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

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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

Low-Loss, Nonvolatile Tuning of Bragg Structures with Sb2Se3

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Low-Loss, Nonvolatile Tuning of Bragg Structures with Sb2Se3

Conference on Lasers and Electro-Optics (CLEO)

作者： Nicholas A. Nobile Chuanyu Lian Hongyi Sun Yi-Siou Huang Brian Mills Cosmin Constantin Popescu Dennis Callahan Juejun Hu Carlos A. Ríos Ocampo Nathan Youngblood Electrical & Computer Engineering Department University of Pittsburgh Pittsburgh PA USA Department of Materials Science & Engineering University of Maryland College Park MD USA Institute for Research in Electronics and Applied Physics University of Maryland College Park MD USA Department of Materials Science & Engineering Massachusetts Institute of Technology Cambridge MA USA Draper Scholar Program The Charles Stark Draper Laboratory Inc Cambridge MA USA The Charles Stark Draper Laboratory Inc Cambridge MA USA

Sb 2 Se 3 is used to switch between broadband transparency and enhanced index contrast in two device types leveraging Bragg gratings for tunable stop-and pass-band functionalities. Experimental results highlight fabr... 详细信息

ISBN: (纸本)9798350369311

关键词： Bragg gratings Waveguide transitions Phase change materials Optical filters Optical switches Refractive index Fabry-Perot Indexes Passband Optical waveguides

Modeling of Measurement Error in Financial Returns Data

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arXiv 2024年

作者： Jasra, Ajay Maama, Mohamed Mijatović, Aleksandar School of Data Science The Chinese University of Hong Kong 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 Department of Statistics University of Warwick United Kingdom

In this paper we consider the modeling of measurement error for fund returns data. In particular, given access to a time-series of discretely observed log-returns and the associated maximum over the observation period, we develop a stochastic model which models the true log-returns and maximum via a Lévy process and the data as a measurement error there-of. The main technical difficulty of trying to infer this model, for instance Bayesian parameter estimation, is that the joint transition density of the return and maximum is seldom known, nor can it be simulated exactly. Based upon the novel stick breaking representation of [12] we provide an approximation of the model. We develop a Markov chain Monte Carlo (MCMC) algorithm to sample from the Bayesian posterior of the approximated posterior and then extend this to a multilevel MCMC method which can reduce the computational cost to approximate posterior expectations, relative to ordinary MCMC. We implement our methodology on several applications including for real data. Copyright © 2024, The Authors. All rights reserved.

关键词： Markov chains

IoT Attack Detection and Prevention Through Machine Learning System

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IoT Attack Detection and Prevention Through Machine Learning...

Communication, Security and Artificial Intelligence (ICCSAI), International Conference on

作者： Kanishk Agrawal Pavan Kumar Reddy Poli Yash Gupta Garv Juneja Adhip Kishen Bopaiah Dinesh Ashok Arani Department of IET CSE Manglayatan University Aligarh Uttar Pradesh India Managing Information Technology Implementations Program management for fortune 6 Healthcare Company USA Department of Computer Science and Information Systems Birla Institute of Technology and Science Pilani India Department of Computer Science and Engineering Maharaja Surajmal Institute of Technology Guru Gobind Singh Indraprastha University Delhi India ICT Trainer Trinity College Bangalore India Manglayatan University Aligarh Uttar Pradesh India

Attacks on web applications are constantly growing in both frequency and severity. Abundant data on the internet stimulates hackers to attempt different types of cyberattacks. Attack detection using conventional approaches and outdated data processing techniques has become outmoded as a result of this development. The purpose of this study is to investigate IoT attacks and discuss the efficient ML technique implementation strategies for restricting security risks. Among different security techniques, Machine learning (ML) systems demonstrated commendable feasibility in improving network and device security for the Internet of Things. The study with contextual research recognises and comprehends that modified “Support Vector Machine (SVM)” as well as “Random Forest (RF)” ML techniques showed optimal performance in IoT attack detection and prevention.

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

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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

TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs

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arXiv 2022年

作者： Li, Alex J. Sundar, Vikram Grigoryan, Gevorg Keating, Amy E. Department of Chemistry Massachusetts Institute of Technology United States Computational and Systems Biology Program Massachusetts Institute of Technology United States Department of Computer Science Dartmouth College United States Departments of Biology and Biological Engineering Massachusetts Institute of Technology United States

Computational protein design has the potential to deliver novel molecular structures, binders, and catalysts for myriad applications. Recent neural graph-based models that use backbone coordinate-derived features show exceptional performance on native sequence recovery tasks and are promising frameworks for design. A statistical framework for modeling protein sequence landscapes using Tertiary Motifs (TERMs), compact units of recurring structure in proteins, has also demonstrated good performance on protein design tasks. In this work, we investigate the use of TERM-derived data as features in neural protein design frameworks. Our graph-based architecture, TERMinator, incorporates TERM-based and coordinate-based information and outputs a Potts model over sequence space. TERMinator outperforms state-of-the-art models on native sequence recovery tasks, suggesting that utilizing TERM-based and coordinate-based features together is beneficial for protein design. © 2022, CC BY.

关键词： Potts model

Coherent Acoustic Phonons in Bi2Se3 Ultrathin Films Probed by Femtosecond, Optical Pump-Probe Spectroscopy

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Coherent Acoustic Phonons in Bi2Se3 Ultrathin Films Probed b...

CLEO: Fundamental Science, CLEO:FS 2024 - Part of Conference on Lasers and Electro-Optics, CLEO 2024

作者： Cheng, Jing Niherysh, Kiryl A. Francis, Peter Chakraborty, Debamitra Lombardi, Floriana Erts, Donats Prischepa, Serghej L. Laszcz, Adam Komissarov, Ivan V. Sobolewski, Roman Materials Science Graduate Program University of Rochester RochesterNY14627 United States Laboratory for Laser Energetics University of Rochester RochesterNY14623-1299 United States Department of Microtechnology and Nanoscience Chalmers University of Technology Gothenburg Sweden Institute of Chemical Physics University of Latvia Riga Latvia Department of Electrical and Computer Engineering University of Rochester RochesterNY14627 United States Dipartimento di Fisica "E.R. Caianiello" Università degli Studi di Salerno Sa FiscianoI-84084 Italy Lukasiewicz Research Network Institute of Microelectronics and Photonics WarszawaPL-02668 Poland

ISBN: (纸本)9781957171395

The dynamics of coherent acoustic phonons in the Bi2Se3 layered crystal system are investigated. The findings reveal that the frequency evolution of breathing modes with the number of the material quintuple layers and the dispersion relation both can be explained by a modified chain model with a nonuniform coupling force. © Optica Publishing Group 2024, © 2024 The Author(s)

关键词： Ultrathin films

Enhancing Diagnostic Accuracy for Knee Osteoarthritis Using a Deep Learning Approach

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Enhancing Diagnostic Accuracy for Knee Osteoarthritis Using ...

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)

A Machine Learning Algorithm to Automate Vehicle Classification and License Plate Detection

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Wireless Communications and Mobile Computing 2022年第0期2022卷

作者： Srividhya, S.R. Kavitha, C. Lai, Wen-Cheng Mani, Vinodhini Khalaf, Osamah Ibrahim Department Of Computer Science And Engineering Sathyabama Institute Of Science And Technology Chennai India Bachelor Program In Industrial Projects National Yunlin University Of Science And Technology Douliu640301 Taiwan Department Electronic Engineering National Yunlin University Of Science And Technology Douliu640301 Taiwan Al-Nahrain University Al-Nahrain Nanorenewable Energy Research Center Baghdad Iraq

In the field of intelligent transportation systems (ITS), video surveillance is a hot research topic;this surveillance is used in a variety of applications, such as detecting the cause of an accident, tracking down a specific vehicle, and discovering routes between major locations. Object detection and shadow elimination are the main tasks in this area. Object detection in computer vision is a critical and vital part of object and scene recognition, and its applications are vast in the fields of surveillance and artificial intelligence. Additionally, other challenges arise in regard to video surveillance, including the recognition of text. Based on shadow elevation, we present in this work an inner-outer outline profile (IOOPL) algorithm for detecting the three levels of object boundaries. A system of video surveillance monitoring of traffic can be incorporated into this method. It is essential to identify the type of detected objects in intelligent transportation systems (ITS) to track safely and estimate traffic parameters correctly. This work addresses the problem of not recognizing object shadows as part of the object itself in-vehicle image segmentation. This paper proposes an approach for detecting and segmenting vehicles by eliminating their shadow counterparts using the delta learning algorithm (Widrow-Hoff learning rule), where the system is trained with various types of vehicles according to their appearance, colors, and build types. An essential aspect of the intelligent transportation system is recognizing the type of the detected object so that it can be tracked reliably and the traffic parameters can be estimated correctly. Furthermore, we propose to classify vehicles using a machine learning algorithm consisting of artificial neural networks trained using the delta learning algorithm, a high-performance machine learning algorithm, to obtain information regarding their travels. The paper also presents a method for recognizing the number plate using tex

关键词： Object detection