Severity Index for Suspected Arbovirus (SISA) : machine learning for accurate prediction of hospitalization in subjects suspected of arboviral infection

Funding: This study was supported, in part, by the Department of Defense Global Emerging Infection Surveillance (https://health.mil/Military-Health-Topics/Combat-Support/Armed-Forces-Health-Surveillance-Branch/Global-Emerging-Infections-Surveillance-and-Response) grant (P0220_13_OT) and the Department of Medicine of SUNY Upstate Medical University (http://www.upstate.edu/medicine/). D.F., M.H. and P.H. were supported by the Ben Kean Fellowship from the American Society for Tropical Medicine and Hygeine (https://www.astmh.org/awards-fellowships-medals/benjamin-h-keen-travel-fellowship-in-tropical-medi). S.J.R and A.M.S-I were supported by NSF DEB EEID 1518681, NSF DEB RAPID 1641145 (https://www.nsf.gov/), A.M.S-I was additionally supported by the Prometeo program of the National Secretary of Higher Education, Science, Technology, and Innovation of Ecuador (http://prometeo.educacionsuperior.gob.ec/).Background: Dengue, chikungunya, and Zika are arboviruses of major global health concern. Decisions regarding the clinical management of suspected arboviral infection are challenging in resource-limited settings, particularly when deciding on patient hospitalization. The objective of this study was to determine if hospitalization of individuals with suspected arboviral infections could be predicted using subject intake data. Methodology/Principal findings: Two prediction models were developed using data from a surveillance study in Machala, a city in southern coastal Ecuador with a high burden of arboviral infections. Data were obtained from subjects who presented at sentinel medical centers with suspected arboviral infection (November 2013 to September 2017). The first prediction model-called the Severity Index for Suspected Arbovirus (SISA)-used only demographic and symptom data. The second prediction model-called the Severity Index for Suspected Arbovirus with Laboratory (SISAL)-incorporated laboratory data. These models were selected by comparing the prediction ability of seven machine learning algorithms; the area under the receiver operating characteristic curve from the prediction of a test dataset was used to select the final algorithm for each model. After eliminating those with missing data, the SISA dataset had 534 subjects, and the SISAL dataset had 98 subjects. For SISA, the best prediction algorithm was the generalized boosting model, with an AUC of 0.91. For SISAL, the best prediction algorithm was the elastic net with an AUC of 0.94. A sensitivity analysis revealed that SISA and SISAL are not directly comparable to one another. Conclusions/Significance: Both SISA and SISAL were able to predict arbovirus hospitalization with a high degree of accuracy in our dataset. These algorithms will need to be tested and validated on new data from future patients. Machine learning is a powerful prediction tool and provides an excellent option for new management tools and clinical assessment of arboviral infection.Publisher PDFPeer reviewe

Global disease monitoring and forecasting with Wikipedia

Infectious disease is a leading threat to public health, economic stability, and other key social structures. Efforts to mitigate these impacts depend on accurate and timely monitoring to measure the risk and progress of disease. Traditional, biologically-focused monitoring techniques are accurate but costly and slow; in response, new techniques based on social internet data such as social media and search queries are emerging. These efforts are promising, but important challenges in the areas of scientific peer review, breadth of diseases and countries, and forecasting hamper their operational usefulness. We examine a freely available, open data source for this use: access logs from the online encyclopedia Wikipedia. Using linear models, language as a proxy for location, and a systematic yet simple article selection procedure, we tested 14 location-disease combinations and demonstrate that these data feasibly support an approach that overcomes these challenges. Specifically, our proof-of-concept yields models with $r^2$ up to 0.92, forecasting value up to the 28 days tested, and several pairs of models similar enough to suggest that transferring models from one location to another without re-training is feasible. Based on these preliminary results, we close with a research agenda designed to overcome these challenges and produce a disease monitoring and forecasting system that is significantly more effective, robust, and globally comprehensive than the current state of the art.Comment: 27 pages; 4 figures; 4 tables. Version 2: Cite McIver & Brownstein and adjust novelty claims accordingly; revise title; various revisions for clarit

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Dengue fever is a worldwide issue, especially in Yemen. Although early detection is critical to reducing dengue disease deaths, accurate dengue diagnosis requires a long time due to the numerous clinical examinations. Thus, this issue necessitates the development of a new diagnostic schema. The objective of this work is to develop a diagnostic model for the earlier diagnosis of dengue disease using Efficient Machine Learning Techniques (EMLT). This paper proposed prediction models for dengue disease based on EMLT. Five different efficient machine learning models, including K-Nearest Neighbor (KNN), Gradient Boosting Classifier (GBC), Extra Tree Classifier (ETC), eXtreme Gradient Boosting (XGB), and Light Gradient Boosting Machine (LightGBM). All classifiers are trained and tested on the dataset using 10-Fold Cross-Validation and Holdout Cross-Validation approaches. On a test set, all models were evaluated using different metrics: accuracy, F1-sore, Recall, Precision, AUC, and operating time. Based on the findings, the ETC model achieved the highest accuracy in Hold-out and 10-fold cross-validation, with 99.12 % and 99.03 %, respectively. In the Holdout cross-validation approach, we conclude that the best classifier with high accuracy is ETC, which achieved 99.12 %. Finally, the experimental results indicate that classifier performance in holdout cross-validation outperforms 10-fold cross-validation. Accordingly, the proposed dengue prediction system demonstrates its efficacy and effectiveness in assisting doctors in accurately predicting dengue disease

Machine learning in drug supply chain management during disease outbreaks: a systematic review

The drug supply chain is inherently complex. The challenge is not only the number of stakeholders and the supply chain from producers to users but also production and demand gaps. Downstream, drug demand is related to the type of disease outbreak. This study identifies the correlation between drug supply chain management and the use of predictive parameters in research on the spread of disease, especially with machine learning methods in the last five years. Using the Publish or Perish 8 application, there are 71 articles that meet the inclusion criteria and keyword search requirements according to Kitchenham's systematic review methodology. The findings can be grouped into three broad groupings of disease outbreaks, each of which uses machine learning algorithms to predict the spread of disease outbreaks. The use of parameters for prediction with machine learning has a correlation with drug supply management in the coronavirus disease case. The area of drug supply risk management has not been heavily involved in the prediction of disease outbreaks

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Currently, novel coronavirus disease 2019 (COVID-19) is a big threat to global health. The rapid spread of the virus has created pandemic, and countries all over the world are struggling with a surge in COVID-19 infected cases. There are no drugs or other therapeutics approved by the US Food and Drug Administration to prevent or treat COVID-19: information on the disease is very limited and scattered even if it exists. This motivates the use of data integration, combining data from diverse sources and eliciting useful information with a unified view of them. In this paper, we propose a Bayesian hierarchical model that integrates global data for real-time prediction of infection trajectory for multiple countries. Because the proposed model takes advantage of borrowing information across multiple countries, it outperforms an existing individual country-based model. As fully Bayesian way has been adopted, the model provides a powerful predictive tool endowed with uncertainty quantification. Additionally, a joint variable selection technique has been integrated into the proposed modeling scheme, which aimed to identify possible country-level risk factors for severe disease due to COVID-19

Healthcare Data Mining: Predicting Hospital Length of Stay of Dengue Patients

Dengue is regarded as the most important mosquito-borne viral disease. Recently dengue has emerged as a public health burden in Southeast Asia and other tropical countries. At times when dengue re-emerges as an epidemic, hospitals are required to be able to handle patient flow fluctuation while maintaining their performance. This research applied a data mining technique to build a model that can predict in-patient hospital length of stay from the time of admission, which can be useful for effective decision-making that may lead to better clinical and resource management in hospitals. Using the C4.5 algorithm and a decision tree classifier, an accuracy of 71.57% and an area under the receiver operating characteristic (ROC) curve value of 0.761 were obtained. The decision tree showed that only 7 out of 21 input attributes affect the hospital length of stay prediction of dengue patients. The attribute with the highest impact was monocytes, followed by diastolic blood pressure, hematocrit, leucocytes, systolic blood pressure, comorbidity score, and lymphocytes. In this research also a prototype of a prediction system using the resulting model was developed

Hydrometeorological Extremes and Its Local Impacts on Human-Environmental Systems

This Special Issue of Atmosphere focuses on hydrometeorological extremes and their local impacts on human–environment systems. Particularly, we accepted submissions on the topics of observational and model-based studies that could provide useful information for infrastructure design, decision making, and policy making to achieve our goals of enhancing the resilience of human–environment systems to climate change and increased variability