This work presents a deep learning-based framework for the solution of partial differential equations on complex computational domains described with computer-aided design tools. To account for the underlying distribution of the training data caused by spline-based projections from the reference to the physical domain, a variational neural solver equipped with an importance sampling scheme is developed, such that the loss function based on the discretized energy functional obtained after the weak formulation is modified according to the sample distribution. To tackle multi-patch domains possibly leading to solution discontinuities, the variational neural solver is additionally combined with a domain decomposition approach based on the Discontinuous Galerkin formulation. The proposed neural solver is verified on a toy problem and then applied to a real-world engineering test case, namely that of electric machine simulation. The numerical results show clearly that the neural solver produces physics-conforming solutions of significantly improved accuracy.
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Specifications of complex, large scale, computer software and hardware systems can be radically simplified by using simple maps from input sequences to output values. These "state machine maps" provide an alternative representation of classical Moore type state machines. Composition of state machine maps corresponds to state machine products and can be used to specify essentially any type of interconnection as well as parallel and distributed computation. State machine maps can also specify abstract properties of systems and are significantly more concise and scalable than traditional representations of automata. Examples included here include specifications of producer/consumer software, network distributed consensus, real-time digital circuits, and operating system scheduling. The motivation for this work comes from experience designing and developing operating systems and real-time software where weak methods for understanding and exploring designs is a well known handicap. The methods introduced here are based on ordinary discrete mathematics, primitive recursive functions and deterministic state machines and are intended, initially, to aid the intuition and understanding of the system developers. Staying strictly within the boundaries of classical deterministic state machines anchors the methods to the algebraic structures of automata and semigroups, obviates any need for axiomatic deduction systems, "formal methods", or extensions to the model, and makes the specifications more faithful to engineering practice. While state machine maps are obvious representations of state machines, the techniques introduced here for defining and composing them are novel.
Stochastic partial differential equations (SPDEs) are the mathematical tool of choice for modelling spatiotemporal PDE-dynamics under the influence of randomness. Based on the notion of mild solution of an SPDE, we introduce a novel neural architecture to learn solution operators of PDEs with (possibly stochastic) forcing from partially observed data. The proposed Neural SPDE model provides an extension to two popular classes of physics-inspired architectures. On the one hand, it extends Neural CDEs and variants -- continuous-time analogues of RNNs -- in that it is capable of processing incoming sequential information arriving irregularly in time and observed at arbitrary spatial resolutions. On the other hand, it extends Neural Operators -- generalizations of neural networks to model mappings between spaces of functions -- in that it can parameterize solution operators of SPDEs depending simultaneously on the initial condition and a realization of the driving noise. By performing operations in the spectral domain, we show how a Neural SPDE can be evaluated in two ways, either by calling an ODE solver (emulating a spectral Galerkin scheme), or by solving a fixed point problem. Experiments on various semilinear SPDEs, including the stochastic Navier-Stokes equations, demonstrate how the Neural SPDE model is capable of learning complex spatiotemporal dynamics in a resolution-invariant way, with better accuracy and lighter training data requirements compared to alternative models, and up to 3 orders of magnitude faster than traditional solvers.
We introduce a filtering technique for Discontinuous Galerkin approximations of hyperbolic problems. Following an approach already proposed for the Hamilton-Jacobi equations by other authors, we aim at reducing the spurious oscillations that arise in presence of discontinuities when high order spatial discretizations are employed. This goal is achieved using a filter function that keeps the high order scheme when the solution is regular and switches to a monotone low order approximation if it is not. The method has been implemented in the framework of the $deal.II$ numerical library, whose mesh adaptation capabilities are also used to reduce the region in which the low order approximation is used. A number of numerical experiments demonstrate the potential of the proposed filtering technique.
Molecular dynamics (MD) has long been the \emph{de facto} choice for modeling complex atomistic systems from first principles, and recently deep learning become a popular way to accelerate it. Notwithstanding, preceding approaches depend on intermediate variables such as the potential energy or force fields to update atomic positions, which requires additional computations to perform back-propagation. To waive this requirement, we propose a novel model called ScoreMD by directly estimating the gradient of the log density of molecular conformations. Moreover, we analyze that diffusion processes highly accord with the principle of enhanced sampling in MD simulations, and is therefore a perfect match to our sequential conformation generation task. That is, ScoreMD perturbs the molecular structure with a conditional noise depending on atomic accelerations and employs conformations at previous timeframes as the prior distribution for sampling. Another challenge of modeling such a conformation generation process is that the molecule is kinetic instead of static, which no prior studies strictly consider. To solve this challenge, we introduce a equivariant geometric Transformer as a score function in the diffusion process to calculate the corresponding gradient. It incorporates the directions and velocities of atomic motions via 3D spherical Fourier-Bessel representations. With multiple architectural improvements, we outperforms state-of-the-art baselines on MD17 and isomers of C7O2H10. This research provides new insights into the acceleration of new material and drug discovery.
The scattering and transmission of harmonic acoustic waves at a penetrable material are commonly modelled by a set of Helmholtz equations. This system of partial differential equations can be rewritten into boundary integral equations defined at the surface of the objects and solved with the boundary element method (BEM). High frequencies or geometrical details require a fine surface mesh, which increases the number of degrees of freedom in the weak formulation. Then, matrix compression techniques need to be combined with iterative linear solvers to limit the computational footprint. Moreover, the convergence of the iterative linear solvers often depends on the frequency of the wave field and the objects' characteristic size. Here, the robust PMCHWT formulation is used to solve the acoustic transmission problem. An operator preconditioner based on on-surface radiation conditions (OSRC) is designed that yields frequency-robust convergence characteristics. Computational benchmarks compare the performance of this novel preconditioned formulation with other preconditioners and boundary integral formulations. The OSRC preconditioned PMCHWT formulation effectively simulates large-scale problems of engineering interest, such as focused ultrasound treatment of osteoid osteoma.
Computing a maximum independent set (MaxIS) is a fundamental NP-hard problem in graph theory, which has important applications in a wide spectrum of fields. Since graphs in many applications are changing frequently over time, the problem of maintaining a MaxIS over dynamic graphs has attracted increasing attention over the past few years. Due to the intractability of maintaining an exact MaxIS, this paper aims to develop efficient algorithms that can maintain an approximate MaxIS with an accuracy guarantee theoretically. In particular, we propose a framework that maintains a $(\frac{\Delta}{2} + 1)$-approximate MaxIS over dynamic graphs and prove that it achieves a constant approximation ratio in many real-world networks. To the best of our knowledge, this is the first non-trivial approximability result for the dynamic MaxIS problem. Following the framework, we implement an efficient linear-time dynamic algorithm and a more effective dynamic algorithm with near-linear expected time complexity. Our thorough experiments over real and synthetic graphs demonstrate the effectiveness and efficiency of the proposed algorithms, especially when the graph is highly dynamic.
The presence of noise is an intrinsic problem in acquisition processes for digital images. One way to enhance images is to combine the forward and backward diffusion equations. However, the latter problem is well known to be exponentially unstable with respect to any small perturbations on the final data. In this scenario, the final data can be regarded as a blurred image obtained from the forward process, and that image can be pixelated as a network. Therefore, we study in this work a regularization framework for the backward diffusion equation on graphs. Our aim is to construct a spectral graph-based solution based upon a cut-off projection. Stability and convergence results are provided together with some numerical experiments.
In this paper, we consider the constrained energy minimizing generalized multiscale finite element method (CEM-GMsFEM) with discontinuous Galerkin (DG) coupling for the linear elasticity equations in highly heterogeneous and high contrast media. We will introduce the construction of a DG version of the CEM-GMsFEM, such as auxiliary basis functions and offline basis functions. The DG version of the method offers some advantages such as flexibility in coarse grid construction and sparsity of resulting discrete systems. Moreover, to our best knowledge, this is the first time where the proof of the convergence of the CEM-GMsFEM in the DG form is given. Some numerical examples will be presented to illustrate the performance of the method.
Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use the variational approach to conformation dynamics to discover the slowest dynamical modes of the simulations. This allows the different metastable states of the system to be located and organized hierarchically. The physical descriptors that characterize metastable states are discovered by means of a machine learning method. We show in the cases of two proteins, Chignolin and Bovine Pancreatic Trypsin Inhibitor, how such analysis can be effortlessly performed in a matter of seconds. Another strength of our approach is that it can be applied to the analysis of both unbiased and biased simulations.
The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.
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