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arXiv 2025年

作者： Kazempour, Ali Sisakht, Esmaeil Taghizadeh Okyay, Mahmut Sait Jiang, Xiao Sato, Shunsuke Park, Noejung Department of physics Payame Noor University PO BOX Tehran119395-3697 Iran Department of Physics Ulsan National Institute of Science and Technology Ulsan689-798 Korea Republic of Materials Science and Engineering Program Department of Chemical and Environmental Engineering University of California-Riverside RiversideCA92521 United States Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan

Ultrafast optical control of ferroelectricity based on short and intense light can be utilized to achieve accurate manipulations of ferroelectric materials, which may pave a basis for future breakthrough in nonvolatile memories. Here, we demonstrate that phase manipulation of electric field in the strong field sub-cycle regime induces a nonlinear injection current, efficiently coupling with the topology of band structure and enabling dynamic reversal of both current and polarization. Our time-dependent first-principles calculations reveal that tuning the phase of linearly or circularly polarized light through time-varying chirp, or constant carrier envelop phases within sub-laser-cycle dynamics effectively breaks the time-reversal symmetry, allowing the control over current and electronic polarization reversal over multi-ferroelectric states. Our time- and momentum-resolved transverse current analysis reveal the significance of Berry curvature higher order poles in the apparent association between the odd (even) orders of Berry curvature multipoles to odd (even) pseudo-harmonics in driving polarization dynamics reversal. We suggest that these phase manipulations of short pulse waveform may lead to unprecedented accurate control of nonlinear photocurrents and polarization states, which facilitate the development of precise ultrafast opto-ferroelectric devices. © 2025, CC BY.

关键词： Ferroelectricity

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A multi-layered defense against adversarial attacks in brain tumor classification using ensemble adversarial training and feature squeezing

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Scientific Reports 2025年第1期15卷 1-11页

作者： Yinusa, Ahmeed Faezipour, Misa Computational and Data Science Program Middle Tennessee State University 1301 East Main Street Murfreesboro 37132 TN United States Department of Engineering Technology Middle Tennessee State University 1301 East Main Street Murfreesboro 37132 TN United States

Deep learning, particularly convolutional neural networks (CNNs), has proven valuable for brain tumor classification, aiding diagnostic and therapeutic decisions in medical imaging. Despite their accuracy, these models are vulnerable to adversarial attacks, compromising their reliability in clinical settings. In this research, we utilized a VGG16-based CNN model to classify brain tumors, achieving 96% accuracy on clean magnetic resonance imaging (MRI) data. To assess robustness, we exposed the model to Fast Gradient Sign Method (FGSM) and Projected Gradient Descent (PGD) attacks, which reduced accuracy to 32% and 13%, respectively. We then applied a multi-layered defense strategy, including adversarial training with FGSM and PGD examples and feature squeezing techniques such as bit-depth reduction and Gaussian blurring. This approach improved model resilience, achieving 54% accuracy on FGSM and 47% on PGD adversarial examples. Our results highlight the importance of proactive defense strategies for maintaining the reliability of AI in medical imaging under adversarial conditions. © The Author(s) 2025.

关键词： Adversarial attacks Adversarial training Artificial intelligence (AI) Brain tumor Feature squeezing Magnetic resonance imaging (MRI)

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Efficient First-Principles Framework for Overdamped Phonon Dynamics and Anharmonic Electron-Phonon Coupling in Superionic Materials

arXiv

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arXiv 2025年

作者： Wang, Yuxuan Zacharias, Marios Zhang, Xiao Pant, Nick Even, Jacky Poudeu, Pierre F.P. Kioupakis, Emmanouil Department of Materials Science and Engineering University of Michigan Ann ArborMI48109 United States Univ Rennes INSA Rennes CNRS Institut FOTON - UMR 6082 RennesF-35000 France Applied Physics Program University of Michigan Ann ArborMI48109 United States Oden Institute for Computational Engineering and Sciences The University of Texas at Austin AustinTX78712 United States

Relying on the anharmonic special displacement method, we introduce an ab initio quasistatic polymorphous framework to describe local disorder, anharmonicity, and electron-phonon coupling in superionic conductors. Using the example of cubic Cu2Se, we show that positional polymorphism yields extremely overdamped anharmonic vibrations while preserving transverse acoustic phonons, consistent with experiments. We also demonstrate well-defined electronic band structures with large band gap openings due to polymorphism of 1.0 eV and calculate anharmonic electron-phonon renormalization, yielding band gap narrowing with increasing temperature in agreement with previous measurements. Our approach opens the way for efficient ab initio electronic structure calculations in superionic crystals to elucidate their compelling high figure-of-merit. © 2025, CC BY-NC-ND.

关键词： Energy gap

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Generalization is not a universal guarantee: Estimating similarity to training data with an ensemble out-of-distribution metric

arXiv

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arXiv 2025年

作者： Schreyer, W. Max Anderson, Christopher Thompson, Reid F. Computational Biology Program Oregon Health & Science University PortlandOR United States Department of Biomedical Engineering Oregon Health & Science University PortlandOR United States Portland VA Research Foundation PortlandOR United States Department of Radiation Medicine Oregon Health & Science University PortlandOR United States Department of Medical Informatics and Clinical Epidemiology Oregon Health & Science University PortlandOR United States Division of Hospital and Specialty Medicine VA Portland Healthcare System PortlandOR United States

Failure of machine learning models to generalize to new data is a core problem limiting the reliability of AI systems, partly due to the lack of simple and robust methods for comparing new data to the original training dataset. We propose a standardized approach for assessing data similarity in a model-agnostic manner by constructing a supervised autoencoder for generalizability estimation (SAGE). We compare points in a low-dimensional embedded latent space, defining empirical probability measures for k-Nearest Neighbors (kNN) distance, reconstruction of inputs and task-based performance. As proof of concept for classification tasks, we use MNIST and CIFAR-10 to demonstrate how an ensemble output probability score can separate deformed images from a mixture of typical test examples, and how this SAGE score is robust to transformations of increasing severity. As further proof of concept, we extend this approach to a regression task using non-imaging data (UCI Abalone). In all cases, we show that out-of-the-box model performance increases after SAGE score filtering, even when applied to data from the model’s own training and test datasets. Our out-of-distribution scoring method can be introduced during several steps of model construction and assessment, leading to future improvements in responsible deep learning implementation. Copyright © 2025, The Authors. All rights reserved.

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Three-dimensional construction of hyperuniform, nonhyperuniform, and antihyperuniform disordered heterogeneous materials and their transport properties via spectral density functions

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Physical Review E 2025年第3期111卷 035310-035310页

作者： Wenlong Shi Yang Jiao Salvatore Torquato Materials Science and Engineering Arizona State University Tempe Arizona 85287 USA Department of Physics Arizona State University Tempe Arizona 85287 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Institute of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Rigorous theories connecting physical properties of a heterogeneous material to its microstructure offer a promising avenue to guide the computational material design and optimization. The spectral density function χ̃V(k), which can be obtained experimentally from scattering data, enables accurate determination of various transport and wave propagation characteristics, including the time-dependent diffusion spreadability S(t) and effective dynamic dielectric constant εe for electromagnetic wave propagation. Moreover, χ̃V(k) determines rigorous upper bounds on the fluid permeability K. Given the importance of χ̃V(k), we present here an efficient Fourier-space based computational framework to construct three-dimensional (3D) statistically isotropic two-phase heterogeneous materials corresponding to targeted spectral density functions. In particular, we employ a variety of analytical functional forms for χ̃V(k) that satisfy all known necessary conditions to construct disordered stealthy hyperuniform, standard hyperuniform, nonhyperuniform, and antihyperuniform two-phase heterogeneous material systems at varying phase volume fractions. We show that by tuning the correlations in the system across length scales via the targeted functions, one can generate a rich spectrum of distinct structures within each of the above classes of materials. Importantly, we present the first realization of antihyperuniform two-phase heterogeneous materials in 3D, which are characterized by autocovariance function χV(r) with a power-law tail, resulting in microstructures that contain clusters of dramatically different sizes and morphologies. We also determine the diffusion spreadability S(t) and estimate the fluid permeability K associated with all of the constructed materials directly from the corresponding spectral densities. Although it is well established that the long-time asymptotic scaling behavior of S(t) only depends on the functional form of χ̃V(k), with the stealthy hyperuniform a

关键词： Spectral density

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Generative AI-Driven Data Augmentation for Robust Virtual Metrology: GANs, VAEs, and Diffusion Models

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IEEE Transactions on Semiconductor Manufacturing 2025年

作者： Lin, Chin-Yi Tseng, Tzu-Liang Emon, Solayman Hossain Tsai, Tsung-Han Department of Industrial Manufacturing and Systems Engineering University of Texas at El Paso El Paso 79968 TX United States Computational Science Program University of Texas at El Paso El Paso 79968 TX United States Institute of Information and Decision Sciences National Taipei University of Business Taipei 10051 Taiwan

Advanced semiconductor manufacturing increasingly depends on Virtual Metrology (VM) for real-time quality monitoring, yet conventional data-driven models rarely capture the scarce or extreme process conditions critical for robust predictions. We propose a Multi-Stage Constrained Data Generative Augmentation (MSC-DGA) framework that integrates Variational Autoencoders (VAE), Normalizing Flows, and Constrained Diffusion to systematically expand coverage of seldom-seen regimes. By embedding strict engineering constraints during generation and applying a two-stage quality filter, MSCDGA ensures physically plausible synthetic samples. We further present theoretical proofs showing that multi-stage generation can approximate complex sensor distributions while enforcing domain validity, thereby improving coverage and preserving essential process physics. Empirically, we demonstrate the approach on real WBG SiC data, incorporating these curated samples into a Generative Foundation Model (GFA-VM) with few-shot finetuning and uncertainty-based active sampling, yielding significant accuracy gains for rarely observed conditions. Experiments confirm notable performance improvements over single-stage augmentation and naive oversampling. By rigorously balancing distribution realism with engineering feasibility, MSC-DGA offers a practical and theoretically grounded advancement for VM, enhancing adaptive control and product quality in next-generation power semiconductor manufacturing. © 2024 IEEE.

关键词： Advanced Process Control (APC) Data augmentation Diffusion models Generative models Physics-informed constraints Rare event coverage Semiconductor manufacturing Variational Autoencoders (VAE) Virtual Metrology (VM)

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CIWARS: A Web Server for Antibiotic Resistance Surveillance Using Longitudinal Metagenomic Data

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Journal of Molecular Biology 2025年

作者： Emon, Muhit Islam Cheung, Yat Fei Stoll, James Rumi, Monjura Afrin Brown, Connor Choi, Joung Min Moumi, Nazifa Ahmed Ahmed, Shafayat Song, Haoqiu Sein, Justin Yao, Shunyu Khan, Ahmad Gupta, Suraj Kulkarni, Rutwik Butt, Ali Vikesland, Peter Pruden, Amy Zhang, Liqing Department of Computer Science Virginia Tech Blacksburg 24060 VA United States Fralin Life Science Institute Virginia Tech Blacksburg 24060 VA United States Department of Civil and Environmental Engineering Virginia Tech Blacksburg 24060 VA United States The Interdisciplinary PhD Program in Genetics Bioinformatics and Computational Biology Virginia Tech Blacksburg 24060 VA United States

The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://***/. © 2025 Elsevier Ltd

关键词： anomaly detection antibiotic resistance (AR) AR indicator profiling longitudinal metagenomics wastewater-based surveillance

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Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation

arXiv

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arXiv 2025年

作者： Tang, Sophia Zhang, Yinuo Tong, Alexander Chatterjee, Pranam Department of Biomedical Engineering Duke University United States Management and Technology Program University of Pennsylvania United States Center of Computational Biology Duke-NUS Medical School Singapore Mila Quebec AI Institute Canada Université de Montréal Canada Department of Computer Science Duke University United States Department of Biostatistics and Bioinformatics Duke University United States

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment. © 2025, CC BY-NC-ND.

关键词： Velocity distribution

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AN INFINITE SUM RELATED TO WKB EIGENVALUES

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JOURNAL OF MATHEMATICAL PHYSICS 1995年第6期36卷 3157-3160页

作者： MILLANE, RP Computational Science and Engineering Program Purdue University West Lafayette Indiana 47907‐1160

An infinite sum that appears in the error term for variational estimates of eigenvalues of the Helmholtz equation is examined. The sum is evaluated directly, confirming a result based on a higher-order variational ana...

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On the particle approximation of lagged Feynman–Kac formulae

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Stochastic Processes and their Applications 2025年 188卷

作者： Awadelkarim, Elsiddig Caffarel, Michel Del Moral, Pierre Jasra, Ajay Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal 23955-6900 Saudi Arabia University of Toulouse CNRS-Lab. de Chimie et Physique Quantiques Toulouse 31062 France Centre de Recherche Inria Bordeaux Sud-Ouest Talence 33405 France School of Data Science The Chinese University of Hong Kong Shenzhen Shenzhen China

In this paper we examine the numerical approximation of the limiting invariant measure associated with Feynman–Kac formulae. These are expressed in a discrete time formulation and are associated with a Markov chain and a potential function. The typical application considered here is the computation of eigenvalues associated with non-negative operators as found, for example, in physics or particle simulation of rare-events. We focus on a novel lagged approximation of this invariant measure, based upon the introduction of a ratio of time-averaged Feynman–Kac marginals associated with a positive operator iterated l∈N times;a lagged Feynman–Kac formula. This estimator and its approximation using Diffusion Monte Carlo (DMC) are commonly used in the physics literature. In short, DMC is an iterative algorithm involving N∈N particles or walkers simulated in parallel, that undergo sampling and resampling operations. In this work, it is shown that for the DMC approximation of the lagged Feynman–Kac formula, one has an almost sure characterization of the L₁-error as the time parameter (iteration) goes to infinity and this is at most of O(exp{−κl}/N), for κ>0. In addition a non-asymptotic in time, and time uniform L₁−bound is proved which is O(l/N). We also prove a novel central limit theorem to give a characterization of the exact asymptotic in time variance. This analysis demonstrates that the strategy used in physics, namely, to run DMC with N and l small and, for long time enough, is mathematically justified. Our results also suggest how one should choose N and l in practice. We emphasize that these results are not restricted to physical applications;they have broad relevance to the general problem of particle simulation of the Feynman–Kac formula, which is utilized in a great variety of scientific and engineering fields. © 2025 Elsevier B.V.

关键词： Diffusion Monte Carlo Eigenvalue approximation Feynman–Kac formula

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