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A finite element based computational scheme is developed and employed to assess a duality based variational approach to the solution of the linear heat and transport PDE in one space dimension and time, and the nonlinear system of ODEs of Euler for the rotation of a rigid body about a fixed point. The formulation turns initial-(boundary) value problems into degenerate elliptic boundary value problems in (space)-time domains representing the Euler-Lagrange equations of suitably designed dual functionals in each of the above problems. We demonstrate reasonable success in approximating solutions of this range of parabolic, hyperbolic, and ODE primal problems, which includes energy dissipation as well as conservation, by a unified dual strategy lending itself to a variational formulation. The scheme naturally associates a family of dual solutions to a unique primal solution; such `gauge invariance' is demonstrated in our computed solutions of the heat and transport equations, including the case of a transient dual solution corresponding to a steady primal solution of the heat equation. Primal evolution problems with causality are shown to be correctly approximated by non-causal dual problems.

We present a machine learning framework capable of consistently inferring mathematical expressions of the hyperelastic energy functionals for incompressible materials from sparse experimental data and physical laws. To achieve this goal, we propose a polyconvex neural additive model (PNAM) that enables us to express the hyperelasticity model in a learnable feature space while enforcing polyconvexity. An upshot of this feature space obtained via PNAM is that (1) it is spanned by a set univariate basis that can be re-parametrized with a more complex mathematical form, and (2) the resultant elasticity model is guaranteed to fulfill the polyconvexity, which ensures that the acoustic tensor remains elliptic for any deformation. To further improve the interpretability, we use genetic programming to convert each univariate basis into a compact mathematical expression. The resultant multi-variable mathematical models obtained from this proposed framework are not only more interpretable but are also proven to fulfill physical laws. By controlling the compactness of the learned symbolic form, the machine learning-generated mathematical model also requires fewer arithmetic operations than the deep neural network counterparts during deployment. This latter attribute is crucial for scaling large-scale simulations where the constitutive responses of every integration point must be updated within each incremental time step. We compare our proposed model discovery framework against other state-of-the-art alternatives to assess the robustness and efficiency of the training algorithms and examine the trade-off between interpretability, accuracy, and precision of the learned symbolic hyperelasticity models obtained from different approaches. Our numerical results suggest that our approach extrapolates well outside the training data regime due to the precise incorporation of physics-based knowledge.

Logical modeling is a powerful tool in biology, offering a system-level understanding of the complex interactions that govern biological processes. A gap that hinders the scalability of logical models is the need to specify the update function of every vertex in the network depending on the status of its predecessors. To address this, we introduce in this paper the concept of strong regulation, where a vertex is only updated to active/inactive if all its predecessors agree in their influences; otherwise, it is set to ambiguous. We explore the interplay between active, inactive, and ambiguous influences in a network. We discuss the existence of phenotype attractors in such networks, where the status of some of the variables is fixed to active/inactive, while the others can have an arbitrary status, including ambiguous.

We present a multigrid algorithm to solve efficiently the large saddle-point systems of equations that typically arise in PDE-constrained optimization under uncertainty. The algorithm is based on a collective smoother that at each iteration sweeps over the nodes of the computational mesh, and solves a reduced saddle-point system whose size depends on the number $N$ of samples used to discretized the probability space. We show that this reduced system can be solved with optimal $O(N)$ complexity. We test the multigrid method on three problems: a linear-quadratic problem, possibly with a local or a boundary control, for which the multigrid method is used to solve directly the linear optimality system; a nonsmooth problem with box constraints and $L^1$-norm penalization on the control, in which the multigrid scheme is used within a semismooth Newton iteration; a risk-adverse problem with the smoothed CVaR risk measure where the multigrid method is called within a preconditioned Newton iteration. In all cases, the multigrid algorithm exhibits excellent performances and robustness with respect to the parameters of interest.

The spectral clustering algorithm is often used as a binary clustering method for unclassified data by applying the principal component analysis. To study theoretical properties of the algorithm, the assumption of conditional homoscedasticity is often supposed in existing studies. However, this assumption is restrictive and often unrealistic in practice. Therefore, in this paper, we consider the allometric extension model, that is, the directions of the first eigenvectors of two covariance matrices and the direction of the difference of two mean vectors coincide, and we provide a non-asymptotic bound of the error probability of the spectral clustering algorithm for the allometric extension model. As a byproduct of the result, we obtain the consistency of the clustering method in high-dimensional settings.

Acceleration of gradient-based optimization methods is an issue of significant practical and theoretical interest, particularly in machine learning applications. Most research has focused on optimization over Euclidean spaces, but given the need to optimize over spaces of probability measures in many machine learning problems, it is of interest to investigate accelerated gradient methods in this context too. To this end, we introduce a Hamiltonian-flow approach that is analogous to moment-based approaches in Euclidean space. We demonstrate that algorithms based on this approach can achieve convergence rates of arbitrarily high order. Numerical examples illustrate our claim.

Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also arise within information-processing molecular systems inside living cells, such as signal transduction cascades and genetic regulatory networks. Might neuromorphic collective modes be found more broadly in other physical and chemical processes, even those that ostensibly play non-information-processing roles such as protein synthesis, metabolism, or structural self-assembly? Here we examine nucleation during self-assembly of multicomponent structures, showing that high-dimensional patterns of concentrations can be discriminated and classified in a manner similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends sensitively on the extent of co-localization of high-concentration tiles within the three structures. The system was trained in-silico to classify a set of 18 grayscale 30 x 30 pixel images into three categories. Experimentally, fluorescence and atomic force microscopy monitoring during and after a 150-hour anneal established that all trained images were correctly classified, while a test set of image variations probed the robustness of the results. While slow compared to prior biochemical neural networks, our approach is surprisingly compact, robust, and scalable. This success suggests that ubiquitous physical phenomena, such as nucleation, may hold powerful information processing capabilities when scaled up as high-dimensional multicomponent systems.

Generative models inspired by dynamical transport of measure -- such as flows and diffusions -- construct a continuous-time map between two probability densities. Conventionally, one of these is the target density, only accessible through samples, while the other is taken as a simple base density that is data-agnostic. In this work, using the framework of stochastic interpolants, we formalize how to \textit{couple} the base and the target densities. This enables us to incorporate information about class labels or continuous embeddings to construct dynamical transport maps that serve as conditional generative models. We show that these transport maps can be learned by solving a simple square loss regression problem analogous to the standard independent setting. We demonstrate the usefulness of constructing dependent couplings in practice through experiments in super-resolution and in-painting.

Hashing has been widely used in approximate nearest search for large-scale database retrieval for its computation and storage efficiency. Deep hashing, which devises convolutional neural network architecture to exploit and extract the semantic information or feature of images, has received increasing attention recently. In this survey, several deep supervised hashing methods for image retrieval are evaluated and I conclude three main different directions for deep supervised hashing methods. Several comments are made at the end. Moreover, to break through the bottleneck of the existing hashing methods, I propose a Shadow Recurrent Hashing(SRH) method as a try. Specifically, I devise a CNN architecture to extract the semantic features of images and design a loss function to encourage similar images projected close. To this end, I propose a concept: shadow of the CNN output. During optimization process, the CNN output and its shadow are guiding each other so as to achieve the optimal solution as much as possible. Several experiments on dataset CIFAR-10 show the satisfying performance of SRH.

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.