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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 Novel Dual-Stage Algorithm for Capacitated Arc Routing Problems with Time-Dependent Service Costs

SSRN

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SSRN 2024年

作者： Li, Qingya Liu, Shengcai Zou, Juan Tang, Ke Guangdong Key Laboratory of Brain-Inspired Intelligent Computation Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China The Key Laboratory of Hunan Province for Internet of Things and Information Security Xiangtan University Xiangtan411105 China The Key Laboratory of Intelligent Computing and Information Processing Ministry of Education Xiangtan University Xiangtan411105 China

This paper focuses on solving the capacitated arc routing problem with time-dependent service costs (CARPTDSC), which is motivated by winter gritting applications. In the current literature, exact algorithms designed for CARPTDSC can only handle small-scale instances, while heuristic algorithms fail to obtain high-quality solutions. To overcome these limitations, we propose a novel dual-stage algorithm, called MAENS-GN, that consists of a routing stage and a vehicle departure time optimization stage. The former obtains the routing plan, while the the latter determines the vehicle departure time. Importantly, existing literature often ignores the characteristic information contained in the relationship between the route cost and the vehicle departure time. The most signiﬁcant innovation in this paper lies in the exploitation of this characteristic information during the vehicle departure time optimization stage. Speciﬁcally, we conduct a detailed analysis of this relationship under various scenarios and employ tailored methods to obtain the (approximately) optimal vehicle departure time. Furthermore, we propose an improved initialization strategy that considers time-dependent characteristics to achieve better solution quality. In addition to the modiﬁed benchmark test sets, we also experiment on a real-world test set. Experimental results demonstrate that MAENS-GN can obtain high-quality solutions on both small-scale and larger-scale instances of CARPTDSC. © 2024, The Authors. All rights reserved.

关键词： Combinatorial optimization

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A novel dual-stage algorithm for capacitated arc routing problems with time-dependent service costs

arXiv

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arXiv 2024年

This paper focuses on solving the capacitated arc routing problem with time-dependent service costs (CARPTDSC), which is motivated by winter gritting applications. In the current literature, exact algorithms designed for CARPTDSC can only handle small-scale instances, while heuristic algorithms fail to obtain high-quality solutions. To overcome these limitations, we propose a novel dual-stage algorithm, called MAENS-GN, that consists of a routing stage and a vehicle departure time optimization stage. The former obtains the routing plan, while the the latter determines the vehicle departure time. Importantly, existing literature often ignores the characteristic information contained in the relationship between the route cost and the vehicle departure time. The most significant innovation in this paper lies in the exploitation of this characteristic information during the vehicle departure time optimization stage. Specifically, we conduct a detailed analysis of this relationship under various scenarios and employ tailored methods to obtain the (approximately) optimal vehicle departure time. Furthermore, we propose an improved initialization strategy that considers time-dependent characteristics to achieve better solution quality. In addition to the modified benchmark test sets, we also experiment on a real-world test set. Experimental results demonstrate that MAENS-GN can obtain high-quality solutions on both small-scale and larger-scale instances of CARPTDSC. Copyright © 2024, The Authors. All rights reserved.

关键词： Combinatorial optimization

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Intracardiac Electrogram Signals Key Feature Points Recognition Using Dense Convolutional Network

Intracardiac Electrogram Signals Key Feature Points Recognit...

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Pattern Recognition and Machine Learning (PRML), IEEE International Conference on

作者： Jiang Yihang Gu Kaihao Wu Xiaomei Department of Biomedical Engineering School of information Science and Technology Fudan University Shanghai China Department of Biomedical Engineering Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention (MICCAI) of Shanghai School of information Science and Technology Fudan University Academy for Engineering and Technology Shanghai Engineering Research Center of Assistive Devices Shanghai China Yiwu Research Institute of Fudan University Zhejiang China

ISBN: (数字)9798350355925

ISBN: (纸本)9798350355932

During radiofrequency ablation procedures for atrial fibrillation patients, physicians can assist in locating ablation targets by analyzing the conduction pathways and low-voltage areas of the intracardiac electrogram signals. The feature points of intracardiac electrogram signals serve as criteria for assessing excitation patterns and low-voltage areas. Therefore, extracting feature points from intracardiac signals is of significant value. To identify key points in intracardiac electrogram signals through deep learning, this experiment collected intracardiac electrogram signals from 21 clinical patients, which were then filtered using wavelet transformation. Subsequently, each excitation was treated as a signal group, indicating the key feature points within. Finally, a total of 36,183 groups of intracardiac electrogram signals annotated with key points were obtained. The dataset consisted of data from 17 patients allocated for training, data from 2 patients reserved for testing, and data from the remaining 2 patients designated for validation purposes. Training was conducted using a DenseNet network incorporating both convolutional attention and feature pyramid modules. The final network successfully identifies the feature points of intracardiac electrogram signals. It outputs six feature points, including the starting point, first rising point, first falling point, peak point, valley point, and termination point, with average absolute errors of only 0.34, 0.27, 0.31, 0.01, 0.27, and 0.42 ms, respectively. The final detection results are highly satisfactory, indicating the potential utility of the findings in assisting the analysis of intracardiac electrogram signals. The research outcomes presented in this paper lay a foundation for the analysis of intracardiac electrogram signals.

关键词： Training Wavelet transforms Radio frequency Low voltage Training data Medical services Myocardium Feature extraction Pattern recognition Testing

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Removing Image Artifacts From Scratched Lens Protectors

Removing Image Artifacts From Scratched Lens Protectors

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： Yufei Wang Renjie Wan Wenhan Yang Bihan Wen Lap-Pui Chau Alex C. Kot School of Electrical and Electronic Engineering Nanyang Technological University Singapore Department of Computer Science Hong Kong Baptist University Hong Kong Distributed High Performance Software Fundamental Research Laboratory Pengcheng National Lab China Department of Electronic and Information Engineering Hong Kong Polytechnic University Hong Kong

A protector is placed in front of the camera lens for mobile devices to avoid damage, while the protector itself can be easily scratched accidentally, especially for plastic ones. The artifacts appear in a wide variety of patterns, making it difficult to see through them clearly. Removing image artifacts from the scratched lens protector is inherently challenging due to the occasional flare artifacts and the co-occurring interference within mixed artifacts. Though different methods have been proposed for some specific distortions, they seldom consider such inherent challenges. In our work, we consider the inherent challenges in a unified framework with two cooperative modules, which facilitate the performance boost of each other. We also collect a new dataset from the real world to facilitate training and evaluation purposes. The experimental results demonstrate that our method outperforms the baselines qualitatively and quantitatively. The code and datasets will be released at https://***/wyf0912/flare-removal

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Removing Image Artifacts From Scratched Lens Protectors

arXiv

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arXiv 2023年

作者： Wang, Yufei Wan, Renjie Yang, Wenhan Wen, Bihan Chau, Lap-Pui Kot, Alex C. School of Electrical and Electronic Engineering Nanyang Technological University Singapore Department of Computer Science Hong Kong Baptist University Hong Kong Distributed High Performance Software Fundamental Research Laboratory Pengcheng National Lab China Department of Electronic and Information Engineering Hong Kong Polytechnic University Hong Kong

关键词： Machine learning

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Adaptive Wavelet Filters as Practical Texture Feature Amplifiers for Parkinson’s Disease Screening in OCT

arXiv

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arXiv 2025年

作者： Zhang, Xiaoqing Shi, Hanfeng Li, Xiangyu Ye, Haili Xu, Tao Li, Na Hu, Yan Lv, Fan Chen, Jiangfan Liu, Jiang Center for High Performance Computing and Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Research Institute of Trustworthy Autonomous Systems Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China State Key Laboratory of Ophthalmology Optometry and Vision Science Wenzhou Medical University Wenzhou China Centre for Computational Science and Mathematical Modelling Coventry University Coventry United Kingdom School of Computer Science University of Nottingham Ningbo China Ningbo315100 China School of Ophthalmology and Optometry Wenzhou Medical University Wenzhou325035 China Department of Electronic and Information Engineering Changchun University Changchun130022 China

Parkinson’s disease (PD) is a prevalent neurodegenerative disorder globally. The eye’s retina is an extension of the brain and has great potential in PD screening. Recent studies have suggested that texture features extracted from retinal layers can be adopted as biomarkers for PD diagnosis under optical coherence tomography (OCT) images. Frequency domain learning techniques can enhance the feature representations of deep neural networks (DNNs) by decomposing frequency components involving rich texture features. Additionally, previous works have not exploited texture features for automated PD screening in OCT. Motivated by the above analysis, we propose a novel Adaptive Wavelet Filter (AWF) that serves as the Practical Texture Feature Amplifier to fully leverage the merits of texture features to boost the PD screening performance of DNNs with the aid of frequency domain learning. Specifically, AWF first enhances texture feature representation diversities via channel mixer, then emphasizes informative texture feature representations with the well-designed adaptive wavelet filtering token mixer. By combining the AWFs with the DNN stem, AWFNet is constructed for automated PD screening. Additionally, we introduce a novel Balanced Confidence (BC) Loss by mining the potential of sample-wise predicted probabilities of all classes and class frequency prior, to further boost the PD screening performance and trustworthiness of AWFNet. The extensive experiments manifest the superiority of our AWFNet and BC over state-of-the-art methods in terms of PD screening performance and trustworthiness. © 2025, CC BY-NC-SA.

关键词： Neurodegenerative diseases

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Optimizing resource allocation in flex-grid entanglement distribution networks

Optimizing resource allocation in flex-grid entanglement dis...

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2022 IEEE Photonics Conference, IPC 2022

作者： Alnas, Jude Alshowkan, Muneer Nageswara Rao, S.V. Peters, Nicholas A. Lukens, Joseph M. University of Alabama Department of Electrical and Computer Engineering TuscaloosaAL35401 United States Quantum Information Science Section Oak Ridge National Laboratory Oak RidgeTN37831 United States Advanced Computing Methods Section Oak Ridge National Laboratory Oak RidgeTN37831 United States

We introduce a model for the distribution of frequency-polarization hyper-entangled photon pairs in a flexible-grid optical network. In order to optimize entanglement fidelity and entangled bit rate, we apply a geneti... 详细信息

ISBN: (数字)9781665434874

ISBN: (纸本)9781665434874

关键词： Genetic algorithms

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Chemical Environment Adaptive Learning for Optical Band Gap Prediction of Doped Graphitic Carbon Nitride Nanosheets

arXiv

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arXiv 2023年

作者： Chen, Chen Xu, Enze Yang, Defu Yan, Chenggang Wei, Tao Chen, Hanning Wei, Yong Chen, Minghan Intelligent Information Processing Laboratory Hangzhou Dianzi University Hangzhou China Department of Computer Science Wake Forest University Winston-SalemNC United States Department of Chemical Engineering Howard University WashingtonDC United States Texas Advanced Computing Center The University of Texas at Austin AustinTX United States Department of Computer Science High Point University High PointNC United States

This study presents a new machine learning algorithm, named Chemical Environment Graph Neural Network (ChemGNN), designed to accelerate materials property prediction and advance new materials discovery. Graphitic carbon nitride (g-C3N4) and its doped variants have gained significant interest for their potential as optical materials. Accurate prediction of their band gaps is crucial for practical applications;however, traditional quantum simulation methods are computationally expensive and challenging to explore the vast space of possible doped molecular structures. The proposed ChemGNN leverages the learning ability of current graph neural networks (GNNs) to satisfactorily capture the characteristics of atoms' chemical environment underlying complex molecular structures. Our experimental results demonstrate more than 100% improvement in band gap prediction accuracy over existing GNNs on g-C3N4. Furthermore, the general ChemGNN model can precisely foresee band gaps of various doped g-C3N4 structures, making it a valuable tool for performing high-throughput prediction in materials design and development. Copyright © 2023, The Authors. All rights reserved.

关键词： Energy gap

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Time-Aware Missing Traffic Flow Prediction for Sensors with Privacy-Preservation 11th

Time-Aware Missing Traffic Flow Prediction for Sensors with ...

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11th International Conference on computer engineering and Networks, CENet2021

作者： Qi, Lianyong Wang, Fan Xu, Xiaolong Dou, Wanchun Zhang, Xuyun Khosravi, Mohammad R. Zhou, Xiaokang School of Computer Science Qufu Normal University Qufu China School of Computer and Software Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology Nanjing University of Information Science and Technology Nanjing China State Key Laboratory for Novel Software Technology Department of Computer Science and Technology Nanjing University Nanjing China Department of Computing Macquarie University SydneyNSW2109 Australia Department of Computer Engineering Persian Gulf University Bushehr Iran Department of Electrical and Electronic Engineering Shiraz University of Technology Shiraz Iran Faculty of Data Science Shiga University Hikone Japan

ISBN: (纸本)9789811665530

With the continuous development of IoT, a number of sensors establish on the roadside to monitor traffic conditions in real time. The continuously traffic data generated by these sensors makes traffic management feasible. However, loss of data may occur due to inevitable sensor failure, impeding traffic managers to understand traffic dynamics clearly. In this situation, it is becoming a necessity to predict missing traffic flow accurately for effective traffic management. Furthermore, the traffic sensor data are often distributed and stored by different agencies, which inhibits the multi-party sensor data sharing significantly due to privacy concerns. Therefore, it has become a major obstacle to balance the tradeoff between data sharing and vehicle privacy. In light of these challenges, we propose a privacy-aware and accurate missing traffic flow prediction approach based on time-aware Locality-Sensitive Hashing technique. At last, we deploy a set of experiments based on a real traffic dataset. Experimental reports demonstrate the feasibility of our proposal in terms of traffic flow prediction accuracy and efficiency while guaranteeing sensor data privacy. © 2022, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Data privacy

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