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We introduce a high-dimensional cubical complex, for any dimension t>0, and apply it to the design of quantum locally testable codes. Our complex is a natural generalization of the constructions by Panteleev and Kalachev and by Dinur et. al of a square complex (case t=2), which have been applied to the design of classical locally testable codes (LTC) and quantum low-density parity check codes (qLDPC) respectively. We turn the geometric (cubical) complex into a chain complex by relying on constant-sized local codes $h_1,\ldots,h_t$ as gadgets. A recent result of Panteleev and Kalachev on existence of tuples of codes that are product expanding enables us to prove lower bounds on the cycle and co-cycle expansion of our chain complex. For t=4 our construction gives a new family of "almost-good" quantum LTCs -- with constant relative rate, inverse-polylogarithmic relative distance and soundness, and constant-size parity checks. Both the distance of the quantum code and its local testability are proven directly from the cycle and co-cycle expansion of our chain complex.

Characterization of joint probability distribution for large networks of random variables remains a challenging task in data science. Probabilistic graph approximation with simple topologies has practically been resorted to; typically the tree topology makes joint probability computation much simpler and can be effective for statistical inference on insufficient data. However, to characterize network components where multiple variables cooperate closely to influence others, model topologies beyond a tree are needed, which unfortunately are infeasible to acquire. In particular, our previous work has related optimal approximation of Markov networks of tree-width k >=2 closely to the graph-theoretic problem of finding maximum spanning k-tree (MSkT), which is a provably intractable task. This paper investigates optimal approximation of Markov networks with k-tree topology that retains some designated underlying subgraph. Such a subgraph may encode certain background information that arises in scientific applications, for example, about a known significant pathway in gene networks or the indispensable backbone connectivity in the residue interaction graphs for a biomolecule 3D structure. In particular, it is proved that the \beta-retaining MSkT problem, for a number of classes \beta of graphs, admit O(n^{k+1})-time algorithms for every fixed k>= 1. These \beta-retaining MSkT algorithms offer efficient solutions for approximation of Markov networks with k-tree topology in the situation where certain persistent information needs to be retained.

A tremendous range of design tasks in materials, physics, and biology can be formulated as finding the optimum of an objective function depending on many parameters without knowing its closed-form expression or the derivative. Traditional derivative-free optimization techniques often rely on strong assumptions about objective functions, thereby failing at optimizing non-convex systems beyond 100 dimensions. Here, we present a tree search method for derivative-free optimization that enables accelerated optimal design of high-dimensional complex systems. Specifically, we introduce stochastic tree expansion, dynamic upper confidence bound, and short-range backpropagation mechanism to evade local optimum, iteratively approximating the global optimum using machine learning models. This development effectively confronts the dimensionally challenging problems, achieving convergence to global optima across various benchmark functions up to 2,000 dimensions, surpassing the existing methods by 10- to 20-fold. Our method demonstrates wide applicability to a wide range of real-world complex systems spanning materials, physics, and biology, considerably outperforming state-of-the-art algorithms. This enables efficient autonomous knowledge discovery and facilitates self-driving virtual laboratories. Although we focus on problems within the realm of natural science, the advancements in optimization techniques achieved herein are applicable to a broader spectrum of challenges across all quantitative disciplines.

Learning approximations to smooth target functions of many variables from finite sets of pointwise samples is an important task in scientific computing and its many applications in computational science and engineering. Despite well over half a century of research on high-dimensional approximation, this remains a challenging problem. Yet, significant advances have been made in the last decade towards efficient methods for doing this, commencing with so-called sparse polynomial approximation methods and continuing most recently with methods based on Deep Neural Networks (DNNs). In tandem, there have been substantial advances in the relevant approximation theory and analysis of these techniques. In this work, we survey this recent progress. We describe the contemporary motivations for this problem, which stem from parametric models and computational uncertainty quantification; the relevant function classes, namely, classes of infinite-dimensional, Banach-valued, holomorphic functions; fundamental limits of learnability from finite data for these classes; and finally, sparse polynomial and DNN methods for efficiently learning such functions from finite data. For the latter, there is currently a significant gap between the approximation theory of DNNs and the practical performance of deep learning. Aiming to narrow this gap, we develop the topic of practical existence theory, which asserts the existence of dimension-independent DNN architectures and training strategies that achieve provably near-optimal generalization errors in terms of the amount of training data.

This work presents a comparative review and classification between some well-known thermodynamically consistent models of hydrogel behavior in a large deformation setting, specifically focusing on solvent absorption/desorption and its impact on mechanical deformation and network swelling. The proposed discussion addresses formulation aspects, general mathematical classification of the governing equations, and numerical implementation issues based on the finite element method. The theories are presented in a unified framework demonstrating that, despite not being evident in some cases, all of them follow equivalent thermodynamic arguments. A detailed numerical analysis is carried out where Taylor-Hood elements are employed in the spatial discretization to satisfy the inf-sup condition and to prevent spurious numerical oscillations. The resulting discrete problems are solved using the FEniCS platform through consistent variational formulations, employing both monolithic and staggered approaches. We conduct benchmark tests on various hydrogel structures, demonstrating that major differences arise from the chosen volumetric response of the hydrogel. The significance of this choice is frequently underestimated in the state-of-the-art literature but has been shown to have substantial implications on the resulting hydrogel behavior.

This work presents a nonintrusive physics-preserving method to learn reduced-order models (ROMs) of Lagrangian systems, which includes nonlinear wave equations. Existing intrusive projection-based model reduction approaches construct structure-preserving Lagrangian ROMs by projecting the Euler-Lagrange equations of the full-order model (FOM) onto a linear subspace. This Galerkin projection step requires complete knowledge about the Lagrangian operators in the FOM and full access to manipulate the computer code. In contrast, the proposed Lagrangian operator inference approach embeds the mechanics into the operator inference framework to develop a data-driven model reduction method that preserves the underlying Lagrangian structure. The proposed approach exploits knowledge of the governing equations (but not their discretization) to define the form and parametrization of a Lagrangian ROM which can then be learned from projected snapshot data. The method does not require access to FOM operators or computer code. The numerical results demonstrate Lagrangian operator inference on an Euler-Bernoulli beam model, the sine-Gordon (nonlinear) wave equation, and a large-scale discretization of a soft robot fishtail with 779,232 degrees of freedom. The learned Lagrangian ROMs generalize well, as they can accurately predict the physical solutions both far outside the training time interval, as well as for unseen initial conditions.

Domain decomposition (DD) methods are a natural way to take advantage of parallel computers when solving large scale linear systems. Their scalability depends on the design of the coarse space used in the two-level method. The analysis of adaptive coarse spaces we present here is quite general since it applies to symmetric and non symmetric problems, to symmetric preconditioners such the additive Schwarz method (ASM) and to the non-symmetric preconditioner restricted additive Schwarz (RAS), as well as to exact or inexact subdomain solves. The coarse space is built by solving generalized eigenvalues in the subdomains and applying a well-chosen operator to the selected eigenvectors.

We propose a method for obtaining parsimonious decompositions of networks into higher order interactions which can take the form of arbitrary motifs.The method is based on a class of analytically solvable generative models, where vertices are connected via explicit copies of motifs, which in combination with non-parametric priors allow us to infer higher order interactions from dyadic graph data without any prior knowledge on the types or frequencies of such interactions. Crucially, we also consider 'degree--corrected' models that correctly reflect the degree distribution of the network and consequently prove to be a better fit for many real world--networks compared to non-degree corrected models. We test the presented approach on simulated data for which we recover the set of underlying higher order interactions to a high degree of accuracy. For empirical networks the method identifies concise sets of atomic subgraphs from within thousands of candidates that cover a large fraction of edges and include higher order interactions of known structural and functional significance. The method not only produces an explicit higher order representation of the network but also a fit of the network to analytically tractable models opening new avenues for the systematic study of higher order network structures.

When building statistical models for Bayesian data analysis tasks, required and optional iterative adjustments and different modelling choices can give rise to numerous candidate models. In particular, checks and evaluations throughout the modelling process can motivate changes to an existing model or the consideration of alternative models to ultimately obtain models of sufficient quality for the problem at hand. Additionally, failing to consider alternative models can lead to overconfidence in the predictive or inferential ability of a chosen model. The search for suitable models requires modellers to work with multiple models without jeopardising the validity of their results. Multiverse analysis offers a framework for transparent creation of multiple models at once based on different sensible modelling choices, but the number of candidate models arising in the combination of iterations and possible modelling choices can become overwhelming in practice. Motivated by these challenges, this work proposes iterative filtering for multiverse analysis to support efficient and consistent assessment of multiple models and meaningful filtering towards fewer models of higher quality across different modelling contexts. Given that causal constraints have been taken into account, we show how multiverse analysis can be combined with recommendations from established Bayesian modelling workflows to identify promising candidate models by assessing predictive abilities and, if needed, tending to computational issues. We illustrate our suggested approach in different realistic modelling scenarios using real data examples.

Functional data analysis is an important research field in statistics which treats data as random functions drawn from some infinite-dimensional functional space, and functional principal component analysis (FPCA) based on eigen-decomposition plays a central role for data reduction and representation. After nearly three decades of research, there remains a key problem unsolved, namely, the perturbation analysis of covariance operator for diverging number of eigencomponents obtained from noisy and discretely observed data. This is fundamental for studying models and methods based on FPCA, while there has not been substantial progress since Hall, M\"uller and Wang (2006)'s result for a fixed number of eigenfunction estimates. In this work, we aim to establish a unified theory for this problem, obtaining upper bounds for eigenfunctions with diverging indices in both the $\mathcal{L}^2$ and supremum norms, and deriving the asymptotic distributions of eigenvalues for a wide range of sampling schemes. Our results provide insight into the phenomenon when the $\mathcal{L}^{2}$ bound of eigenfunction estimates with diverging indices is minimax optimal as if the curves are fully observed, and reveal the transition of convergence rates from nonparametric to parametric regimes in connection to sparse or dense sampling. We also develop a double truncation technique to handle the uniform convergence of estimated covariance and eigenfunctions. The technical arguments in this work are useful for handling the perturbation series with noisy and discretely observed functional data and can be applied in models or those involving inverse problems based on FPCA as regularization, such as functional linear regression.