We present a physics-informed neural network (PINN) approach for the discovery of slow invariant manifolds (SIMs), for the most general class of fast/slow dynamical systems of ODEs. In contrast to other machine learning (ML) approaches that construct reduced order black box surrogate models using simple regression, and/or require a priori knowledge of the fast and slow variables, our approach, simultaneously decomposes the vector field into fast and slow components and provides a functional of the underlying SIM in a closed form. The decomposition is achieved by finding a transformation of the state variables to the fast and slow ones, which enables the derivation of an explicit, in terms of fast variables, SIM functional. The latter is obtained by solving a PDE corresponding to the invariance equation within the Geometric Singular Perturbation Theory (GSPT) using a single-layer feedforward neural network with symbolic differentiation. The performance of the proposed physics-informed ML framework is assessed via three benchmark problems: the Michaelis-Menten, the target mediated drug disposition (TMDD) reaction model and a fully competitive substrate-inhibitor(fCSI) mechanism. We also provide a comparison with other GPST methods, namely the quasi steady state approximation (QSSA), the partial equilibrium approximation (PEA) and CSP with one and two iterations. We show that the proposed PINN scheme provides SIM approximations, of equivalent or even higher accuracy, than those provided by QSSA, PEA and CSP, especially close to the boundaries of the underlying SIMs.
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Physics-informed neural networks (PINN) is a extremely powerful paradigm used to solve equations encountered in scientific computing applications. An important part of the procedure is the minimization of the equation residual which includes, when the equation is time-dependent, a time sampling. It was argued in the literature that the sampling need not be uniform but should overweight initial time instants, but no rigorous explanation was provided for these choice. In this paper we take some prototypical examples and, under standard hypothesis concerning the neural network convergence, we show that the optimal time sampling follows a truncated exponential distribution. In particular we explain when the time sampling is best to be uniform and when it should not be. The findings are illustrated with numerical examples on linear equation, Burgers' equation and the Lorenz system.
Physics-Informed Neural Networks (PINNs) have emerged as a highly active research topic across multiple disciplines in science and engineering, including computational geomechanics. PINNs offer a promising approach in different applications where faster, near real-time or real-time numerical prediction is required. Examples of such areas in geomechanics include geotechnical design optimization, digital twins of geo-structures and stability prediction of monitored slopes. But there remain challenges in training of PINNs, especially for problems with high spatial and temporal complexity. In this paper, we study how the training of PINNs can be improved by using an idealized poroelasticity problem as a demonstration example. A curriculum training strategy is employed where the PINN model is trained gradually by dividing the training data into intervals along the temporal dimension. We find that the PINN model with curriculum training takes nearly half the time required for training compared to conventional training over the whole solution domain. For the particular example here, the quality of the predicted solution was found to be good in both training approaches, but it is anticipated that the curriculum training approach has the potential to offer a better prediction capability for more complex problems, a subject for further research.
Domain decomposition provides an effective way to tackle the dilemma of physics-informed neural networks (PINN) which struggle to accurately and efficiently solve partial differential equations (PDEs) in the whole domain, but the lack of efficient tools for dealing with the interfaces between two adjacent sub-domains heavily hinders the training effects, even leads to the discontinuity of the learned solutions. In this paper, we propose a symmetry group based domain decomposition strategy to enhance the PINN for solving the forward and inverse problems of the PDEs possessing a Lie symmetry group. Specifically, for the forward problem, we first deploy the symmetry group to generate the dividing-lines having known solution information which can be adjusted flexibly and are used to divide the whole training domain into a finite number of non-overlapping sub-domains, then utilize the PINN and the symmetry-enhanced PINN methods to learn the solutions in each sub-domain and finally stitch them to the overall solution of PDEs. For the inverse problem, we first utilize the symmetry group acting on the data of the initial and boundary conditions to generate labeled data in the interior domain of PDEs and then find the undetermined parameters as well as the solution by only training the neural networks in a sub-domain. Consequently, the proposed method can predict high-accuracy solutions of PDEs which are failed by the vanilla PINN in the whole domain and the extended physics-informed neural network in the same sub-domains. Numerical results of the Korteweg-de Vries equation with a translation symmetry and the nonlinear viscous fluid equation with a scaling symmetry show that the accuracies of the learned solutions are improved largely.
Advanced Krylov subspace methods are investigated for the solution of large sparse linear systems arising from stiff adjoint-based aerodynamic shape optimization problems. A special attention is paid to the flexible inner-outer GMRES strategy combined with most relevant preconditioning and deflation techniques. The choice of this specific class of Krylov solvers for challenging problems is based on its outstanding convergence properties. Typically in our implementation the efficiency of the preconditioner is enhanced with a domain decomposition method with overlapping. However, maintaining the performance of the preconditioner may be challenging since scalability and efficiency of a preconditioning technique are properties often antagonistic to each other. In this paper we demonstrate how flexible inner-outer Krylov methods are able to overcome this critical issue. A numerical study is performed considering either a Finite Volume (FV), or a high-order Discontinuous Galerkin (DG) discretization which affect the arithmetic intensity and memory-bandwith of the algebraic operations. We consider test cases of transonic turbulent flows with RANS modelling over the two-dimensional supercritical OAT15A airfoil and the three-dimensional ONERA M6 wing. Benefits in terms of robustness and convergence compared to standard GMRES solvers are obtained. Strong scalability analysis shows satisfactory results. Based on these representative problems a discussion of the recommended numerical practices is proposed.
The main challenge of large-scale numerical simulation of radiation transport is the high memory and computation time requirements of discretization methods for kinetic equations. In this work, we derive and investigate a neural network-based approximation to the entropy closure method to accurately compute the solution of the multi-dimensional moment system with a low memory footprint and competitive computational time. We extend methods developed for the standard entropy-based closure to the context of regularized entropy-based closures. The main idea is to interpret structure-preserving neural network approximations of the regularized entropy closure as a two-stage approximation to the original entropy closure. We conduct a numerical analysis of this approximation and investigate optimal parameter choices. Our numerical experiments demonstrate that the method has a much lower memory footprint than traditional methods with competitive computation times and simulation accuracy. The code and all trained networks are provided on GitHub //github.com/ScSteffen/neuralEntropyClosures and //github.com/CSMMLab/KiT-RT.
Scopus and the Web of Science have been the foundation for research in the science of science even though these traditional databases systematically underrepresent certain disciplines and world regions. In response, new inclusive databases, notably OpenAlex, have emerged. While many studies have begun using OpenAlex as a data source, few critically assess its limitations. This study, conducted in collaboration with the OpenAlex team, addresses this gap by comparing OpenAlex to Scopus across a number of dimensions. The analysis concludes that OpenAlex is a superset of Scopus and can be a reliable alternative for some analyses, particularly at the country level. Despite this, issues of metadata accuracy and completeness show that additional research is needed to fully comprehend and address OpenAlex's limitations. Doing so will be necessary to confidently use OpenAlex across a wider set of analyses, including those that are not at all possible with more constrained databases.
Twin nodes in a static network capture the idea of being substitutes for each other for maintaining paths of the same length anywhere in the network. In dynamic networks, we model twin nodes over a time-bounded interval, noted $(\Delta,d)$-twins, as follows. A periodic undirected time-varying graph $\mathcal G=(G_t)_{t\in\mathbb N}$ of period $p$ is an infinite sequence of static graphs where $G_t=G_{t+p}$ for every $t\in\mathbb N$. For $\Delta$ and $d$ two integers, two distinct nodes $u$ and $v$ in $\mathcal G$ are $(\Delta,d)$-twins if, starting at some instant, the outside neighbourhoods of $u$ and $v$ has non-empty intersection and differ by at most $d$ elements for $\Delta$ consecutive instants. In particular when $d=0$, $u$ and $v$ can act during the $\Delta$ instants as substitutes for each other in order to maintain journeys of the same length in time-varying graph $\mathcal G$. We propose a distributed deterministic algorithm enabling each node to enumerate its $(\Delta,d)$-twins in $2p$ rounds, using messages of size $O(\delta_\mathcal G\log n)$, where $n$ is the total number of nodes and $\delta_\mathcal G$ is the maximum degree of the graphs $G_t$'s. Moreover, using randomized techniques borrowed from distributed hash function sampling, we reduce the message size down to $O(\log n)$ w.h.p.
Calls to make scientific research more open have gained traction with a range of societal stakeholders. Open Science practices include but are not limited to the early sharing of results via preprints and openly sharing outputs such as data and code to make research more reproducible and extensible. Existing evidence shows that adopting Open Science practices has effects in several domains. In this study, we investigate whether adopting one or more Open Science practices leads to significantly higher citations for an associated publication, which is one form of academic impact. We use a novel dataset known as Open Science Indicators, produced by PLOS and DataSeer, which includes all PLOS publications from 2018 to 2023 as well as a comparison group sampled from the PMC Open Access Subset. In total, we analyze circa 122'000 publications. We calculate publication and author-level citation indicators and use a broad set of control variables to isolate the effect of Open Science Indicators on received citations. We show that Open Science practices are adopted to different degrees across scientific disciplines. We find that the early release of a publication as a preprint correlates with a significant positive citation advantage of about 20.2% on average. We also find that sharing data in an online repository correlates with a smaller yet still positive citation advantage of 4.3% on average. However, we do not find a significant citation advantage for sharing code. Further research is needed on additional or alternative measures of impact beyond citations. Our results are likely to be of interest to researchers, as well as publishers, research funders, and policymakers.
When and why can a neural network be successfully trained? This article provides an overview of optimization algorithms and theory for training neural networks. First, we discuss the issue of gradient explosion/vanishing and the more general issue of undesirable spectrum, and then discuss practical solutions including careful initialization and normalization methods. Second, we review generic optimization methods used in training neural networks, such as SGD, adaptive gradient methods and distributed methods, and theoretical results for these algorithms. Third, we review existing research on the global issues of neural network training, including results on bad local minima, mode connectivity, lottery ticket hypothesis and infinite-width analysis.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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