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Stress prediction in porous materials and structures is challenging due to the high computational cost associated with direct numerical simulations. Convolutional Neural Network (CNN) based architectures have recently been proposed as surrogates to approximate and extrapolate the solution of such multiscale simulations. These methodologies are usually limited to 2D problems due to the high computational cost of 3D voxel based CNNs. We propose a novel geometric learning approach based on a Graph Neural Network (GNN) that efficiently deals with three-dimensional problems by performing convolutions over 2D surfaces only. Following our previous developments using pixel-based CNN, we train the GNN to automatically add local fine-scale stress corrections to an inexpensively computed coarse stress prediction in the porous structure of interest. Our method is Bayesian and generates densities of stress fields, from which credible intervals may be extracted. As a second scientific contribution, we propose to improve the extrapolation ability of our network by deploying a strategy of online physics-based corrections. Specifically, we condition the posterior predictions of our probabilistic predictions to satisfy partial equilibrium at the microscale, at the inference stage. This is done using an Ensemble Kalman algorithm, to ensure tractability of the Bayesian conditioning operation. We show that this innovative methodology allows us to alleviate the effect of undesirable biases observed in the outputs of the uncorrected GNN, and improves the accuracy of the predictions in general.

This work presents a comparative study to numerically compute impulse approximate controls for parabolic equations with various boundary conditions. Theoretical controllability results have been recently investigated using a logarithmic convexity estimate at a single time based on a Carleman commutator approach. We propose a numerical algorithm for computing the impulse controls with minimal $L^2$-norms by adapting a penalized Hilbert Uniqueness Method (HUM) combined with a Conjugate Gradient (CG) method. We consider static boundary conditions (Dirichlet and Neumann) and dynamic boundary conditions. Some numerical experiments based on our developed algorithm are given to validate and compare the theoretical impulse controllability results.

In an era where scientific experiments can be very costly, multi-fidelity emulators provide a useful tool for cost-efficient predictive scientific computing. For scientific applications, the experimenter is often limited by a tight computational budget, and thus wishes to (i) maximize predictive power of the multi-fidelity emulator via a careful design of experiments, and (ii) ensure this model achieves a desired error tolerance with some notion of confidence. Existing design methods, however, do not jointly tackle objectives (i) and (ii). We propose a novel stacking design approach that addresses both goals. A multi-level reproducing kernel Hilbert space (RKHS) interpolator is first introduced to build the emulator, under which our stacking design provides a sequential approach for designing multi-fidelity runs such that a desired prediction error of $\epsilon > 0$ is met under regularity assumptions. We then prove a novel cost complexity theorem that, under this multi-level interpolator, establishes a bound on the computation cost (for training data simulation) needed to achieve a prediction bound of $\epsilon$. This result provides novel insights on conditions under which the proposed multi-fidelity approach improves upon a conventional RKHS interpolator which relies on a single fidelity level. Finally, we demonstrate the effectiveness of stacking designs in a suite of simulation experiments and an application to finite element analysis.

Scientists continue to develop increasingly complex mechanistic models to reflect their knowledge more realistically. Statistical inference using these models can be challenging since the corresponding likelihood function is often intractable and model simulation may be computationally burdensome. Fortunately, in many of these situations, it is possible to adopt a surrogate model or approximate likelihood function. It may be convenient to conduct Bayesian inference directly with the surrogate, but this can result in bias and poor uncertainty quantification. In this paper we propose a new method for adjusting approximate posterior samples to reduce bias and produce more accurate uncertainty quantification. We do this by optimizing a transform of the approximate posterior that maximizes a scoring rule. Our approach requires only a (fixed) small number of complex model simulations and is numerically stable. We demonstrate good performance of the new method on several examples of increasing complexity.

We address speech enhancement based on variational autoencoders, which involves learning a speech prior distribution in the time-frequency (TF) domain. A zero-mean complex-valued Gaussian distribution is usually assumed for the generative model, where the speech information is encoded in the variance as a function of a latent variable. In contrast to this commonly used approach, we propose a weighted variance generative model, where the contribution of each spectrogram time-frame in parameter learning is weighted. We impose a Gamma prior distribution on the weights, which would effectively lead to a Student's t-distribution instead of Gaussian for speech generative modeling. We develop efficient training and speech enhancement algorithms based on the proposed generative model. Our experimental results on spectrogram auto-encoding and speech enhancement demonstrate the effectiveness and robustness of the proposed approach compared to the standard unweighted variance model.

Academic writing is an indispensable yet laborious part of the research enterprise. This Perspective maps out principles and methods for using generative artificial intelligence (AI), specifically large language models (LLMs), to elevate the quality and efficiency of academic writing. We introduce a human-AI collaborative framework that delineates the rationale (why), process (how), and nature (what) of AI engagement in writing. The framework pinpoints both short-term and long-term reasons for engagement and their underlying mechanisms (e.g., cognitive offloading and imaginative stimulation). It reveals the role of AI throughout the writing process, conceptualized through a two-stage model for human-AI collaborative writing, and the nature of AI assistance in writing, represented through a model of writing-assistance types and levels. Building on this framework, we describe effective prompting techniques for incorporating AI into the writing routine (outlining, drafting, and editing) as well as strategies for maintaining rigorous scholarship, adhering to varied journal policies, and avoiding overreliance on AI. Ultimately, the prudent integration of AI into academic writing can ease the communication burden, empower authors, accelerate discovery, and promote diversity in science.

The evaluation of clustering algorithms can involve running them on a variety of benchmark problems, and comparing their outputs to the reference, ground-truth groupings provided by experts. Unfortunately, many research papers and graduate theses consider only a small number of datasets. Also, the fact that there can be many equally valid ways to cluster a given problem set is rarely taken into account. In order to overcome these limitations, we have developed a framework whose aim is to introduce a consistent methodology for testing clustering algorithms. Furthermore, we have aggregated, polished, and standardised many clustering benchmark dataset collections referred to across the machine learning and data mining literature, and included new datasets of different dimensionalities, sizes, and cluster types. An interactive datasets explorer, the documentation of the Python API, a description of the ways to interact with the framework from other programming languages such as R or MATLAB, and other details are all provided at <//clustering-benchmarks.gagolewski.com>.

Neuromorphic computing relies on spike-based, energy-efficient communication, inherently implying the need for conversion between real-valued (sensory) data and binary, sparse spiking representation. This is usually accomplished using the real valued data as current input to a spiking neuron model, and tuning the neuron's parameters to match a desired, often biologically inspired behaviour. We developed a tool, the WaLiN-GUI, that supports the investigation of neuron models and parameter combinations to identify suitable configurations for neuron-based encoding of sample-based data into spike trains. Due to the generalized LIF model implemented by default, next to the LIF and Izhikevich neuron models, many spiking behaviors can be investigated out of the box, thus offering the possibility of tuning biologically plausible responses to the input data. The GUI is provided open source and with documentation, being easy to extend with further neuron models and personalize with data analysis functions.

Infinite-dimensional, holomorphic functions have been studied in detail over the last several decades, due to their relevance to parametric differential equations and computational uncertainty quantification. The approximation of such functions from finitely many samples is of particular interest, due to the practical importance of constructing surrogate models to complex mathematical models of physical processes. In a previous work, [5] we studied the approximation of so-called Banach-valued, $(\boldsymbol{b},\varepsilon)$-holomorphic functions on the infinite-dimensional hypercube $[-1,1]^{\mathbb{N}}$ from $m$ (potentially adaptive) samples. In particular, we derived lower bounds for the adaptive $m$-widths for classes of such functions, which showed that certain algebraic rates of the form $m^{1/2-1/p}$ are the best possible regardless of the sampling-recovery pair. In this work, we continue this investigation by focusing on the practical case where the samples are pointwise evaluations drawn identically and independently from a probability measure. Specifically, for Hilbert-valued $(\boldsymbol{b},\varepsilon)$-holomorphic functions, we show that the same rates can be achieved (up to a small polylogarithmic or algebraic factor) for essentially arbitrary tensor-product Jacobi (ultraspherical) measures. Our reconstruction maps are based on least squares and compressed sensing procedures using the corresponding orthonormal Jacobi polynomials. In doing so, we strengthen and generalize past work that has derived weaker nonuniform guarantees for the uniform and Chebyshev measures (and corresponding polynomials) only. We also extend various best $s$-term polynomial approximation error bounds to arbitrary Jacobi polynomial expansions. Overall, we demonstrate that i.i.d.\ pointwise samples are near-optimal for the recovery of infinite-dimensional, holomorphic functions.

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.