HASLab - Indexed Articles in Journals

Permanent URI for this collection

http://localhost:4000/handle/123456789/167

Browse

Browsing HASLab - Indexed Articles in Journals by Author "5596"
  • Item
    Consistent comparison of symptom-based methods for COVID-19 infection detection
    ( 2023) Carlos Baquero ; 5596
    Background: During the global pandemic crisis, various detection methods of COVID-19-positive cases based on self-reported information were introduced to provide quick diagnosis tools for effectively planning and managing healthcare resources. These methods typically identify positive cases based on a particular combination of symptoms, and they have been evaluated using different datasets.Purpose: This paper presents a comprehensive comparison of various COVID-19 detection methods based on self-reported information using the University of Maryland Global COVID-19 Trends and Impact Survey (UMD-CTIS), a large health surveillance platform, which was launched in partnership with Facebook.Methods: Detection methods were implemented to identify COVID-19-positive cases among UMD-CTIS participants reporting at least one symptom and a recent antigen test result (positive or negative) for six countries and two periods. Multiple detection methods were implemented for three different categories: rule-based approaches, logistic regression techniques, and tree-based machine-learning models. These methods were evaluated using different metrics including F1-score, sensitivity, specificity, and precision. An explainability analysis has also been conducted to compare methods.Results: Fifteen methods were evaluated for six countries and two periods. We identify the best method for each category: rule-based methods (F1-score: 51.48% -71.11%), logistic regression techniques (F1-score: 39.91% -71.13%), and tree-based machine learning models (F1-score: 45.07% -73.72%). According to the explainability analysis, the relevance of the reported symptoms in COVID-19 detection varies between countries and years. However, there are two variables consistently relevant across approaches: stuffy or runny nose, and aches or muscle pain.Conclusions: Regarding the categories of detection methods, evaluating detection methods using homogeneous data across countries and years provides a solid and consistent comparison. An explainability analysis of a tree-based machine-learning model can assist in identifying infected individuals specifically based on their relevant symptoms. This study is limited by the self-report nature of data, which cannot replace clinical diagnosis.
  • Item
    The CoronaSurveys System for COVID-19 Incidence Data Collection and Processing
    ( 2021) Agundez,AG ; Sanchez,I ; Roberts,JC ; Ojo,O ; Stavrakis,E ; Nicolaou,N ; Hernández Roig,HA ; Goessens,M ; Ortega,A ; Girault,B ; Georgiou,C ; Carlos Baquero ; Casari,P ; Anta,AF ; García,AG ; Frey,D ; 5596
  • Item
    The CoronaSurveys System for COVID-19 Incidence Data Collection and Processing
    ( 2021) Carlos Baquero ; Casari,P ; Anta,AF ; Garcia Garcia,A ; Frey,D ; Garcia Agundez,A ; Georgiou,C ; Girault,B ; Ortega,A ; Goessens,M ; Hernandez Roig,HA ; Nicolaou,N ; Stavrakis,E ; Ojo,O ; Roberts,JC ; Sanchez,I ; 5596
    CoronaSurveys is an ongoing interdisciplinary project developing a system to infer the incidence of COVID-19 around the world using anonymous open surveys. The surveys have been translated into 60 languages and are continuously collecting participant responses from any country in the world. The responses collected are pre-processed, organized, and stored in a version-controlled repository, which is publicly available to the scientific community. In addition, the CoronaSurveys team has devised several estimates computed on the basis of survey responses and other data, and makes them available on the project's website in the form of tables, as well as interactive plots and maps. In this paper, we describe the computational system developed for the CoronaSurveys project. The system includes multiple components and processes, including the web survey, the mobile apps, the cleaning and aggregation process of the survey responses, the process of storage and publication of the data, the processing of the data and the computation of estimates, and the visualization of the results. In this paper we describe the system architecture and the major challenges we faced in designing and deploying it.
  • Item
    Delta State Replicated Data Types
    ( 2018) Paulo Sérgio Almeida ; Ali Shoker ; Carlos Baquero ; 5607 ; 6172 ; 5596
  • Item
    Using survey data to estimate the impact of the omicron variant on vaccine efficacy against COVID-19 infection
    ( 2023) Carlos Baquero ; 5596
    Symptoms-based detection of SARS-CoV-2 infection is not a substitute for precise diagnostic tests but can provide insight into the likely level of infection in a given population. This study uses symptoms data collected in the Global COVID-19 Trends and Impact Surveys (UMD Global CTIS), and data on variants sequencing from GISAID. This work, conducted in January of 2022 during the emergence of the Omicron variant (subvariant BA.1), aims to improve the quality of infection detection from the available symptoms and to use the resulting estimates of infection levels to assess the changes in vaccine efficacy during a change of dominant variant; from the Delta dominant to the Omicron dominant period. Our approach produced a new symptoms-based classifier, Random Forest, that was compared to a ground-truth subset of cases with known diagnostic test status. This classifier was compared with other competing classifiers and shown to exhibit an increased performance with respect to the ground-truth data. Using the Random Forest classifier, and knowing the vaccination status of the subjects, we then proceeded to analyse the evolution of vaccine efficacy towards infection during different periods, geographies and dominant variants. In South Africa, where the first significant wave of Omicron occurred, a significant reduction of vaccine efficacy is observed from August-September 2021 to December 2021. For instance, the efficacy drops from 0.81 to 0.30 for those vaccinated with 2 doses (of Pfizer/BioNTech), and from 0.51 to 0.09 for those vaccinated with one dose (of Pfizer/BioNTech or Johnson & Johnson). We also extended the study to other countries in which Omicron has been detected, comparing the situation in October 2021 (before Omicron) with that of December 2021. While the reduction measured is smaller than in South Africa, we still found, for instance, an average drop in vaccine efficacy from 0.53 to 0.45 among those vaccinated with two doses. Moreover, we found a significant negative (Pearson) correlation of around - 0.6 between the measured prevalence of Omicron in several countries and the vaccine efficacy in those same countries. This prediction, in January of 2022, of the decreased vaccine efficacy towards Omicron is in line with the subsequent increase of Omicron infections in the first half of 2022.