Architected materials possessing physico-chemical properties adaptable to disparate environmental conditions embody a disruptive new domain of materials science. Fueled by advances in digital design and fabrication, materials shaped into lattice topologies enable a degree of property customization not afforded to bulk materials. A promising venue for inspiration toward their design is in the irregular micro-architectures of nature. However, the immense design variability unlocked by such irregularity is challenging to probe analytically. Here, we propose a new computational approach using graph-based representation for regular and irregular lattice materials. Our method uses differentiable message passing algorithms to calculate mechanical properties, therefore allowing automatic differentiation with surrogate derivatives to adjust both geometric structure and local attributes of individual lattice elements to achieve inversely designed materials with desired properties. We further introduce a graph neural network surrogate model for structural analysis at scale. The methodology is generalizable to any system representable as heterogeneous graphs.
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Permutation tests enable testing statistical hypotheses in situations when the distribution of the test statistic is complicated or not available. In some situations, the test statistic under investigation is multivariate, with the multiple testing problem being an important example. The corresponding multivariate permutation tests are then typically based on a suitableone-dimensional transformation of the vector of partial permutation p-values via so called combining functions. This paper proposes a new approach that utilizes the optimal measure transportation concept. The final single p-value is computed from the empirical center-outward distribution function of the permuted multivariate test statistics. This method avoids computation of the partial p-values and it is easy to be implemented. In addition, it allows to compute and interpret contributions of the components of the multivariate test statistic to the non-conformity score and to the rejection of the null hypothesis. Apart from this method, the measure transportation is applied also to the vector of partial p-values as an alternative to the classical combining functions. Both techniques are compared with the standard approaches using various practical examples in a Monte Carlo study. An application on a functional data set is provided as well.
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.
This work presents a novel global digital image correlation (DIC) method, based on a newly developed convolution finite element (C-FE) approximation. The convolution approximation can rely on the mesh of linear finite elements and enables arbitrarily high order approximations without adding more degrees of freedom. Therefore, the C-FE based DIC can be more accurate than {the} usual FE based DIC by providing highly smooth and accurate displacement and strain results with the same element size. The detailed formulation and implementation of the method have been discussed in this work. The controlling parameters in the method include the polynomial order, patch size, and dilation. A general choice of the parameters and their potential adaptivity have been discussed. The proposed DIC method has been tested by several representative examples, including the DIC challenge 2.0 benchmark problems, with comparison to the usual FE based DIC. C-FE outperformed FE in all the DIC results for the tested examples. This work demonstrates the potential of C-FE and opens a new avenue to enable highly smooth, accurate, and robust DIC analysis for full-field displacement and strain measurements.
We describe a quantum algorithm based on an interior point method for solving a linear program with $n$ inequality constraints on $d$ variables. The algorithm explicitly returns a feasible solution that is $\epsilon$-close to optimal, and runs in time $\sqrt{n}\, \mathrm{poly}(d,\log(n),\log(1/\varepsilon))$ which is sublinear for tall linear programs (i.e., $n \gg d$). Our algorithm speeds up the Newton step in the state-of-the-art interior point method of Lee and Sidford [FOCS '14]. This requires us to efficiently approximate the Hessian and gradient of the barrier function, and these are our main contributions. To approximate the Hessian, we describe a quantum algorithm for the spectral approximation of $A^T A$ for a tall matrix $A \in \mathbb R^{n \times d}$. The algorithm uses leverage score sampling in combination with Grover search, and returns a $\delta$-approximation by making $O(\sqrt{nd}/\delta)$ row queries to $A$. This generalizes an earlier quantum speedup for graph sparsification by Apers and de Wolf [FOCS '20]. To approximate the gradient, we use a recent quantum algorithm for multivariate mean estimation by Cornelissen, Hamoudi and Jerbi [STOC '22]. While a naive implementation introduces a dependence on the condition number of the Hessian, we avoid this by pre-conditioning our random variable using our quantum algorithm for spectral approximation.
Computing equilibrium shapes of crystals (ESC) is a challenging problem in materials science that involves minimizing an orientation-dependent (i.e., anisotropic) surface energy functional subject to a prescribed mass constraint. The highly nonlinear and singular anisotropic terms in the problem make it very challenging from both the analytical and numerical aspects. Especially, when the strength of anisotropy is very strong (i.e., strongly anisotropic cases), the ESC will form some singular, sharp corners even if the surface energy function is smooth. Traditional numerical approaches, such as the $H^{-1}$ gradient flow, are unable to produce true sharp corners due to the necessary addition of a high-order regularization term that penalizes sharp corners and rounds them off. In this paper, we propose a new numerical method based on the Davis-Yin splitting (DYS) optimization algorithm to predict the ESC instead of using gradient flow approaches. We discretize the infinite-dimensional phase-field energy functional in the absence of regularization terms and transform it into a finite-dimensional constraint minimization problem. The resulting optimization problem is solved using the DYS method which automatically guarantees the mass-conservation and bound-preserving properties. We also prove the global convergence of the proposed algorithm. These desired properties are numerically observed. In particular, the proposed method can produce real sharp corners with satisfactory accuracy. Finally, we present numerous numerical results to demonstrate that the ESC can be well simulated under different types of anisotropic surface energies, which also confirms the effectiveness and efficiency of the proposed method.
This paper introduces an extended tensor decomposition (XTD) method for model reduction. The proposed method is based on a sparse non-separated enrichment to the conventional tensor decomposition, which is expected to improve the approximation accuracy and the reducibility (compressibility) in highly nonlinear and singular cases. The proposed XTD method can be a powerful tool for solving nonlinear space-time parametric problems. The method has been successfully applied to parametric elastic-plastic problems and real time additive manufacturing residual stress predictions with uncertainty quantification. Furthermore, a combined XTD-SCA (self-consistent clustering analysis) strategy has been presented for multi-scale material modeling, which enables real time multi-scale multi-parametric simulations. The efficiency of the method is demonstrated with comparison to finite element analysis. The proposed method enables a novel framework for fast manufacturing and material design with uncertainties.
Implicit models for magnetic coenergy have been proposed by Pera et al. to describe the anisotropic nonlinear material behavior of electrical steel sheets. This approach aims at predicting magnetic response for any direction of excitation by interpolating measured of B--H curves in the rolling and transverse directions. In an analogous manner, an implicit model for magnetic energy is proposed. We highlight some mathematical properties of these implicit models and discuss their numerical realization, outline the computation of magnetic material laws via implicit differentiation, and discuss the potential use for finite element analysis in the context of nonlinear magnetostatics.
Quadratic NURBS-based discretizations of the Galerkin method suffer from volumetric locking when applied to nearly-incompressible linear elasticity. Volumetric locking causes not only smaller displacements than expected, but also large-amplitude spurious oscillations of normal stresses. Continuous-assumed-strain (CAS) elements have been recently introduced to remove membrane locking in quadratic NURBS-based discretizations of linear plane curved Kirchhoff rods (Casquero et al., CMAME, 2022). In this work, we propose two generalizations of CAS elements (named CAS1 and CAS2 elements) to overcome volumetric locking in quadratic NURBS-based discretizations of nearly-incompressible linear elasticity. CAS1 elements linearly interpolate the strains at the knots in each direction for the term in the variational form involving the first Lam\'e parameter while CAS2 elements linearly interpolate the dilatational strains at the knots in each direction. For both element types, a displacement vector with C1 continuity across element boundaries results in assumed strains with C0 continuity across element boundaries. In addition, the implementation of the two locking treatments proposed in this work does not require any additional global or element matrix operations such as matrix inversions or matrix multiplications. The locking treatments are applied at the element level and the nonzero pattern of the global stiffness matrix is preserved. The numerical examples solved in this work show that CAS1 and CAS2 elements, using either two or three Gauss-Legrendre quadrature points per direction, are effective locking treatments since they not only result in more accurate displacements for coarse meshes, but also remove the spurious oscillations of normal stresses.
We study the canonical momentum based discretizations of a hybrid model with kinetic ions and mass-less electrons. Two equivalent formulations of the hybrid model are presented, in which the vector potentials are in different gauges and the distribution functions depend on canonical momentum (not velocity). Particle-in-cell methods are used for the distribution functions, and the vector potentials are discretized by the finite element methods in the framework of finite element exterior calculus. Splitting methods are used for the time discretizations. It is illustrated that the second formulation is numerically superior and the schemes constructed based on the anti-symmetric bracket proposed have better conservation properties, although the filters can be used to improve the schemes of the first formulation.
This paper investigates the multiple testing problem for high-dimensional sparse binary sequences, motivated by the crowdsourcing problem in machine learning. We study the empirical Bayes approach for multiple testing on the high-dimensional Bernoulli model with a conjugate spike and uniform slab prior. We first show that the hard thresholding rule deduced from the posterior distribution is suboptimal. Consequently, the $\ell$-value procedure constructed using this posterior tends to be overly conservative in estimating the false discovery rate (FDR). We then propose two new procedures based on $\adj\ell$-values and $q$-values to correct this issue. Sharp frequentist theoretical results are obtained, demonstrating that both procedures can effectively control the FDR under sparsity. Numerical experiments are conducted to validate our theory in finite samples. To our best knowledge, this work provides the first uniform FDR control result in multiple testing for high-dimensional sparse binary data.
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