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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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NOBGP: A Novel Optimized Balanced Graph Partitioning Algorithm 19th

NOBGP: A Novel Optimized Balanced Graph Partitioning Algorit...

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19th CCF Conference on Computer Supported Cooperative Work and Social computing, ChineseCSCW 2024

作者： Chen, Jiebin Hu, Ziqiang Ye, Renjie Zhang, Qishan Guo, Kun College of Computer and Data Science Fuzhou University Fuzhou350108 China Engineering Research Center of Big Data Intelligence Ministry of Education Fuzhou350108 China Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou350108 China Xianda College of Economics and Humanities Shanghai International Studies University Shanghai China

ISBN: (纸本)9789819623723

Large-scale graphs have become prevalent with the advent of the big data era. Distributed graph computing systems are commonly used for processing and analyzing large-scale graphs, with graph partitioning being a key prerequisite for their efficient computation. Graph partitioning aims to balance the load across partitions while minimizing the number of cut-edges. Moreover, it should achieve high efficiency and scalability. However, the existing popular graph partitioning algorithms do not fully take into account the internal topology of real-world graphs, which affects the final partition quality and convergence. Meanwhile, they easily fall into the local optimum due to partition load constraints. This paper introduces a Novel Optimized Balanced Graph Partitioning algorithm (NOBGP). First, we propose an initialization strategy based on label propagation of core vertices to achieve initial partitions with good locality and accelerate convergence. Second, we optimize the label propagation process to ensure balanced partitions and propose a probability-based disruption strategy to avoid the local optimum. We implement NOBGP on the distributed graph computing framework GraphX. Extensive experimental results on real-world graphs show that the proposed algorithm is scalable and performs better than the existing algorithms. We also run PageRank and Louvain applications using the graph partitioning results to demonstrate the efficiency of our algorithm. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： Graph algorithms

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WiViPose: A Video-aided Wi-Fi Framework for Environment-Independent 3D Human Pose Estimation

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IEEE Transactions on Multimedia 2025年

作者： Zhang, Lei Ning, Haoran Tang, Jiaxin Chen, Zhenxiang Zhong, Yaping Han, Yahong Tianjin University College of Intelligence and Computing the Tianjin Key Laboratory of Advanced Network Technology and Application Tianjin300050 China Key Laboratory of Computing Power Network and Information Security Ministry of Education China University of Jinan Shandong Provincial Key Laboratory of Ubiquitous Intelligent Computing the School of Information Science and Engineering Jinan250022 China Wuhan Sports University Sports Big-data Research Center Wuhan430079 China Tianjin University College of Intelligence and Computing the Tianjin Key Laboratory of Machine Learning Tianjin300350 China

The inherent complexity of Wi-Fi signals makes video-aided Wi-Fi 3D pose estimation difficult. The challenges include the limited generalizability of the task across diverse environments, its significant signal heterogeneity, and its inadequate ability to analyze local and geometric information. To overcome these challenges, we introduce WiViPose, a video-aided Wi-Fi framework for 3D pose estimation, which attains enhanced cross-environment generalization through cross-layer optimization. Bilinear temporal-spectral fusion (BTSF) is initially used to fuse the time-domain and frequency-domain features derived from Wi-Fi. Video features are derived from a multiresolution convolutional pose machine and enhanced by local self-attention. Cross-modality data fusion is facilitated through an attention-based transformer, with the process further refined under a supervisory mechanism. WiViPose demonstrates effectiveness by achieving an average percentage of correct keypoints (PCK)@50 of 91.01% across three typical indoor environments. © 2025 IEEE.

关键词： Frequency domain analysis

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PUTraceAD: Trace Anomaly Detection with Partial Labels based on GNN and PU Learning

PUTraceAD: Trace Anomaly Detection with Partial Labels based...

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International Symposium on Software Reliability Engineering (ISSRE)

作者： Ke Zhang Chenxi Zhang Xin Peng Chaofeng Sha School of Computer Science Fudan University China Shanghai Key Laboratory of Data Science Fudan University China Shanghai Collaborative Innovation Center of Intelligent Visual Computing China

ISBN: (数字)9781665451321

ISBN: (纸本)9781665451338

Distributed tracing has been an important part of microservice infrastructure and learning-based trace analysis has been used to detect anomalies in microservice systems. Existing learning-based trace anomaly detection approaches ei-ther assume that trace patterns can be learned from normal execution or rely on fault injection to produce labeled traces (i.e., normal/anomalous ones). However, in practice it is often difficult to ensure that the normal execution does not involve anomalous traces or obtain a large variety of normal and anomalous traces through fault injection. In this paper, we propose PUTraceAD, a trace anomaly detection approach that can alleviate the above problems. PUTraceAD represents a trace as a span causal graph with node features such as operation name, response code, duration time. Based on the graph representation, PUTraceAD trains a GNN- and PU learning-based trace anomaly detection model. During the process, PU (Positive and Unlabeled) learning optimizes model parameters through estimating the data distribution. Therefore, PUTraceAD can train the model based on a small set of labeled anomalous traces and a large set of unlabeled traces. Our evaluation shows that PUTraceAD outperforms existing unsupervised trace anomaly detection approaches and only slightly underperforms a supervised learning-based approach that takes full advantage of labeled traces.

关键词： Codes Microservice architectures data models Software reliability Time factors Anomaly detection

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Reliable Indoor Localization in Multi-Building Environments: Leveraging Environment-Invariant and Position-Related Features

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IEEE Internet of Things Journal 2025年

作者： Long, Wenhan Wen, Xinlong Liu, Hao Li, Mengyao Li, Songquan Wu, Yonghui Chen, Fuxiang Liu, Lu Zhu, Rongbo Huazhong Agricultural University College of Informatics Wuhan430070 China Ministry of Education Engineering Research Center of Intelligent Technology for Agriculture Wuhan430070 China Hubei Engineering Technology Research Center of Agricultural Big Data Wuhan430070 China University of Leicester School of Computing and Mathematical Sciences Leicester United Kingdom University of Exeter Department of Computer Science Exeter United Kingdom

Received Signal Strength Indicator (RSSI)-based indoor localization offers a cost-effective solution for autonomous mobile robot navigation in 3D indoor environments, including cross-floor and multi-building structures. However, localization accuracy is fundamentally constrained by the low sampling density and unstable measurement of RSSI data. So far, existing methods neglect cross-environment RSSI coherence (e.g., repeated signal patterns in geometrically similar areas), resulting in unreliable fingerprint databases. What’s more, most approaches fail to model the spatial hierarchy of buildings, floors, and coordinates, which leads to lower accuracy in indoor positioning model predictions. To address these issues, we propose EP-3DLoc, a novel 3D indoor localization framework that combines an Environment-Invariant feature-based data Completion (EIC) method with a Position-Related feature-based Localization (PRL) method. The EIC enhances data quality by filling in sparse RSSI data using environment-invariant features, which are recurring RSSI patterns found in similar environmental structures. The PRL module combines multi-scale RSSI signal processing (raw data and image-like data) with a multi-task network that analyzes location relationships, enhancing localization accuracy in 3D environments. Experimental results on public datasets (TUT2018, UTSIndoorLoc, and UJIIndoorLoc) have demonstrated that EP-3DLoc achieves state-of-the-art performance on indoor localization in multi-building environments. Further testing on the self-constructed dataset HZAUIndoorLoc have revealed that EP-3DLoc not only outperforms existing methods in localization accuracy but also maintains low energy consumption and strong resistance to interference. © 2014 IEEE.

关键词： Floors

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DFGET: Displacement-Field Assisted Graph Energy Transmitter for Gland Instance Segmentation

DFGET: Displacement-Field Assisted Graph Energy Transmitter ...

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International Conference on Signal Processing Proceedings (ICSP)

作者： Caiqing Jian Yongbin Qin Lihui Wang Chen Ye Xinyu Cheng GState Key Laboratory of Public Big Data College of Computer Science and Technology Engineering Research Center of Text Computing & Cognitive Intelligence Ministry of Education Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province Guizhou University Guiyang China

ISBN: (数字)9798350387384

ISBN: (纸本)9798350387391

Gland instance segmentation is an essential but challenging task in the diagnosis of adenocarcinoma. The existing models usually achieve gland instance segmentation through multi-task learning and boundary loss constraint. However, how to deal with the problems of gland adhesion and inaccurate boundary in segmenting the complex samples remains a challenge. In this work, we propose a novel geometric feature named displacement field (DF), which can represent the geometric information such as shape, size, and orientation of the glands. Based on the explicit constraint of DF, a displacement-field assisted graph energy transmitter (DFGET) framework is proposed for solving the above problems. Using such graph framework, the gland semantic segmentation map and the displacement field of the graph nodes are estimated with two graph network branches. With the constraint of DF, a graph cluster module is presented to improve the intra-class feature consistency and inter-class feature discrepancy, as well as to separate the adherent glands. Extensive comparison and ablation experiments on the GlaS dataset demonstrate the effectiveness of the displacement field and the superiority of DFGET. Compared to the best comparative model, DFGET increases the object-Dice and object-F1 score by 2.27% and 3.11% respectively, while decreases the object-HD by 15.58, achieving state-of-the-art performance, which indicates that DFGET can serve as an auxiliary tool for the diagnosis of adenocarcinoma.

关键词： Instance segmentation Measurement Visualization Adhesives Shape Semantic segmentation Glands Signal processing algorithms Signal processing Market research

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A Multi-tier Offloading Optimization Strategy for Consumer Electronics in Vehicular Edge computing

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IEEE Transactions on Consumer Electronics 2025年

作者： Lin, Haiyang Xiao, Bo Zhou, Xiaokang Zhang, Yonghong Liu, Xiaodong the School of Software Nanjing University of Information Science and Technology Nanjing210044 China Jiangsu Province Engineering Research Center of Advanced Computing and Intelligent Services Nanjing210044 China the School of Chemistry and Materials Science Nanjing University of Information Science and Technology Nanjing210044 China the Faculty of Business Data Science Kansai University Osaka565-0823 Japan the School of Automation Nanjing University of Information Science and Technology Nanjing210044 China the School of Computing Edinburgh Napier University EdinburghEH10 5DT United Kingdom

—In the domain of consumer electronics, vehicular edge computing (VEC) technology is emerging as a novel data processing paradigm within vehicular networks. By sending tasks related to vehicular applications to the edge, this model makes it easier for computing power to be spread out. This lets interactive services respond quickly. Nevertheless, the computational resources at edge servers are inherently limited and often tasked with handling multiple concurrent operations. The inefficacious allocation of these resources significantly impairs the efficiency of task offloading. Additionally, indiscriminate offloading could overwhelm the servers, detrimentally impacting the performance of subsequent tasks. To circumvent these challenges, this study introduces a multi-tier offloading model predicated on game theory principles. This framework aims to optimize resource utilization at the edge while accounting for server load to ensure the timely execution of latency-sensitive tasks. To evaluate this model, this paper created a simulation environment specifically for video game tasks in consumer electronics. The experimental results show that the multi-tier offloading model can effectively relieve the load pressure on the edge server. The task failure rate of the multi-tier offloading model remains at the lowest level compared with several state-of-the-art algorithms, significantly reducing the execution delay of tasks and being able to meet the requirements of consumer electronics applications. © 2025 IEEE.

关键词： Computation offloading

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Fast Latent Factor Analysis via a Fuzzy PID-Incorporated Stochastic Gradient Descent Algorithm

arXiv

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arXiv 2023年

作者： Li, Jinli Yuan, Ye School of Computer Science and Technology Chongqing University of Posts and Telecommunications Chongqing400065 China Chongqing Key Laboratory of Big Data and Intelligent Computing Chongqing Engineering Research Center of Big Data Application for Smart Cities Chongqing Institute of Green and Intelligent Technology Chinese Academy of Sciences Chongqing400714 China College of Computer and Information Science Southwest University Chongqing400715 China

A high-dimensional and incomplete (HDI) matrix can describe the complex interactions among numerous nodes in various big data-related applications. A stochastic gradient descent (SGD)-based latent factor analysis (LFA) model is remarkably effective in extracting valuable information from an HDI matrix. However, such a model commonly encounters the problem of slow convergence because a standard SGD algorithm learns a latent factor relying on the stochastic gradient of current instance error only without considering past update information. To address this critical issue, this paper innovatively proposes a Fuzzy PID-incorporated SGD (FPS) algorithm with two-fold ideas: 1) rebuilding the instance learning error by considering the past update information in an efficient way following the principle of PID, and 2) implementing hyper-parameters and gain parameters adaptation following the fuzzy rules. With it, an FPS-incorporated LFA model is further achieved for fast processing an HDI matrix. Empirical studies on six HDI datasets demonstrate that the proposed FPS-incorporated LFA model significantly outperforms the state-of-the-art LFA models in terms of computational efficiency for predicting the missing data of an HDI matrix with competitive accuracy. Copyright © 2023, The Authors. All rights reserved.

关键词： Matrix algebra

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A Weighted Flat Lattice Transformer-based Knowledge Extraction Architecture for Chinese Named Entity Recognition

A Weighted Flat Lattice Transformer-based Knowledge Extracti...

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International Conference on Computer Supported Cooperative Work in Design

作者： Hengwei Zhang Yuejia Wu Jian-Tao Zhou Inner Mongolia University College of Computer Science Hohhot China Ministry of Education National & Local Joint Engineering Research Center of Intelligent Information Processing Technology for Mongolian Engineering Research Center of Ecological Big Data Hohhot China Inner Mongolia Engineering Laboratory for Cloud Computing and Service Software Hohhot China Inner Mongolia Key Laboratory of Social Computing and Data Processing Hohhot China Inner Mongolia Key Laboratory of Discipline Inspection and Supervision Big Data Hohhot China Inner Mongolia Engineering Laboratory for Big Data Analysis Technology Hohhot China

ISBN: (数字)9798350349184

ISBN: (纸本)9798350349191

Named Entity Recognition (NER) is one of the contents of Knowledge Extraction (KE) that transforms data into knowledge representation. However, Chinese NER faces the problem of lacking clear word boundaries that limit the effectiveness of the KE. Although the flat lattice Transformer (FLAT) framework, which converts lattice structure into a flat structure including a set of spans, can effectively improve this problem and obtain advanced results, there still exist the problems of insensitivity to entity importance weights and insufficient feature learning. This paper proposes a weighted flat lattice Transformer architecture for Chinese NER, namely WFLAT. The WFLAT first adds a weight matrix into self-attention calculation, which can obtain finer-grained partitioning of entities to improve experimental performance, and then adopts a multi-layer Transformer encoder with each layer using a multi-head self-attention mechanism. Extensive experimental results on benchmarks demonstrate that our proposed KE model can obtain state-of-the-art performance for the Chinese NER task.

关键词： Representation learning Computational modeling Memory management Lattices Named entity recognition Transforms Knowledge representation

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Dfier: A Directed Vulnerability Verifier for Ethereum Smart Contracts

SSRN

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SSRN 2023年

作者： Wang, Zeli Dai, Weiqi Li, Ming Choo, Kim-Kwang Raymond Zou, Deqing Chongqing Key Laboratory of Computational Intelligence Key Laboratory of Big Data Intelligent Computing Key Laboratory of Cyberspace Big Data Intelligent Security Ministry of Education College of Computer Science and Technology Chongqing University of Posts and Telecommunications Chongqing40065 China National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Hubei Engineering Research Center on Big Data Security Hubei Key Laboratory of Distributed System Security Hubei Engineering Research Center on Big Data Security School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan430074 China Department of Information Systems and Cyber Security University of Texas at San Antonio San Antonio United States

Existing smart contract vulnerability identification approaches mainly focus on complete program detection. Consequently, lots of known potentially vulnerable locations need manual verification, which is energy-exhaustive and error-prone. Fuzzing is an effective way to detect vulnerabilities. However, current fuzzers cannot effectively probe these suspicious targets because they overlook two key factors: exploring all paths toward the targets and providing high-quality directed seed inputs. This paper presents a Directed vulnerability veriFier (DFier), elaborating effective transaction sequences with directed inputs for the fuzzer, to focus on analyzing target paths and automatically detect whether the given locations are vulnerable. Specifically, DFier fuses the effectiveness of static analysis and the efficiency of fuzzing. The static analysis helps locate target paths and generate directed inputs for the fuzzer under three heuristic strategies. The first prefers inputs with the larger possibility of triggering potential vulnerabilities based on target features. The second guides the value mutation to satisfy the path constraints. The third adequately leverages execution information to help find exploits faster. Extensive experiments demonstrate that DFier is effective in verifying contract security, compared with three existing contract fuzzers (i.e., contractFuzzer, sFuzz, and conFuzzius). And the performance losses are in an acceptable range. © 2023, The Authors. All rights reserved.

关键词： Smart contract

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