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  1. Article ; Online: Solving inverse problems in physics by optimizing a discrete loss: Fast and accurate learning without neural networks.

    Karnakov, Petr / Litvinov, Sergey / Koumoutsakos, Petros

    PNAS nexus

    2024  Volume 3, Issue 1, Page(s) pgae005

    Abstract: In recent years, advances in computing hardware and computational methods have prompted a wealth of activities for solving inverse problems in physics. These problems are often described by systems of partial differential equations (PDEs). The advent of ... ...

    Abstract In recent years, advances in computing hardware and computational methods have prompted a wealth of activities for solving inverse problems in physics. These problems are often described by systems of partial differential equations (PDEs). The advent of machine learning has reinvigorated the interest in solving inverse problems using neural networks (NNs). In these efforts, the solution of the PDEs is expressed as NNs trained through the minimization of a loss function involving the PDE. Here, we show how to accelerate this approach by five orders of magnitude by deploying, instead of NNs, conventional PDE approximations. The framework of optimizing a discrete loss (ODIL) minimizes a cost function for discrete approximations of the PDEs using gradient-based and Newton's methods. The framework relies on grid-based discretizations of PDEs and inherits their accuracy, convergence, and conservation properties. The implementation of the method is facilitated by adopting machine-learning tools for automatic differentiation. We also propose a multigrid technique to accelerate the convergence of gradient-based optimizers. We present applications to PDE-constrained optimization, optical flow, system identification, and data assimilation. We compare ODIL with the popular method of physics-informed neural networks and show that it outperforms it by several orders of magnitude in computational speed while having better accuracy and convergence rates. We evaluate ODIL on inverse problems involving linear and nonlinear PDEs including the Navier-Stokes equations for flow reconstruction problems. ODIL bridges numerical methods and machine learning and presents a powerful tool for solving challenging, inverse problems across scientific domains.
    Language English
    Publishing date 2024-01-11
    Publishing country England
    Document type Journal Article
    ISSN 2752-6542
    ISSN (online) 2752-6542
    DOI 10.1093/pnasnexus/pgae005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Flow reconstruction by multiresolution optimization of a discrete loss with automatic differentiation.

    Karnakov, Petr / Litvinov, Sergey / Koumoutsakos, Petros

    The European physical journal. E, Soft matter

    2023  Volume 46, Issue 7, Page(s) 59

    Abstract: We present a potent computational method for the solution of inverse problems in fluid mechanics. We consider inverse problems formulated in terms of a deterministic loss function that can accommodate data and regularization terms. We introduce a ... ...

    Abstract We present a potent computational method for the solution of inverse problems in fluid mechanics. We consider inverse problems formulated in terms of a deterministic loss function that can accommodate data and regularization terms. We introduce a multigrid decomposition technique that accelerates the convergence of gradient-based methods for optimization problems with parameters on a grid. We incorporate this multigrid technique to the Optimizing a DIscrete Loss (ODIL) framework. The multiresolution ODIL (mODIL) accelerates by an order of magnitude the original formalism and improves the avoidance of local minima. Moreover, mODIL accommodates the use of automatic differentiation for calculating the gradients of the loss function, thus facilitating the implementation of the framework. We demonstrate the capabilities of mODIL on a variety of inverse and flow reconstruction problems: solution reconstruction for the Burgers equation, inferring conductivity from temperature measurements, and inferring the body shape from wake velocity measurements in three dimensions. We also provide a comparative study with the related, popular Physics-Informed Neural Networks (PINNs) method. We demonstrate that mODIL has three to five orders of magnitude lower computational cost than PINNs in benchmark problems including simple PDEs and lid-driven cavity problems. Our results suggest that mODIL is a very potent, fast and consistent method for solving inverse problems in fluid mechanics.
    Language English
    Publishing date 2023-07-24
    Publishing country France
    Document type Journal Article
    ZDB-ID 2004003-9
    ISSN 1292-895X ; 1292-8941
    ISSN (online) 1292-895X
    ISSN 1292-8941
    DOI 10.1140/epje/s10189-023-00313-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Computing foaming flows across scales: From breaking waves to microfluidics.

    Karnakov, Petr / Litvinov, Sergey / Koumoutsakos, Petros

    Science advances

    2022  Volume 8, Issue 5, Page(s) eabm0590

    Abstract: Crashing ocean waves, cappuccino froths, and microfluidic bubble crystals are examples of foamy flows. Foamy flows are critical in numerous natural and industrial processes and remain notoriously difficult to compute as they involve coupled, multiscale ... ...

    Abstract Crashing ocean waves, cappuccino froths, and microfluidic bubble crystals are examples of foamy flows. Foamy flows are critical in numerous natural and industrial processes and remain notoriously difficult to compute as they involve coupled, multiscale physical processes. Computations need to resolve the interactions of the bubbles separated by stable thin liquid films. We present the multilayer volume-of-fluid method (Multi-VOF) that advances the state of the art in simulation capabilities of foamy flows. The method introduces a scheme to handle multiple bubbles that do not coalesce. Multi-VOF is verified and validated with experimental results and complemented with open-source software. We demonstrate capturing of crystalline structures of bubbles in realistic microfluidics devices and foamy flows involving tens of thousands of bubbles in a waterfall. The present technique extends the classical volume-of-fluid methodology and allows for large-scale predictive simulations of flows with multiple interfaces.
    Language English
    Publishing date 2022-02-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abm0590
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Computing foaming flows across scales

    Karnakov, Petr / Litvinov, Sergey / Koumoutsakos, Petros

    from breaking waves to microfluidics

    2021  

    Abstract: Crashing ocean waves, cappuccino froths and microfluidic bubble crystals are examples of foamy flows. Foamy flows are critical in numerous natural and industrial processes and remain notoriously difficult to compute as they involve coupled, multiscale ... ...

    Abstract Crashing ocean waves, cappuccino froths and microfluidic bubble crystals are examples of foamy flows. Foamy flows are critical in numerous natural and industrial processes and remain notoriously difficult to compute as they involve coupled, multiscale physical processes. Computations need to resolve the interactions of the bubbles with the fluid and complex boundaries, while capturing the drainage and rupture of the microscopic liquid films at their interface. We present a novel multilayer simulation framework (Multi-VOF) that advances the state of the art in simulation capabilities of foamy flows. The framework introduces a novel scheme for the distinct handling of multiple neighboring bubbles and a new regularization method that produces sharp interfaces and removes spurious fragments. Multi-VOF is verified and validated with experimental results and complemented with open source, efficient scalable software. We demonstrate capturing of bubble crystalline structures in realistic microfluidics devices and foamy flows involving tens of thousands of bubbles in a waterfall. The present multilayer framework extends the classical volume-of-fluid methodology and allows for unprecedented large scale, predictive simulations of flows with multiple interfaces.

    Comment: 11 pages, 7 figures, supplementary information, software https://github.com/cselab/aphros
    Keywords Physics - Computational Physics ; Computer Science - Computational Engineering ; Finance ; and Science ; Mathematics - Numerical Analysis ; Physics - Fluid Dynamics
    Subject code 532
    Publishing date 2021-03-02
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Data-driven inference of the reproduction number for COVID-19 before and after interventions for 51 European countries.

    Karnakov, Petr / Arampatzis, Georgios / Kičić, Ivica / Wermelinger, Fabian / Wälchli, Daniel / Papadimitriou, Costas / Koumoutsakos, Petros

    Swiss medical weekly

    2020  Volume 150, Page(s) w20313

    Abstract: The reproduction number is broadly considered as a key indicator for the spreading of the COVID-19 pandemic. Its estimated value is a measure of the necessity and, eventually, effectiveness of interventions imposed in various countries. Here we present ... ...

    Abstract The reproduction number is broadly considered as a key indicator for the spreading of the COVID-19 pandemic. Its estimated value is a measure of the necessity and, eventually, effectiveness of interventions imposed in various countries. Here we present an online tool for the data-driven inference and quantification of uncertainties for the reproduction number, as well as the time points of interventions for 51 European countries. The study relied on the Bayesian calibration of the SIR model with data from reported daily infections from these countries. The model fitted the data, for most countries, without individual tuning of parameters. We also compared the results of SIR and SEIR models, which give different estimates of the reproduction number, and provided an analytical relationship between the respective numbers. We deployed a Bayesian inference framework with efficient sampling algorithms, to present a publicly available graphical user interface (https://cse-lab.ethz.ch/coronavirus) that allows the user to assess and compare predictions for pairs of European countries. The results quantified the rate of the disease’s spread before and after interventions, and provided a metric for the effectiveness of non-pharmaceutical interventions in different countries. They also indicated how geographic proximity and the times of interventions affected the progression of the epidemic.
    MeSH term(s) Basic Reproduction Number/statistics & numerical data ; Bayes Theorem ; Betacoronavirus/isolation & purification ; COVID-19 ; Communicable Disease Control/methods ; Communicable Disease Control/statistics & numerical data ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/transmission ; Disease Transmission, Infectious/prevention & control ; Disease Transmission, Infectious/statistics & numerical data ; Epidemiologic Measurements ; Epidemiological Monitoring ; Europe/epidemiology ; Humans ; Pandemics/prevention & control ; Pandemics/statistics & numerical data ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/transmission ; SARS-CoV-2 ; Uncertainty
    Keywords covid19
    Language English
    Publishing date 2020-07-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2036179-8
    ISSN 1424-3997 ; 1424-7860
    ISSN (online) 1424-3997
    ISSN 1424-7860
    DOI 10.4414/smw.2020.20313
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Data-driven inference of the reproduction number for COVID-19 before and after interventions for 51 European countries

    Karnakov, Petr / Arampatzis, Georgios / Kii, Ivica / Wermelinger, Fabian / Wlchli, Daniel / Papadimitriou, Costas / Koumoutsakos, Petros

    Swiss Medical Weekly ; ISSN 1424-3997

    2020  

    Keywords General Medicine ; covid19
    Language English
    Publisher EMH Swiss Medical Publishers, Ltd.
    Publishing country ch
    Document type Article ; Online
    DOI 10.4414/smw.2020.20313
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Optimal allocation of limited test resources for the quantification of COVID-19 infections.

    Chatzimanolakis, Michail / Weber, Pascal / Arampatzis, Georgios / Wälchli, Daniel / Kičić, Ivica / Karnakov, Petr / Papadimitriou, Costas / Koumoutsakos, Petros

    Swiss medical weekly

    2020  Volume 150, Page(s) w20445

    Abstract: The systematic identification of infected individuals is critical for the containment of the COVID-19 pandemic. Currently, the spread of the disease is mostly quantified by the reported numbers of infections, hospitalisations, recoveries and deaths; ... ...

    Abstract The systematic identification of infected individuals is critical for the containment of the COVID-19 pandemic. Currently, the spread of the disease is mostly quantified by the reported numbers of infections, hospitalisations, recoveries and deaths; these quantities inform epidemiology models that provide forecasts for the spread of the epidemic and guide policy making. The veracity of these forecasts depends on the discrepancy between the numbers of reported, and unreported yet infectious, individuals. We combine Bayesian experimental design with an epidemiology model and propose a methodology for the optimal allocation of limited testing resources in space and time, which maximises the information gain for such unreported infections. The proposed approach is applicable at the onset and spread of the epidemic and can forewarn of a possible recurrence of the disease after relaxation of interventions. We examine its application in Switzerland; the open source software is, however, readily adaptable to countries around the world. We find that following the proposed methodology can lead to vastly less uncertain predictions for the spread of the disease, thus improving estimates of the effective reproduction number and the future number of unreported infections. This information can provide timely and systematic guidance for the effective identification of infectious individuals and for decision-making regarding lockdown measures and the distribution of vaccines.
    MeSH term(s) Bayes Theorem ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/transmission ; COVID-19 Testing/methods ; Communicable Disease Control/methods ; Diagnostic Services/supply & distribution ; Epidemiological Monitoring ; Forecasting ; Health Policy ; Humans ; Random Allocation ; Resource Allocation/methods ; SARS-CoV-2 ; Switzerland/epidemiology
    Language English
    Publishing date 2020-12-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2036179-8
    ISSN 1424-3997 ; 1424-7860
    ISSN (online) 1424-3997
    ISSN 1424-7860
    DOI 10.4414/smw.2020.20445
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book ; Online: Individualizing Glioma Radiotherapy Planning by Optimization of a Data and Physics Informed Discrete Loss

    Balcerak, Michal / Ezhov, Ivan / Karnakov, Petr / Litvinov, Sergey / Koumoutsakos, Petros / Weidner, Jonas / Zhang, Ray Zirui / Lowengrub, John S. / Wiestler, Bene / Menze, Bjoern

    2023  

    Abstract: The growth and progression of brain tumors is governed by patient-specific dynamics. Even when the tumor appears well-delineated in medical imaging scans, tumor cells typically already have infiltrated the surrounding brain tissue beyond the visible ... ...

    Abstract The growth and progression of brain tumors is governed by patient-specific dynamics. Even when the tumor appears well-delineated in medical imaging scans, tumor cells typically already have infiltrated the surrounding brain tissue beyond the visible lesion boundaries. Quantifying and understanding these growth dynamics promises to reveal this otherwise hidden spread and is key to individualized therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a standard uniform margin around the visible tumor on imaging scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. Here, we present the framework GliODIL which infers the full spatial distribution of tumor cell concentration from available imaging data based on PDE-constrained optimization. The framework builds on the newly introduced method of Optimizing the Discrete Loss (ODIL), data are assimilated in the solution of the Partial Differential Equations (PDEs) by optimizing a cost function that combines the discrete form of the equations and data as penalty terms. By utilizing consistent and stable discrete approximations of the PDEs, employing a multigrid method, and leveraging automatic differentiation, we achieve computation times suitable for clinical application such as radiotherapy planning. Our method performs parameter estimation in a manner that is consistent with the PDEs. Through a harmonious blend of physics-based constraints and data-driven approaches, GliODIL improves the accuracy of estimating tumor cell distribution and, clinically highly relevant, also predicting tumor recurrences, outperforming all other studied benchmarks.

    Comment: 19 pages, 6 figures. Associated GitHub: https://github.com/m1balcerak/GliODIL
    Keywords Physics - Medical Physics ; Mathematics - Numerical Analysis ; Quantitative Biology - Quantitative Methods
    Subject code 612
    Publishing date 2023-12-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Data driven inference of the reproduction number (R0) for COVID-19 before and after interventions for 51 European countries

    Karnakov, Petr / Arampatzis, Georgios / Kičić, Ivica / Wermelinger, Fabian / Wälchli, Daniel / Papadimitriou, Costas / Koumoutsakos, Petros

    medRxiv

    Abstract: The reproduction number (R0) is broadly considered as a key indicator for the spreading of the COVID-19 pandemic. The estimation of its value with respect to the key threshold of 1.0 is a measure of the need, and eventually effectiveness, of ... ...

    Abstract The reproduction number (R0) is broadly considered as a key indicator for the spreading of the COVID-19 pandemic. The estimation of its value with respect to the key threshold of 1.0 is a measure of the need, and eventually effectiveness, of interventions imposed in various countries. Here we present an online tool for the data driven inference and quantification of uncertainties for R0 as well as the time points of interventions for 51 European countries. The study relies on the Bayesian calibration of the simple and well established SIR model with data from reported daily infections. The model is able to fit the data for most countries without individual tuning of parameters. We deploy an open source Bayesian inference framework and efficient sampling algorithms to present a publicly available GUI (https://www.cse-lab.ethz.ch/coronavirus/) that allows the user to assess custom data and compare predictions for pairs of European countries. The results provide a ranking based on the rate of the disease9s spread suggesting a metric for the effectiveness of social distancing measures. They also serve to demonstrate how geographic proximity and related times of interventions can lead to similarities in the progression of the epidemic.
    Keywords covid19
    Language English
    Publishing date 2020-05-23
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.05.21.20109314
    Database COVID19

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  10. Book ; Online: Korali

    Martin, Sergio M. / Wälchli, Daniel / Arampatzis, Georgios / Economides, Athena E. / Karnakov, Petr / Koumoutsakos, Petros

    Efficient and Scalable Software Framework for Bayesian Uncertainty Quantification and Stochastic Optimization

    2020  

    Abstract: We present Korali, an open-source framework for large-scale Bayesian uncertainty quantification and stochastic optimization. The framework relies on non-intrusive sampling of complex multiphysics models and enables their exploitation for optimization and ...

    Abstract We present Korali, an open-source framework for large-scale Bayesian uncertainty quantification and stochastic optimization. The framework relies on non-intrusive sampling of complex multiphysics models and enables their exploitation for optimization and decision-making. In addition, its distributed sampling engine makes efficient use of massively-parallel architectures while introducing novel fault tolerance and load balancing mechanisms. We demonstrate these features by interfacing Korali with existing high-performance software such as Aphros, Lammps (CPU-based), and Mirheo (GPU-based) and show efficient scaling for up to 512 nodes of the CSCS Piz Daint supercomputer. Finally, we present benchmarks demonstrating that Korali outperforms related state-of-the-art software frameworks.

    Comment: 12 pages, 12 figures
    Keywords Computer Science - Distributed ; Parallel ; and Cluster Computing ; 60-08 ; G.3
    Subject code 006
    Publishing date 2020-05-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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