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We propose a new simple and explicit numerical scheme for time-homogeneous stochastic differential equations. The scheme is based on sampling increments at each time step from a skew-symmetric probability distribution, with the level of skewness determined by the drift and volatility of the underlying process. We show that as the step-size decreases the scheme converges weakly to the diffusion of interest. We then consider the problem of simulating from the limiting distribution of an ergodic diffusion process using the numerical scheme with a fixed step-size. We establish conditions under which the numerical scheme converges to equilibrium at a geometric rate, and quantify the bias between the equilibrium distributions of the scheme and of the true diffusion process. Notably, our results do not require a global Lipschitz assumption on the drift, in contrast to those required for the Euler--Maruyama scheme for long-time simulation at fixed step-sizes. Our weak convergence result relies on an extension of the theory of Milstein \& Tretyakov to stochastic differential equations with non-Lipschitz drift, which could also be of independent interest. We support our theoretical results with numerical simulations.

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.

Optimization constrained by high-fidelity computational models has potential for transformative impact. However, such optimization is frequently unattainable in practice due to the complexity and computational intensity of the model. An alternative is to optimize a low-fidelity model and use limited evaluations of the high-fidelity model to assess the quality of the solution. This article develops a framework to use limited high-fidelity simulations to update the optimization solution computed using the low-fidelity model. Building off a previous article [22], which introduced hyper-differential sensitivity analysis with respect to model discrepancy, this article provides novel extensions of the algorithm to enable uncertainty quantification of the optimal solution update via a Bayesian framework. Specifically, we formulate a Bayesian inverse problem to estimate the model discrepancy and propagate the posterior model discrepancy distribution through the post-optimality sensitivity operator for the low-fidelity optimization problem. We provide a rigorous treatment of the Bayesian formulation, a computationally efficient algorithm to compute posterior samples, a guide to specify and interpret the algorithm hyper-parameters, and a demonstration of the approach on three examples which highlight various types of discrepancy between low and high-fidelity models.

We consider a prototypical problem of Bayesian inference for a structured spiked model: a low-rank signal is corrupted by additive noise. While both information-theoretic and algorithmic limits are well understood when the noise is i.i.d. Gaussian, the more realistic case of structured noise still proves to be challenging. To capture the structure while maintaining mathematical tractability, a line of work has focused on rotationally invariant noise. However, existing studies either provide sub-optimal algorithms or they are limited to a special class of noise ensembles. In this paper, we establish the first characterization of the information-theoretic limits for a noise matrix drawn from a general trace ensemble. These limits are then achieved by an efficient algorithm inspired by the theory of adaptive Thouless-Anderson-Palmer (TAP) equations. Our approach leverages tools from statistical physics (replica method) and random matrix theory (generalized spherical integrals), and it unveils the equivalence between the rotationally invariant model and a surrogate Gaussian model.

Successive image generation using cyclic transformations is demonstrated by extending the CycleGAN model to transform images among three different categories. Repeated application of the trained generators produces sequences of images that transition among the different categories. The generated image sequences occupy a more limited region of the image space compared with the original training dataset. Quantitative evaluation using precision and recall metrics indicates that the generated images have high quality but reduced diversity relative to the training dataset. Such successive generation processes are characterized as chaotic dynamics in terms of dynamical system theory. Positive Lyapunov exponents estimated from the generated trajectories confirm the presence of chaotic dynamics, with the Lyapunov dimension of the attractor found to be comparable to the intrinsic dimension of the training data manifold. The results suggest that chaotic dynamics in the image space defined by the deep generative model contribute to the diversity of the generated images, constituting a novel approach for multi-class image generation. This model can be interpreted as an extension of classical associative memory to perform hetero-association among image categories.

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.

Simulation of the monodomain equation, crucial for modeling the heart's electrical activity, faces scalability limits when traditional numerical methods only parallelize in space. To optimize the use of large multi-processor computers by distributing the computational load more effectively, time parallelization is essential. We introduce a high-order parallel-in-time method addressing the substantial computational challenges posed by the stiff, multiscale, and nonlinear nature of cardiac dynamics. Our method combines the semi-implicit and exponential spectral deferred correction methods, yielding a hybrid method that is extended to parallel-in-time employing the PFASST framework. We thoroughly evaluate the stability, accuracy, and robustness of the proposed parallel-in-time method through extensive numerical experiments, using practical ionic models such as the ten-Tusscher-Panfilov. The results underscore the method's potential to significantly enhance real-time and high-fidelity simulations in biomedical research and clinical applications.

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.

Temporal reasoning with conditionals is more complex than both classical temporal reasoning and reasoning with timeless conditionals, and can lead to some rather counter-intuitive conclusions. For instance, Aristotle's famous "Sea Battle Tomorrow" puzzle leads to a fatalistic conclusion: whether there will be a sea battle tomorrow or not, but that is necessarily the case now. We propose a branching-time logic LTC to formalise reasoning about temporal conditionals and provide that logic with adequate formal semantics. The logic LTC extends the Nexttime fragment of CTL*, with operators for model updates, restricting the domain to only future moments where antecedent is still possible to satisfy. We provide formal semantics for these operators that implements the restrictor interpretation of antecedents of temporalized conditionals, by suitably restricting the domain of discourse. As a motivating example, we demonstrate that a naturally formalised in our logic version of the `Sea Battle' argument renders it unsound, thereby providing a solution to the problem with fatalist conclusion that it entails, because its underlying reasoning per cases argument no longer applies when these cases are treated not as material implications but as temporal conditionals. On the technical side, we analyze the semantics of LTC and provide a series of reductions of LTC-formulae, first recursively eliminating the dynamic update operators and then the path quantifiers in such formulae. Using these reductions we obtain a sound and complete axiomatization for LTC, and reduce its decision problem to that of the modal logic KD.

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.