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1. Data assimilation of synthetic data as a novel strategy for predicting disease progression in alopecia areata

   https://doi.org/10.1093/imammb/dqab008  

   Cogan, NG; Bao, Feng; Paus, Ralf; Dobreva, Atanaska (June 2021, Mathematical Medicine and Biology: A Journal of the IMA)

   null (Ed.)

   Abstract The goal of patient-specific treatment of diseases requires a connection between clinical observations with models that are able to accurately predict the disease progression. Even when realistic models are available, it is very difficult to parameterize them and often parameter estimates that are made using early time course data prove to be highly inaccurate. Inaccuracies can cause different predictions, especially when the progression depends sensitively on the parameters. In this study, we apply a Bayesian data assimilation method, where the data are incorporated sequentially, to a model of the autoimmune disease alopecia areata that is characterized by distinct spatial patterns of hair loss. Using synthetic data as simulated clinical observations, we show that our method is relatively robust with respect to variations in parameter estimates. Moreover, we compare convergence rates for parameters with different sensitivities, varying observational times and varying levels of noise. We find that this method works better for sparse observations, sensitive parameters and noisy observations. Taken together, we find that our data assimilation, in conjunction with our biologically inspired model, provides directions for individualized diagnosis and treatments. 

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2. Recovering Missing Component Dependence for System Reliability Prediction via Synergy Between Physics and Data

   https://doi.org/10.1115/1.4052624  

   Li, Huiru; Du, Xiaoping (April 2022, Journal of Mechanical Design)

   Abstract Predicting system reliability is often a core task in systems design. System reliability depends on component reliability and dependence of components. Component reliability can be predicted with a physics-based approach if the associated physical models are available. If the models do not exist, component reliability may be estimated from data. When both types of components coexist, their dependence is often unknown, and therefore, the component states are assumed independent by the traditional method, which can result in a large error. This study proposes a new system reliability method to recover the missing component dependence, thereby leading to a more accurate estimate of the joint probability density function (PDF) of all the component states. The method works for series systems whose load is shared by its components that may fail due to excessive loading. For components without physical models available, the load data are recorded upon failure, and equivalent physical models are created; the model parameters are estimated by the proposed Bayesian approach. Then models of all component states become available, and the dependence of component states, as well as their joint PDF, can be estimated. Four examples are used to evaluate the proposed method, and the results indicate that the method can produce more accurate predictions of system reliability than the traditional method that assumes independent component states. 

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3. A Bayesian Approach to Recovering Missing Component Dependence for System Reliability Prediction via Synergy Between Physics and Data

   https://doi.org/10.1115/DETC2021-67958  

   Li, Huiru; Du, Xiaoping (August 2021, Proceedings of the ASME 2021 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference)

   Abstract Predicting system reliability is often a core task in systems design. System reliability depends on component reliability and dependence of components. Component reliability can be predicted with a physics-based approach if the associated physical models are available. If the models do not exist, component reliability may be estimated from data. When both types of components coexist, their dependence is often unknown, and the component states are therefore assumed independent by the traditional method, which can result in a large error. This work proposes a new system reliability method to recover the missing component dependence, thereby leading to a more accurate estimate of the joint probability density (PDF) of all the component states. The method works for series systems whose load is shared by its components that may fail due to excessive loading. For components without physical models available, the load data are recorded upon failure, and equivalent physical models are created; the model parameters are estimated by the proposed Bayesian approach. Then models of all component states become available, and the dependence of component states, as well as their joint PDF, can be estimated. Four examples are used to evaluate the proposed method, and the results indicate that the proposed method can produce more accurate predictions of system reliability than the traditional method that assumes independent component states. 

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4. Ensemble inference of unobserved infections in networks using partial observations

   https://doi.org/10.1371/journal.pcbi.1011355  

   Zhang, Renquan; Tai, Jilei; Pei, Sen (August 2023, PLOS Computational Biology)

   Fu, Feng (Ed.)

   Undetected infections fuel the dissemination of many infectious agents. However, identification of unobserved infectious individuals remains challenging due to limited observations of infections and imperfect knowledge of key transmission parameters. Here, we use an ensemble Bayesian inference method to infer unobserved infections using partial observations. The ensemble inference method can represent uncertainty in model parameters and update model states using all ensemble members collectively. We perform extensive experiments in both model-generated and real-world networks in which individuals have differential but unknown transmission rates. The ensemble method outperforms several alternative approaches for a variety of network structures and observation rates, despite that the model is mis-specified. Additionally, the computational complexity of this algorithm scales almost linearly with the number of nodes in the network and the number of observations, respectively, exhibiting the potential to apply to large-scale networks. The inference method may support decision-making under uncertainty and be adapted for use for other dynamical models in networks. 

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5. Detecting disturbances in network-coupled dynamical systems with machine learning

   https://doi.org/10.1063/5.0169237  

   Skardal, Per Sebastian; Restrepo, Juan G (October 2023, Chaos: An Interdisciplinary Journal of Nonlinear Science)

   Identifying disturbances in network-coupled dynamical systems without knowledge of the disturbances or underlying dynamics is a problem with a wide range of applications. For example, one might want to know which nodes in the network are being disturbed and identify the type of disturbance. Here, we present a model-free method based on machine learning to identify such unknown disturbances based only on prior observations of the system when forced by a known training function. We find that this method is able to identify the locations and properties of many different types of unknown disturbances using a variety of known forcing functions. We illustrate our results with both linear and nonlinear disturbances using food web and neuronal activity models. Finally, we discuss how to scale our method to large networks. 

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