Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease.
<h4>Background</h4>Chagas disease is a long-lasting disease with a prolonged asymptomatic period. Cumulative indices of infection such as prevalence do not shed light on the current epidemiological situation, as they integrate infection over long periods. Instead, metrics such as the For...
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Public Library of Science (PLoS)
2022-07-01
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| Series: | PLoS Neglected Tropical Diseases |
| Online Access: | https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0010594&type=printable |
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| author | Julia Ledien Zulma M Cucunubá Gabriel Parra-Henao Eliana Rodríguez-Monguí Andrew P Dobson Susana B Adamo María-Gloria Basáñez Pierre Nouvellet |
| author_facet | Julia Ledien Zulma M Cucunubá Gabriel Parra-Henao Eliana Rodríguez-Monguí Andrew P Dobson Susana B Adamo María-Gloria Basáñez Pierre Nouvellet |
| author_sort | Julia Ledien |
| collection | DOAJ |
| description | <h4>Background</h4>Chagas disease is a long-lasting disease with a prolonged asymptomatic period. Cumulative indices of infection such as prevalence do not shed light on the current epidemiological situation, as they integrate infection over long periods. Instead, metrics such as the Force-of-Infection (FoI) provide information about the rate at which susceptible people become infected and permit sharper inference about temporal changes in infection rates. FoI is estimated by fitting (catalytic) models to available age-stratified serological (ground-truth) data. Predictive FoI modelling frameworks are then used to understand spatial and temporal trends indicative of heterogeneity in transmission and changes effected by control interventions. Ideally, these frameworks should be able to propagate uncertainty and handle spatiotemporal issues.<h4>Methodology/principal findings</h4>We compare three methods in their ability to propagate uncertainty and provide reliable estimates of FoI for Chagas disease in Colombia as a case study: two Machine Learning (ML) methods (Boosted Regression Trees (BRT) and Random Forest (RF)), and a Linear Model (LM) framework that we had developed previously. Our analyses show consistent results between the three modelling methods under scrutiny. The predictors (explanatory variables) selected, as well as the location of the most uncertain FoI values, were coherent across frameworks. RF was faster than BRT and LM, and provided estimates with fewer extreme values when extrapolating to areas where no ground-truth data were available. However, BRT and RF were less efficient at propagating uncertainty.<h4>Conclusions/significance</h4>The choice of FoI predictive models will depend on the objectives of the analysis. ML methods will help characterise the mean behaviour of the estimates, while LM will provide insight into the uncertainty surrounding such estimates. Our approach can be extended to the modelling of FoI patterns in other Chagas disease-endemic countries and to other infectious diseases for which serosurveys are regularly conducted for surveillance. |
| format | Article |
| id | doaj-art-4b2e48639374461e8697b99e74cb3b72 |
| institution | OA Journals |
| issn | 1935-2727 1935-2735 |
| language | English |
| publishDate | 2022-07-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Neglected Tropical Diseases |
| spelling | doaj-art-4b2e48639374461e8697b99e74cb3b722025-08-20T02:33:27ZengPublic Library of Science (PLoS)PLoS Neglected Tropical Diseases1935-27271935-27352022-07-01167e001059410.1371/journal.pntd.0010594Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease.Julia LedienZulma M CucunubáGabriel Parra-HenaoEliana Rodríguez-MonguíAndrew P DobsonSusana B AdamoMaría-Gloria BasáñezPierre Nouvellet<h4>Background</h4>Chagas disease is a long-lasting disease with a prolonged asymptomatic period. Cumulative indices of infection such as prevalence do not shed light on the current epidemiological situation, as they integrate infection over long periods. Instead, metrics such as the Force-of-Infection (FoI) provide information about the rate at which susceptible people become infected and permit sharper inference about temporal changes in infection rates. FoI is estimated by fitting (catalytic) models to available age-stratified serological (ground-truth) data. Predictive FoI modelling frameworks are then used to understand spatial and temporal trends indicative of heterogeneity in transmission and changes effected by control interventions. Ideally, these frameworks should be able to propagate uncertainty and handle spatiotemporal issues.<h4>Methodology/principal findings</h4>We compare three methods in their ability to propagate uncertainty and provide reliable estimates of FoI for Chagas disease in Colombia as a case study: two Machine Learning (ML) methods (Boosted Regression Trees (BRT) and Random Forest (RF)), and a Linear Model (LM) framework that we had developed previously. Our analyses show consistent results between the three modelling methods under scrutiny. The predictors (explanatory variables) selected, as well as the location of the most uncertain FoI values, were coherent across frameworks. RF was faster than BRT and LM, and provided estimates with fewer extreme values when extrapolating to areas where no ground-truth data were available. However, BRT and RF were less efficient at propagating uncertainty.<h4>Conclusions/significance</h4>The choice of FoI predictive models will depend on the objectives of the analysis. ML methods will help characterise the mean behaviour of the estimates, while LM will provide insight into the uncertainty surrounding such estimates. Our approach can be extended to the modelling of FoI patterns in other Chagas disease-endemic countries and to other infectious diseases for which serosurveys are regularly conducted for surveillance.https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0010594&type=printable |
| spellingShingle | Julia Ledien Zulma M Cucunubá Gabriel Parra-Henao Eliana Rodríguez-Monguí Andrew P Dobson Susana B Adamo María-Gloria Basáñez Pierre Nouvellet Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease. PLoS Neglected Tropical Diseases |
| title | Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease. |
| title_full | Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease. |
| title_fullStr | Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease. |
| title_full_unstemmed | Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease. |
| title_short | Linear and Machine Learning modelling for spatiotemporal disease predictions: Force-of-Infection of Chagas disease. |
| title_sort | linear and machine learning modelling for spatiotemporal disease predictions force of infection of chagas disease |
| url | https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0010594&type=printable |
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