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Predicting circRNA-Disease Associations by Using Multi-Biomolecular Networks Based on Variational Graph Auto-Encoder with Attention Mechanism

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Chinese Journal of Electronics 2024年第6期33卷 1526-1537页

作者： Jing YANG Xiujuan LEI Yi PAN School of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology

CircRNA-disease association(CDA) can provide a new direction for the treatment of diseases. However,traditional biological experiment is time-consuming and expensive, this urges us to propose the reliable computational model to predict the associations between circRNAs and diseases. And there is existing more and more evidence indicates that the combination of multi-biomolecular information can improve the prediction accuracy. We propose a novel computational model for CDA prediction named MBCDA, we collect the multi-biomolecular information including circRNA, disease, miRNA and lncRNA based on 6 databases, and construct three heterogeneous network among them, then the multi-heads graph attention networks are applied to these three networks to extract the features of circRNAs and diseases from different views, the obtained features are put into variational graph auto-encoder(VGAE) network to learn the latent distributions of the nodes, a fully connected neural network is adopted to further process the output of VGAE and uses sigmoid function to obtain the predicted probabilities of circRNA-disease *** a result, MBCDA achieved the values of AUC and AUPR under 5-fold cross-validation of 0.893 and 0.887. MBCDA was applied to the analysis of the top-25 predicted associations between circRNAs and diseases, these experimental results show that our proposed MBCDA is a powerful computational model for CDA prediction.

关键词： Knowledge engineering Attention mechanisms Computational modeling Biological system modeling Predictive models Feature extraction Heterogeneous networks Topology Data mining Diseases

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Molecular Generation and Optimization of Molecular Properties Using a Transformer Model

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Big Data Mining and Analytics 2024年第1期7卷 142-155页

作者： Zhongyin Xu Xiujuan Lei Mei Ma Yi Pan School of Computer Science Shaanxi Normal UniversityXi'an 710119China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Generating novel molecules to satisfy specific properties is a challenging task in modern drug discovery,which requires the optimization of a specific objective based on satisfying chemical ***,we aim to optimize the properties of a specific molecule to satisfy the specific properties of the generated *** Matched Molecular Pairs(MMPs),which contain the source and target molecules,are used herein,and logD and solubility are selected as the optimization *** main innovative work lies in the calculation related to a specific transformer from the perspective of a matrix *** intervals and state changes are then used to encode logD and solubility for subsequent *** the experiments,we screen the data based on the proportion of heavy atoms to all atoms in the groups and select 12365,1503,and 1570 MMPs as the training,validation,and test sets,*** models are compared with the baseline models with respect to their abilities to generate molecules with specific *** show that the transformer model can accurately optimize the source molecules to satisfy specific properties.

关键词： molecular optimization transformer Matched Molecular Pairs(MMPs) logD solubility

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Learning from Heterogeneity: A Dynamic Learning Framework for Hypergraphs

IEEE Transactions on Artificial Intelligence

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IEEE Transactions on Artificial Intelligence 2025年第06期6卷 1513-1528页

作者： Zhang, Tiehua Liu, Yuze Shen, Zhishu Ma, Xingjun Qi, Peng Ding, Zhijun Jin, Jiong Tongji University School of Computer Science and Technology Shanghai China Ant Group Shanghai China Wuhan University of Technology School of Computer Science and Artificial Intelligence Wuhan China Fudan University School of Computer Science Shanghai China Tongji University Department of Control Science and Engineering Shanghai China Swinburne University of Technology School of Science Computing and Engineering Technologies Melbourne Australia

Graph neural network (GNN) has gained increasing popularity in recent years owing to its capability and flexibility in modeling complex graph structure data. Among all graph learning methods, hypergraph learning is a technique for exploring the implicit higher-order correlations when training the embedding space of the graph. In this paper, we propose a hypergraph learning framework named Learning from Heterogeneity (LFH) that is capable of dynamic hyperedge construction and attentive embedding update utilizing the heterogeneity attributes of the graph. Specifically, in our framework, the high-quality features are first generated by the pairwise fusion strategy that utilizes explicit graph structure information when generating initial node embedding. Afterwards, a hypergraph is constructed through the dynamic grouping of implicit hyperedges, followed by the type-specific hypergraph learning process. To evaluate the effectiveness of our proposed framework, we conduct comprehensive experiments on several popular datasets with twelve state-of-the- art models on both node classification and link prediction tasks, which fall into categories of homogeneous pairwise graph learning, heterogeneous pairwise graph learning, and hypergraph learning. The experiment results demonstrate a significant performance gain (an average of 12.9% in node classification and 12.8% in link prediction) compared with recent state-of-the-art methods. © 2020 IEEE.

关键词： Contrastive Learning

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Leakage Localization of Gas Pipelines Based on Modal Acoustic Emission and Cross-power Spectrum Peak Optimization

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IEEE Sensors Journal 2025年第11期25卷 19982-19992页

作者： Zhang, Wenbiao Gong, Kezheng Cui, Xiwang North China Electric Power University School of Control and Computer Engineering Beijing102206 China Beijing Information Science and Technology University School of Instrument Science and OptoElectronics Engineering Beijing100192 China

Leakage accidents in natural gas pipelines bring huge property losses and pose serious safety risks. Therefore, faster and more accurate leakage localization is of great significance. In this paper, a new method based on modal acoustic emission (MAE) and peak optimization of cross-power spectrum is proposed to enhance the performance of leakage localization. When a pipeline leakage occurs, the sensors installed on the pipelines receive the acoustic emission (AE) signals, which have various modes. Instead of extracting a single mode through complex algorithms, the proposed method directly extracts the cross-power spectrum of a specified mode by choosing the appropriate window function and window parameters to locate the leakage with velocity information from dispersion curves. Gaussian, Hamming and Blackman window functions are compared in the extraction of the cross-power spectrum of L(0,1) mode, among which the Blackman window function is found to be the most effective. The artificial fish swarm algorithm combined with the iteration criterion for peak optimization is used to obtain suitable window parameters. Finally, the localization error of the above method is less than 5.2%. In addition, the performance of the iteration criterion for peak optimization of cross-power spectrum combined with other intelligent swarm algorithms are investigated. The results show that the maximum errors of other intelligent methods are still less than 9%, demonstrating the great compatibility of the proposed method. © 2001-2012 IEEE.

关键词： Acoustic emissions

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Harnessing Trend Theory to Enhance Distributed Proximal Point Algorithm Approaches for Multi-Area Economic Dispatch Optimization

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computers, Materials & Continua 2025年第3期82卷 4503-4533页

作者： Yaming Ren Xing Deng College of Mechanical and Control Engineering Guilin University of TechnologyGuilin541006China School of Computer Jiangsu University of Science and TechnologyZhenjiang212003China

The exponential growth in the scale of power systems has led to a significant increase in the complexity of dispatch problem resolution,particularly within multi-area interconnected power *** complexity necessitates the employment of distributed solution methodologies,which are not only essential but also highly *** the realm of computational modelling,the multi-area economic dispatch problem(MAED)can be formulated as a linearly constrained separable convex optimization *** proximal point algorithm(PPA)is particularly adept at addressing such mathematical constructs *** study introduces parallel(PPPA)and serial(SPPA)variants of the PPA as distributed algorithms,specifically designed for the computational modelling of the *** PPA introduces a quadratic term into the objective function,which,while potentially complicating the iterative updates of the algorithm,serves to dampen oscillations near the optimal solution,thereby enhancing the convergence ***,the convergence efficiency of the PPA is significantly influenced by the parameter *** address this parameter sensitivity,this research draws on trend theory from stock market analysis to propose trend theory-driven distributed PPPA and SPPA,thereby enhancing the robustness of the computational *** computational models proposed in this study are anticipated to exhibit superior performance in terms of convergence behaviour,stability,and robustness with respect to parameter selection,potentially outperforming existing methods such as the alternating direction method of multipliers(ADMM)and Auxiliary Problem Principle(APP)in the computational simulation of power system dispatch *** simulation results demonstrate that the trend theory-based PPPA,SPPA,ADMM and APP exhibit significant robustness to the initial value of parameter c,and show superior convergence characteristics compared to the residual balancing ADMM.

关键词： Multi-area economic dispatch problem proximal point algorithm trend theory

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Two-Way Neural Network Performance PredictionModel Based onKnowledge Evolution and Individual Similarity

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computer Modeling in engineering & sciences 2024年第2期138卷 1183-1206页

作者： Xinzheng Wang Bing Guo Yan Shen College of Computer Science Sichuan UniversityChengdu610065China School of Information Science and Engineering Guilin University of TechnologyGuilin541004China School of Control Engineering Chengdu University of Information TechnologyChengdu610225China

Predicting students’academic achievements is an essential issue in education,which can benefit many stakeholders,for instance,students,teachers,managers,*** with online courses such asMOOCs,students’academicrelateddata in the face-to-face physical teaching environment is usually sparsity,and the sample size is *** makes building models to predict students’performance accurately in such an environment even *** paper proposes a Two-WayNeuralNetwork(TWNN)model based on the bidirectional recurrentneural network and graph neural network to predict students’next semester’s course performance using only theirprevious course *** experiments on a real dataset show that our model performs better thanthe baselines in many indicators.

关键词： computer education performance prediction deep learning

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Joint V2V Group Association and Transmission Power control in Federated Vehicular Networks

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IEEE Internet of Things Journal 2025年第11期12卷 18167-18182页

作者： Liu, Su Guan, Peiyuan Li, Yushuai Li, Tianyi Zolfagharian, Zolaikha Yu, Jiong Huang, Tingwen Xinjiang University School of Computer Science and Technology Urumqi830046 China University of Oslo Department of Informatics Oslo0316 Norway Aalborg University Department of Computer Science Aalborg9220 Denmark University of Tehran School of Electrical and Computer Engineering Iran Shenzhen University of Advanced Technology Faculty of Computer Science and Control Engineering Shenzhen518055 China

With growing awareness of privacy protection, Federated Learning (FL) in vehicular network scenarios effectively addresses privacy concerns, leading to the development of Federated Vehicular Networks (FVN). In FVN, vehicles maintain a global model by transmitting local models and iterative processing, resulting in significant communication overhead. In the Internet of Vehicles (IoV), as the majority of the spectrum resources are allocated to Vehicle-to-Vehicle (V2V) communication, vehicles engaged in FL encounter uplink interference when these resources are reused. This compromises the efficacy of FL vehicle communication. To address this issue, we propose FedCDC, a new Federated learning framework with adaptive weight Clustering with knowledge Distillation and Channel sharing-based resource allocation. First, we implement a communication compression strategy based on clustering and distillation to alleviate transmission load. Then, we develop a resource allocation strategy to maximize the Signal-to-Interference-plus-Noise Ratio (SINR) for both FL vehicles and V2V groups, which investigates two critical components: channel pairing and power coordination. We formulate the optimization issue as a multi-objective optimization problem that is solved offline using the MIDACO solver. Due to the dynamic characteristics of FVN, we employ a Multi-Agent Deep Deterministic Policy Gradient (MADDPG) to enhance efficiency. Finally, extensive experiments demonstrate that our approach significantly reduces data transmission and offers an efficient resource coordination plan, thus improving FL communication efficiency and ensuring the Quality of Service (QoS) for both V2V groups and FL vehicles. © 2014 IEEE.

关键词： Differential privacy

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circ2CBA: prediction of circRNA-RBP binding sites combining deep learning and attention mechanism

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Frontiers of computer science 2023年第5期17卷 217-225页

作者： Yajing GUO Xiujuan LEI Lian LIU Yi PAN School of Computer Science Shaanxi Normal UniversityXi’an 710119China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Circular RNAs(circRNAs)are RNAs with closed circular structure involved in many biological processes by key interactions with RNA binding proteins(RBPs).Existing methods for predicting these interactions have limitations in feature *** view of this,we propose a method named circ2CBA,which uses only sequence information of circRNAs to predict circRNA-RBP binding *** have constructed a data set which includes eight ***,circ2CBA encodes circRNA sequences using the one-hot ***,a two-layer convolutional neural network(CNN)is used to initially extract the *** CNN,circ2CBA uses a layer of bidirectional long and short-term memory network(BiLSTM)and the self-attention mechanism to learn the *** AUC value of circ2CBA reaches *** of circ2CBA with other three methods on our data set and an ablation experiment confirm that circ2CBA is an effective method to predict the binding sites between circRNAs and RBPs.

关键词： circRNAs RBPs CNN BiLSTM self-attention mechanism

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Medical Knowledge Graph:Data Sources,Construction,Reasoning,and Applications

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Big Data Mining and Analytics 2023年第2期6卷 201-217页

作者： Xuehong Wu Junwen Duan Yi Pan Min Li Computer Science and Engineering Central South UniversityChangsha 410083China School of Computer Science Hunan First Normal UniversityChangsha 410006China School of Computer Science and Engineering Central South UniversityChangsha 410083China Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518000China

Medical knowledge graphs(MKGs)are the basis for intelligent health care,and they have been in use in a variety of intelligent medical ***,understanding the research and application development of MKGs will be crucial for future relevant research in the biomedical *** this end,we offer an in-depth review of MKG in this *** research begins with the examination of four types of medical information sources,knowledge graph creation methodologies,and six major themes for MKG ***,three popular models of reasoning from the viewpoint of knowledge reasoning are discussed.A reasoning implementation path(RIP)is proposed as a means of expressing the reasoning procedures for *** addition,we explore intelligent medical applications based on RIP and MKG and classify them into nine major ***,we summarize the current state of MKG research based on more than 130 publications and future challenges and opportunities.

关键词： medical knowledge graph knowledge graph construction knowledge reasoning intelligent medical applications intelligent healthcare

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Predicting Traffic Flow Using Dynamic Spatial-Temporal Graph Convolution Networks

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computers, Materials & Continua 2024年第3期78卷 4343-4361页

作者： Yunchang Liu Fei Wan Chengwu Liang School of Computer and Data Science Henan University of Urban ConstructionPingdingshan467036China School of Electrical and Control Engineering Henan University of Urban ConstructionPingdingshan467036China

Traffic flow prediction plays a key role in the construction of intelligent transportation ***,due to its complex spatio-temporal dependence and its uncertainty,the research becomes very *** of the existing studies are based on graph neural networks that model traffic flow graphs and try to use fixed graph structure to deal with the relationship between ***,due to the time-varying spatial correlation of the traffic network,there is no fixed node relationship,and these methods cannot effectively integrate the temporal and spatial *** paper proposes a novel temporal-spatial dynamic graph convolutional network(TSADGCN).The dynamic time warping algorithm(DTW)is introduced to calculate the similarity of traffic flow sequence among network nodes in the time dimension,and the spatiotemporal graph of traffic flow is constructed to capture the spatiotemporal characteristics and dependencies of traffic *** combining graph attention network and time attention network,a spatiotemporal convolution block is constructed to capture spatiotemporal characteristics of traffic *** on open data sets PEMSD4 and PEMSD8 show that TSADGCN has higher prediction accuracy than well-known traffic flow prediction algorithms.

关键词： Intelligent transportation graph convolutional network traffic flow DTW algorithm attention mechanism

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