Approximate Bayesian Computation and simulation-based inference for complex stochastic epidemic models

McKinley, T.J.; Vernon, I.; Andrianakis, I.; McCreesh, N.; Oakley, J.E.; Nsubuga, R.; Goldstein, M.; White, R.G.

doi:10.1214/17-sts618

Systematic structural discrepancy assessment for computer models (2025)
Journal Article
Goldstein, M., Vernon, I., & Cumming, J. A. (2025). Systematic structural discrepancy assessment for computer models. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 383(2293), Article 20240214. https://doi.org/10.1098/rsta.2024.0214

Model or structural discrepancy is an essential component in the analysis of computer simulators, representing the differences between the outputs of the simulator and the real-world system that the simulator seeks to represent. This discrepancy can... Read More about Systematic structural discrepancy assessment for computer models.

Bayesian Emulation for Computer Models with Multiple Partial Discontinuities (2024)
Journal Article
Vernon, I., Owen, J., & Carter, J. (online). Bayesian Emulation for Computer Models with Multiple Partial Discontinuities. Bayesian Analysis, https://doi.org/10.1214/24-BA1456

Computer models are widely used across a range of scientific disciplines to describe various complex physical systems, however to perform full uncertainty quantification we often need to employ emulators. An emulator is a fast statistical construct t... Read More about Bayesian Emulation for Computer Models with Multiple Partial Discontinuities.

Emulation and History Matching using the hmer Package (2024)
Journal Article
Iskauskas, A., Vernon, I., Goldstein, M., Scarponi, D., McKinley, T. J., White, R. G., & McCreesh, N. (2024). Emulation and History Matching using the hmer Package. Journal of Statistical Software, 109(10), 1–48. https://doi.org/10.18637/jss.v109.i10

Modeling complex real-world situations such as infectious diseases, geological phenomena, and biological processes can present a dilemma: the computer model (referred to as a simulator) needs to be complex enough to capture the dynamics of the system... Read More about Emulation and History Matching using the hmer Package.

FLAMINGO: calibrating large cosmological hydrodynamical simulations with machine learning. (2023)
Journal Article
Kugel, R., Schaye, J., Schaller, M., Helly, J. C., Braspenning, J., Elbers, W., …Vernon, I. (2023). FLAMINGO: calibrating large cosmological hydrodynamical simulations with machine learning. Monthly Notices of the Royal Astronomical Society, 526(4), 6103-6127. https://doi.org/10.1093/mnras/stad2540

To fully take advantage of the data provided by large-scale structure surveys, we need to quantify the potential impact of baryonic effects, such as feedback from active galactic nuclei (AGN) and star formation, on cosmological observables. In simula... Read More about FLAMINGO: calibrating large cosmological hydrodynamical simulations with machine learning..

First observation of 28O (2023)
Journal Article
Kondo, Y., Achouri, N. L., Falou, H. A., Atar, L., Aumann, T., Baba, H., …Yoshida, S. (2023). First observation of 28O. Nature, 620(7976), 965-970. https://doi.org/10.1038/s41586-023-06352-6

Subjecting a physical system to extreme conditions is one of the means often used to obtain a better understanding and deeper insight into its organization and structure. In the case of the atomic nucleus, one such approach is to investigate isotopes... Read More about First observation of 28O.

Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer (2023)
Journal Article
Scarponi, D., Iskauskas, A., Clark, R. A., Vernon, I., McKinley, T. J., Goldstein, M., Mukandavire, C., Deol, A., Weerasuriya, C., Bakker, R., White, R. G., & McCreesh, N. (2023). Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer. Epidemics, 43, Article 100678. https://doi.org/10.1016/j.epidem.2023.100678

Infectious disease models are widely used by epidemiologists to improve the understanding of transmission dynamics and disease natural history, and to predict the possible effects of interventions. As the complexity of such models increases, however,... Read More about Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer.

A Bayesian Computer Model Analysis of Robust Bayesian Analyses (2022)
Journal Article
Vernon, I., & Gosling, J. (2023). A Bayesian Computer Model Analysis of Robust Bayesian Analyses. Bayesian Analysis, 18(4), 1367-1399. https://doi.org/10.1214/22-ba1340

We harness the power of Bayesian emulation techniques, designed to aid the analysis of complex computer models, to examine the structure of complex Bayesian analyses themselves. These techniques facilitate robust Bayesian analyses and/or sensitivity... Read More about A Bayesian Computer Model Analysis of Robust Bayesian Analyses.

Ab initio predictions link the neutron skin of 208Pb to nuclear forces (2022)
Journal Article
Hu, B., Jaing, W., Miyagi, T., Sun, Z., Ekström, A., Forssén, C., Hagen, G., Holt, J. D., Papenbrock, T., Stroberg, S. R., & Vernon, I. (2022). Ab initio predictions link the neutron skin of 208Pb to nuclear forces. Nature Physics, 18(10), 1196-1200. https://doi.org/10.1038/s41567-022-01715-8

Heavy atomic nuclei have an excess of neutrons over protons, which leads to the formation of a neutron skin whose thickness is sensitive to details of the nuclear force. This links atomic nuclei to properties of neutron stars, thereby relating object... Read More about Ab initio predictions link the neutron skin of 208Pb to nuclear forces.

Bayesian Emulation and History Matching of JUNE (2022)
Journal Article
Vernon, I., Owen, J., Aylett-Bullock, J., Cuestra-Lazaro, C., Frawley, J., Quera-Bofarull, A., Sedgewick, A., Shi, D., Truong, H., Turner, M., Walker, J., Caulfield, T., Fong, K., & Krauss, F. (2022). Bayesian Emulation and History Matching of JUNE. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233), Article 20220039. https://doi.org/10.1098/rsta.2022.0039

We analyse JUNE: a detailed model of Covid-19 transmission with high spatial and demographic resolution, developed as part of the RAMP initiative. JUNE requires substantial computational resources to evaluate, making model calibration and general unc... Read More about Bayesian Emulation and History Matching of JUNE.

Complex model calibration through emulation, a worked example for a stochastic epidemic model (2022)
Journal Article
Dunne, M., Mohammadi, H., Challenor, P., Borgo, R., Porphyre, T., Vernon, I., Firat, E. E., Turkay, C., Torsney-Weir, T., Goldstein, M., Reeve, R., Fang, H., & Swallow, B. (2022). Complex model calibration through emulation, a worked example for a stochastic epidemic model. Epidemics, 39, Article 100574. https://doi.org/10.1016/j.epidem.2022.100574

Uncertainty quantification is a formal paradigm of statistical estimation that aims to account for all uncertainties inherent in the modelling process of real-world complex systems. The methods are directly applicable to stochastic models in epidemio... Read More about Complex model calibration through emulation, a worked example for a stochastic epidemic model.

Efficient Emulation of Computer Models Utilising Multiple Known Boundaries of Differing Dimension (2022)
Journal Article
Jackson, S. E., & Vernon, I. (2023). Efficient Emulation of Computer Models Utilising Multiple Known Boundaries of Differing Dimension. Bayesian Analysis, 18(1), 165-191. https://doi.org/10.1214/22-ba1304

Emulation has been successfully applied across a wide variety of scientific disciplines for efficiently analysing computationally intensive models. We develop known boundary emulation strategies which utilise the fact that, for many computer models,... Read More about Efficient Emulation of Computer Models Utilising Multiple Known Boundaries of Differing Dimension.

Challenges in estimation, uncertainty quantification and elicitation for pandemic modelling (2022)
Journal Article
Swallow, B., Birrell, P., Blake, J., Burgman, M., Challenor, P., Coffeng, L. E., Dawid, P., De Angelis, D., Goldstein, M., Hemming, V., Marion, G., McKinley, T. J., Overton, C. E., Panovska-Griffiths, J., Pellis, L., Probert, W., Shea, K., Villela, D., & Vernon, I. (2022). Challenges in estimation, uncertainty quantification and elicitation for pandemic modelling. Epidemics, 38, https://doi.org/10.1016/j.epidem.2022.100547

The estimation of parameters and model structure for informing infectious disease response has become a focal point of the recent pandemic. However, it has also highlighted a plethora of challenges remaining in the fast and robust extraction of infor... Read More about Challenges in estimation, uncertainty quantification and elicitation for pandemic modelling.

JUNE: open-source individual-based epidemiology simulation (2021)
Journal Article
Aylett-Bullock, J., Cuesta-Lazaro, C., Quera-Bofarull, A., Icaza-Lizaola, M., Sedgewick, A., Truong, H., Curran, A., Elliott, E., Caulfield, T., Fong, K., Vernon, I., Williams, J., Bower, R., & Krauss, F. (2021). JUNE: open-source individual-based epidemiology simulation. Royal Society Open Science, 8(7), https://doi.org/10.1098/rsos.210506

We introduce June, an open-source framework for the detailed simulation of epidemics on the basis of social interactions in a virtual population constructed from geographically granular census data, reflecting age, sex, ethnicity and socio-economic i... Read More about JUNE: open-source individual-based epidemiology simulation.

Efficient Selection of Reservoir Model Outputs within an Emulation-Based Bayesian History Matching Uncertainty Analysis (2020)
Journal Article
Ferreira, C., Vernon, I., Caiado, C., Formentin, H., Avansi, G., Goldstein, M., & Schiozer, D. (2020). Efficient Selection of Reservoir Model Outputs within an Emulation-Based Bayesian History Matching Uncertainty Analysis. SPE Journal, 25(4), 2119-2142. https://doi.org/10.4043/29801-ms

When performing classic uncertainty reduction based on dynamic data, a large number of reservoir simulations need to be evaluated at high computational cost. As an alternative, we construct Bayesian emulators that mimic the dominant behaviour of the... Read More about Efficient Selection of Reservoir Model Outputs within an Emulation-Based Bayesian History Matching Uncertainty Analysis.

Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching (2020)
Journal Article
Jackson, S., Vernon, I., Liu, J., & Lindsey, K. (2020). Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching. Statistical Applications in Genetics and Molecular Biology, 19(2), Article 20180053. https://doi.org/10.1515/sagmb-2018-0053

A major challenge in plant developmental biology is to understand how plant growth is coordinated by interacting hormones and genes. To meet this challenge, it is important to not only use experimental data, but also formulate a mathematical model. F... Read More about Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching.

Gaining more understanding about reservoir behavior through assimilation of breakthrough time and productivity deviation in the history matching process (2019)
Journal Article
Formentin, H. N., Almeida, F. L. R., Avansi, G. D., Maschio, C., Schiozer, D. J., Caiado, C., Vernon, I., & Goldstein, M. (2019). Gaining more understanding about reservoir behavior through assimilation of breakthrough time and productivity deviation in the history matching process. Journal of Petroleum Science and Engineering, 173, 1080-1096. https://doi.org/10.1016/j.petrol.2018.10.045

History matching (HM) is an inverse problem where uncertainties in attributes are reduced by comparison with observed dynamic data. Typically, normalized misfit summarizes dissimilarities between observed and simulation data. Especially for long-time... Read More about Gaining more understanding about reservoir behavior through assimilation of breakthrough time and productivity deviation in the history matching process.

Known Boundary Emulation of Complex Computer Models (2019)
Journal Article
Vernon, I., Jackson, S., & Cumming, J. (2019). Known Boundary Emulation of Complex Computer Models. SIAM/ASA Journal on Uncertainty Quantification, 7(3), 838-876. https://doi.org/10.1137/18m1164457

Computer models are now widely used across a range of scientific disciplines to describe various complex physical systems, however to perform full uncertainty quantification we often need to employ emulators. An emulator is a fast statistical constru... Read More about Known Boundary Emulation of Complex Computer Models.

Choice of time horizon critical in estimating costs and effects of changes to HIV programmes (2018)
Journal Article
McCreesh, N., Andrianakis, I., Nsubuga, R. N., Strong, M., Vernon, I., McKinley, T. J., Oakley, J. E., Goldstein, M., Hayes, R., & White, R. G. (2018). Choice of time horizon critical in estimating costs and effects of changes to HIV programmes. PLoS ONE, 13(5), Article e0196480. https://doi.org/10.1371/journal.pone.0196480

Background: Uganda changed its antiretroviral therapy guidelines in 2014, increasing the CD4 threshold for antiretroviral therapy initiation from 350 cells/μl to 500 cells/μl. We investigate what effect this change in policy is likely to have on HIV... Read More about Choice of time horizon critical in estimating costs and effects of changes to HIV programmes.

Emulation of reservoir production forecast considering variation in petrophysical properties (2018)
Journal Article
Moreno, R., Avansi, G., Schiozer, D., Vernon, I., Goldstein, M., & Caiado, C. (2018). Emulation of reservoir production forecast considering variation in petrophysical properties. Journal of Petroleum Science and Engineering, 165, 711-725. https://doi.org/10.1016/j.petrol.2018.02.056

Implementation of proxy models, such as emulators might reduce the computational time required in a variety of reservoir simulation studies. By definition, an emulator uses reservoir properties as input parameters in a statistical model constructed f... Read More about Emulation of reservoir production forecast considering variation in petrophysical properties.

Approximate Bayesian Computation and simulation-based inference for complex stochastic epidemic models (2018)
Journal Article
McKinley, T., Vernon, I., Andrianakis, I., McCreesh, N., Oakley, J., Nsubuga, R., …White, R. (2018). Approximate Bayesian Computation and simulation-based inference for complex stochastic epidemic models. Statistical Science, 33(1), 4-18. https://doi.org/10.1214/17-sts618

Approximate Bayesian Computation (ABC) and other simulation-based inference methods are becoming increasingly used for inference in complex systems, due to their relative ease-of-implementation. We briefly review some of the more popular variants of... Read More about Approximate Bayesian Computation and simulation-based inference for complex stochastic epidemic models.

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