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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: The volume of healthy red blood cells is optimal for advective oxygen transport in arterioles.

    Amoudruz, Lucas / Economides, Athena / Koumoutsakos, Petros

    Biophysical journal

    2024  

    Abstract: Red blood cells (RBCs) are vital for transporting oxygen from the lungs to the body's tissues through the intricate circulatory system. They achieve this by binding and releasing oxygen molecules to the abundant hemoglobin within their cytosol. The ... ...

    Abstract Red blood cells (RBCs) are vital for transporting oxygen from the lungs to the body's tissues through the intricate circulatory system. They achieve this by binding and releasing oxygen molecules to the abundant hemoglobin within their cytosol. The volume of RBCs affects the amount of oxygen they can carry, yet whether this volume is optimal for transporting oxygen through the circulatory system remains an open question. This study explores, through high-fidelity numerical simulations, the impact of RBC volume on advective oxygen transport efficiency through arterioles, which form the area of greatest flow resistance in the circulatory system. The results show that, strikingly, RBCs with volumes similar to those found in vivo are most efficient to transport oxygen through arterioles. The flow resistance is related to the cell-free layer thickness, which is influenced by the shape and the motion of the RBCs: at low volumes, RBCs deform and fold, while at high volumes, RBCs collide and follow more diffuse trajectories. In contrast, RBCs with a healthy volume maximize the cell-free layer thickness, resulting in a more efficient advective transport of oxygen.
    Language English
    Publishing date 2024-04-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2024.04.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Scientific multi-agent reinforcement learning for wall-models of turbulent flows.

    Bae, H Jane / Koumoutsakos, Petros

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 1443

    Abstract: The predictive capabilities of turbulent flow simulations, critical for aerodynamic design and weather prediction, hinge on the choice of turbulence models. The abundance of data from experiments and simulations and the advent of machine learning have ... ...

    Abstract The predictive capabilities of turbulent flow simulations, critical for aerodynamic design and weather prediction, hinge on the choice of turbulence models. The abundance of data from experiments and simulations and the advent of machine learning have provided a boost to turbulence modeling efforts. However, simulations of turbulent flows remain hindered by the inability of heuristics and supervised learning to model the near-wall dynamics. We address this challenge by introducing scientific multi-agent reinforcement learning (SciMARL) for the discovery of wall models for large-eddy simulations (LES). In SciMARL, discretization points act also as cooperating agents that learn to supply the LES closure model. The agents self-learn using limited data and generalize to extreme Reynolds numbers and previously unseen geometries. The present simulations reduce by several orders of magnitude the computational cost over fully-resolved simulations while reproducing key flow quantities. We believe that SciMARL creates unprecedented capabilities for the simulation of turbulent flows.
    Language English
    Publishing date 2022-03-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-28957-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Learning from Predictions

    Vlachas, Pantelis R. / Koumoutsakos, Petros

    Fusing Training and Autoregressive Inference for Long-Term Spatiotemporal Forecasts

    2023  

    Abstract: Recurrent Neural Networks (RNNs) have become an integral part of modeling and forecasting frameworks in areas like natural language processing and high-dimensional dynamical systems such as turbulent fluid flows. To improve the accuracy of predictions, ... ...

    Abstract Recurrent Neural Networks (RNNs) have become an integral part of modeling and forecasting frameworks in areas like natural language processing and high-dimensional dynamical systems such as turbulent fluid flows. To improve the accuracy of predictions, RNNs are trained using the Backpropagation Through Time (BPTT) method to minimize prediction loss. During testing, RNNs are often used in autoregressive scenarios where the output of the network is fed back into the input. However, this can lead to the exposure bias effect, as the network was trained to receive ground-truth data instead of its own predictions. This mismatch between training and testing is compounded when the state distributions are different, and the train and test losses are measured. To address this, previous studies have proposed solutions for language processing networks with probabilistic predictions. Building on these advances, we propose the Scheduled Autoregressive BPTT (BPTT-SA) algorithm for predicting complex systems. Our results show that BPTT-SA effectively reduces iterative error propagation in Convolutional RNNs and Convolutional Autoencoder RNNs, and demonstrate its capabilities in long-term prediction of high-dimensional fluid flows.

    Comment: 18 pages
    Keywords Computer Science - Machine Learning ; Nonlinear Sciences - Chaotic Dynamics ; Physics - Computational Physics ; Physics - Fluid Dynamics
    Subject code 006
    Publishing date 2023-02-21
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: The stress-free state of human erythrocytes: Data-driven inference of a transferable RBC model.

    Amoudruz, Lucas / Economides, Athena / Arampatzis, Georgios / Koumoutsakos, Petros

    Biophysical journal

    2023  Volume 122, Issue 8, Page(s) 1517–1525

    Abstract: The stress-free state (SFS) of red blood cells (RBCs) is a fundamental reference configuration for the calibration of computational models, yet it remains unknown. Current experimental methods cannot measure the SFS of cells without affecting their ... ...

    Abstract The stress-free state (SFS) of red blood cells (RBCs) is a fundamental reference configuration for the calibration of computational models, yet it remains unknown. Current experimental methods cannot measure the SFS of cells without affecting their mechanical properties, whereas computational postulates are the subject of controversial discussions. Here, we introduce data-driven estimates of the SFS shape and the visco-elastic properties of RBCs. We employ data from single-cell experiments that include measurements of the equilibrium shape of stretched cells and relaxation times of initially stretched RBCs. A hierarchical Bayesian model accounts for these experimental and data heterogeneities. We quantify, for the first time, the SFS of RBCs and use it to introduce a transferable RBC (t-RBC) model. The effectiveness of the proposed model is shown on predictions of unseen experimental conditions during the inference, including the critical stress of transitions between tumbling and tank-treading cells in shear flow. Our findings demonstrate that the proposed t-RBC model provides predictions of blood flows with unprecedented accuracy and quantified uncertainties.
    MeSH term(s) Humans ; Bayes Theorem ; Computer Simulation ; Erythrocytes/physiology ; Viscosity
    Language English
    Publishing date 2023-03-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2023.03.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. 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
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  7. 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
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  8. Book ; Online: Interpretable reduced-order modeling with time-scale separation

    Kaltenbach, Sebastian / Koutsourelakis, Phaedon-Stelios / Koumoutsakos, Petros

    2023  

    Abstract: Partial Differential Equations (PDEs) with high dimensionality are commonly encountered in computational physics and engineering. However, finding solutions for these PDEs can be computationally expensive, making model-order reduction crucial. We propose ...

    Abstract Partial Differential Equations (PDEs) with high dimensionality are commonly encountered in computational physics and engineering. However, finding solutions for these PDEs can be computationally expensive, making model-order reduction crucial. We propose such a data-driven scheme that automates the identification of the time-scales involved and can produce stable predictions forward in time as well as under different initial conditions not included in the training data. To this end, we combine a non-linear autoencoder architecture with a time-continuous model for the latent dynamics in the complex space. It readily allows for the inclusion of sparse and irregularly sampled training data. The learned, latent dynamics are interpretable and reveal the different temporal scales involved. We show that this data-driven scheme can automatically learn the independent processes that decompose a system of linear ODEs along the eigenvectors of the system's matrix. Apart from this, we demonstrate the applicability of the proposed framework in a hidden Markov Model and the (discretized) Kuramoto-Shivashinsky (KS) equation. Additionally, we propose a probabilistic version, which captures predictive uncertainties and further improves upon the results of the deterministic framework.
    Keywords Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Numerical Analysis
    Subject code 006
    Publishing date 2023-03-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Book ; Online: The volume of healthy red blood cells maximizes oxygen transport

    Amoudruz, Lucas / Economides, Athena / Koumoutsakos, Petros

    2023  

    Abstract: Red blood cells (RBCs) play a crucial role in oxygen transport in living organisms as the vast majority of oxygen in the blood is bound to the hemoglobin molecules in their cytosol. Healthy RBCs have a biconcave shape and a flexible membrane enabling ... ...

    Abstract Red blood cells (RBCs) play a crucial role in oxygen transport in living organisms as the vast majority of oxygen in the blood is bound to the hemoglobin molecules in their cytosol. Healthy RBCs have a biconcave shape and a flexible membrane enabling them to undergo substantial reversible elastic deformation as they traverse narrow capillaries during microcirculation. This RBC deformability is critical for efficient circulation while the unique biconcave shape of healthy RBCs is attributed to their specific volume, which affects the amount of oxygen they can carry. However, despite extensive research, the underlying mechanism that determines the optimal RBC volume remains unknown. This paper examines the impact of RBC volume on the efficiency of oxygen transport from a fluid dynamics standpoint. Our investigation reveals that RBCs with volumes similar to those observed in vivo demonstrate superior oxygen transport efficiency in circular tubes similar to arterioles, which represent areas of the circulatory system with the highest flow resistance. Furthermore, we identify mechanisms that impair oxygen transport when the RBC volume deviates from the optimal value. While healthy RBCs produce a maximum cell-free layer thickness that affects flow dissipation, smaller RBC volumes result in greater deformations and thus dissipate more energy. Strikingly, the flow resistance is minimized at the reduced volume of healthy RBCs. Our study highlights that the volume of healthy RBCs maximizes oxygen transport efficiency and may offer insight into developing targeted treatments for circulatory disorders.
    Keywords Physics - Biological Physics ; Condensed Matter - Soft Condensed Matter
    Subject code 612
    Publishing date 2023-04-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Discovering Individual Rewards in Collective Behavior through Inverse Multi-Agent Reinforcement Learning

    Waelchli, Daniel / Weber, Pascal / Koumoutsakos, Petros

    2023  

    Abstract: The discovery of individual objectives in collective behavior of complex dynamical systems such as fish schools and bacteria colonies is a long-standing challenge. Inverse reinforcement learning is a potent approach for addressing this challenge but its ... ...

    Abstract The discovery of individual objectives in collective behavior of complex dynamical systems such as fish schools and bacteria colonies is a long-standing challenge. Inverse reinforcement learning is a potent approach for addressing this challenge but its applicability to dynamical systems, involving continuous state-action spaces and multiple interacting agents, has been limited. In this study, we tackle this challenge by introducing an off-policy inverse multi-agent reinforcement learning algorithm (IMARL). Our approach combines the ReF-ER techniques with guided cost learning. By leveraging demonstrations, our algorithm automatically uncovers the reward function and learns an effective policy for the agents. Through extensive experimentation, we demonstrate that the proposed policy captures the behavior observed in the provided data, and achieves promising results across problem domains including single agent models in the OpenAI gym and multi-agent models of schooling behavior. The present study shows that the proposed IMARL algorithm is a significant step towards understanding collective dynamics from the perspective of its constituents, and showcases its value as a tool for studying complex physical systems exhibiting collective behaviour.
    Keywords Computer Science - Machine Learning ; Computer Science - Artificial Intelligence ; Computer Science - Multiagent Systems
    Subject code 006
    Publishing date 2023-05-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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