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      Neural parameter calibration for large-scale multiagent models

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          Significance

          In this work, we consider multiagent models, widely used across the quantitative sciences to analyze complex systems. These often contain parameters which must be estimated from data. While many methods to do so have been developed, they can be mathematically involved or computationally expensive. We present an alternative using neural networks that addresses both these issues. Our method can make accurate predictions from various kinds of data in seconds where more classical techniques, such as MCMC, take hours, thereby presenting researchers across the quantitative disciplines with a valuable tool to estimate relevant parameters and produce more meaningful simulations at a greatly reduced computational cost.

          Abstract

          Computational models have become a powerful tool in the quantitative sciences to understand the behavior of complex systems that evolve in time. However, they often contain a potentially large number of free parameters whose values cannot be obtained from theory but need to be inferred from data. This is especially the case for models in the social sciences, economics, or computational epidemiology. Yet, many current parameter estimation methods are mathematically involved and computationally slow to run. In this paper, we present a computationally simple and fast method to retrieve accurate probability densities for model parameters using neural differential equations. We present a pipeline comprising multiagent models acting as forward solvers for systems of ordinary or stochastic differential equations and a neural network to then extract parameters from the data generated by the model. The two combined create a powerful tool that can quickly estimate densities on model parameters, even for very large systems. We demonstrate the method on synthetic time series data of the SIR model of the spread of infection and perform an in-depth analysis of the Harris–Wilson model of economic activity on a network, representing a nonconvex problem. For the latter, we apply our method both to synthetic data and to data of economic activity across Greater London. We find that our method calibrates the model orders of magnitude more accurately than a previous study of the same dataset using classical techniques, while running between 195 and 390 times faster.

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          Estimates of the severity of coronavirus disease 2019: a model-based analysis

          Summary Background In the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting for censoring and ascertainment biases. Methods We collected individual-case data for patients who died from COVID-19 in Hubei, mainland China (reported by national and provincial health commissions to Feb 8, 2020), and for cases outside of mainland China (from government or ministry of health websites and media reports for 37 countries, as well as Hong Kong and Macau, until Feb 25, 2020). These individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. We also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland China. Using data on the prevalence of PCR-confirmed cases in international residents repatriated from China, we obtained age-stratified estimates of the infection fatality ratio. Furthermore, data on age-stratified severity in a subset of 3665 cases from China were used to estimate the proportion of infected individuals who are likely to require hospitalisation. Findings Using data on 24 deaths that occurred in mainland China and 165 recoveries outside of China, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval [CrI] 16·9–19·2) and to hospital discharge to be 24·7 days (22·9–28·1). In all laboratory confirmed and clinically diagnosed cases from mainland China (n=70 117), we estimated a crude case fatality ratio (adjusted for censoring) of 3·67% (95% CrI 3·56–3·80). However, after further adjusting for demography and under-ascertainment, we obtained a best estimate of the case fatality ratio in China of 1·38% (1·23–1·53), with substantially higher ratios in older age groups (0·32% [0·27–0·38] in those aged <60 years vs 6·4% [5·7–7·2] in those aged ≥60 years), up to 13·4% (11·2–15·9) in those aged 80 years or older. Estimates of case fatality ratio from international cases stratified by age were consistent with those from China (parametric estimate 1·4% [0·4–3·5] in those aged <60 years [n=360] and 4·5% [1·8–11·1] in those aged ≥60 years [n=151]). Our estimated overall infection fatality ratio for China was 0·66% (0·39–1·33), with an increasing profile with age. Similarly, estimates of the proportion of infected individuals likely to be hospitalised increased with age up to a maximum of 18·4% (11·0–7·6) in those aged 80 years or older. Interpretation These early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and show a strong age gradient in risk of death. Funding UK Medical Research Council.
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            Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe

            Following the detection of the new coronavirus1 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics of coronavirus disease 2019 (COVID-19). In response, many European countries have implemented non-pharmaceutical interventions, such as the closure of schools and national lockdowns. Here we study the effect of major interventions across 11 European countries for the period from the start of the COVID-19 epidemics in February 2020 until 4 May 2020, when lockdowns started to be lifted. Our model calculates backwards from observed deaths to estimate transmission that occurred several weeks previously, allowing for the time lag between infection and death. We use partial pooling of information between countries, with both individual and shared effects on the time-varying reproduction number (Rt). Pooling allows for more information to be used, helps to overcome idiosyncrasies in the data and enables more-timely estimates. Our model relies on fixed estimates of some epidemiological parameters (such as the infection fatality rate), does not include importation or subnational variation and assumes that changes in Rt are an immediate response to interventions rather than gradual changes in behaviour. Amidst the ongoing pandemic, we rely on death data that are incomplete, show systematic biases in reporting and are subject to future consolidation. We estimate that-for all of the countries we consider here-current interventions have been sufficient to drive Rt below 1 (probability Rt < 1.0 is greater than 99%) and achieve control of the epidemic. We estimate that across all 11 countries combined, between 12 and 15 million individuals were infected with SARS-CoV-2 up to 4 May 2020, representing between 3.2% and 4.0% of the population. Our results show that major non-pharmaceutical interventions-and lockdowns in particular-have had a large effect on reducing transmission. Continued intervention should be considered to keep transmission of SARS-CoV-2 under control.
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              Physics-Informed Neural Networks: A Deep Learning Framework for Solving Forward and Inverse Problems Involving Nonlinear Partial Differential Equations

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                Author and article information

                Contributors
                Journal
                Proc Natl Acad Sci U S A
                Proc Natl Acad Sci U S A
                PNAS
                Proceedings of the National Academy of Sciences of the United States of America
                National Academy of Sciences
                0027-8424
                1091-6490
                10 February 2023
                14 February 2023
                10 February 2023
                : 120
                : 7
                : e2216415120
                Affiliations
                [1] aDepartment of Applied Mathematics and Theoretical Physics , University of Cambridge , Cambridge CB3 0WA, UK
                [2] bDepartment of Mathematics , Imperial College London , London SW7 2AZ, UK
                [3] cDepartment of Engineering , University of Cambridge , Cambridge CB2 1PZ, UK
                [4] dThe Alan Turing Institute , London NW1 2DB, UK
                Author notes
                1To whom correspondence may be addressed. Email: trg34@ 123456cam.ac.uk .

                Edited by David Donoho, Stanford University, Stanford, CA; received September 28, 2022; accepted January 9, 2023

                Author information
                https://orcid.org/0000-0002-5644-4431
                https://orcid.org/0000-0002-3468-9227
                https://orcid.org/0000-0003-3008-253X
                Article
                202216415
                10.1073/pnas.2216415120
                9963791
                36763529
                d57fda3a-532e-44e2-b03e-1b02aeed9a89
                Copyright © 2023 the Author(s). Published by PNAS.

                This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).

                History
                : 28 September 2022
                : 9 January 2023
                Page count
                Pages: 10, Words: 6703
                Funding
                Funded by: UKRI | Engineering and Physical Sciences Research Council (EPSRC), FundRef 501100000266;
                Award ID: EP/P020720/2
                Award Recipient : Thomas Gaskin Award Recipient : Grigorios A Pavliotis Award Recipient : Mark Girolami
                Funded by: UKRI | Engineering and Physical Sciences Research Council (EPSRC), FundRef 501100000266;
                Award ID: EP/P031587/1
                Award Recipient : Thomas Gaskin Award Recipient : Grigorios A Pavliotis Award Recipient : Mark Girolami
                Funded by: UKRI | Engineering and Physical Sciences Research Council (EPSRC), FundRef 501100000266;
                Award ID: EP/T000414/1
                Award Recipient : Thomas Gaskin Award Recipient : Grigorios A Pavliotis Award Recipient : Mark Girolami
                Funded by: UKRI | Engineering and Physical Sciences Research Council (EPSRC), FundRef 501100000266;
                Award ID: EP/R018413/2
                Award Recipient : Thomas Gaskin Award Recipient : Grigorios A Pavliotis Award Recipient : Mark Girolami
                Funded by: UKRI | Engineering and Physical Sciences Research Council (EPSRC), FundRef 501100000266;
                Award ID: EP/P020720/2
                Award Recipient : Thomas Gaskin Award Recipient : Grigorios A Pavliotis Award Recipient : Mark Girolami
                Funded by: UKRI | Engineering and Physical Sciences Research Council (EPSRC), FundRef 501100000266;
                Award ID: EP/R034710/1
                Award Recipient : Thomas Gaskin Award Recipient : Grigorios A Pavliotis Award Recipient : Mark Girolami
                Funded by: UKRI | Engineering and Physical Sciences Research Council (EPSRC), FundRef 501100000266;
                Award ID: EP/R004889/1
                Award Recipient : Thomas Gaskin Award Recipient : Grigorios A Pavliotis Award Recipient : Mark Girolami
                Categories
                research-article, Research Article
                app-math, Applied Mathematics
                404
                Physical Sciences
                Applied Mathematics

                multiagent systems,neural differential equations,model calibration,parameter density estimation

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