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DMFVAE:miRNA-disease associations prediction based on deep matrix factorization method with variational autoencoder

Frontiers of Computer Science 2024年第6期18卷 259-270页

作者： Pijing WEI Qianqian WANG Zhen GAO Ruifen CAO Chunhou ZHENG Information Materials and Intelligent Sensing Laboratory of Anhui Province Institutes of Physical Science and Information TechnologyAnhui UniversityHefei 230601China Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and TechnologyAnhui UniversityHefei 230601China Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Artificial IntelligenceAnhui UniversityHefei 230601China

MicroRNAs(miRNAs)are closely related to numerous complex human diseases,therefore,exploring miRNA-disease associations(MDAs)can help people gain a better understanding of complex disease *** increasing number of computational methods have been developed to predict ***,the sparsity of the MDAs may hinder the performance of many *** addition,many methods fail to capture the nonlinear relationships of miRNA-disease network and inadequately leverage the features of network and neighbor *** this study,we propose a deep matrix factorization model with variational autoencoder(DMFVAE)to predict potential *** first decomposes the original association matrix and the enhanced association matrix,in which the enhanced association matrix is enhanced by self-adjusting the nearest neighbor method,to obtain sparse vectors and dense vectors,***,the variational encoder is employed to obtain the nonlinear latent vectors of miRNA and disease for the sparse vectors,and meanwhile,node2vec is used to obtain the network structure embedding vectors of miRNA and disease for the dense ***,sample features are acquired by combining the latent vectors and network structure embedding vectors,and the final prediction is implemented by convolutional neural network with channel *** evaluate the performance of DMFVAE,we conduct five-fold cross validation on the HMDD v2.0 and HMDD v3.2 datasets and the results show that DMFVAE performs ***,case studies on lung neoplasms,colon neoplasms,and esophageal neoplasms confirm the ability of DMFVAE in identifying potential miRNAs for human diseases.

关键词： miRNA-disease association deep matrix factorization self-adjusted nearest neighbor variational encoder network structure

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A knowledge-enhanced interest segment division attention network for click-through rate prediction

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Neural computing and Applications 2024年第34期36卷 21817-21837页

作者： Liu, Zhanghui Chen, Shijie Chen, Yuzhong Su, Jieyang Zhong, Jiayuan Dong, Chen College of Computer and Data Science Fuzhou University Fujian Province Fuzhou350108 China Fujian Provincial Key Laboratory of Network Computing and Intelligent Information Processing Fujian Province Fuzhou350108 China

Click-through rate (CTR) prediction aims to estimate the probability of a user clicking on a particular item, making it one of the core tasks in various recommendation platforms. In such systems, user behavior data are crucial for capturing user interests, which has garnered significant attention from both academia and industry, leading to the development of various user behavior modeling methods. However, existing models still face unresolved issues, as they fail to capture the complex diversity of user interests at the semantic level, refine user interests effectively, and uncover users’ potential interests. To address these challenges, we propose a novel model called knowledge-enhanced Interest segment division attention network (KISDAN), which can effectively and comprehensively model user interests. Specifically, to leverage the semantic information within user behavior sequences, we employ the structure of a knowledge graph to divide user behavior sequence into multiple interest segments. To provide a comprehensive representation of user interests, we further categorize user interests into strong and weak interests. By leveraging both the knowledge graph and the item co-occurrence graph, we explore users’ potential interests from two perspectives. This methodology allows KISDAN to better understand the diversity of user interests. Finally, we extensively evaluate KISDAN on three benchmark datasets, and the experimental results consistently demonstrate that the KISDAN model outperforms state-of-the-art models across various evaluation metrics, which validates the effectiveness and superiority of KISDAN. © The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2024.

关键词： Contrastive Learning

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Imputation of Compound Property Assay Data Using a Gene Expression Programming-Based Method 1st

Imputation of Compound Property Assay Data Using a Gene Expr...

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1st International Conference on Applied Intelligence, ICAI 2023

作者： Zhou, Hongliang Lin, Yanmei Chen, Nan Peng, Yuzhong Key Lab of Scientific Computing and Intelligent Information Processing Nanning Normal University Guangxi Nanning5300001 China Guangxi Academy of Sciences Guangxi Nanning530007 China

ISBN: (纸本)9789819709021

Compound property assays are an important part of drug development, but incomplete data may occur for a variety of reasons. To deal with these incomplete data and improve the success rate of drug development, researchers often need to effectively impute the missing data. Therefore, this paper proposes a gene expression programming-based method, called GEP-CPI, for imputing missing compound property assay data. In GEP-CPI, the missing data imputation model is expressed by the parse tree of a chromosome, and then the optimal missing data imputation model is mined by iterative evolution of the chromosome population. Experimental results on three compound property assay related datasets demonstrates that the proposed method generally outperforms the state-of-the-art methods in imputing missing data of compound property assays. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

关键词： Trees (mathematics)

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DisenGCD: A Meta Multigraph-assisted Disentangled Graph Learning Framework for Cognitive Diagnosis 38

DisenGCD: A Meta Multigraph-assisted Disentangled Graph Lear...

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38th Conference on Neural information processing Systems, NeurIPS 2024

作者： Yang, Shangshang Chen, Mingyang Wang, Ziwen Yu, Xiaoshan Zhang, Panpan Ma, Haiping Zhang, Xingyi Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Anhui Hefei230601 China Anhui Province Key Laboratory of Intelligent Computing and Applications China Department of Information Materials and Intelligent Sensing Laboratory of Anhui Province China

Existing graph learning-based cognitive diagnosis (CD) methods have made relatively good results, but their student, exercise, and concept representations are learned and exchanged in an implicit unified graph, which makes the interaction-agnostic exercise and concept representations be learned poorly, failing to provide high robustness against noise in students' interactions. Besides, lower-order exercise latent representations obtained in shallow layers are not well explored when learning the student representation. To tackle the issues, this paper suggests a meta multigraph-assisted disentangled graph learning framework for CD (DisenGCD), which learns three types of representations on three disentangled graphs: student-exercise-concept interaction, exercise-concept relation, and concept dependency graphs, respectively. Specifically, the latter two graphs are first disentangled from the interaction graph. Then, the student representation is learned from the interaction graph by a devised meta multigraph learning module;multiple learnable propagation paths in this module enable current student latent representation to access lower-order exercise latent representations, which can lead to more effective nad robust student representations learned;the exercise and concept representations are learned on the relation and dependency graphs by graph attention modules. Finally, a novel diagnostic function is devised to handle three disentangled representations for prediction. Experiments show better performance and robustness of DisenGCD than state-of-the-art CD methods and demonstrate the effectiveness of the disentangled learning framework and meta multigraph module. The source code is available at https://***/BIMK/intelligent-Education/tree/main/DisenGCD. © 2024 Neural information processing systems foundation. All rights reserved.

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An Improved Compressive Sensing-Based Model for Efficient Analysis of Monostatic Electromagnetic Scattering Problems

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IEEE Microwave and Wireless Technology Letters 2025年第4期35卷 388-391页

作者： Qi, Qi Fan, Yunuo Cao, Xinyuan Liu, Yi Kong, Meng Huang, Zhixiang Wu, Xianliang Hefei Normal University Anhui Province Key Laboratory of Simulation Calculation and Design for Electronic Information System Hefei230601 China Anhui University Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Hefei230601 China

To further accelerate the analysis of monostatic electromagnetic (EM) scattering problems of objects, an improved compressive sensing (CS)-based model is proposed. First, an orthogonal subspace spanned by the wide-angle induced currents is identified by means of the wide-angle incident sources. Then, the sparse transform of the induced currents is replaced by the subspace projection. In addition, an optimal number of measurements is determined, only slightly larger than the dimension of the subspace. Finally, the recovery algorithm is simplified to the least-squares method to solve the resulting overdetermined system. Compared with the traditional CS-based model, the proposed model significantly improves the efficiency of the recovery step and optimizes both the requirement for and the way of determining the number of measurements. © 2023 IEEE.

关键词： Least squares approximations

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Amplified emission and lasing enabled by high-Q quasi-bound states in asymmetric dielectric metasurfaces via eigenfield perturbation

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Optics Express 2025年第10期33卷 21551-21565页

作者： Xu, Ke Fei, Yuhang Sun, Yingying Feng, Jian Deng, Xuesong Fang, Ming Huang, Zhixiang The Information Materials and Intelligent Sensing Laboratory of Anhui Province Anhui University Anhui Hefei230039 China The Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei230039 China

Symmetry-protected bound states in the continuum represent a distinct class of nonradiative modes in continuous media. By introducing asymmetric parameters into a symmetric metasurface, the inherent symmetry can be broken, transforming BICs—originally decoupled from external radiation channels—into high-Q quasi-BICs with controlled radiation capabilities. However, manufacturing constraints pose a significant challenge in fabricating nanostructures with ultra-small asymmetric parameters, thereby limiting the achievable Q-factor. In this work, we propose an asymmetric perforated metasurface structure that supports BICs. When the perforations are shifted along the x or y axis to a specific position, the linewidth vanishes, and simulations confirm the emergence of a BIC in the system, with a quality factor reaching up to 109. Furthermore, we demonstrate that selective eigenmode perturbation can effectively transform BICs into practical quasi-BICs. Notably, for the same structure, perturbing the weak-field region yields higher Q-factors, offering a flexible approach to optimizing performance. This approach enables precise Q-factor control and enhanced radiation properties. Furthermore, we design a laser cavity structure based on these quasi-BICs, achieving amplified emission and lasing with excellent agreement between simulations and theoretical predictions. These findings expand the BIC library and offer new methods for Q-factor manipulation, paving the way for high-performance optoelectronic devices such as nanolasers, biosensors, and nonlinear harmonic generators. © 2025 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement.

关键词： Q factor measurement

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Overlapping community‐based particle swarm optimization algorithm for influence maximization in social networks

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CAAI Transactions on Intelligence Technology 2023年第3期8卷 893-913页

作者： Lei Zhang Yutong Liu Haipeng Yang Fan Cheng Qi Liu Xingyi Zhang Information Materials and Intelligent Sensing Laboratory of Anhui Province Key Laboratory of Intelligent Computing and Signal Processing of Ministry of EducationSchool of Computer Science and TechnologyAnhui UniversityHefeiChina School of Computer Science and Technology University of Science and Technology of ChinaHefeiChina

Influence maximization,whose aim is to maximise the expected number of influenced nodes by selecting a seed set of k influential nodes from a social network,has many applications such as goods advertising and rumour *** the existing influence maximization methods,the community‐based ones can achieve a good balance between effectiveness and ***,this kind of algorithm usually utilise the network community structures by viewing each node as a non‐overlapping *** fact,many nodes in social networks are overlapping ones,which play more important role in influence *** this end,an overlapping community‐based particle swarm opti-mization algorithm named OCPSO for influence maximization in social networks,which can make full use of overlapping nodes,non‐overlapping nodes,and their interactive information is ***,an overlapping community detection algorithm is used to obtain the information of overlapping community structures,based on which three novel evolutionary strategies,such as initialisation,mutation,and local search are designed in OCPSO for better finding influential *** results in terms of influence spread and running time on nine real‐world social networks demonstrate that the proposed OCPSO is competitive and promising comparing to several state‐of‐the‐arts(***,CMA‐IM,CIM,CDH‐SHRINK,CNCG,and CFIN).

关键词： computational intelligence data mining social network

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A numerical magnitude aware multi-channel hierarchical encoding network for math word problem solving

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Neural computing and Applications 2025年第3期37卷 1651-1672页

作者： Xu, Junjie Chen, Yuzhong Xiao, Lingsheng Liao, Hongmiao Zhong, Jiayuan Dong, Chen College of Computer and Data Science Fuzhou University Fujian Province Fuzhou350108 China Engineering Research Center of Big Data Intelligence Ministry of Education Fuzhou China Fujian Provincial Key Laboratory of Network Computing and Intelligent Information Processing Fujian Province Fuzhou350108 China

Math word problem (MWP) represents a critical research area within reading comprehension, where accurate comprehension of math problem text is crucial for generating math expressions. However, current approaches still grapple with unresolved challenges in grasping the sensitivity of math problem text and delineating distinct roles across various clause types, and enhancing numerical representation. To address these challenges, this paper proposes a Numerical Magnitude Aware Multi-Channel Hierarchical Encoding Network (NMA-MHEA) for math expression generation. Firstly, NMA-MHEA implements a multi-channel hierarchical context encoding module to learn context representations at three different channels: intra-clause channel, inter-clause channel, and context-question interaction channel. NMA-MHEA constructs hierarchical constituent-dependency graphs for different levels of sentences and employs a Hierarchical Graph Attention Neural Network (HGAT) to learn syntactic and semantic information within these graphs at the intra-clause and inter-clause channels. NMA-MHEA then refines context clauses using question information at the context-question interaction channel. Secondly, NMA-MHEA designs a number encoding module to enhance the relative magnitude information among numerical values and type information of numerical values. Experimental results on two public benchmark datasets demonstrate that NMA-MHEA outperforms other state-of-the-art models. © The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2024.

关键词： Semantics

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Linear Subspace Surrogate Modeling for Large-Scale Expensive Single/Multi-Objective Optimization

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IEEE Transactions on Evolutionary Computation 2023年第3期29卷 1-1页

作者： Si, Langchun Zhang, Xingyi Tian, Ye Yang, Shangshang Zhang, Limiao Jin, Yaochu School of Computer Science and Technology Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei China School of Artificial Intelligence Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei China Information Materials and Intelligent Sensing Laboratory of Anhui Province Anhui University Hefei China Faculty of Technology Bielefeld University Bielefeld Germany

Despite that the surrogate-assisted evolutionary algorithms have achieved great success in addressing expensive optimization problems, they still suffer from stiff challenges when the number of dimensions of problems becomes large. The primary reason lies in that it is very hard to build an acceptable surrogate model in the high-dimensional search space with small amounts of evaluated historical data in evolution. To tackle this issue, we suggest an effective surrogate modeling method for large-scale expensive optimization in this paper, where the models are built on a number of linear subspaces instead of the original search space. Specifically, a linear subspace is constructed by a pair of points/solutions which are generated based on the set of elite solutions. For each linear subspace, several historical solutions are first associated according to their distance to the linear subspace, and then a surrogate model is trained by the associated solutions and used to evaluate the offspring. To ensure the exploration and exploitation capacity of the proposed method, these linear subspaces and the surrogate models are updated after a few iterations. Experimental results on CEC’2010 and CEC’2013 single-objective optimization problems with up to 1500 decision variables show that the proposed algorithm is superior over six comparison algorithms. Moreover, we also extend the proposed algorithm to multi-objective optimization problems and verified its competitiveness on problems with up to 1500 decision variables. IEEE

关键词： Evolutionary algorithms

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Parallel finite element computation of incompressible magnetohydrodynamics based on three iterations

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Applied Mathematics and Mechanics(English Edition) 2022年第1期43卷 141-154页

作者： Qili TANG Yunqing HUANG Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing&Information Processing of Ministry of EducationSchool of Mathematics and Computational ScienceXiangtan UniversityXiangtanHunan Province411105China

Based on local algorithms,some parallel finite element(FE)iterative methods for stationary incompressible magnetohydrodynamics(MHD)are *** approaches are on account of two-grid skill include two major phases:find the FE solution by solving the nonlinear system on a globally coarse mesh to seize the low frequency component of the solution,and then locally solve linearized residual subproblems by one of three iterations(Stokes-type,Newton,and Oseen-type)on subdomains with fine grid in parallel to approximate the high frequency *** error estimates with regard to two mesh sizes and iterative steps of the proposed algorithms are *** numerical examples are implemented to verify the algorithm.

关键词： local and parallel algorithm finite element(FE)method iteration stationary incompressible magnetohydrodynamics(MHD)

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