Reiker, T. and Golumbeanu, M. and Shattock, A. and Burgert, L. and Smith, T. A. and Filippi, S. and Cameron, E. and Penny, M. A.. (2021) Emulator-based Bayesian optimization for efficient multi-objective calibration of an individual-based model of malaria. Nat Commun, 12. p. 7212.
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Official URL: https://edoc.unibas.ch/89285/
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Abstract
Individual-based models have become important tools in the global battle against infectious diseases, yet model complexity can make calibration to biological and epidemiological data challenging. We propose using a Bayesian optimization framework employing Gaussian process or machine learning emulator functions to calibrate a complex malaria transmission simulator. We demonstrate our approach by optimizing over a high-dimensional parameter space with respect to a portfolio of multiple fitting objectives built from datasets capturing the natural history of malaria transmission and disease progression. Our approach quickly outperforms previous calibrations, yielding an improved final goodness of fit. Per-objective parameter importance and sensitivity diagnostics provided by our approach offer epidemiological insights and enhance trust in predictions through greater interpretability.
Faculties and Departments: | 09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) 09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Former Units within Swiss TPH > Infectious Disease Modelling > Epidemiology and Transmission Dynamics (Smith) 09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Epidemiology and Public Health (EPH) > Disease Modelling > Disease Modelling and Intervention Dynamics (Penny) |
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UniBasel Contributors: | Reiker, Theresa and Golumbeanu, Monica and Shattock, Andrew James and Burgert, Lydia and Smith, Thomas A. and Penny, Melissa |
Item Type: | Article, refereed |
Article Subtype: | Research Article |
ISSN: | 2041-1723 (Electronic)2041-1723 (Linking) |
Note: | Publication type according to Uni Basel Research Database: Journal article |
Language: | English |
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Last Modified: | 20 Dec 2022 15:04 |
Deposited On: | 20 Dec 2022 15:04 |
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