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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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Multi-MedVit: a deep learning approach for the diagnosis of COVID-19 with the CT images

Multi-MedVit: a deep learning approach for the diagnosis of ...

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2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

作者： Cai, Yunjie Zheng, Zeqi Nie, Shanling Guo, Yue Zhang, Ruijie Yang, Hai East China University of Science and Technology Department of Computer Science and Engineering Shanghai200237 China Shanghai Key Laboratory of Computer Software Evaluating and Testing Shanghai China University of Southampton School of Electronics and Computer Science United Kingdom

ISBN: (纸本)9781665468190

The grim situation of novel coronavirus pneumonia 2019 (COVID-19) and its terrible spreading speed have already constituted a severe risk to human life, so it is ultimately essential to rapidly and accurately diagnose for COVID-19 pneumonia. Based on this study's 746 lung CT images, we propose Multi-MedVit, a novel auxiliary COVID-19 diagnosis framework based on the multi-input Transformer. We compare Multi-MedVit with state-of-the-art deep learning methods, such as CNN, VGG16, and ResNet50. Multi-MedVit outperformed the other methods on the benchmark dataset and proved that multiscale data input for data augmentation helped enhance model stability. Based on an interpretable analysis of the input and output of Multi-MedVit, we found that with the support of the training set data, the model has been possible to accurately focus on the lesion area for diagnosis of COVID-19 without expert annotations, which can provide initial references containing more potential information to doctors more precisely and fleetly. © 2022 IEEE.

关键词： COVID-19

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Improving the Robustness of Knowledge-Grounded Dialogue via Contrastive Learning

arXiv

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arXiv 2024年

作者： Wang, Jiaan Qu, Jianfeng Wang, Kexin Li, Zhixu Hua, Wen Li, Ximing Liu, An School of Computer Science and Technology Soochow University Suzhou China Shanghai Key Laboratory of Data Science School of Computer Science Fudan University Shanghai China The Hong Kong Polytechnic University Hong Kong College of Computer Science and Technology Jilin University China

Knowledge-grounded dialogue (KGD) learns to generate an informative response based on a given dialogue context and external knowledge (e.g., knowledge graphs;KGs). Recently, the emergence of large language models (LLMs) and pre-training techniques has brought great success to knowledge-grounded dialogue. However, when building KGD systems in real applications, there are various real-world noises that are inevitable to face. For example, the dialogue context might involve perturbations such as misspellings and abbreviations. In addition, KGs typically suffer from incompletion and also might contain erroneous and outdated facts. Such real-world noises pose a challenge to the robustness of KGD systems and hinder their applications in the real world. In this paper, we propose an entity-based contrastive learning framework for improving the robustness of KGD. Specifically, we make use of the entity information in a KGD sample to create both its positive and negative samples which involve semantic-irrelevant and semantic-relevant perturbations, respectively. The contrastive learning framework ensures the KGD model is aware of these two types of perturbations, thus generating informative responses with the potentially noisy inputs in real applications. Experimental results on three benchmark datasets show that our method achieves new state-of-the-art performance in terms of automatic evaluation scores, verifying its effectiveness and potentiality. Furthermore, we show that our method can generate better responses than comparison models in both the noisy and the few-shot settings. Copyright © 2024, The Authors. All rights reserved.

关键词： Knowledge graph

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A secure quantum homomorphic encryption ciphertext retrieval scheme

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Soft Computing 2025年第3期29卷 1497-1509页

作者： Cheng, Zhen-Wen Chen, Xiu-Bo Xu, Gang Chang, Yan Miao, Li-Hua Yang, Yi-Xian Wang, Ya-Lan School of Data and Computer Science Shandong Women’s University Jinan250300 China Information Security Center State Key Laboratory of Networking and Switching Technology Beijing University of Posts and Telecommunications Beijing100876 China School of Information Science and Technology North China University of Technology Beijing100144 China School of Cybersecurity Chengdu University of Information Technology Chengdu610225 China Huawei Technologies Co. Ltd Shenzhen518129 China Department of Computer Science Faculty of Engineering and Physical Sciences University of Surrey Surrey GuildfordGU2 7XH United Kingdom

In a recent paper (Gong et al. Quantum Inf Process 19:3, 2020), a novel ciphertext retrieval scheme based on the Grover algorithm and quantum homomorphic encryption was presented. In this scheme, when the server performs the operation of marking the solution on the user’s encrypted state in the Grover iteration, it needs to remove many gate-errors generated in the homomorphic evaluation of the T gate. And the server could judge this specific solution from the quantum circuit of marking the solution. It makes this scheme unable to achieve the low-cost and secure ciphertext retrieval. Therefore, we improve the Gong et al.’s scheme and propose a secure quantum homomorphic encryption ciphertext retrieval scheme. In our scheme, the trusted third party is introduced to cooperate with the server to execute the Grover algorithm. In each Grover iteration, the trusted third party can quickly mark the solution on the plaintext state, encrypt the marked state, and transmit it to the server. Then the server performs the remaining operations of this Grover iteration on the encrypted state. The trusted third party finally decrypts the iterated state. This cooperative approach ensures that the number of auxiliary qubits required and extra quantum gates executed in our scheme are lower than the Gong et al.’s scheme. By analyzing the security of our scheme, we confirm that the server and the trusted third party will not be informed of this solution. Thus, our scheme realizes the secure ciphertext retrieval with low computational overhead. We utilize IBM’s Qiskit framework to simulate our scheme, and the experimental result shows that our scheme is correct. It is worth noting that the low-cost and secure ciphertext retrieval will play a crucial role in modern information security and privacy protection. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.

关键词： Ciphertext

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EmotionQueen: A Benchmark for Evaluating Empathy of Large Language Models

arXiv

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arXiv 2024年

作者： Chen, Yuyan Wang, Hao Yan, Songzhou Liu, Sijia Li, Yueze Zhao, Yi Xiao, Yanghua Shanghai Key Laboratory of Data Science School of Computer Science Fudan University China Beijing Yuandian Technology China School of Engineering and Applied Science University of Pennsylvania United States

Emotional intelligence in large language models (LLMs) is of great importance in Natural Language Processing. However, the previous research mainly focus on basic sentiment analysis tasks, such as emotion recognition, which is not enough to evaluate LLMs' overall emotional intelligence. Therefore, this paper presents a novel framework named Emotion- Queen for evaluating the emotional intelligence of LLMs. The framework includes four distinctive tasks: key Event Recognition, Mixed Event Recognition, Implicit Emotional Recognition, and Intention Recognition. LLMs are requested to recognize important event or implicit emotions and generate empathetic response. We also design two metrics to evaluate LLMs' capabilities in recognition and response for emotion-related statements. Experiments yield significant conclusions about LLMs' capabilities and limitations in emotion intelligence. © 2024, CC BY.

关键词： Emotional intelligence

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Federated Hybrid-Supervised Learning for Universal Medical Image Segmentation

Federated Hybrid-Supervised Learning for Universal Medical I...

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2025 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2025

作者： Zheng, Shenhai Wen, Sian Li, Congyu Chen, Qing Li, Laquan College of Computer Science and Technology Chongqing University of Posts and Telecommunications Chongqing China Key Laboratory of Cyberspace Big Data Intelligent Security Ministry of Education Chongqing China School of Science Chongqing University of Posts and Telecommunications Chongqing China

ISBN: (纸本)9798350368741

Federated Learning (FL) is an advanced technology that tackles the challenge of blocked data arising from privacy concerns, enabling the training of deep learning models without the need for data sharing. However, FL faces difficulties with heterogeneous data and limited annotations in medical image segmentation. Motivated by this discovery, this study proposes a novel hybrid-supervised federated learning method (FedSLAG) that explores various types of annotations in medical imaging. To focus more on weakly-supervised and unsupervised scenarios within hybrid-supervised learning, a federated Gaussian enhancement module was proposed for heterogeneous sparse annotations (points and scribbles). The feature extraction module combines the features of multiple weakly-supervised clients and establishes the correlation of similar pixels, thus making up for the deficiency of scarce annotations and the insufficient feature extraction capability of a single machine. Then, a two-stage broadcast mechanism based on supervision sparsity was proposed to alleviate optimization deviation in local models. Experiments on breast tumor and skin lesion segmentation tasks demonstrate significant efficiency gains as well as highly competitive segmentation accuracy in many hybrid-supervised situations. Our codes are available at: https://***/TrivenDev/FedSLAG. © 2025 IEEE.

关键词： federated learning hybrid-supervised learning medical image segmentation

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Approximation Designs for Energy Harvesting Relay Deployment in Wireless Sensor Networks

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Journal of computer science & Technology 2022年第4期37卷 779-796页

作者： Yi Wang Yi-Xue Liu Shun-Jia Zhu Xiao-Feng Gao Chen Tian School of Modern Posts Nanjing University of Posts and TelecommunicationsNanjing 210003China State Key Laboratory for Novel Software Technology Nanjing UniversityNanjing 210023China ByteDance Inc. Shanghai 201100China Key Laboratory of Artificial Intelligence of Ministry of Education Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai 200240China

Energy harvesting technologies allow wireless devices to be recharged by the surrounding environment, providing wireless sensor networks (WSNs) with higher performance and longer lifetime. However, directly building a wireless sensor network with energy harvesting nodes is very costly. A compromise is upgrading existing networks with energy harvesting technologies. In this paper, we focus on prolonging the lifetime of WSNs with the help of energy harvesting relays (EHRs). EHRs are responsible for forwarding data for sensor nodes, allowing them to become terminals and thus extending their lifetime. We aim to deploy a minimum number of relays covering the whole network. As EHRs have several special properties such as the energy harvesting and depletion rate, it brings great research challenges to seek an optimal deployment strategy. To this end, we propose an approximation algorithm named Effective Relay Deployment Algorithm, which can be divided into two phases: disk covering and connector insertion using the partitioning technique and the Steinerization technique, respectively. Based on probabilistic analysis, we further optimize the performance ratio of our algorithm to (5 + 6/K) where K is an integer denoting the side length of a cell after partitioning. Our extensive simulation results show that our algorithm can reduce the number of EHRs to be deployed by up to 45% compared with previous work and thus validate the efficiency and effectiveness of our solution.

关键词： approximation algorithm constraint relay deployment energy harvesting wireless sensor network

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Dynamic Tracking with Fuzzy Rules for Evolutionary Dynamic Constrained Optimization

Dynamic Tracking with Fuzzy Rules for Evolutionary Dynamic C...

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2023 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2023

作者： Bu, Chenyang Liu, Yuxin Zhang, Lizhong Zhu, Tao Luo, Wenjian School of Computer Science and Information Engineering Hefei University of Technology Ministry of Education Key Laboratory of Knowledge Engineering with Big Data Anhui Hefei230027 China School of Computer Science and Information Engineering University of South China Hunan Hengyang421200 China School of Computer Science and Technology Harbin Institute of Technology Guangdong Shenzhen518000 China

ISBN: (纸本)9798350337020

Nature-inspired population-based stochastic search algorithms (SSA) have demonstrated effectiveness in solving many real-world dynamic optimization problems (DOPs), such as dynamic optimal power flow (DOPF) problems. The basic idea of solving DOPs using SSAs is to 'track the moving optima', rather than solving the changed problems from scratch. Its hidden assumption is that the problems are slightly changed in general, and it is expected that the search process can be accelerated by learning from past search experiences. However, the hidden assumption that the current search process can always benefit from previous search experiences might not be true for certain cases. For example, if the current problem is not similar to any of its previous problems, the historical solutions might not be helpful for the current search. To reduce such negative transfer, the following issues are worthy of study: how to choose which historical problems to learn from, and how to determine the degree of learning from historical problems. To solve the above problems, we propose a dynamic processing framework based on fuzzy rules from the perspective of incorporating human knowledge for optima tracking. The experimental results on the DOPF problems show that the SSA with the proposed optima tracking strategy outperforms other comparative algorithms. We open up the code and data of our algorithm44https://***/DMiC-Lab-HFUT/SMDE-Transfer. © 2023 IEEE.

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CDGNet: A Cross-Time Dynamic Graph-Based Deep Learning Model for Vehicle-Based Traffic Speed Forecasting

IEEE Transactions on Intelligent Vehicles

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IEEE Transactions on Intelligent Vehicles 2024年 1-14页

作者： Fang, Yuchen Luo, Haiyong Zhao, Fang Sun, Poly Z.H. Qin, Yanjun Zeng, Liang Hui, Bo Wang, Chenxing School of Computer Science National Pilot Software Engineering School Beijing University of Posts and Telecommunications Beijing China Beijing Key Laboratory of Mobile Computing and Pervasive Device Institute of Computing Technology Chinese Academy of Sciences Beijing China Department of Industrial Engineering School of Mechanical Engineering Shanghai Jiao Tong University Shanghai China Tsinghua University Beijing China University of Tulsa Tulsa USA

Vehicle-based traffic speed forecasting aims to predict the average speed of vehicles on the road in the future, which is an essential side information in intelligent vehicles and beneficial to safe autonomous driving, yet is very challenging due to the complex and dynamic spatio-temporal dependencies in real-world vehicle-based traffic. To extract intricate correlations among multiple vehicle-based speed time series, previous methods have used graph convolution networks. However, the conventional static and dynamic graphs fail to reflect the traffic evolution and the hysteresis spatial influence caused by vehicle movement. To address this issue, we propose a novel cross-time dynamic graph-based deep learning model, named CDGNet, for vehicle-based traffic speed forecasting. The model is able to effectively capture hysteresis spatial dependencies between each time slice and its historical time slices through the cross-time dynamic graph-based GCN. Meanwhile, a gating mechanism is integrated into our cross-time dynamic graph, which conforms to the sparse correlation in the real world. Besides, GCNs are incorporated into a novel encoder-decoder architecture to forecast multi-step speed. Experimental results on three real-world vehicle-based traffic speed datasets demonstrate the superiority of our CDGNet over various state-of-the-art spatio-temporal forecasting methods and the effectiveness of each component. We additionally provide a visualization of our cross-time dynamic graph to show the capability of assisting intelligent vehicles to avoid congestion. IEEE

关键词： Forecasting

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PVG: Progressive Vision Graph for Vision Recognition

arXiv

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arXiv 2023年

作者： Wu, Jiafu Chi, Mingmin Li, Jian Wang, Yabiao Zhang, Jiangning Zhang, Boshen Wang, Chengjie School of Computer Science Shanghai Key Laboratory of Data Science Fudan University Shanghai China School of Computer Science Shanghai Key Laboratory of Data Science Fudan University Zhongshan PoolNet Technology Ltd Shanghai China Tencent Youtu Lab Shanghai China Zhejiang University Tencent Youtu Lab China

Convolution-based and Transformer-based vision backbone networks process images into the grid or sequence structures, respectively, which are inflexible for capturing irregular objects. Though Vision GNN (ViG) adopts graph-level features for complex images, it has some issues, such as inaccurate neighbor node selection, expensive node information aggregation calculation, and over-smoothing in the deep layers. To address the above problems, we propose a Progressive Vision Graph (PVG) architecture for vision recognition task. Compared with previous works, PVG contains three main components: 1) Progressively Separated Graph Construction (PSGC) to introduce second-order similarity by gradually increasing the channel of the global graph branch and decreasing the channel of local branch as the layer deepens;2) Neighbor nodes information aggregation and update module by using Max pooling and mathematical Expectation (MaxE) to aggregate rich neighbor information;3) Graph error Linear Unit (GraphLU) to enhance low-value information in a relaxed form to reduce the compression of image detail information for alleviating the over-smoothing. Extensive experiments on mainstream benchmarks demonstrate the superiority of PVG over state-of-the-art methods, e.g., our PVG-S obtains 83.0% Top-1 accuracy on ImageNet-1K that surpasses GNN-based ViG-S by +0.9↑ with the parameters reduced by 18.5%, while the largest PVG-B obtains 84.2% that has +0.5↑ improvement than ViG-B. Furthermore, our PVG-S obtains +1.3↑ box AP and +0.4↑ mask AP gains than ViG-S on COCO ***://***/wujiafu007/PVG/tree/main Copyright © 2023, The Authors. All rights reserved.

关键词： Image compression

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