Formulating dynamical models for physical phenomena is essential for understanding the interplay between the different mechanisms and predicting the evolution of physical states. However, a dynamical model alone is often insufficient to address these fundamental tasks, as it suffers from model errors and uncertainties. One common remedy is to rely on data assimilation, where the state estimate is updated with observations of the true system. Ensemble filters sequentially assimilate observations by updating a set of samples over time. They operate in two steps: a forecast step that propagates each sample through the dynamical model and an analysis step that updates the samples with incoming observations. For accurate and robust predictions of dynamical systems, discrete solutions must preserve their critical invariants. While modern numerical solvers satisfy these invariants, existing invariant-preserving analysis steps are limited to Gaussian settings and are often not compatible with classical regularization techniques of ensemble filters, e.g., inflation and covariance tapering. The present work focuses on preserving linear invariants, such as mass, stoichiometric balance of chemical species, and electrical charges. Using tools from measure transport theory (Spantini et al., 2022, SIAM Review), we introduce a generic class of nonlinear ensemble filters that automatically preserve desired linear invariants in non-Gaussian filtering problems. By specializing this framework to the Gaussian setting, we recover a constrained formulation of the Kalman filter. Then, we show how to combine existing regularization techniques for the ensemble Kalman filter (Evensen, 1994, J. Geophys. Res.) with the preservation of the linear invariants. Finally, we assess the benefits of preserving linear invariants for the ensemble Kalman filter and nonlinear ensemble filters.
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The main challenge of large-scale numerical simulation of radiation transport is the high memory and computation time requirements of discretization methods for kinetic equations. In this work, we derive and investigate a neural network-based approximation to the entropy closure method to accurately compute the solution of the multi-dimensional moment system with a low memory footprint and competitive computational time. We extend methods developed for the standard entropy-based closure to the context of regularized entropy-based closures. The main idea is to interpret structure-preserving neural network approximations of the regularized entropy closure as a two-stage approximation to the original entropy closure. We conduct a numerical analysis of this approximation and investigate optimal parameter choices. Our numerical experiments demonstrate that the method has a much lower memory footprint than traditional methods with competitive computation times and simulation accuracy.
Model-based clustering of moderate or large dimensional data is notoriously difficult. We propose a model for simultaneous dimensionality reduction and clustering by assuming a mixture model for a set of latent scores, which are then linked to the observations via a Gaussian latent factor model. This approach was recently investigated by Chandra et al. (2023). The authors use a factor-analytic representation and assume a mixture model for the latent factors. However, performance can deteriorate in the presence of model misspecification. Assuming a repulsive point process prior for the component-specific means of the mixture for the latent scores is shown to yield a more robust model that outperforms the standard mixture model for the latent factors in several simulated scenarios. The repulsive point process must be anisotropic to favor well-separated clusters of data, and its density should be tractable for efficient posterior inference. We address these issues by proposing a general construction for anisotropic determinantal point processes. We illustrate our model in simulations as well as a plant species co-occurrence dataset.
Many combinatorial optimization problems can be formulated as the search for a subgraph that satisfies certain properties and minimizes the total weight. We assume here that the vertices correspond to points in a metric space and can take any position in given uncertainty sets. Then, the cost function to be minimized is the sum of the distances for the worst positions of the vertices in their uncertainty sets. We propose two types of polynomial-time approximation algorithms. The first one relies on solving a deterministic counterpart of the problem where the uncertain distances are replaced with maximum pairwise distances. We study in details the resulting approximation ratio, which depends on the structure of the feasible subgraphs and whether the metric space is Ptolemaic or not. The second algorithm is a fully-polynomial time approximation scheme for the special case of $s-t$ paths.
Symplectic integrators are widely implemented numerical integrators for Hamiltonian mechanics, which preserve the Hamiltonian structure (symplecticity) of the system. Although the symplectic integrator does not conserve the energy of the system, it is well known that there exists a conserving modified Hamiltonian, called the shadow Hamiltonian. For the Nambu mechanics, which is a kind of generalized Hamiltonian mechanics, we can also construct structure-preserving integrators by the same procedure used to construct the symplectic integrators. In the structure-preserving integrator, however, the existence of shadow Hamiltonians is nontrivial. This is because the Nambu mechanics is driven by multiple Hamiltonians and it is nontrivial whether the time evolution by the integrator can be cast into the Nambu mechanical time evolution driven by multiple shadow Hamiltonians. In this paper we present a general procedure to calculate the shadow Hamiltonians of structure-preserving integrators for Nambu mechanics, and give an example where the shadow Hamiltonians exist. This is the first attempt to determine the concrete forms of the shadow Hamiltonians for a Nambu mechanical system. We show that the fundamental identity, which corresponds to the Jacobi identity in Hamiltonian mechanics, plays an important role in calculating the shadow Hamiltonians using the Baker-Campbell-Hausdorff formula. It turns out that the resulting shadow Hamiltonians have indefinite forms depending on how the fundamental identities are used. This is not a technical artifact, because the exact shadow Hamiltonians obtained independently have the same indefiniteness.
Multivariate Cryptography is one of the main candidates for Post-quantum Cryptography. Multivariate schemes are usually constructed by applying two secret affine invertible transformations $\mathcal S,\mathcal T$ to a set of multivariate polynomials $\mathcal{F}$ (often quadratic). The secret polynomials $\mathcal{F}$ posses a trapdoor that allows the legitimate user to find a solution of the corresponding system, while the public polynomials $\mathcal G=\mathcal S\circ\mathcal F\circ\mathcal T$ look like random polynomials. The polynomials $\mathcal G$ and $\mathcal F$ are said to be affine equivalent. In this article, we present a more general way of constructing a multivariate scheme by considering the CCZ equivalence, which has been introduced and studied in the context of vectorial Boolean functions.
Differential abundance analysis is a key component of microbiome studies. While dozens of methods for it exist, currently, there is no consensus on the preferred methods. Correctness of results in differential abundance analysis is an ambiguous concept that cannot be evaluated without employing simulated data, but we argue that consistency of results across datasets should be considered as an essential quality of a well-performing method. We compared the performance of 14 differential abundance analysis methods employing datasets from 54 taxonomic profiling studies based on 16S rRNA gene or shotgun sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from independent studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, the highest consistency without unnecessary reduction in sensitivity was attained by analyzing relative abundances with a non-parametric method (Wilcoxon test or ordinal regression model) or linear regression (MaAsLin2). Comparable performance was also attained by analyzing presence/absence of taxa with logistic regression.
The problems of optimal recovering univariate functions and their derivatives are studied. To solve these problems, two variants of the truncation method are constructed, which are order-optimal both in the sense of accuracy and in terms of the amount of involved Galerkin information. For numerical summation, it has been established how the parameters characterizing the problem being solved affect its stability.
Conventional computing paradigm struggles to fulfill the rapidly growing demands from emerging applications, especially those for machine intelligence, because much of the power and energy is consumed by constant data transfers between logic and memory modules. A new paradigm, called "computational random-access memory (CRAM)" has emerged to address this fundamental limitation. CRAM performs logic operations directly using the memory cells themselves, without having the data ever leave the memory. The energy and performance benefits of CRAM for both conventional and emerging applications have been well established by prior numerical studies. However, there lacks an experimental demonstration and study of CRAM to evaluate its computation accuracy, which is a realistic and application-critical metrics for its technological feasibility and competitiveness. In this work, a CRAM array based on magnetic tunnel junctions (MTJs) is experimentally demonstrated. First, basic memory operations as well as 2-, 3-, and 5-input logic operations are studied. Then, a 1-bit full adder with two different designs is demonstrated. Based on the experimental results, a suite of modeling has been developed to characterize the accuracy of CRAM computation. Scalar addition, multiplication, and matrix multiplication, which are essential building blocks for many conventional and machine intelligence applications, are evaluated and show promising accuracy performance. With the confirmation of MTJ-based CRAM's accuracy, there is a strong case that this technology will have a significant impact on power- and energy-demanding applications of machine intelligence.
Given a finite set of matrices with integer entries, the matrix mortality problem asks if there exists a product of these matrices equal to the zero matrix. We consider a special case of this problem where all entries of the matrices are nonnegative. This case is equivalent to the NFA mortality problem, which, given an NFA, asks for a word $w$ such that the image of every state under $w$ is the empty set. The size of the alphabet of the NFA is then equal to the number of matrices in the set. We study the length of shortest such words depending on the size of the alphabet. We show that this length for an NFA with $n$ states can be at least $2^n - 1$, $2^{(n - 4)/2}$ and $2^{(n - 2)/3}$ if the size of the alphabet is, respectively, equal to $n$, three and two.
Within distributed learning, workers typically compute gradients on their assigned dataset chunks and send them to the parameter server (PS), which aggregates them to compute either an exact or approximate version of $\nabla L$ (gradient of the loss function $L$). However, in large-scale clusters, many workers are slower than their promised speed or even failure-prone. A gradient coding solution introduces redundancy within the assignment of chunks to the workers and uses coding theoretic ideas to allow the PS to recover $\nabla L$ (exactly or approximately), even in the presence of stragglers. Unfortunately, most existing gradient coding protocols are inefficient from a computation perspective as they coarsely classify workers as operational or failed; the potentially valuable work performed by slow workers (partial stragglers) is ignored. In this work, we present novel gradient coding protocols that judiciously leverage the work performed by partial stragglers. Our protocols are efficient from a computation and communication perspective and numerically stable. For an important class of chunk assignments, we present efficient algorithms for optimizing the relative ordering of chunks within the workers; this ordering affects the overall execution time. For exact gradient reconstruction, our protocol is around $2\times$ faster than the original class of protocols and for approximate gradient reconstruction, the mean-squared-error of our reconstructed gradient is several orders of magnitude better.
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