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Single-cell technologies: current and near future

Science China(Life Sciences) 2025年第1期68卷 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi KeyLaboratory of Spine and Spinal CordInjury Repairand Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchoolofLifeSciencesandTechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Key Laboratory of Advanced Theory and Application in Statistics and Data Science(MOE) School of StatisticsEast China Normal UniversityShanghai 200062China

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity,tissue organization,and overall organism function(Sun et al.,2024).In 2009,single-cell RNA sequencing(scRNA-seq)was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology,single-cell approaches have expanded to encompass other omics,such as genomics,epigenomics,proteomics,and ***,multimodal technologies including spatially resolved transcriptomics and clustered regularly interspaced short palindromic repeats(CRISPR)screening at the single-cell level further advanced our ability to comprehensively understand cellular ***-cell methods provide deeper insights into disease mechanisms across various conditions,including cancer,developmental disorders,and aging-associated *** this issue,we focus on topics related to single-cell methods,covering the following four aspects:(i)single-cell multi-omic sequencing technology;(ii)single-cell spatial technology;(iii)singlecell CRISPR screening technology;(iv)applications of single-cell technology.

关键词： expanded enable insight

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Fusion recommendation algorithm based on DeepWalk and Item-Based collaborative filtering

Fusion recommendation algorithm based on DeepWalk and Item-B...

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Computer Science and Management Technology (ICCSMT), International Conference on

作者： Yicheng Yu Rongbin Li Jun Yin School of Computing Qinghai Normal University Xi’Ning China The State Key Laboratory of Tibetan Intelligent Information Processing and Application Xi’Ning China

Collaborative filtering techniques have been applied to personalised recommendation systems in recommender systems. However, with the gradual increase in the number of platform users and goods, the user rating data on the entire project matrix is extremely sparse, resulting in the inaccuracy of the prediction results. DeepWalk, on the other hand, still performs well when the data is sparse. Therefore, DeepWalk is introduced into collaborative filtering, and a fusion recommendation algorithm based on DeepWalk and collaborative filtering is proposed to reduce the impact of cold start and sparsity on the recommendation results. Experiments show that the proposed fusion recommendation algorithm has higher recommendation accuracy when the data is sparse compared with other traditional algorithms, which improves the recommendation quality to a certain extent.

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Adaptive Neural Tracking Control for Nonlinear Servo System with Unknown Time-Varying Parameters and Uncertainties

Adaptive Neural Tracking Control for Nonlinear Servo System ...

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Chinese Control Conference (CCC)

作者： Faxiang Zhang Guanbin Gao Jing Na Jiande Wu Faculty of Mechanical and Electrical Engineering and Yunnan International Joint Laboratory of Intelligent Control and Application of Advanced Equipment Kunming University of Science and Technology Kunming P. R. China Yunnan Key Laboratory of Intelligent Systems and Computing Yunnan University Kunming P. R. China

This paper solves the neural network (NN) tracking control problem for uncertain nonlinear servo system with time-varying parameters and uncertainties. To address the uncertain nonlinear function with unknown time-varying parameters (i.e., unknown nonlinear spatiotemporal function), the time-varying parameter extraction method is used to separate the time-varying parameters from uncertain nonlinear spatiotemporal function, which yields an unknown state-based boundary function. By the tools of NN and adaptive technology, an adaptive neural tracking controller is designed, which guarantees the uniformly ultimately bounded (UUB) performance of the resulting closed-loop system. The effectiveness of the designed method is verified by simulations.

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Single-cell omics: experimental workflow, data analyses and applications

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Science China(Life Sciences) 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University(The Second People’s Hospital of Wuhu City)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** exploration of how the genomes orchestrate the formation and maintenance of each cell,and control the cellular phenotypes of various organismsis,is both captivating and *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** technologies have expanded horizontally to include single-cell genome,epigenome,proteome,and metabolome,while vertically,they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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A Reference Vector-Assisted Many-Objective Optimization Algorithm with Adaptive Niche Dominance Relation

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intelligent Automation & Soft computing 2024年第2期39卷 189-211页

作者： Fangzhen Ge Yating Wu Debao Chen Longfeng Shen School of Computer Science and Technology Huaibei Normal UniversityHuaibei340604China School of Physic and Electronic Information Huaibei Normal UniversityHuaibei340604China Anhui Engineering Research Center for Intelligent Computing and Application on Cognitive Behavior(ICACB) Huaibei Normal UniversityHuaibei340604China Anhui Province Key Laboratory of Intelligent Computing and Applications Huaibei Normal UniversityHuaibei340604China Institute of Artificial Intelligence Hefei Comprehensive National Science CenterHefei230000China

It is still a huge challenge for traditional Pareto-dominatedmany-objective optimization algorithms to solve manyobjective optimization problems because these algorithms hardly maintain the balance between convergence and diversity and can only find a group of solutions focused on a small area on the Pareto front,resulting in poor performance of those *** this reason,we propose a reference vector-assisted algorithmwith an adaptive niche dominance relation,for short *** new dominance relation forms a niche based on the angle between candidate *** comparing these solutions,the solutionwith the best convergence is found to be the non-dominated solution to improve the selection *** reproduction,a mutation strategy of k-bit crossover and hybrid mutation is used to generate high-quality *** 23 test problems with up to 15-objective,we compared the proposed algorithm with five state-of-the-art *** experimental results verified that the proposed algorithm is competitive.

关键词： Many-objective optimization evolutionary algorithm Pareto dominance reference vector adaptive niche

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A New Predefined Time Stability Theorem and its application in Multi-Modal Memristive Neural Network Synchronization

A New Predefined Time Stability Theorem and its Application ...

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Memristive computing and applications (ICMCA), IEEE International Conference on

作者： Hui Zhao Lei Zhou Qingjie Wang Aidi Liu Jingliang Peng Shandong Provincial Key Laboratory of Network Based Intelligent Computing School of Information Science and Engineering University of Jinan Jinan China College of Information Science and Engineering Northeastern University Shenyang China Collaborative Innovation Center of Memristive Computing Application Qilu Institute of Technology Jinan China

This article proposes a new predefined-time (PDT) stability theorem, which offers more evident advantages compared to previous predefined-time stability. Firstly, based on the limitations of existing PDT stability, this theorem relaxed the limitations of sufficient conditions, which fill the gap in the research on PDT stability. Secondly, the PDT synchronization of multi-modal memristive neural networks (MM-MNN) is analyzed by the usability of the new judgment theorem. A matching PDT controller is designed and sufficient synchronization control conditions is obtained by utilizing generalized Lyapunov functional method, set-valued mapping, inequality analysis technique and differential inclusion theory. Meanwhile, the topological characteristics of multi-modal neuron and its impact on network synchronization behavior are presented. Finally, we provide some confirmatory numerical simulations.

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Label Distribution Learning with Correlation Information

SSRN

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SSRN 2024年

作者： Wu, Yilin Lin, Yaojin Guo, Wenzhong Ding, Weiping College of Computer and Data Science Fuzhou University Fuzhou350116 China Fujian Provincial Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou350116 China Key Laboratory of Data Science and Intelligence Application Minnan Normal University Zhangzhou363000 China School of Information Science and Technology Nantong University Nantong226019 China

Label distribution learning quantifies the label space for each instance and has widely applicability in different fields. However, most existing works primarily focus on label correlation, but they still have a limitation in capturing instance correlation. Meanwhile, traditional label distribution learning operates on individual labels sequentially, leading to limitation in applying common features. Therefore, in this paper, we propose a novel approach for label distribution learning with correlation information i.e. instance correlation and label correlation. Specifically, the instance correlation and label correlation are identified by an optimization function and Pearson correlation coefficient, respectively. Besides, we conduct $\ell_{2,1}-$norm regularization to exploit common features. Comprehensive experiments manifest the superiority of our proposed approach against other well-established label distribution learning algorithms. © 2024, The Authors. All rights reserved.

关键词： Learning algorithms

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RIESZ TYPE THEOREMS FOR κ-PLURIHARMONIC MAPPINGS, INVARIANT HARMONIC QUASIREGULAR MAPPINGS AND HARMONIC QUASIREGULAR MAPPINGS

arXiv

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arXiv 2023年

作者： Chen, Shaolin Huang, Manzi College of Mathematics and Statistics Hengyang Normal University Hunan Hengyang421002 China Hunan Provincial Key Laboratory of Intelligent Information Processing and Application 421002 China Key Laboratory of High Performance Computing and Stochastic Information Processing College of Mathematics and Statistics Hunan Normal University Hunan Changsha410081 China

The main purpose of this paper is to develop some methods to improve and generalize the main results in a recent paper by Liu and Zhu (Adv. Math., 2023, i.e., [19]). The paper consists of two parts. In the first part, we discuss the Riesz type theorem in the setting of n-dimensional complex spaces for all n ≥ 1. In this part, we first introduce the family of κ-pluriharmonic mappings of the n-dimensional complex unit ball. Then we establish two Riesz type theorems for these mappings, which are the n-dimensional versions of Theorems 1.1 and 1.2 in [19], respectively. Furthermore, even when n = 1, our first result shows that the assumption of the real parts of the mappings not being negative (or being negative) in [19, Theorem 1.1] is redundant;and our second result illustrates that the assumption of "quasiconformality" on the mappings in [19, Theorem 1.2] can be replaced by the weaker one of "quasiregularity". In the second part, we investigate the Riesz type theorem in the setting of n-dimensional real spaces for all n ≥ 2. In this part, first, we prove a Riesz type theorem for invariant harmonic quasiregular mappings of the unit n-dimensional real ball. Our result indicates that (i) the range of the parameter p discussed in [19, Theorem 1.3] can be changed from (1, 2) to (1, ∞);(ii) the assumption of the first coordinate functions of the mappings being non-zero in [19, Theorem 1.3] is redundant. In this way, we complete the discussions carried out in [19, Theorems 1.3 and 1.4]. Second, we obtain a Riesz type theorem for harmonic K-quasiregular mappings of the unit n-dimensional real ball. Our result demonstrates that the range of the parameter p discussed in [15, Theorem 2.1] can be changed from (1, 2) to (1, ∞).MSC Codes 30H10, 30C62 Copyright © 2023, The Authors. All rights reserved.

关键词： Harmonic analysis

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A DECOUPLED STRUCTURE PRESERVING SCHEME FOR THE POISSON-NERNST-PLANCK NAVIER-STOKES EQUATIONS AND ITS ERROR ANALYSIS

arXiv

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arXiv 2023年

作者： Yu, Ziyao Cheng, Qing Shen, Jie Wang, Changyou Department of Mathematics West LafayetteIN47907 United States Key Laboratory of Intelligent Computing and Application Tongji University Ministry of Education Department of Mathematics Tongji University Shanghai200092 China Eastern Institute of Technology Zhejiang Ningbo315200 China

We consider in this paper a numerical approximation of Poisson-Nernst-Planck-Navier-Stokes (PNP-NS) system. We construct a decoupled semi-discrete and fully discrete scheme that enjoys the properties of positivity preserving, mass conserving, and unconditionally energy stability. Then, we establish the well-posedness and regularity for the initial and (periodic) boundary value problem of the PNP-NS system under suitable assumptions on the initial data, and carry out a rigorous convergence analysis for the fully discretized scheme. We also present some numerical results to validate the positivity preserving property and the accuracy of our scheme. Copyright © 2023, The Authors. All rights reserved.

关键词： Navier Stokes equations

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Provably Secure Authenticated key-Management Mechanism for e-Healthcare Environment

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IEEE Internet of Things Journal 2025年

作者： Saleem, Muhammad Asad Li, Xiong Mahmood, Khalid Ghaffar, Zahid Xie, Yong Wang, Guijuan University of Electronic Science and Technology of China School of Computer Science and Engineering Sichuan Chengdu611731 China National Yunlin University of Science and Technology Graduate School of Intelligent Data Science Yunlin Douliu64002 Taiwan National Yunlin University of Science and Technology Graduate School of Engineering Science and Technology Douliu64002 Taiwan Qinghai Institute of Technology School of Computer and Information Science China Qinghai Provincial Laboratory for Intelligent Computing and Application China Key Laboratory of Computing Power Network and Information Security Jinan250353 China Shandong Provincial Key Laboratory of Industrial Network and Information System Security China Shandong Fundamental Research Center for Computer Science Jinan250353 China

The Internet of Things (IoT) is rapidly permeating all aspects of human life, involving a network of devices that share sensitive data. A notable application is the e-healthcare systems, which employ connected sensors, medical servers, and wearable devices. However, the public nature of communication in e-healthcare systems poses challenges such as security, privacy, and authentication of participating entities. Recently, many authentication protocols have been introduced to address these challenges. However, most of these protocols remain vulnerable to various security attacks, including device or medical server impersonation, denial of service, physical or cloning, and de-synchronization attacks. Therefore, we introduce an authenticated key-management protocol utilizing hash functions and Cipher-Block Chaining-Advanced Encryption Standard encryption (CBC-AES) encryption. The proposed protocol also employs the Physical Unclonable Function (PUF), which makes it more robust and efficient in resisting physical or cloning attacks. Additionally, the proposed scheme resists various security threats, including impersonation, session key leakage, ephemeral secret leakage, and de-synchronization attacks. We analyze the scheme’s security and reliability through formal and informal analysis. The informal analysis demonstrates that the scheme encompasses crucial security features, while the formal analysis substantiates. Moreover, performance analysis of the proposed protocol with various competing results indicates that our protocol achieves an average reduction in communication and computation overheads by 36.03.% and 41.79%, respectively. © 2014 IEEE.

关键词： Electronic health record

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