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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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An Encoding-Decoding Framework Based on CNN for circ RNA-RBP Binding Sites Prediction

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Chinese Journal of Electronics 2024年第1期33卷 256-263页

作者： Yajing GUO 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 Department of Computer Science Georgia State University

Predicting RNA binding protein(RBP) binding sites on circular RNAs(circ RNAs) is a fundamental step to understand their interaction mechanism. Numerous computational methods are developed to solve this problem, but they cannot fully learn the features. Therefore, we propose circ-CNNED, a convolutional neural network(CNN)-based encoding and decoding framework. We first adopt two encoding methods to obtain two original matrices. We preprocess them using CNN before fusion. To capture the feature dependencies, we utilize temporal convolutional network(TCN) and CNN to construct encoding and decoding blocks, respectively. Then we introduce global expectation pooling to learn latent information and enhance the robustness of circ-CNNED. We perform circ-CNNED across 37 datasets to evaluate its effect. The comparison and ablation experiments demonstrate that our method is superior. In addition, motif enrichment analysis on four datasets helps us to explore the reason for performance improvement of circ-CNNED.

关键词： Circular RNAs (circRNAs) RNA binding proteins Convolutional neural network Temporal convolutional network Encoder-decoder network

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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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Neuroadaptive Containment control for Nonlinear Multiagent Systems With Input Saturation: An Event-Triggered Communication Approach

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IEEE Transactions on Systems, Man, and Cybernetics: Systems 2025年第5期55卷 3163-3173页

作者： Wang, Xin Zhang, Sen Li, Huaqing Zhang, Wei Li, Hongyi Huang, Tingwen Southwest University College of Electronic and Information Engineering Chongqing400715 China Shenzhen University of Advanced Technology Faculty of Computer Science and Control Engineering Shenzhen518055 China

In this article, a neuroadaptive event-triggered containment control strategy combined with the dynamic surface control (DSC) approach is proposed for nonlinear multiagent systems (MASs) with input saturation. Based on the event-triggered communication mechanisms, the updates of neural network weight and controllers are implemented solely under triggering conditions of violation, which markedly reduces unnecessary communication resources and minimizes inefficient control costs compared with the traditional control method. Radial basis function neural networks (RBF NNs) are employed to handle the nonlinear uncertainties of MASs. Simultaneously, an adaptive compensatory mechanism is incorporated within the backstepping process to address the nonlinear effect posed by input saturation. Additionally, we demonstrate the system stability by extending the Lyapunov theorem to jump and continuous scenarios while excluding Zeno behavior, realizing that all followers can enter the convex hull constructed by leaders. Finally, the effectiveness of the proposed methodology is verified through application simulations. © 2013 IEEE.

关键词： Radial basis function networks

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Drug-Target Interactions Prediction Based on Signed Heterogeneous Graph Neural Networks

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Chinese Journal of Electronics 2024年第1期33卷 231-244页

作者： Ming CHEN Yajian JIANG Xiujuan LEI Yi PAN Chunyan JI Wei JIANG College of Information Science and Engineering Hunan Normal University School of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Computer Science Department BNU-HKBU United International College

Drug-target interactions(DTIs) prediction plays an important role in the process of drug *** computational methods treat it as a binary prediction problem, determining whether there are connections between drugs and targets while ignoring relational types information. Considering the positive or negative effects of DTIs will facilitate the study on comprehensive mechanisms of multiple drugs on a common target, in this work, we model DTIs on signed heterogeneous networks, through categorizing interaction patterns of DTIs and additionally extracting interactions within drug pairs and target protein pairs. We propose signed heterogeneous graph neural networks(SHGNNs), further put forward an end-to-end framework for signed DTIs prediction, called SHGNN-DTI,which not only adapts to signed bipartite networks, but also could naturally incorporate auxiliary information from drug-drug interactions(DDIs) and protein-protein interactions(PPIs). For the framework, we solve the message passing and aggregation problem on signed DTI networks, and consider different training modes on the whole networks consisting of DTIs, DDIs and PPIs. Experiments are conducted on two datasets extracted from Drug Bank and related databases, under different settings of initial inputs, embedding dimensions and training modes. The prediction results show excellent performance in terms of metric indicators, and the feasibility is further verified by the case study with two drugs on breast cancer.

关键词： Drug-target interactions Signed heterogeneous network Link sign prediction Graph neural networks

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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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A New Benchmark and Algorithm for Clothes-Changing Video Person Re-Identification

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IEEE Transactions on Information Forensics and Security 2025年 20卷 1993-2005页

作者： Wang, Likai Zhang, Xiangqun Han, Ruize Wei, Yanjie Wang, Song Feng, Wei Tianjin University College of Intelligence and Computing Tianjin300350 China Shenzhen University of Advanced Technology Faculty of Computer Science and Control Engineering Shenzhen518107 China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China

Person re-identification (Re-ID) is a classical computer vision task and has significant applications for public security and information forensics. Recently, long-term Re-ID with clothes-changing has attracted increasing attention. However, existing methods mainly focus on image-based setting, where richer temporal information is overlooked. In this paper, we focus on the relatively new yet practical problem of Clothes-Changing Video-based Re-ID (CCVReID), which is less studied. First, given the dataset shortage, we build two new benchmark datasets for CCVReID problem, including a large-scale synthetic video dataset and a real-world one, both containing human sequences with various clothing changes. Moreover, we systematically study this problem by simultaneously considering the classical appearance feature and temporal feature contained in the video. We develop a dual-branch fusion framework that makes use of the information from both clothes-aware appearance feature and clothes-free gait feature. For better information fusion, a confidence-guided re-ranking strategy is proposed to adaptively balance the weight of these two categories of features. We have released the benchmark and code proposed in this work to the public at https://***/kkw98/CCVReID. © 2025 IEEE.

关键词： Reamers

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Indoor Uncertain Semantic Trajectory Similarity Join

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Journal of computer science & technology 2024年第6期39卷 1441-1465页

作者： Hong-Bo Yin Dong-Hua Yang Kai-Qi Zhang Hong Gao Jian-Zhong Li Faculty of Computing Harbin Institute of TechnologyHarbin 150001China Center of Analysis Measurement and ComputingHarbin Institute of TechnologyHarbin 150001China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

With the widespread deployment of indoor positioning systems, an unprecedented scale of indoor trajectories is being produced. By considering the inherent uncertainties and the text information contained in such an indoor trajectory, a new definition named Indoor Uncertain Semantic Trajectory is defined in this paper. In this paper, we focus on a new primitive, yet quite essential query named Indoor Uncertain Semantic Trajectory Similarity Join (IUST-Join for short), which is to match all similar pairs of indoor uncertain semantic trajectories from two sets. IUST-Join targets a number of essential indoor applications. With these applications in mind, we provide a purposeful definition of an indoor uncertain semantic trajectory similarity metric named IUS. To process IUST-Join more efficiently, both an inverted index on indoor uncertain semantic trajectories named 3IST and the first acceleration strategy are proposed to form a filtering-and-verification framework, where most invalid pairs of indoor uncertain semantic trajectories are pruned at quite low computation cost. And based on this filtering-and-verification framework, we present a highly-efficient algorithm named Indoor Uncertain Semantic Trajectory Similarity Join Processing (USP for short). In addition, lots of novel and effective acceleration strategies are proposed and embedded in the USP algorithm. Thanks to these techniques, both the time complexity and the time overhead of the USP algorithm are further reduced. The results of extensive experiments demonstrate the superior performance of the proposed work.

关键词： filtering-and-verification framework indoor uncertain semantic trajectory inverted index trajectory similarity join

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Continuous and Discrete Similarity Coefficient for Identifying Essential Proteins Using Gene Expression Data

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Big Data Mining and Analytics 2023年第2期6卷 185-200页

作者： Jiancheng Zhong Zuohang Qu Ying Zhong Chao Tang Yi Pan College of Information Science and Engineering Hunan Normal UniversityChangsha 410081China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences ShenzhenGuangzhou 518055China

Essential proteins play a vital role in biological processes,and the combination of gene expression profiles with Protein-Protein Interaction(PPI)networks can improve the identification of essential ***,gene expression data are prone to significant fluctuations due to noise interference in topological *** this work,we discretized gene expression data and used the discrete similarities of the gene expression spectrum to eliminate noise *** then proposed the Pearson Jaccard coefficient(PJC)that consisted of continuous and discrete similarities in the gene expression *** the graph theory as the basis,we fused the newly proposed similarity coefficient with the existing network topology prediction algorithm at each protein node to recognize essential *** strategy exhibited a high recognition rate and good *** validated the new similarity coefficient PJC on PPI datasets of Krogan,Gavin,and DIP of yeast species and evaluated the results by receiver operating characteristic analysis,jackknife analysis,top analysis,and accuracy *** with that of node-based network topology centrality and fusion biological information centrality methods,the new similarity coefficient PJC showed a significantly improved prediction performance for essential proteins in DC,IC,Eigenvector centrality,subgraph centrality,betweenness centrality,closeness centrality,NC,PeC,and *** also compared the PJC coefficient with other methods using the NF-PIN algorithm,which predicts proteins by constructing active PPI networks through dynamic gene *** experimental results proved that our newly proposed similarity coefficient PJC has superior advantages in predicting essential proteins.

关键词： Protein-Protein Interaction(PPI)network continuous and discrete similarity coefficient essential proteins

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QTFN:A General End-to-End Time-Frequency Network to Reveal the Time-Varying Signatures of the Time Series

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Big Data Mining and Analytics 2024年第3期7卷 905-919页

作者： Tao Chen Yang Jiao Lei Xie Hongye Su State Key Laboratory of Industrial Control Technology Zhejiang UniversityHangzhou 310027China Shenzhen Key Laboratory of Intelligent Bioinformatics and College of Computer Science and Control EngineeringShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Nonstationary time series are ubiquitous in almost all natural and engineering *** the time-varying signatures from nonstationary time series is still a challenging problem for data *** Time-Frequency Distribution(TFD)provides a powerful tool to analyze these ***,they suffer from Cross-Term(CT)issues that impair the readability of ***,to achieve high-resolution and CT-free TFDs,an end-to-end architecture termed Quadratic TF-Net(QTFN)is proposed in this *** by classic TFD theory,the design of this deep learning architecture is heuristic,which firstly generates various basis functions through ***,more comprehensive TF features can be extracted by these basis ***,to balance the results of various basis functions adaptively,the Efficient Channel Attention(ECA)block is also embedded into ***,a new structure called Muti-scale Residual Encoder-Decoder(MRED)is also proposed to improve the learning ability of the model by highly integrating the multi-scale learning and encoder-decoder ***,although the model is only trained by synthetic signals,both synthetic and real-world signals are tested to validate the generalization capability and superiority of the proposed QTFN.

关键词： Time-Frequency Analysis(TFA) Multi-scale Residual Encoder-Decoder(MRED) quadratic Time-Frequency Distribution(TFD)

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