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Thanks to their universal approximation properties and new efficient training strategies, Deep Neural Networks are becoming a valuable tool for the approximation of mathematical operators. In the present work, we introduce Mesh-Informed Neural Networks (MINNs), a class of architectures specifically tailored to handle mesh based functional data, and thus of particular interest for reduced order modeling of parametrized Partial Differential Equations (PDEs). The driving idea behind MINNs is to embed hidden layers into discrete functional spaces of increasing complexity, obtained through a sequence of meshes defined over the underlying spatial domain. The approach leads to a natural pruning strategy which enables the design of sparse architectures that are able to learn general nonlinear operators. We assess this strategy through an extensive set of numerical experiments, ranging from nonlocal operators to nonlinear diffusion PDEs, where MINNs are compared against more traditional architectures, such as classical fully connected Deep Neural Networks, but also more recent ones, such as DeepONets and Fourier Neural Operators. Our results show that MINNs can handle functional data defined on general domains of any shape, while ensuring reduced training times, lower computational costs, and better generalization capabilities, thus making MINNs very well-suited for demanding applications such as Reduced Order Modeling and Uncertainty Quantification for PDEs.

In this paper we consider the generalized inverse iteration for computing ground states of the Gross-Pitaevskii eigenvector problem (GPE). For that we prove explicit linear convergence rates that depend on the maximum eigenvalue in magnitude of a weighted linear eigenvalue problem. Furthermore, we show that this eigenvalue can be bounded by the first spectral gap of a linearized Gross-Pitaevskii operator, recovering the same rates as for linear eigenvector problems. With this we establish the first local convergence result for the basic inverse iteration for the GPE without damping. We also show how our findings directly generalize to extended inverse iterations, such as the Gradient Flow Discrete Normalized (GFDN) proposed in [W. Bao, Q. Du, SIAM J. Sci. Comput., 25 (2004)] or the damped inverse iteration suggested in [P. Henning, D. Peterseim, SIAM J. Numer. Anal., 53 (2020)]. Our analysis also reveals why the inverse iteration for the GPE does not react favourably to spectral shifts. This empirical observation can now be explained with a blow-up of a weighting function that crucially contributes to the convergence rates. Our findings are illustrated by numerical experiments.

The purpose of this work is to present an improved energy conservation method for hyperelastodynamic contact problems based on specific normal compliance conditions. In order to determine this Improved Normal Compliance (INC) law, we use a Moreau--Yosida $\alpha$-regularization to approximate the unilateral contact law. Then, based on the work of Hauret--LeTallec \cite{hauret2006energy}, we propose in the discrete framework a specific approach allowing to respect the energy conservation of the system in adequacy with the continuous case. This strategy (INC) is characterized by a conserving behavior for frictionless impacts and admissible dissipation for friction phenomena while limiting penetration. Then, we detail the numerical treatment within the framework of the semi-smooth Newton method and primal-dual active set strategy for the normal compliance conditions with friction. We finally provide some numerical experiments to bring into light the energy conservation and the efficiency of the INC method by comparing with different classical methods from the literature throught representative contact problems.

In this paper we discuss potentially practical ways to produce expander graphs with good spectral properties and a compact description. We focus on several classes of uniform and bipartite expander graphs defined as random Schreier graphs of the general linear group over the finite field of size two. We perform numerical experiments and show that such constructions produce spectral expanders that can be useful for practical applications. To find a theoretical explanation of the observed experimental results, we used the method of moments to prove upper bounds for the expected second largest eigenvalue of the random Schreier graphs used in our constructions. We focus on bounds for which it is difficult to study the asymptotic behaviour but it is possible to compute non-trivial conclusions for relatively small graphs with parameters from our numerical experiments (e.g., with less than 2^200 vertices and degree at least logarithmic in the number of vertices).

Recombination is a fundamental evolutionary force, but it is difficult to quantify because the effect of a recombination event on patterns of variation in a sample of genetic data can be hard to discern. Estimators for the recombination rate, which are usually based on the idea of integrating over the unobserved possible evolutionary histories of a sample, can therefore be noisy. Here we consider a related question: how would an estimator behave if the evolutionary history actually was observed? This would offer an upper bound on the performance of estimators used in practice. In this paper we derive an expression for the maximum likelihood estimator for the recombination rate based on a continuously observed, multi-locus, Wright--Fisher diffusion of haplotype frequencies, complementing existing work for an estimator of selection. We show that, contrary to selection, the estimator has unusual properties because the observed information matrix can explode in finite time whereupon the recombination parameter is learned without error. We also show that the recombination estimator is robust to the presence of selection in the sense that incorporating selection into the model leaves the estimator unchanged. We study the properties of the estimator by simulation and show that its distribution can be quite sensitive to the underlying mutation rates.

Inverse rendering methods that account for global illumination are becoming more popular, but current methods require evaluating and automatically differentiating millions of path integrals by tracing multiple light bounces, which remains expensive and prone to noise. Instead, this paper proposes a radiometric prior as a simple alternative to building complete path integrals in a traditional differentiable path tracer, while still correctly accounting for global illumination. Inspired by the Neural Radiosity technique, we use a neural network as a radiance function, and we introduce a prior consisting of the norm of the residual of the rendering equation in the inverse rendering loss. We train our radiance network and optimize scene parameters simultaneously using a loss consisting of both a photometric term between renderings and the multi-view input images, and our radiometric prior (the residual term). This residual term enforces a physical constraint on the optimization that ensures that the radiance field accounts for global illumination. We compare our method to a vanilla differentiable path tracer, and more advanced techniques such as Path Replay Backpropagation. Despite the simplicity of our approach, we can recover scene parameters with comparable and in some cases better quality, at considerably lower computation times.

Empirical likelihood enables a nonparametric, likelihood-driven style of inference without restrictive assumptions routinely made in parametric models. We develop a framework for applying empirical likelihood to the analysis of experimental designs, addressing issues that arise from blocking and multiple hypothesis testing. In addition to popular designs such as balanced incomplete block designs, our approach allows for highly unbalanced, incomplete block designs. We derive an asymptotic multivariate chi-square distribution for a set of empirical likelihood test statistics and propose two single-step multiple testing procedures: asymptotic Monte Carlo and nonparametric bootstrap. Both procedures asymptotically control the generalised family-wise error rate and efficiently construct simultaneous confidence intervals for comparisons of interest without explicitly considering the underlying covariance structure. A simulation study demonstrates that the performance of the procedures is robust to violations of standard assumptions of linear mixed models. We also present an application to experiments on a pesticide.

This article introduces new multiplicative updates for nonnegative matrix factorization with the $\beta$-divergence and sparse regularization of one of the two factors (say, the activation matrix). It is well known that the norm of the other factor (the dictionary matrix) needs to be controlled in order to avoid an ill-posed formulation. Standard practice consists in constraining the columns of the dictionary to have unit norm, which leads to a nontrivial optimization problem. Our approach leverages a reparametrization of the original problem into the optimization of an equivalent scale-invariant objective function. From there, we derive block-descent majorization-minimization algorithms that result in simple multiplicative updates for either $\ell_{1}$-regularization or the more "aggressive" log-regularization. In contrast with other state-of-the-art methods, our algorithms are universal in the sense that they can be applied to any $\beta$-divergence (i.e., any value of $\beta$) and that they come with convergence guarantees. We report numerical comparisons with existing heuristic and Lagrangian methods using various datasets: face images, an audio spectrogram, hyperspectral data, and song play counts. We show that our methods obtain solutions of similar quality at convergence (similar objective values) but with significantly reduced CPU times.

Algorithmic self-assembly occurs when disorganized components autonomously combine to form structures and, by their design and the dynamics of the system, are forced to follow the execution of algorithms. Motivated by applications in DNA-nanotechnology, investigations in algorithmic tile-based self-assembly have blossomed into a mature theory with research leveraging tools from computability theory, complexity theory, information theory, and graph theory to develop a wide range of models and show that many are computationally universal, while also exposing powers and limitations of each. Beyond computational universality, the abstract Tile Assembly Model (aTAM) was shown to be intrinsically universal (IU), a strong notion of completeness where a single tile set is capable of simulating all systems within the model; however, this result required non-deterministic tile attachments. This was later confirmed necessary when it was shown that the class of directed aTAM systems is not IU. Building on these results to further investigate the impacts of other dynamics, Hader et al. examined several tile-assembly models which varied across (1) the numbers of dimensions used, (2) restrictions based on diffusion of tiles through space, and (3) whether each system is directed, and showed which models are IU. Such results have shed much light on the roles of various aspects of the dynamics of tile-assembly and their effects on the intrinsic universality of each model. Here we provide direct comparisons of the various models by considering intrinsic simulations between models. We show that in some cases one model is more powerful than another, and in others, pairs of models have mutually exclusive capabilities. This comparison helps to expose the impacts of these three important aspects and further helps define a hierarchy of tile-assembly models.

High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.