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MR2CPPIS: Accurate prediction of protein–protein interaction sites based on multi-scale Res2Net with coordinate attention mechanism

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computers in Biology and Medicine 2024年 176卷 108543-108543页

作者： Gong, Yinyin Li, Rui Liu, Yan Wang, Jilong Cao, Buwen Fu, Xiangzheng Li, Renfa Chen, Danny Z. College of Computer Science and Electronic Engineering Hunan University Changsha410082 China Hunan Engineering Research Center of Advanced Embedded Computing and Intelligent Medical Systems Hunan University Changsha410082 China Peng Cheng Laboratory Shenzhen518066 China College of Information and Electronic Engineering Hunan City University Yiyang413002 China Department of Computer Science and Engineering University of Notre Dame Notre DameIN46556 United States

Proteins play a vital role in various biological processes and achieve their functions through protein–protein interactions (PPIs). Thus, accurate identification of PPI sites is essential. Traditional biological methods for identifying PPIs are costly, labor-intensive, and time-consuming. The development of computational prediction methods for PPI sites offers promising alternatives. Most known deep learning (DL) methods employ layer-wise multi-scale CNNs to extract features from protein sequences. But, these methods usually neglect the spatial positions and hierarchical information embedded within protein sequences, which are actually crucial for PPI site prediction. In this paper, we propose MR2CPPIS, a novel sequence-based DL model that utilizes the multi-scale Res2Net with coordinate attention mechanism to exploit multi-scale features and enhance PPI site prediction capability. We leverage the multi-scale Res2Net to expand the receptive field for each network layer, thus capturing multi-scale information of protein sequences at a granular level. To further explore the local contextual features of each target residue, we employ a coordinate attention block to characterize the precise spatial position information, enabling the network to effectively extract long-range dependencies. We evaluate our MR2CPPIS on three public benchmark datasets (Dset 72, Dset 186, and PDBset 164), achieving state-of-the-art performance. The source codes are available at https://***/YyinGong/MR2CPPIS. © 2024 Elsevier Ltd

关键词： Forecasting

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A Data-Informed Analysis of Scalable Supervision for Safety in Autonomous Vehicle Fleets

arXiv

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arXiv 2024年

作者： Hickert, Cameron Yan, Zhongxia Wu, Cathy The Institute for Data Systems and Society Massachusetts Institute of Technology CambridgeMA02139 United States The Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States The Laboratory for Information & Decision Systems The Institute for Data Systems and Society The Department of Civil and Environmental Engineering Massachusetts Institute of Technology CambridgeMA02139 United States

Autonomous driving is a highly anticipated approach toward eliminating roadway fatalities. At the same time, the bar for safety is both high and costly to verify. This work considers the role of remotely-located human operators supervising a fleet of autonomous vehicles (AVs) for safety. Such a 'scalable supervision' concept was previously proposed to bridge the gap between still-maturing autonomy technology and the pressure to begin commercial offerings of autonomous driving. The present article proposes DISCES, a framework for Data-Informed Safety-Critical Event Simulation, to investigate the practicality of this concept from a dynamic network loading standpoint. With a focus on the safety-critical context of AVs merging into mixed-autonomy traffic, vehicular arrival processes at 1,097 highway merge points are modeled using microscopic traffic reconstruction with historical data from interstates across three California counties. Combined with a queuing theoretic model, these results characterize the dynamic supervision requirements and thereby scalability of the teleoperation approach. Across all scenarios we find reductions in operator requirements greater than 99% as compared to in-vehicle supervisors for the time period analyzed. The work also demonstrates two methods for reducing these empirical supervision requirements: (i) the use of cooperative connected AVs - which are shown to produce an average 3.67 orders-of-magnitude system reliability improvement across the scenarios studied - and (ii) aggregation across larger regions. Copyright © 2024, The Authors. All rights reserved.

关键词： Autonomous vehicles

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State Derivative Normalization for Continuous-Time Deep Neural Networks

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IFAC-PapersOnLine 2024年第15期58卷 253-258页

作者： Jonas Weigand Gerben I. Beintema Jonas Ulmen Daniel Görges Roland Tóth Maarten Schoukens Martin Ruskowski Chair of Machine Tools and Control Systems RPTU Kaiserslautern and the German Research Center for Artificial Intelligence Kaiserslautern Germany Control Systems (CS) Group at the Department of Electrical Engineering Eindhoven University of Technology Netherlands. R. Tóth is also affiliated to the Systems and Control Laboratory at the Institute for Computer Science and Control Budapest Hungary Institute for Electromobility RPTU Kaiserslautern Germany

The importance of proper data normalization for deep neural networks is well known. However, in continuous-time state-space model estimation, it has been observed that improper normalization of either the hidden state or hidden state derivative of the model estimate, or even of the time interval can lead to numerical and optimization challenges with deep learning based methods. This results in a reduced model quality. In this contribution, we show that these three normalization tasks are inherently coupled. Due to the existence of this coupling, we propose a solution to all three normalization challenges by introducing a normalization constant at the state derivative level. We show that the appropriate choice of the normalization constant is related to the dynamics of the to-be-identified system and we derive multiple methods of obtaining an effective normalization constant. We compare and discuss all the normalization strategies on a benchmark problem based on experimental data from a cascaded tanks system and compare our results with other methods of the identification literature.

关键词： System Identification Continuous-Time Neural Ordinary Differential Equations Nonlinear State-Space

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INNSE: Invertible neural network-based DNA image storage with self-correction encoding

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Computational and Structural Biotechnology Journal 2025年 27卷 2492-2502页

作者： Zheng, Yanfen Zhang, Xiaokang Sun, Lijun Cao, Ben Wang, Bin Zhang, Qiang Zheng, Pan School of Computer Science and Technology Dalian University of Technology Liaoning Dalian116024 China The Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Liaoning Dalian116622 China Department of Accounting and Information Systems University of Canterbury Upper Riccarton Christchurch8140 New Zealand

DNA storage has become an alternative to silicon-based storage of media. However, when used to store multimodal data such as images, it fails to take full advantage of the characteristics of high correlation and variability present in such data, and currently remains inferior in terms of encoding density and time complexity. It also has the shortcoming of weak performance in terms of error correction methods to address insertion and deletion errors caused by error crosstalk. Therefore, we proposed an invertible neural network-based DNA image storage self-correction encoding method (INNSE) that uses the invertibility of network to perform up-down sampling processing on image and video data, thereby greatly reducing the number of DNA sequences required for data storage. A codebook generator was then designed to encode low-dimensional vectors into DNA sequences that meet various constraints. Finally, a self-correction method was constructed to achieve DNA sequence error correction at the base level without adding any redundant information. Our experimental results showed that, compared to the Yin-Yang algorithm, the encoding density of INNSE was increased by 3×, encoding time complexity was reduced by 95.26%. Under a simulated error rate of 2%, PSNR and SSIM were raised by 80.88% and 63.82%, respectively, proving that INNSE has significant advantages in encoding performance and error correction ability. © 2025

关键词： Network coding

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POVNav: A Pareto-Optimal Mapless Visual Navigator

arXiv

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arXiv 2023年

作者： Pushp, Durgakant Chen, Zheng Luo, Chaomin Gregory, Jason M. Liu, Lantao Luddy School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States The Department of Electrical and Computer Engineering Mississippi State University MS39762 United States DEVCOM Army Research Laboratory United States

Mapless navigation has emerged as a promising approach for enablingautonomous robots to navigate in environments where pre-existing maps may beinaccurate, outdated, or unavailable. In this work, we propose an image-basedlocal representation of the environment immediately around a robot to parsenavigability. We further develop a local planning and control framework, aPareto-optimal mapless visual navigator (POVNav), to use this representationand enable autonomous navigation in various challenging and real-worldenvironments. In POVNav, we choose a Pareto-optimal sub-goal in the image byevaluating all the navigable pixels, finding a safe visual path, and generatingactions to follow the path using visual servo control. In addition to providingcollision-free motion, our approach enables selective navigation behavior, suchas restricting navigation to select terrain types, by only changing thenavigability definition in the local representation. The ability of POVNav tonavigate a robot to the goal using only a monocular camera without relying on amap makes it computationally light and easy to implement on various roboticplatforms. Real-world experiments in diverse challenging environments, rangingfrom structured indoor environments to unstructured outdoor environments suchas forest trails and roads after a heavy snowfall, using various imagesegmentation techniques demonstrate the remarkable efficacy of our proposedframework. © 2023, CC BY-NC-SA.

关键词： Visual servoing

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arXiv

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arXiv 2024年

作者： Ren, Yingying Li, Qiuli Guo, Yangyang Pedrycz, Witold Xing, Lining Liu, Anfeng Song, Yanjie School of Computer Electronics and Information Guangxi University Nanning China Guangxi Key Laboratory of Multimedia Communications and Network Technology China Key Laboratory of Parallel Distributed and Intelligent Computing Guangxi University China School of Systems Science Beijing Jiaotong University Beijing China Department of Electrical and Computer Engineering University of Alberta Edmonton Canada Systems Research Institute Polish Academy of Sciences Poland Faculty of Engineering and Natural Sciences Department of Computer Engineering Sariyer Istanbul Turkey School of Electronic Engineering Xidian University Xian China School of Electronic Engineering Central South University Changsha China National Engineering Research Center of Maritime Navigation System Dalian Maritime University Dalian China

With the rapid development of the satellite industry, the information transmission network based on communication satellites has gradually become a major and important part of the future satellite ground integration network. However, the low transmission efficiency of the satellite data relay back mission has become a problem that is currently constraining the construction of the system and needs to be solved urgently. Effectively planning the task of satellite ground networking by reasonably scheduling resources is crucial for the efficient transmission of task data. In this paper, we hope to provide a task execution scheme that maximizes the profit of the networking task for satellite ground network planning considering feeding mode (SGNPFM). To solve the SGNPFM problem, a mixed-integer planning model with the objective of maximizing the gain of the link-building task is constructed, which considers various constraints of the satellite in the feed-switching mode. Based on the problem characteristics, we propose a distance similarity-based genetic optimization algorithm (DSGA), which considers the state characteristics between the tasks and introduces a weighted Euclidean distance method to determine the similarity between the tasks. To obtain more high-quality solutions, different similarity evaluation methods are designed to assist the algorithm in intelligently screening individuals. The DSGAalso uses an adaptive crossover strategy based on similarity mechanism, which guides the algorithm to achieve efficient population search. In addition, a task scheduling algorithm considering the feed-switching mode is designed for decoding the algorithm to generate a highquality scheme. The results of simulation experiments show that the DSGA can effectively solve the SGNPFM problem. Compared to other algorithms, the proposed algorithm not only obtains higher quality planning schemes but also has faster algorithm convergence speed. The proposed algorithm improves data trans

关键词： Profitability

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Stealthy Attacks on Sampled-Data Control and Encryption-Based Countermeasures

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IEEE Transactions on Automatic Control 2025年

作者： Shang, Jun Li, Yuzhe Chen, Tongwen Tongji University Department of Control Science and Engineering Shanghai Institute of Intelligent Science and Technology National Key Laboratory of Autonomous Intelligent Unmanned Systems Frontiers Science Center for Intelligent Autonomous Systems Shanghai200092 China Northeastern University State Key Laboratory of Synthetical Automation for Process Industries Shenyang110004 China University of Alberta Department of Electrical and Computer Engineering EdmontonABT6G 1H9 Canada

This paper investigates stealthy attacks on sampled-data control systems, where a continuous process is sampled periodically, and the resultant discrete output and control signals are transmitted through dual channels in wireless communication networks. Acknowledging the vulnerability of these transmitted data to cyber threats, we analyze two types of stealthy attacks that compromise either one or both channels. We explicitly present the necessary and sufficient conditions for the existence of stealthy single-channel attacks. To mitigate these security risks, we implement encryption-based countermeasures, including linear time-invariant and periodic encryption methods. We detail sufficient conditions under which these encryption strategies effectively thwart single- and dual-channel stealthy attacks. The effectiveness of these approaches and the theoretical findings are demonstrated through numerical simulations. © 1963-2012 IEEE.

关键词： Cyber attacks

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Energy-Efficient Probabilistic Semantic Communication over Space-Air-Ground Integrated Networks

arXiv

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arXiv 2024年

作者： Zhao, Zhouxiang Yang, Zhaohui Chen, Mingzhe Zhang, Zhaoyang Xu, Wei Huang, Kaibin College of Information Science and Electronic Engineering Zhejiang University China Hangzhou310027 China Department of Electrical and Computer Engineering Institute for Data Science and Computing University of Miami Coral GablesFL33146 United States National Mobile Communications Research Laboratory Southeast University Nanjing211189 China The Department of Electrical and Electronic Engineering The University of Hong Kong Hong Kong

Space-air-ground integrated networks (SAGINs) are emerging as a pivotal element in the evolution of future wireless networks. Despite their potential, the joint design of communication and computation within SAGINs remains a formidable challenge. In this paper, the problem of energy efficiency in SAGIN-enabled probabilistic semantic communication (PSC) system is investigated. In the considered model, a satellite needs to transmit data to multiple ground terminals (GTs) via an unmanned aerial vehicle (UAV) acting as a relay. During transmission, the satellite and the UAV can use PSC technique to compress the transmitting data, while the GTs can automatically recover the missing information. The PSC is underpinned by shared probability graphs that serve as a common knowledge base among the transceivers, allowing for resource-saving communication at the expense of increased computation resource. Through analysis, the computation overhead function in PSC is a piecewise function with respect to the semantic compression ratio. Therefore, it is important to make a balance between communication and computation to achieve optimal energy efficiency. The joint communication and computation problem is formulated as an optimization problem aiming to minimize the total communication and computation energy consumption of the network under latency, power, computation capacity, bandwidth, semantic compression ratio, and UAV location constraints. To solve this non-convex non-smooth problem, we propose an iterative algorithm where the closed-form solutions for computation capacity allocation and UAV altitude are obtained at each iteration. Numerical results show the effectiveness of the proposed algorithm. Copyright © 2024, The Authors. All rights reserved.

关键词： Energy efficiency

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Statistical 3D Device Simulation of Full Fluctuations of Gate-All-Around Silicon Nanosheet MOSFETs at Sub-3-nm Technology Nodes

Statistical 3D Device Simulation of Full Fluctuations of Gat...

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2022 International Symposium on VLSI Technology, systems and Applications, VLSI-TSA 2022

作者： Kola, Sekhar Reddy Li, Yiming Chen, Chieh-Yang Chuang, Min-Hui National Yang-Ming Chiao Tung University Electrical Engineering and Computer Science International Graduate Program Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Institute of Communications Engineering Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Department of Electrical Engineering and Computer Engineering Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Institute of Biomedical Engineering Hsinchu300 Taiwan National Yang-Ming Chiao Tung University Parallel and Scientific Computing Laboratory Hsinchu300 Taiwan

ISBN: (纸本)9781665409230

We for the first time study characteristic fluctuation of gate-all-around silicon nanosheet MOSFETs induced by random dopants fluctuation (RDF), interface trap fluctuation (ITF), and work function fluctuation (WKF), and their combinations. The explored devices affected by the WKF and its combination result in sizeable variability. Because of enigmatical interactions among the aforementioned random factors, overestimated variabilities occur if we only consider one random source each time, compared with the statistical 3D device simulation for full RDF, ITF and WKF at the same time. Notably, 10.78% and 103% overestimations are found for the threshold voltage and off-state current fluctuations. © 2022 IEEE.

关键词： Nanosheets

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A 3D Implementation of Convolutional Neural Network for Fast Inference

A 3D Implementation of Convolutional Neural Network for Fast...

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IEEE International Symposium on Circuits and systems (ISCAS)

作者： Narasinga Rao Miniskar Pruek Vanna-Iampikul Aaron Young Sung Kyu Lim Frank Liu Jieun Yoo Corrinne Mills Nhan Tran Farah Fahim Jeffrey S Vetter Computer Science and Mathematic Division Oak Ridge National Laboratory Oak Ridge USA Department of Electrical and Computer Engineering Georgia Institute of Technology Atlanta USA Department of Physics University of Illinois Chicago Chicago USA Scientific Computing Division Fermi National Accelerator Laboratory Chicago USA

Low latency inference has many applications in edge machine learning. In this paper, we present a run-time configurable convolutional neural network (CNN) inference ASIC design for low-latency edge machine learning. By implementing a 5-stage pipelined CNN inference model in a 3D ASIC technology, we demonstrate that the model distributed on two dies utilizing face-to-face (F2F) 3D integration achieves superior performance. Our experimental results show that the design based on 3D integration achieves 43% better energy-delay product when compared to the traditional 2D technology.

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