The scalar auxiliary variable (SAV)-type methods are very popular techniques for solving various nonlinear dissipative systems. Compared to the semi-implicit method, the baseline SAV method can keep a modified energy dissipation law but doubles the computational cost. The general SAV approach does not add additional computation but needs to solve a semi-implicit solution in advance, which may potentially compromise the accuracy and stability. In this paper, we construct a novel first- and second-order unconditional energy stable and positivity-preserving stabilized SAV (PS-SAV) schemes for $L^2$ and $H^{-1}$ gradient flows. The constructed schemes can reduce nearly half computational cost of the baseline SAV method and preserve its accuracy and stability simultaneously. Meanwhile, the introduced auxiliary variable is always positive while the baseline SAV cannot guarantee this positivity-preserving property. Unconditionally energy dissipation laws are derived for the proposed numerical schemes. We also establish a rigorous error analysis of the first-order scheme for the Allen-Cahn type equation in $l^{\infty}(0,T; H^1(\Omega) ) $ norm. In addition we propose an energy optimization technique to optimize the modified energy close to the original energy. Several interesting numerical examples are presented to demonstrate the accuracy and effectiveness of the proposed methods.
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High-dimensional variable selection, with many more covariates than observations, is widely documented in standard regression models, but there are still few tools to address it in non-linear mixed-effects models where data are collected repeatedly on several individuals. In this work, variable selection is approached from a Bayesian perspective and a selection procedure is proposed, combining the use of a spike-and-slab prior and the Stochastic Approximation version of the Expectation Maximisation (SAEM) algorithm. Similarly to Lasso regression, the set of relevant covariates is selected by exploring a grid of values for the penalisation parameter. The SAEM approach is much faster than a classical MCMC (Markov chain Monte Carlo) algorithm and our method shows very good selection performances on simulated data. Its flexibility is demonstrated by implementing it for a variety of nonlinear mixed effects models. The usefulness of the proposed method is illustrated on a problem of genetic markers identification, relevant for genomic-assisted selection in plant breeding.
We propose novel optimal and parameter-free algorithms for computing an approximate solution with small (projected) gradient norm. Specifically, for computing an approximate solution such that the norm of its (projected) gradient does not exceed $\varepsilon$, we obtain the following results: a) for the convex case, the total number of gradient evaluations is bounded by $O(1)\sqrt{L\|x_0 - x^*\|/\varepsilon}$, where $L$ is the Lipschitz constant of the gradient and $x^*$ is any optimal solution; b) for the strongly convex case, the total number of gradient evaluations is bounded by $O(1)\sqrt{L/\mu}\log(\|\nabla f(x_0)\|/\epsilon)$, where $\mu$ is the strong convexity modulus; and c) for the nonconvex case, the total number of gradient evaluations is bounded by $O(1)\sqrt{Ll}(f(x_0) - f(x^*))/\varepsilon^2$, where $l$ is the lower curvature constant. Our complexity results match the lower complexity bounds of the convex and strongly cases, and achieve the above best-known complexity bound for the nonconvex case for the first time in the literature. Moreover, for all the convex, strongly convex, and nonconvex cases, we propose parameter-free algorithms that do not require the input of any problem parameters. To the best of our knowledge, there do not exist such parameter-free methods before especially for the strongly convex and nonconvex cases. Since most regularity conditions (e.g., strong convexity and lower curvature) are imposed over a global scope, the corresponding problem parameters are notoriously difficult to estimate. However, gradient norm minimization equips us with a convenient tool to monitor the progress of algorithms and thus the ability to estimate such parameters in-situ.
We show that the known list-decoding algorithms for univariate multiplicity and folded Reed-Solomon (FRS) codes can be made to run in nearly-linear time. This yields, to our knowledge, the first known family of codes that can be decoded in nearly linear time, even as they approach the list decoding capacity. Univariate multiplicity codes and FRS codes are natural variants of Reed-Solomon codes that were discovered and studied for their applications to list-decoding. It is known that for every $\epsilon >0$, and rate $R \in (0,1)$, there exist explicit families of these codes that have rate $R$ and can be list-decoded from a $(1-R-\epsilon)$ fraction of errors with constant list size in polynomial time (Guruswami & Wang (IEEE Trans. Inform. Theory, 2013) and Kopparty, Ron-Zewi, Saraf & Wootters (SIAM J. Comput. 2023)). In this work, we present randomized algorithms that perform the above tasks in nearly linear time. Our algorithms have two main components. The first builds upon the lattice-based approach of Alekhnovich (IEEE Trans. Inf. Theory 2005), who designed a nearly linear time list-decoding algorithm for Reed-Solomon codes approaching the Johnson radius. As part of the second component, we design nearly-linear time algorithms for two natural algebraic problems. The first algorithm solves linear differential equations of the form $Q\left(x, f(x), \frac{df}{dx}, \dots,\frac{d^m f}{dx^m}\right) \equiv 0$ where $Q$ has the form $Q(x,y_0,\dots,y_m) = \tilde{Q}(x) + \sum_{i = 0}^m Q_i(x)\cdot y_i$. The second solves functional equations of the form $Q\left(x, f(x), f(\gamma x), \dots,f(\gamma^m x)\right) \equiv 0$ where $\gamma$ is a high-order field element. These algorithms can be viewed as generalizations of classical algorithms of Sieveking (Computing 1972) and Kung (Numer. Math. 1974) for computing the modular inverse of a power series, and might be of independent interest.
Compiling large datasets from published resources, such as archaeological find catalogues presents fundamental challenges: identifying relevant content and manually recording it is a time-consuming, repetitive and error-prone task. For the data to be useful, it must be of comparable quality and adhere to the same recording standards, which is hardly ever the case in archaeology. Here, we present a new data collection method exploiting recent advances in Artificial Intelligence. Our software uses an object detection neural network combined with further classification networks to speed up, automate, and standardise data collection from legacy resources, such as archaeological drawings and photographs in large unsorted PDF files. The AI-assisted workflow detects common objects found in archaeological catalogues, such as graves, skeletons, ceramics, ornaments, stone tools and maps, and spatially relates and analyses these objects on the page to extract real-life attributes, such as the size and orientation of a grave based on the north arrow and the scale. A graphical interface allows for and assists with manual validation. We demonstrate the benefits of this approach by collecting a range of shapes and numerical attributes from richly-illustrated archaeological catalogues, and benchmark it in a real-world experiment with ten users. Moreover, we record geometric whole-outlines through contour detection, an alternative to landmark-based geometric morphometrics not achievable by hand.
Physics-informed neural networks (PINNs) effectively embed physical principles into machine learning, but often struggle with complex or alternating geometries. We propose a novel method for integrating geometric transformations within PINNs to robustly accommodate geometric variations. Our method incorporates a diffeomorphism as a mapping of a reference domain and adapts the derivative computation of the physics-informed loss function. This generalizes the applicability of PINNs not only to smoothly deformed domains, but also to lower-dimensional manifolds and allows for direct shape optimization while training the network. We demonstrate the effectivity of our approach on several problems: (i) Eikonal equation on Archimedean spiral, (ii) Poisson problem on surface manifold, (iii) Incompressible Stokes flow in deformed tube, and (iv) Shape optimization with Laplace operator. Through these examples, we demonstrate the enhanced flexibility over traditional PINNs, especially under geometric variations. The proposed framework presents an outlook for training deep neural operators over parametrized geometries, paving the way for advanced modeling with PDEs on complex geometries in science and engineering.
In semi-supervised learning, the prevailing understanding suggests that observing additional unlabeled samples improves estimation accuracy for linear parameters only in the case of model misspecification. This paper challenges this notion, demonstrating its inaccuracy in high dimensions. Initially focusing on a dense scenario, we introduce robust semi-supervised estimators for the regression coefficient without relying on sparse structures in the population slope. Even when the true underlying model is linear, we show that leveraging information from large-scale unlabeled data improves both estimation accuracy and inference robustness. Moreover, we propose semi-supervised methods with further enhanced efficiency in scenarios with a sparse linear slope. Diverging from the standard semi-supervised literature, we also allow for covariate shift. The performance of the proposed methods is illustrated through extensive numerical studies, including simulations and a real-data application to the AIDS Clinical Trials Group Protocol 175 (ACTG175).
Regression with random data objects is becoming increasingly common in modern data analysis. Unfortunately, like the traditional regression setting with Euclidean data, random response regression is not immune to the trouble caused by unusual observations. A metric Cook's distance extending the classical Cook's distances of Cook (1977) to general metric-valued response objects is proposed. The performance of the metric Cook's distance in both Euclidean and non-Euclidean response regression with Euclidean predictors is demonstrated in an extensive experimental study. A real data analysis of county-level COVID-19 transmission in the United States also illustrates the usefulness of this method in practice.
Threshold selection is a fundamental problem in any threshold-based extreme value analysis. While models are asymptotically motivated, selecting an appropriate threshold for finite samples can be difficult through standard methods. Inference can also be highly sensitive to the choice of threshold. Too low a threshold choice leads to bias in the fit of the extreme value model, while too high a choice leads to unnecessary additional uncertainty in the estimation of model parameters. In this paper, we develop a novel methodology for automated threshold selection that directly tackles this bias-variance trade-off. We also develop a method to account for the uncertainty in this threshold choice and propagate this uncertainty through to high quantile inference. Through a simulation study, we demonstrate the effectiveness of our method for threshold selection and subsequent extreme quantile estimation. We apply our method to the well-known, troublesome example of the River Nidd dataset.
Current AI-based methods do not provide comprehensible physical interpretations of the utilized data, extracted features, and predictions/inference operations. As a result, deep learning models trained using high-resolution satellite imagery lack transparency and explainability and can be merely seen as a black box, which limits their wide-level adoption. Experts need help understanding the complex behavior of AI models and the underlying decision-making process. The explainable artificial intelligence (XAI) field is an emerging field providing means for robust, practical, and trustworthy deployment of AI models. Several XAI techniques have been proposed for image classification tasks, whereas the interpretation of image segmentation remains largely unexplored. This paper offers to bridge this gap by adapting the recent XAI classification algorithms and making them usable for muti-class image segmentation, where we mainly focus on buildings' segmentation from high-resolution satellite images. To benchmark and compare the performance of the proposed approaches, we introduce a new XAI evaluation methodology and metric based on "Entropy" to measure the model uncertainty. Conventional XAI evaluation methods rely mainly on feeding area-of-interest regions from the image back to the pre-trained (utility) model and then calculating the average change in the probability of the target class. Those evaluation metrics lack the needed robustness, and we show that using Entropy to monitor the model uncertainty in segmenting the pixels within the target class is more suitable. We hope this work will pave the way for additional XAI research for image segmentation and applications in the remote sensing discipline.
We analyse the geometric instability of embeddings produced by graph neural networks (GNNs). Existing methods are only applicable for small graphs and lack context in the graph domain. We propose a simple, efficient and graph-native Graph Gram Index (GGI) to measure such instability which is invariant to permutation, orthogonal transformation, translation and order of evaluation. This allows us to study the varying instability behaviour of GNN embeddings on large graphs for both node classification and link prediction.
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