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Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization

National science Review 2023年第5期10卷 240-250页

作者： Sijie Zhou Yi Wu Yu Zhao Zhen Zhang Limin Jiang Lin Liu Yan Zhang Jijun Tang Ying-Jin Yuan Frontiers Science Center for Synthetic Biology (Ministry of Education) Tianjin University Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin University Institute for Systems Genetics NYU Langone Health School of Computer Science and Technology College of Intelligence and ComputingTianjin University Epigenetic Group Frasergen Bioinformatics Co.Ltd. Department of Computer Science University of South Carolina

Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary *** Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural ***,we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes(synⅡ,synⅢ,synⅤ,circular synⅥ,synⅨR and synⅩ).Remarkably,we find that the rearrangement events exhibit a specific landscape of *** further reveal that the landscape is shaped by the combined effects of chromatin accessibili and spatial contact *** rearrangements tend to occur in 3D spatially proximal and chromatin-accessible *** enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution,and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

关键词： synthetic biology genome rearrangement hierarchical chromatin organization synthetic yeast genome SCRaMbLE Saccharomyces cerevisiae

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A survey on deep learning for polyp segmentation: techniques, challenges and future trends

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Visual Intelligence 2025年第1期3卷 1-20页

作者： Mei, Jiaxin Zhou, Tao Huang, Kaiwen Zhang, Yizhe Zhou, Yi Wu, Ye Fu, Huazhu PCA Lab Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education Nanjing China School of Computer Science and Engineering Nanjing University of Science and Technology Nanjing China School of Computer Science and Engineering Southeast University Nanjing China Institute of High Performance Computing A*STAR Singapore Singapore

Early detection and assessment of polyps play a crucial role in the prevention and treatment of colorectal cancer (CRC). Polyp segmentation provides an effective solution to assist clinicians in accurately locating and segmenting polyp regions. In the past, people often relied on manually extracted lower-level features such as color, texture, and shape, which often had problems capturing global context and lacked robustness to complex scenarios. With the advent of deep learning, more and more medical image segmentation algorithms based on deep learning networks have emerged, making significant progress in the field. This paper provides a comprehensive review of polyp segmentation algorithms. We first review some traditional algorithms based on manually extracted features and deep segmentation algorithms, and then describe benchmark datasets related to the topic. Specifically, we carry out a comprehensive evaluation of recent deep learning models and results based on polyp size, taking into account the focus of research topics and differences in network structures. Finally, we discuss the challenges of polyp segmentation and future trends in the field. © The Author(s) 2025.

关键词： Comprehensive evaluation Deep learning Medical imaging Polyp segmentation

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BERD+: A Generic Sequential Recommendation Framework by Eliminating Unreliable Data with Item- and Attribute-level Signals

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ACM Transactions on Information systems 2023年第2期42卷 1-33页

作者： Sun, Yatong Yang, Xiaochun Sun, Zhu Wang, Bin School of Computer Science and Engineering Northeastern University School of Computing Macquarie University China Australia Institute of High Performance Computing Centre for Frontier AI Research A*STAR Singapore School of Computer Science and Engineering Northeastern University China National Frontiers Science Center for Industrial Intelligence and Systems Optimization China Key Laboratory of Data Analytics and Optimization for Smart Industry [Northeastern University Ministry of Education China

A preliminary work of our study was published at IJCAI’21 [47], which is substantially extended in the following aspects: (1) In Section 1, we analyze the necessity of introducing item attributes for detecting unreliable instances, together with the problems and challenges that attributes may bring in. (2) In Section 2, we add discussions about the limitations of existing attribute-aware recommender systems (Section 2.2) and denoising methods (Section 2.3) in the context of detecting unreliable instances. (3) In Section 4.2, we further conduct an in-depth analysis at the attribute level to demonstrate the capability of attributes for rectifying instance loss and uncertainty, as well as the disturbance caused by attributes. (4) We generalize BERD to a generic framework BERD+ in Section 5.1, equipped with novel modules, i.e., HU-GCN (Section 5.2) and EPE (Section 5.4), which properly incorporate item attributes while reducing their disturbance for rectifying instance uncer tainty (Section 5.5) and loss (Section 5.6). The generic BERD+ can be flexibly plugged into existing SRSs for performance enhanced recommendation via eliminating unreliable data. (5) In Section 6.2, we apply our BERD+ framework to seven state-of-the-art SRSs on five real-world datasets to illustrate its superiority. (6) To avoid unfair comparison caused by item attributes, we build and compare with the baseline that combines the original BERD and an advanced attribute-aware recommender system, KSR [19]. (7) For more comprehensive comparison, in Section 6.2.2, we compare BRED+ with two state-of-the-art denoising approaches;in Section 6.2.3, to examine the efficacy of HU-GCN and EPE, we compare HU-GCN with various attribute embedding techniques, i.e., variants of graph neural networks, and compare EPE with different attribute fusing methods, i.e., adding, concatenation, and weighted sum. (8) In Section 6.2.4, a detailed ablation study is conducted to verify the effectiveness of each module of BERD+. (

关键词： Convolution

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A Counterfactual Ultrasound Anti-Interference Self-Supervised Network for B-mode Ultrasound Tongue Extraction

A Counterfactual Ultrasound Anti-Interference Self-Supervise...

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

作者： Jia, Yan Cheng, Yuqing Xu, Kele Dou, Yong Qiao, Peng He, Zhouyu National Key Laboratory of Parallel and Distributed Computing College of Computer Science and Technology National University of Defense Technology Changsha China College of Systems Engineering National University of Defense Technology Changsha China

ISBN: (纸本)9798350368741

B-mode ultrasound tongue imaging is a non-invasive and real-time method for visualizing vocal tract deformation. However, accurately extracting the tongue's surface contour remains a significant challenge due to the low signal-to-noise ratio (SNR) and prevalent speckle noise in ultrasound images. Traditional supervised learning models often require large labeled datasets, which are labor-intensive to produce and susceptible to noise interference. To address these limitations, we present a novel Counterfactual Ultrasound Anti-Interference Self-Supervised Network (CUAI-SSN), which integrates self-supervised learning (SSL) with counterfactual data augmentation, progressively disentangles confounding factors, ensuring that the model generalizes well across varied ultrasound conditions. Our approach leverages causal reasoning to decouple noise from relevant features, enabling the model to learn robust representations that focus on essential tongue structures. By generating counterfactual image-label pairs, our method introduces alternative, noise-independent scenarios that enhance model training. Furthermore, we introduce attention mechanisms to enhance the network's ability to capture fine-grained details even in noisy conditions. Extensive experiments on real ultrasound tongue images demonstrate that CUAI-SSN outperforms existing methods, setting a new benchmark for automated contour extraction in ultrasound tongue imaging. Our code is publicly available at https://***/inexhaustible419/CounterfactualultrasoundAI. © 2025 IEEE.

关键词： contour extraction counterfactual inference self-supervised learning speech production ultrasound image

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Continuous-Time Prediction of Industrial Paste Thickener System With Differential ODE-Net

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IEEE/CAA Journal of Automatica Sinica 2022年第4期9卷 686-698页

作者： Zhaolin Yuan Xiaorui Li Di Wu Xiaojuan Ban Nai-Qi Wu Hong-Ning Dai Hao Wang the Beijing Advanced Innovation Center for Materials Genome Engineering Institute of Artificial IntelligenceBeijing Key Laboratory of Knowledge Engineering for Materials ScienceSchool of Computer and Communication EngineeringUniversity of Science and Technology Beijing the Department of ICT and Natural Science Norwegian University of Science and Technology IEEE the Institute of Systems Engineering and Collaborative Laboratory for Intelligent Science and SystemsMacao University of Science and Technology the Department of Computing and Decision Sciences Lingnan University the Department of Computer Science Norwegian University of Science and Technology

It is crucial to predict the outputs of a thickening system,including the underflow concentration(UC)and mud pressure,for optimal control of the *** proliferation of industrial sensors and the availability of thickening-system data make this ***,the unique properties of thickening systems,such as the non-linearities,long-time delays,partially observed data,and continuous time evolution pose challenges on building data-driven predictive *** address the above challenges,we establish an integrated,deep-learning,continuous time network structure that consists of a sequential encoder,a state decoder,and a derivative module to learn the deterministic state space model from thickening *** a case study,we examine our methods with a tailing thickener manufactured by the FLSmidth installed with massive sensors and obtain extensive experimental *** results demonstrate that the proposed continuous-time model with the sequential encoder achieves better prediction performances than the existing discrete-time models and reduces the negative effects from long time delays by extracting features from historical system *** proposed method also demonstrates outstanding performances for both short and long term prediction tasks with the two proposed derivative types.

关键词： Industrial 24 paste thickener ordinary differential equation(ODE)-net recurrent neural network time series prediction

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Cooperative Air-Ground Instant Delivery by UAVs and Crowdsourced Taxis 40

Cooperative Air-Ground Instant Delivery by UAVs and Crowdsou...

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40th IEEE International Conference on Data engineering, ICDE 2024

作者： Gao, Junhui Wang, Qianru Zhang, Xin Shi, Juan Zhao, Xiang Han, Qingye Pan, Yan School of Computer Science Northwestern Polytechnical University China School of Computer Science and Technology Xidian University China Air Force Engineering University China National University of Defense Technology Laboratory for Big Data and Decision China School of Management Science and Real Estate Chongqing University China National University of Defense Technology National Key Laboratory of Information Systems Engineering China National University of Defense Technology National Key Laboratory of Parallel and Distributed Computing China

ISBN: (纸本)9798350317152

Instant delivery has become a fundamental service in people's daily lives. Different from the traditional express service, the instant delivery has a strict shipping time constraint after being ordered. However, the labor shortage makes it challenging to realize efficient instant delivery. To tackle the problem, researchers have studied to introduce vehicles (i.e., taxis) or Unmanned Aerial Vehicles (UAVs or drones) into instant delivery tasks. Unfortunately, the delivery detour of taxis and the limited battery of UAVs make it hard to meet the rapidly increasing instant delivery demands. Under this circumstance, this paper proposes an air-ground cooperative instant delivery paradigm to maximize the delivery performance and meanwhile minimize the negative effects on the taxi passengers. Specifically, a data-driven delivery potential-demands-aware cooperative strategy is designed to improve the overall delivery performance of both UAVs and taxis as well as the taxi passengers' experience. The experimental results show that the proposed method improves the delivery number by 30.1% and 114.5% compared to the taxi-based and UAV-based instant delivery respectively, and shortens the delivery time by 35.7% compared to the taxi-based instant delivery. © 2024 IEEE.

关键词： Unmanned aerial vehicles (UAV)

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FedIERF: Federated Incremental Extremely Random Forest for Wearable Health Monitoring

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Journal of computer science & Technology 2023年第5期38卷 970-984页

作者：胡春雨忽丽莎袁林陆佃杰吕蕾陈益强 Key Laboratory of Computing Power Network and Information Security Ministry of EducationShandong Computer Science Center(National Supercomputer Center in Jinan)Qilu University of Technology(Shandong Academy of Sciences)Jinan 250353China Shandong Provincial Key Laboratory of Computer Networks Shandong Fundamental Research Center for Computer ScienceJinan 250000China Shandong Provincial Key Laboratory for Novel Distributed Computer Software Technology Jinan 25000China Institute of Information Technology Hebei University of Economics and BusinessShijiazhuang 050061China School of Information Science and Engineering Shandong Normal UniversityJinan 250358China Institute of Computing Technology Chinese Academy of SciencesBeijing 100190China

Wearable health monitoring is a crucial technical tool that offers early warning for chronic diseases due to its superior portability and low power ***,most wearable health data is distributed across dfferent organizations,such as hospitals,research institutes,and companies,and can only be accessed by the owners of the data in compliance with data privacy *** first challenge addressed in this paper is communicating in a privacy-preserving manner among different *** second technical challenge is handling the dynamic expansion of the federation without model *** address the first challenge,we propose a horizontal federated learning method called Federated Extremely Random Forest(FedERF).Its contribution-based splitting score computing mechanism significantly mitigates the impact of privacy protection constraints on model *** on FedERF,we present a federated incremental learning method called Federated Incremental Extremely Random Forest(FedIERF)to address the second technical *** introduces a hardness-driven weighting mechanism and an importance-based updating scheme to update the existing federated model *** experiments show that FedERF achieves comparable performance with non-federated methods,and FedIERF effectively addresses the dynamic expansion of the *** opens up opportunities for cooperation between different organizations in wearable health monitoring.

关键词： federated learning incremental learning random forest wearable health monitoring

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Pushing AI to wireless network edge: an overview on integrated sensing, communication, and computation towards 6G

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science China(Information sciences) 2023年第3期66卷 7-25页

作者： Guangxu ZHU Zhonghao LYU Xiang JIAO Peixi LIU Mingzhe CHEN Jie XU Shuguang CUI Ping ZHANG Shenzhen Research Institute of Big Data Future Network of Intelligence Institute (FNii) The Chinese University of Hong Kong (Shenzhen) School of Science and Engineering (SSE) The Chinese University of Hong Kong (Shenzhen) State Key Laboratory of Advanced Optical Communication Systems and Networks School of Electronics Peking University Department of Electrical and Computer Engineering and Institute for Data Science and Computing University of Miami Peng Cheng Laboratory State Key Laboratory of Networking and Switching Technology Beijing University of Posts and Telecommunications

Pushing artificial intelligence(AI) from central cloud to network edge has reached board consensus in both industry and academia for materializing the vision of artificial intelligence of things(AIoT) in the sixth-generation(6G) era. This gives rise to an emerging research area known as edge intelligence, which concerns the distillation of human-like intelligence from the vast amount of data scattered at the wireless network edge. Typically, realizing edge intelligence corresponds to the processes of sensing, communication,and computation, which are coupled ingredients for data generation, exchanging, and processing, ***, conventional wireless networks design the three mentioned ingredients separately in a task-agnostic manner, which leads to difficulties in accommodating the stringent demands of ultra-low latency, ultra-high reliability, and high capacity in emerging AI applications like auto-driving and metaverse. This thus prompts a new design paradigm of seamlessly integrated sensing, communication, and computation(ISCC) in a taskoriented manner, which comprehensively accounts for the use of the data in downstream AI tasks. In view of its growing interest, this study provides a timely overview of ISCC for edge intelligence by introducing its basic concept, design challenges, and enabling techniques, surveying the state-of-the-art advancements, and shedding light on the road ahead.

关键词： sixth-generation (6G) edge intelligence artificial intelligence of things (AIoT) integrated sensing communication and computation (ISCC)

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Edge-Driven Industrial computing Power Networks: Digital Twin-Empowered Service Provisioning by Hybrid Soft Actor-Critic

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IEEE Transactions on Vehicular Technology 2025年第5期74卷 8095-8109页

作者： Zhang, Long Song, Deng-Ao Zhang, Hongliang Tian, Ni Zhuang, Zirui Niyato, Dusit Han, Zhu Hebei University of Engineering School of Information and Electrical Engineering Handan056038 China Peking University State Key Laboratory of Advanced Optical Communication Systems and Networks School of Electronics Beijing100871 China Beijing University of Posts and Telecommunications State Key Laboratory of Networking and Switching Technology Beijing100876 China Nanyang Technological University College of Computing and Data Science 639798 Singapore University of Houston Department of Electrical and Computer Engineering HoustonTX77004 United States Kyung Hee University Department of Computer Science and Engineering Seoul446-701 Korea Republic of

With the proliferation of data-intensive industrial applications, the collaboration of computing powers among standalone edge servers is vital to provision such services for smart devices. In this paper, we propose an edge-driven industrial computing power network (CPN) by orchestrating the computing and network resources of edge servers through the centralized resource scheduling and decentralized task computing. However, efficient task offloading and collaborative processing is challenging, which requires higher degrees of network automation and intelligence. Therefore, we incorporate digital twins (DTs) into the edge-driven CPN architecture, where the DTs are created as the digital replicas to assist both the computation offloading and collaborative processing. A joint optimization problem of the computing power assignment, service association, task partition, and transmit power control is formulated for maximizing the system average weighted utility. Due to the temporal-spatial variability of tasks and the resulted dynamic environment, we transform the original problem as a Markov decision process aiming at maximizing the long-term average weighted utility. To efficiently handle the high-dimensional discrete-continuous action space, a hybrid soft actor-critic based deep reinforcement learning algorithm is developed for optimizing the joint design. Simulation results validate the superiority of our proposed algorithm over the benchmarks, showing the significant gains obtained by integrating DTs into the edge-driven CPN. © 1967-2012 IEEE.

关键词： Markov processes

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Interest Points Analysis for Internet Forum Based on Long-Short Windows Similarity

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computers, Materials & Continua 2022年第8期72卷 3247-3267页

作者： Xinghai Ju Jicang Lu Xiangyang Luo Gang Zhou Shiyu Wang Shunhang Li Yang Yang State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou450001China School of Computing and Information Systems Singapore Management University188065Singapore College of Computer Science and Big Data Fuzhou UniversityFuzhou350116China

For Internet forum Points of Interest(PoI),existing analysis methods are usually lack of usability analysis under different conditions and ignore the long-term variation,which lead to blindness in method *** address this problem,this paper proposed a PoI variation prediction framework based on similarity analysis between long and short *** on the framework,this paper presented 5 PoI analysis algorithms which can be categorized into 2 types,i.e.,the traditional sequence analysis methods such as autoregressive integrated moving average model(ARIMA),support vector regressor(SVR),and the deep learning methods such as convolutional neural network(CNN),long-short term memory network(LSTM),Transformer(TRM).Specifically,this paper firstly divides observed data into long and short windows,and extracts key words as PoI of each ***,the PoI similarities between long and short windows are calculated for training and ***,series of experiments is conducted based on real Internet forum *** results show that,all the 5 algorithms could predict PoI variations well,which indicate effectiveness of the proposed *** the length of long window is small,traditional methods perform better,and SVR is the *** the contrary,the deep learning methods show superiority,and LSTM performs *** results could provide beneficial references for PoI variation analysis and prediction algorithms selection under different parameter configurations.

关键词： Point of interest(PoI)analysis long and short windows sequential analysis deep learning

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