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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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A Conceptual Exploration of Generative AI-Induced Cognitive Dissonance and its Emergence in University-Level Academic Writing

arXiv

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arXiv 2025年

作者： Seran, Carl Errol Tan, Myles Joshua Toledo Karim, Hezerul Abdul AlDahoul, Nouar Biology Program College of Arts and Sciences University of St. La Salle Bacolod Philippines Department of Natural Sciences College of Arts and Sciences University of St. La Salle Bacolod Philippines Faculty of Education University of the Philippines Open University Los Baños Philippines Department of Electrical and Computer Engineering Herbert Wertheim College of Engineering University of Florida GainesvilleFL United States Department of Epidemiology College of Public Health and Health Professions College of Medicine University of Florida GainesvilleFL United States Department of Chemical Engineering College of Engineering and Technology University of St. La Salle Bacolod Philippines Department of Electronics Engineering College of Engineering and Technology University of St. La Salle Bacolod Philippines Yo-Vivo Corporation Bacolod Philippines Faculty of Engineering Multimedia University Persiaran Multimedia Cyberjaya Malaysia Department of Computer Science Division of Science New York University Abu Dhabi Abu Dhabi United Arab Emirates

The integration of Generative Artificial Intelligence (GenAI) intouniversity-level academic writing presents both opportunities and challenges,particularly in relation to cognitive dissonance (CD). This work explores howGenAI serves as both a trigger and amplifier of CD, as students navigateethical concerns, academic integrity, and self-efficacy in their writingpractices. By synthesizing empirical evidence and theoretical insights, weintroduce a hypothetical construct of GenAI-induced CD, illustrating thepsychological tension between AI-driven efficiency and the principles oforiginality, effort, and intellectual ownership. We further discuss strategiesto mitigate this dissonance, including reflective pedagogy, AI literacyprograms, transparency in GenAI use, and discipline-specific task *** approaches reinforce critical engagement with AI, fostering a balancedperspective that integrates technological advancements while safeguarding humancreativity and learning. Our findings contribute to ongoing discussions on AIin education, self-regulated learning, and ethical AI use, offering aconceptual framework for institutions to develop guidelines that align AIadoption with academic values. © 2025, CC BY.

关键词： Generative adversarial networks

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Three-dimensional computation of light scattering from cells

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IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS 1996年第4期2卷 898-905页

作者： Dunn, A RichardsKortum, R Biomedical Engineering Program Department of Electrical and Computer Engineering University of Technology Austin TX USA

Using the finite-difference time-domain method, three-dimensional scattering patterns are computed for cells containing multiple organelles. The scattering cross section and average cosine of the scattering angle are computed for cells as a function of volume fraction of melanin granules and mitochondria, Results show that small organelles play a significant role in light scattering from cells, and the volume fraction of organelles affects both the total amount of scattered light and the angular distribution of scattered light.

关键词： Light scattering Optical scattering Mie scattering Electromagnetic scattering Cells (biology) Optical refraction Finite difference methods Time domain analysis Biomedical optical imaging High-resolution imaging

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Enhancing Diagnostic Accuracy for Knee Osteoarthritis Using a Deep Learning Approach

Enhancing Diagnostic Accuracy for Knee Osteoarthritis Using ...

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International Symposium on Applied Science 2024, ISAS 2024

作者： Raza, Aquib Ching, Congo Tak Shing Liu, Peng-Ta Phan, Thien-Luan Tran, Ngoc-Luan Nguyen, Ha Anh T. Rameez, Mohammad Li, Hung-Chung Linh, Dao Nguyen Phuong Van Hieu, Nguyen Tran, Trung Nghia National Taiwan University Taipei City10673 Taiwan Research Center for Information Technology Academia Sinica Taipei City11529 Taiwan Graduate Institute of Biomedical Engineering National Chung Hsing University Taichung402 Taiwan Department of Electrical Engineering National Chi Nan University Nantou County Taiwan Advanced Plant and Food Crop Biotechnology Center National Chung Hsing University Taichung402 Taiwan International Doctoral Program in Agriculture National Chung Hsing University Taichung402 Taiwan Fall Prevention Center Department of Physical Medicine & Rehabilitation Changhua Christian Hospital Changhua500 Taiwan Department of Physics and Electronic Engineering University of Science Vietnam National University - Ho Chi Minh City Ho Chi Minh City70000 Viet Nam Department of Computer Science University of York York HeslingtonYO10 5DD United Kingdom Undergraduate Program of Intellectual Creativity Engineering National Chung Hsing University Taichung402 Taiwan Ho Chi Minh City72409 Viet Nam HCMUT Vietnam National University Ho Chi Minh City Thu Duc Ho Chi Minh City71308 Viet Nam

This research introduces a deep learning framework that combines convolutional neural networks with autoencoders to improve the diagnostic accuracy of knee osteoarthritis. The study utilized a publicly available dataset from the Mendeley Data repository, where knee joint images were preprocessed using Contrast Limited Adaptive Histogram Equalization to enhance contrast and ensure consistent image sizing. Initially, an autoencoder was employed in an unsupervised manner to learn compressed representations of the data. These representations were then used to train a CNN to classify knee images into 'healthy' and 'osteoarthritic' categories. The model was trained using an 80:20 split for training and testing data, incorporating early stopping and data augmentation techniques to prevent overfitting and enhance generalization. Performance metrics such as accuracy, precision, recall, and the area under the Receiver Operating Characteristic curve (ROCAUC) were used to evaluate the model, resulting in a high test accuracy of 98.95%. The high precision and recall rates further confirmed the model's robustness in diagnosing KOA. To enhance interpretability, Gradient-weighted Class Activation Mapping (Grad-CAM) was applied to identify critical regions in the images that influenced the model's decisions. Additionally, t-Distributed Stochastic Neighbor Embedding (t-SNE) was used to visualize the high-dimensional encoded features in a two-dimensional space, providing deeper insights into how the model differentiates between classes. The promising results of this deep learning approach suggest its potential for broader applications in medical imaging diagnostics. By providing healthcare professionals with a tool that enhances diagnostic accuracy and operational efficiency, this framework lays the foundation for developing scalable, AI-driven diagnostic systems for various complex medical conditions. © 2025 Institute of Physics Publishing. All rights reserved.

关键词： Joints (anatomy)

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Crack Catcher AI — Enabling Smart Fracture Mechanics Approach for Damage Control in Thin Silicon Wafers for 3D Semiconductor Integrated Devices/Packages

Crack Catcher AI — Enabling Smart Fracture Mechanics Approa...

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Annual International Symposium on Reliability Physics

作者： Gabriel Preston Greer Gonzolez Andrea S. Karnyoto Fitya S. Mozar Matthew M. Henry Mahmud Isnan Kuncahyo S. Nugroho Henry Candra Muhamad Doris Dianing N. N. Putri Tyas K Sari Bens Pardamean Endang Djuana Derrric Speaks Arief S. Budiman Oregon Renewable Energy Center (OREC) Oregon Institute of Technology (Oregon Tech) Klamath Falls OR USA Dept. of Manufacturing & Mechanical Eng. & Tech. (MMET) Oregon Institute of Technology Klamath Falls OR USA Bioinformatics & Data Science Research Center (BDSRC) Bina Nusantara University Jakarta Indonesia Computer Sci. Dept. BINUS Grad. Program - Master of Computer Sci. Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Center for Artificial Intelligence and Advanced Technology (CAPTIVATE) Universitas TRISAKTI Jakarta Indonesia Department of Electrical Engineering Faculty of Industrial Technology Universitas TRISAKTI Jakarta Indonesia Industrial Eng. Dept. BINUS Grad. Program – Master of Industrial Eng. Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331504779

ISBN: (纸本)9798331504786

The importance of silicon cannot be undermined - in photovoltaics (PV) as well as in semiconductor industries. However, silicon is very brittle. Silicon cells/wafers crack easily during manufacturing assembly and/or during device operations. Crack Catcher AI uses novel smart fracture mechanics approach with Artificial Intelligence (AI) methodologies to predict and control crack/damage evolution in thin silicon cells/wafers. This is critical as semiconductor 3D integration technology calls for wafer-to-wafer bonding with utmost alignment accuracy and yield/reliability.

关键词： Semiconductor device measurement Three-dimensional displays Accuracy Semiconductor device reliability Silicon Artificial intelligence Bonding Stress Three-dimensional integrated circuits Stress measurement

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Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches

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computers in Biology and Medicine 2025年 190卷 110044-110044页

作者： Saif, Ahmed Islam, Md. Tarikul Raihan, Md. Obayed Yousefi, Niloofar Rahman, Md. Ajijur Faridi, Hafeez Hasan, Al Riyad Hossain, Mirza Mahfuj Saleem, Rasha Mohammed Albadrani, Ghadeer M. Al-Ghadi, Muath Q. Ahasan Setu, Md. Ali Kamel, Mohamed Abdel-Daim, Mohamed M. Aktaruzzaman, Md. Department of Pharmacy Faculty of Science University of Rajshahi Rajshahi6205 Bangladesh Department of Genetic Engineering and Biotechnology Faculty of Biological Science and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Jashore7408 Bangladesh Department of Pharmaceutical Sciences College of Health Sciences and Pharmacy Chicago State University ChicagoIL United States Department of Industrial Engineering and Management Systems University of Central Florida USA OrlandoFL United States Department of Pharmacy Faculty of Biological Science and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Department of Computer Science and Engineering Faculty of Engineering and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Department of Laboratory Medicine Faculty of Applied Medical Sciences Al-Baha University Al-Baha65431 Saudi Arabia Department of Biology College of Science Princess Nourah bint Abdulrahman University 84428 Riyadh11671 Saudi Arabia Department of Zoology College of Science King Saud University P.O. Box 2455 Riyadh11451 Saudi Arabia Department of Microbiology Faculty of Biological Science and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Department of Medicine and Infectious Diseases Faculty of Veterinary Medicine Cairo University Giza12211 Egypt Department of Pharmaceutical Sciences Pharmacy Program Batterjee Medical College P.O. Box 6231 Jeddah21442 Saudi Arabia Pharmacology Department Faculty of Veterinary Medicine Suez Canal University Ismailia41522 Egypt

Cancer remains a significant global health challenge, with the Cell Division Cycle 7 (CDC7) protein emerging as a potential therapeutic target due to its critical role in tumor proliferation, survival, and resistance. However, a comprehensive analysis of CDC7 across multiple cancers is lacking, and existing therapeutic options have come with limited clinical success. The aim of this is to integrate a comprehensive pan-cancer analysis of CDC7 with the identification of novel marine-derived inhibitors, bridging the understanding of CDC7's role as a prognostic biomarker and therapeutic target across diverse cancer types. In this study, we conducted a pan-cancer analysis of CDC7 across 33 tumor types using publicly available datasets to evaluate its expression, genetic alterations, immune interactions, survival, and prognostic significance. Additionally, a marine-derived compound library of 31,492 molecules was screened to identify potential CDC7 inhibitors using chemoinformatics and machine learning. The top candidates underwent rigorous evaluations, including molecular docking, pharmacokinetics, toxicity, Density Functional Theory (DFT) calculations, and Molecular Dynamics (MD) simulations. The findings revealed that CDC7 is overexpressed in several cancers and is associated with poor survival outcomes and unfavorable prognosis. Enrichment analysis linked CDC7 to critical DNA replication pathways, while its role in modulating tumor-immune interactions highlighted its potential as a target for immunotherapy. Among all tested compounds, Tetrahydroaltersolanol D (CMNPD21999) exhibited the strongest binding affinity and stability, along with better drug-likeness and zero toxicity. These attributes highlight its potential as a promising drug candidate for CDC7 inhibition and future cancer treatment development. Furthermore, additional in vitro and in vivo studies are required to confirm the effectiveness of this drug candidate against the CDC7 protein. © 2025

关键词： Gene expression

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engineering Andreev Bound States for Thermal Sensing in Proximity Josephson Junctions

arXiv

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arXiv 2025年

作者： Jung, Woochan Arnault, Ethan G. Huang, Bevin Park, Jinho Jang, Seong Watanabe, Kenji Taniguchi, Takashi Englund, Dirk Fong, Kin Chung Lee, Gil-Ho Physics Department Pohang University of Science and Technology Pohang37673 Korea Republic of Research Laboratory of Electronics Massachusetts Institute of Technology CambridgeMA02139 United States Intelligence Community Postdoctoral Research Fellowship Program Massachusetts Institute of Technology CambridgeMA02139 United States Department of Mechanical Engineering Columbia University New YorkNY10027 United States Research Center for Functional Materials National Institute for Materials Science Tsukuba Japan International Center for Materials Nanoarchitectonics National Institute for Materials Science Tsukuba Japan Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Department of Electrical and Computer Engineering Northeastern University BostonMA02115 United States Department of Physics Northeastern University BostonMA02115 United States Quantum Materials and Sensing Institute BurlingtonMA01803 United States

The thermal response of proximity Josephson junctions (JJs) is governed by the temperature (T)- dependent occupation of Andreev bound states (ABS), making them promising candidates for sensitive thermal detection. In this study, we systematically engineer ABS to enhance the thermal sensitivity of critical current (lc) of proximity JJs, quantified as |dlc/dT/| for threshold readout scheme and |dlc/***−1| for inductive readout scheme. Using a gate-tunable graphene-based JJ platform, we explore the impact of key parameters—including channel length, transparency, carrier density, and superconducting material—on the thermal response. Our results reveal that the proximity-induced superconducting gap plays a crucial role in optimizing thermal sensitivity. Notably, we see a maximum |dlc/***−1| value of 0.6 K−1 at low temperatures with titanium-based graphene JJs. By demonstrating a systematic approach to engineering ABS in proximity JJs, this work establishes a versatile framework for optimizing thermal sensors and advancing the study of ABS-mediated transport. © 2025, CC BY.

关键词： Superconducting materials

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Unbiased Parameter Estimation for Bayesian Inverse Problems

arXiv

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arXiv 2025年

作者： Chada, Neil K. Jasra, Ajay Maama, Mohamed Tempone, Raul Department of Mathematics City University of Hong Kong China School of Data Science The Chinese University of Hong Kong Shenzhen CN Shenzhen China Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this paper we consider the estimation of unknown parameters in Bayesian inverse problems. In most cases of practical interest, there are several barriers to performing such estimation, This includes a numerical approximation of a solution of a differential equation and, even if exact solutions are available, an analytical intractability of the marginal likelihood and its associated gradient, which is used for parameter estimation. The focus of this article is to deliver unbiased estimates of the unknown parameters, that is, stochastic estimators that, in expectation, are equal to the maximizer of the marginal likelihood, and possess no numerical approximation error. Based upon the ideas of [4] we develop a new approach for unbiased parameter estimation for Bayesian inverse problems. We prove unbiasedness and establish numerically that the associated estimation procedure is faster than the current state-of-the-art methodology for this problem. We demonstrate the performance of our methodology on a range of problems which include a PDE and ODE. Copyright © 2025, The Authors. All rights reserved.

关键词： Markov processes

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Imaging the evolution of lithium-solid electrolyte interface using operando scanning electron microscopy

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Nature Communications 2025年第1期16卷 1-11页

作者： Zhao, Lihong Feng, Min Wu, Chaoshan Guo, Liqun Chen, Zhaoyang Risal, Samprash Ai, Qing Lou, Jun Fan, Zheng Qi, Yue Yao, Yan Department of Electrical and Computer Engineering and Texas Center for Superconductivity at the University of Houston University of Houston Houston TX United States School of Engineering Brown University Providence RI United States Materials Science and Engineering Program University of Houston Houston TX United States Department of Materials Science and Nanoengineering and the Rice Advanced Materials Institute Rice University Houston TX United States Department of Engineering Technology University of Houston Houston TX United States

The quality of Li–solid electrolyte interface is crucial for the performance of solid-state lithium metal batteries, particularly at low stack pressure, but its dynamics during cell operation remain poorly understood due to a lack of reliable operando characterization techniques. Here, we report the evolution of Li–electrolyte interface with high spatial resolution using operando scanning electron microscopy under realistic operating conditions. By tracking the stripping process of both Li and Li-rich Li-Mg alloy anodes, we show that multiple voids coalesce into a single gap and eventually delaminate the interface in Li, whereas the voids split and collapse to partially recover interfacial contact in Li-Mg. Density functional theory calculations show that the stronger Mg-S interaction at the metal–electrolyte interface attracts Mg toward the interface and repels Li-vacancies into the bulk, resulting in a reduced number of voids. The pressure-dependent voltage profiles of Li and Li-Mg stripping suggest that loss of contact due to void formation, rather than Mg accumulation at the interface, is the origin of high overpotential that limits the utilization of metal anodes. Improved interfacial contact enables stable cycling of all-solid-state lithium full cell at low stack pressure (1 MPa) and moderate rate (2 mA cm⁻²) simultaneously. The real-time visualization of Li–electrolyte interface dynamics provides critical insights into the rational design of solid-state battery interfaces. © The Author(s) 2025.

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BENCHMARKING COMMUNITY DRUG RESPONSE PREDICTION MODELS: DATASETS, MODELS, TOOLS, AND METRICS FOR CROSS-DATASET GENERALIZATION ANALYSIS

arXiv

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arXiv 2025年

作者： Partin, Alexander Vasanthakumari, Priyanka Narykov, Oleksandr Wilke, Andreas Koussa, Natasha Jones, Sara E. Zhu, Yitan Overbeek, Jamie C. Jain, Rajeev Fernando, Gayara Demini Sanchez-Villalobos, Cesar Garcia-Cardona, Cristina Mohd-Yusof, Jamaludin Chia, Nicholas Wozniak, Justin M. Ghosh, Souparno Pal, Ranadip Brettin, Thomas S. Weil, M. Ryan Stevens, Rick L. Division of Data Science and Learning Argonne National Laboratory LemontIL United States Frederick National Laboratory for Cancer Research Cancer Data Science Initiatives Cancer Research Technology Program FrederickMD United States Department of Statistics University of Nebraska–Lincoln LincolnNE United States Department of Electrical & Computer Engineering Texas Tech University LubbockTX United States Division of Computer Computational and Statistical Sciences Los Alamos National Laboratory Los AlamosNM United States Department of Computer Science The University of Chicago ChicagoIL United States

Deep learning (DL) and machine learning (ML) models have shown promise in drug response prediction (DRP), yet their ability to generalize across datasets remains an open question, raising concerns about their real-world applicability. Due to the lack of standardized benchmarking approaches, model evaluations and comparisons often rely on inconsistent datasets and evaluation criteria, making it difficult to assess true predictive capabilities. In this work, we introduce a benchmarking framework for evaluating cross-dataset prediction generalization in DRP models. Our framework incorporates five publicly available drug screening datasets, six standardized DRP models, and a scalable workflow for systematic evaluation. To assess model generalization, we introduce a set of evaluation metrics that quantify both absolute performance (e.g., predictive accuracy across datasets) and relative performance (e.g., performance drop compared to within-dataset results), enabling a more comprehensive assessment of model transferability. Our results reveal substantial performance drops when models are tested on unseen datasets, underscoring the importance of rigorous generalization assessments. While several models demonstrate relatively strong cross-dataset generalization, no single model consistently outperforms across all datasets. Furthermore, we identify CTRPv2 as the most effective source dataset for training, yielding higher generalization scores across target datasets. By sharing this standardized evaluation framework with the community, our study aims to establish a rigorous foundation for model comparison, and accelerate the development of robust DRP models for real-world applications. © 2025, CC BY.

关键词： Prediction models

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