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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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Multi-modal Data based Semi-Supervised Learning for Vehicle Positioning

arXiv

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arXiv 2024年

作者： Huan, Ouwen Yang, Yang Luo, Tao Chen, Mingzhe Beijing Laboratory of Advanced Information Network Beijing University of Posts and Telecommunications Beijing100876 China Department of Electrical and Computer Engineering Institute for Data Science and Computing University of Miami Coral GablesFL33146 United States Beijing Key Laboratory of Network System Architecture and Convergence School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing100876 China

In this paper, a multi-modal data based semisupervised learning (SSL) framework that jointly use channel state information (CSI) data and RGB images for vehicle positioning is designed. In particular, an outdoor positioning system where the vehicle locations are determined by a base station (BS) is considered. The BS equipped with several cameras can collect a large amount of unlabeled CSI data and a small number of labeled CSI data of vehicles, and the images taken by cameras. Although the collected images contain partial information of vehicles (i.e. azimuth angles of vehicles), the relationship between the unlabeled CSI data and its azimuth angle, and the distances between the BS and the vehicles captured by images are both unknown. Therefore, the images cannot be directly used as the labels of unlabeled CSI data to train a positioning model. To exploit unlabeled CSI data and images, a SSL framework that consists of a pretraining stage and a downstream training stage is proposed. In the pretraining stage, the azimuth angles obtained from the images are considered as the labels of unlabeled CSI data to pretrain the positioning model. In the downstream training stage, a small sized labeled dataset in which the accurate vehicle positions are considered as labels is used to retrain the model. Simulation results show that the proposed method can reduce the positioning error by up to 30% compared to a baseline where the model is not pretrained. Copyright © 2024, The Authors. All rights reserved.

关键词： Self-supervised learning

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Clustering Interval and Triangular Granular Data: Modeling, Execution, and Assessment

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IEEE Transactions on Neural Networks and Learning systems 2024年第6期36卷 10000-10014页

作者： Yiming Tang Wenbin Wu Witold Pedrycz Jianwei Gao Xianghui Hu Zhaohong Deng Rui Chen Anhui Province Key Laboratory of Affective Computing and Advanced Intelligent Machine School of Computer and Information Hefei University of Technology Hefei China Department of Electrical and Computer Engineering University of Alberta Edmonton AB Canada School of Computer and Information Hefei University of Technology Hefei China Faculty of Automatic Control Electronics and Computer Science Silesian University of Tecghnology Gliwice Poland Research Center of Performance and Productivity Analysis Istinye University Istanbul TÃrkiye School of Computer Science and Engineering Southeast University Nanjing China School of Artificial Intelligence and Computer Jiangnan University Wuxi Jiangsu China

In current granular clustering algorithms, numeric representatives were selected by users or an ordinary strategy, which seemed simple; meanwhile, weight settings for granular data could not adequately express their structural characteristics. Aiming at these problems, in this study, a new scheme called a granular weighted kernel fuzzy clustering (GWKFC) algorithm is put forward. We propose the representative selection and granularity generation (RSGG) algorithm enlightened by the density peak clustering (DPC) algorithm. We build interval and triangular granular data on the strength of numeric representatives obtained by RSGG under the principle of justifiable granularity (PJG), in which we establish some combinations of functions and boundary constraints and prove their properties. Furthermore, we present a novel distance formula via the kernel function for granular data and design new weights to affect the coverage and specificity of granular data. In addition, based upon these factors, we come up with the GWKFC algorithm of granular clustering, and its performance with different granularity is assessed. To sum up, a macro framework involving granular modeling, granular clustering, and assessment has been set up. Lastly, the GWKFC algorithm and ten other granular clustering algorithms are compared by experiments on some artificial and UCI datasets together with datasets with large data or those of high dimensionality. It is found that the GWKFC algorithm can provide better granular clustering results by contrast with other algorithms. The originality is embodied as follows. First, we improve the previous density radius and present the RSGG algorithm to acquire numeric representatives. Second, we propose a new strategy to determine granular data boundaries and further obtain novel weights enlightened by the idea of volume. Lastly, we employ the kernel function to calculate the distance between granular data, which has a stronger spatial division ability than the pr

关键词： Clustering algorithms Data models Computational modeling Numerical models Kernel Phase change materials Granular computing Uncertainty Fuzzy sets Noise

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AI/ML Based Detection and Categorization of Covert Communication in IPv6 Network

arXiv

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arXiv 2025年

作者： Rahman, Mohammad Wali Ur Lin, Yu-Zheng Weeks, Carter Ruddell, David Gabriellini, Jeff Hayes, Bill Hariri, Salim Ziegler, Edward V. Department of Electrical and Computer Engineering University of Arizona TucsonAZ85721 United States Department of Management Information Systems University of Arizona TucsonAZ85721 United States Department of Systems and Industrial Engineering University of Arizona TucsonAZ85721 United States Laboratory for Advanced Cybersecurity Research National Security Agency United States

The flexibility and complexity of IPv6 extension headers allow attackers to create covert channels or bypass security mechanisms, leading to potential data breaches or system compromises. The mature development of machine learning has become the primary detection technology option used to mitigate covert communication threats. However, the complexity of detecting covert communication, evolving injection techniques, and scarcity of data make building machine-learning models challenging. In previous related research, machine learning has shown good performance in detecting covert communications, but oversimplified attack scenario assumptions cannot represent the complexity of modern covert technologies and make it easier for machine learning models to detect covert communications. To bridge this gap, in this study, we analyzed the packet structure and network traffic behavior of IPv6, used encryption algorithms, and performed covert communication injection without changing network packet behavior to get closer to real attack scenarios. In addition to analyzing and injecting methods for covert communications, this study also uses comprehensive machine learning techniques to train the model proposed in this study to detect threats, including traditional decision trees such as random forests and gradient boosting, as well as complex neural network architectures such as CNNs and LSTMs, to achieve detection accuracy of over 90%. This study details the methods used for dataset augmentation and the comparative performance of the applied models, reinforcing insights into the adaptability and resilience of the machine learning application in IPv6 covert communication. In addition, we also proposed a Generative AI-assisted interpretation concept based on prompt engineering as a preliminary study of the role of Generative AI agents in covert communication. © 2025, CC BY-NC-ND.

关键词： Decision trees

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Shields for Digital Images: A Watermarking Method with KAN Block and Simulation-Enhanced Noise Pool to Resist Screen-Camera Attacks

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IEEE Transactions on Circuits and systems for Video Technology 2025年

作者： Guo, Daidou Qin, Chuan Luo, Xiangyang Feng, Guorui Zhang, Xinpeng University of Shanghai for Science and Technology School of Optical-Electrical and Computer Engineering Shanghai 200093 China State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou 450000 China Henan Key Laboratory of Cyberspace Situation Awareness Zhengzhou 450001 China Shanghai University School of Communication and Information Engineering Shanghai 200444 China

To address the issues of privacy leakage and copyright infringement in screen-camera scenarios, we propose a robust image watermarking method, which incorporates kolmogorov-arnold network (KAN) blocks and a simulation-enhanced noise pool to resist screen-camera noise attacks. Specifically, we first modify the traditional convolutional blocks for processing high-dimensional features in the U-Net-based encoder to KAN blocks. This operation enhances the ability of encoder to model nonlinear relationships between complex features, while preserving global structure of the original image and minimizing the damage to local details caused by watermark embedding, thereby improving visual quality of the watermarked image. Additionally, to enhance the robustness of the proposed method against complex screen-camera noise attacks, a simulation-enhanced noise pool containing mathematical models and a deep noise simulation network, called NSim-Net, is designed. Especially, in NSim-Net, adversarial training between the simulator based on the improved U-Net and the discriminator based on PatchGAN effectively improves the ability to simulate complex noise. Experimental results demonstrate that, compared to typical screen-camera resilient watermarking methods, the watermarked image generated by the proposed method achieves a maximum peak signal-to-noise ratio (PSNR) improvement of 4.78 dB. Furthermore, based on our simulation-enhanced noise pool, the watermark extraction accuracy of the proposed method exceeds 98% under various screen-camera noise attacks. © 1991-2012 IEEE.

关键词： Imperceptibility Robustness Screen-Camera Resilient Watermarking Simulation-Enhanced Noise Pool

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Continual Reinforcement Learning for Digital Twin Synchronization Optimization

arXiv

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arXiv 2025年

作者： Tong, Haonan Chen, Mingzhe Zhao, Jun Hu, Ye Yang, Zhaohui Liu, Yuchen Yin, Changchuan The Beijing Key Laboratory of Network System Architecture and Convergence The Beijing Advanced Information Network Laboratory Beijing University of Posts and Telecommunications Beijing China Singapore The Department of Electrical and Computer Engineering Frost Institute for Data Science and Computing University of Miami Coral GablesFL33146 United States The Department of Industrial and Systems Engineering University of Miami Coral GablesFL33146 United States The College of Information Science and Electronic Engineering Zhejiang University Zhejiang Hangzhou310027 China The Department of Computer Science North Carolina State University RaleighNC27695 United States The Beijing Key Laboratory of Network System Architecture and Convergence China The Beijing Advanced Information Network Laboratory Beijing University of Posts and Telecommunications Beijing100876 China

This article investigates the adaptive resource allocation scheme for digital twin (DT) synchronization optimization over dynamic wireless networks. In our considered model, a base station (BS) continuously collects factory physical object state data from wireless devices to build a real-time virtual DT system for factory event analysis. Due to continuous data transmission, maintaining DT synchronization must use extensive wireless resources. To address this issue, a subset of devices is selected to transmit their sensing data, and resource block (RB) allocation is optimized. This problem is formulated as a constrained Markov process (CMDP) problem that minimizes the long-term mismatch between the physical and virtual systems. To solve this CMDP, we first transform the problem into a dual problem that refines RB constraint impacts on device scheduling strategies. We then propose a continual reinforcement learning (CRL) algorithm to solve the dual problem. The CRL algorithm learns a stable policy across historical experiences for quick adaptation to dynamics in physical states and network capacity. Simulation results show that the CRL can adapt quickly to network capacity changes and reduce normalized root mean square error (NRMSE) between physical and virtual states by up to 55.2%, using the same RB number as traditional methods. © 2025, CC BY-NC-SA.

关键词： Markov processes

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CM-MLP: Cascade Multi-scale MLP with Axial Context Relation Encoder for Edge Segmentation of Medical Image

CM-MLP: Cascade Multi-scale MLP with Axial Context Relation ...

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2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

作者： Lv, Jinkai Hu, Yuyong Fu, Quanshui Zhang, Zhiwang Hu, Yuqiang Lv, Lin Yang, Guoqing Li, Jinpeng Zhao, Yi Henan Institute of Advanced Technology Zhengzhou University Zhengzhou China The Research Center for Ubiquitous Computing Systems Institute of Computing Technology Chinese Academy of Sciences Beijing China Suining Central Hospital Suining China Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China School of Electrical and Information Engineering The University of Sydney Sydney Australia School of Mathematics and Computer Sciences NanChang University Nanchang China School of Information and Software Engineering University of Electronic Science and Technology of China Chengdu China

ISBN: (纸本)9781665468190

The convolutional-based methods provide good segmentation performance in the medical image segmentation task. However, those methods have the following challenges when dealing with the edges of the medical images: (1) Previous convolutional-based methods do not focus on the boundary relationship between foreground and background around the segmentation edge, which leads to the degradation of segmentation performance when the edge changes complexly. (2) The inductive bias of the convolutional layer cannot be adapted to complex edge changes and the aggregation of multiple-segmented areas, resulting in its performance improvement mostly limited to segmenting the body of segmented areas instead of the edge. To address these challenges, we propose the CM-MLP framework on MFI (Multiscale Feature Interaction) block and ACRE (axial context relation encoder) block for accurate segmentation of the edge of medical image. In the MFI block, we propose the cascade multi-scale MLP (Cascade MLP) to process all local information from the deeper layers of the network simultaneously and utilize a cascade multiscale mechanism to fuse discrete local information gradually. Then, the ACRE block is used to make the deep supervision focus on exploring the boundary relationship between foreground and background to modify the edge of the medical image. The segmentation accuracy (Dice) of our proposed CM-MLP framework reaches 96.96%, 96.76%, and 82.54% on three benchmark datasets: CVC-ClinicDB dataset, sub-Kvasir dataset, and our inhouse dataset, respectively, which significantly outperform the state-of-the-art method. The source code and trained models will be available at https://***/ProgrammerHyy/CM-MLP. © 2022 IEEE.

关键词： Semantic Segmentation

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Joint Optimization of Sensing and Communications in Vehicular Networks: A Graph Neural Network-Based Approach

Joint Optimization of Sensing and Communications in Vehicula...

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IEEE International Conference on Communications (ICC)

作者： Xuefei Li Mingzhe Chen Zhilong Zhang Danpu Liu Yuchen Liu Shiwen Mao Beijing Laboratory of Advanced Information Network Beijing University of Posts and Telecommunications Beijing China Department of Electrical and Computer Engineering Institute for Data Science and Computing University of Miami Coral Gables FL USA Department of Computer Science North Carolina State University Raleigh NC USA Department of Electrical and Computer Engineering Auburn University Auburn AL USA

In this paper, the problem of joint sensing and communications is studied over terahertz (THz) vehicular networks. In the studied model, a set of service provider vehicles provide either communication service or sensing service to communication target vehicles or sensing target vehicles, respectively. Therefore, it is necessary to determine the service mode (i.e., providing sensing or communication service) for each service provider vehicle and the subset of target vehicles that each service provider vehicle will serve. The problem is formulated as an optimization problem aiming to maximize the sum of the data rates of all communication target vehicles while satisfying the sensing service requirements of all sensing target vehicles by determining the service mode and the user association for each service provider vehicle. To solve this problem, a graph neural network (GNN) based algorithm with a heterogeneous graph representation is proposed. The proposed algorithm enables the central controller to extract each vehicle's graph information related to its location, connection, and communication interference. Using the extracted graph information, the joint service mode selection and user association strategy will be determined. Simulation results show that the proposed GNN-based scheme can achieve 94% of the sum rate produced by the optimal solution, and yield up to 3.95% and 36.16% improvements in sum rate, respectively, compared to a homogeneous GNN-based algorithm and the conventional optimization algorithm without using GNNs.

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Fundus Image Quality Assessment and Enhancement: a Systematic Review

arXiv

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arXiv 2025年

作者： Li, Heng Li, Haojin Ou, Mingyang Yu, Xiangyang Zhang, Xiaoqing Niu, Ke Fu, Huazhu Liu, Jiang Research Institute of Trustworthy Autonomous Systems SUSTech Shenzhen China Department of Computer Science and Engineering SUSTech Shenzhen China Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Computer School Beijing Information Science and Technology University Beijing China Singapore

As an affordable and convenient eye scan, fundus photography holds the potential for preventing vision impairment, especially in resource-limited regions. However, fundus image degradation is common under intricate imaging environments, impacting following diagnosis and treatment. Consequently, image quality assessment (IQA) and enhancement (IQE) are essential for ensuring the clinical value and reliability of fundus images. While existing reviews offer some overview of this field, a comprehensive analysis of the interplay between IQA and IQE, along with their clinical deployment challenges, is lacking. This paper addresses this gap by providing a thorough review of fundus IQA and IQE algorithms, research advancements, and practical applications. We outline the fundamentals of the fundus photography imaging system and the associated interferences, and then systematically summarize the paradigms in fundus IQA and IQE. Furthermore, we discuss the practical challenges and solutions in deploying IQA and IQE, as well as offer insights into potential future research directions. Copyright © 2025, The Authors. All rights reserved.

关键词： Photography

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Visible Light Positioning Based on a Single Luminaire: A Novel Visual Odometry Assisted Algorithm

Visible Light Positioning Based on a Single Luminaire: A Nov...

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IEEE International Conference on Communications (ICC)

作者： Zhiyu Zhu Yang Yang Mingzhe Chen Caili Guo Yipeng Bai Beijing Key Laboratory of Network System Architecture and Convergence School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing China Department of Electrical and Computer Engineering Institute for Data Science and Computing University of Miami Coral Gables FL USA Beijing Laboratory of Advanced Information Networks School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing China

Visible light positioning (VLP) is a promising positioning technique, which, however, typically requires multiple luminaires to achieve accurate positioning. This paper proposes a novel visual odometry (VO) assisted visible light positioning algorithm (VO-VLP) in achieving positioning with only a single luminaire. In the considered model, a user equipped with a camera jointly uses geometric features in the captured images and coordinates information obtained via visible light communication (VLC) for positioning. The proposed VLP algorithm does not rely on any extra inertial measurement unit and relaxes the tilted angle limitation at the user. In particular, VO-VLP first uses the circle feature of a luminaire to obtain dual normal vectors of the luminaire. Then, the basic principle of VO is used to eliminate the wrong normal vector by exploiting the geometric features in two consecutive images captured when the user moves. Finally, the pose and location of the user are obtained by using an artificially marked point on the luminaire's contour. VO-VLP can achieve accurate positioning with only a single luminaire and a camera. Simulation results show that the proposed indoor positioning algorithm can achieve a 97th-percentile positioning accuracy of around 10 cm.

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