https://doi.org/10.54751/revistafoco.v17n3-079.

Carvalho da Silva, R. et al. Análise dos fatores meteorológicos, socioambientais e socioeconômicos relacionados à incidência de dengue em Joinville – SC nos anos de 2020 e 2021. Hygeia: Revista Brasileira de Geografia Médica e da Saúde, v. 20, p. 1–12, 2024. DOI: 10.14393/Hygeia2071212.

Felix, 2024 [Referência completa não encontrada no documento original]

Gui, H.; Gwee, S.; Koh, J.; Pang, J. Weather factors associated with

World Health Organization, 2025 [Full reference not found in the original document]

To generate the final bibliographic list, I performed data cross-referencing according to the established rules.

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