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An algebraic framework for structured epidemic modelling

Pandemic management requires that scientists rapidly formulate and analyse epidemiological models in order to forecast the spread of disease and the effects of mitigation strategies. Scientists must modify existing models and create novel ones in light of new biological data and policy changes such...

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Detalles Bibliográficos
Autores principales: Libkind, Sophie, Baas, Andrew, Halter, Micah, Patterson, Evan, Fairbanks, James P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9376710/
https://www.ncbi.nlm.nih.gov/pubmed/35965465
http://dx.doi.org/10.1098/rsta.2021.0309
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author Libkind, Sophie
Baas, Andrew
Halter, Micah
Patterson, Evan
Fairbanks, James P.
author_facet Libkind, Sophie
Baas, Andrew
Halter, Micah
Patterson, Evan
Fairbanks, James P.
author_sort Libkind, Sophie
collection PubMed
description Pandemic management requires that scientists rapidly formulate and analyse epidemiological models in order to forecast the spread of disease and the effects of mitigation strategies. Scientists must modify existing models and create novel ones in light of new biological data and policy changes such as social distancing and vaccination. Traditional scientific modelling workflows detach the structure of a model—its submodels and their interactions—from its implementation in software. Consequently, incorporating local changes to model components may require global edits to the code base through a manual, time-intensive and error-prone process. We propose a compositional modelling framework that uses high-level algebraic structures to capture domain-specific scientific knowledge and bridge the gap between how scientists think about models and the code that implements them. These algebraic structures, grounded in applied category theory, simplify and expedite modelling tasks such as model specification, stratification, analysis and calibration. With their structure made explicit, models also become easier to communicate, criticize and refine in light of stakeholder feedback. This article is part of the theme issue ‘Technical challenges of modelling real-life epidemics and examples of overcoming these’.
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spelling pubmed-93767102022-08-22 An algebraic framework for structured epidemic modelling Libkind, Sophie Baas, Andrew Halter, Micah Patterson, Evan Fairbanks, James P. Philos Trans A Math Phys Eng Sci Articles Pandemic management requires that scientists rapidly formulate and analyse epidemiological models in order to forecast the spread of disease and the effects of mitigation strategies. Scientists must modify existing models and create novel ones in light of new biological data and policy changes such as social distancing and vaccination. Traditional scientific modelling workflows detach the structure of a model—its submodels and their interactions—from its implementation in software. Consequently, incorporating local changes to model components may require global edits to the code base through a manual, time-intensive and error-prone process. We propose a compositional modelling framework that uses high-level algebraic structures to capture domain-specific scientific knowledge and bridge the gap between how scientists think about models and the code that implements them. These algebraic structures, grounded in applied category theory, simplify and expedite modelling tasks such as model specification, stratification, analysis and calibration. With their structure made explicit, models also become easier to communicate, criticize and refine in light of stakeholder feedback. This article is part of the theme issue ‘Technical challenges of modelling real-life epidemics and examples of overcoming these’. The Royal Society 2022-10-03 2022-08-15 /pmc/articles/PMC9376710/ /pubmed/35965465 http://dx.doi.org/10.1098/rsta.2021.0309 Text en © 2022 The Authors. https://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, provided the original author and source are credited.
spellingShingle Articles
Libkind, Sophie
Baas, Andrew
Halter, Micah
Patterson, Evan
Fairbanks, James P.
An algebraic framework for structured epidemic modelling
title An algebraic framework for structured epidemic modelling
title_full An algebraic framework for structured epidemic modelling
title_fullStr An algebraic framework for structured epidemic modelling
title_full_unstemmed An algebraic framework for structured epidemic modelling
title_short An algebraic framework for structured epidemic modelling
title_sort algebraic framework for structured epidemic modelling
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9376710/
https://www.ncbi.nlm.nih.gov/pubmed/35965465
http://dx.doi.org/10.1098/rsta.2021.0309
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