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AlphaFold2 and its applications in the fields of biology and medicine

Signal Transduction and Targeted Therapy 2023年第4期8卷 1630-1643页

作者： Zhenyu Yang Xiaoxi Zeng Yi Zhao Runsheng Chen West China Biomedical Big Data Center West China HospitalSichuan UniversityChengdu 610041China Key Laboratory of Intelligent Information Processing Advanced Computer Research CenterInstitute of Computing TechnologyChinese Academy of SciencesBeijing 100190China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China Pingshan Translational Medicine Center Shenzhen Bay LaboratoryShenzhen 518118China

AlphaFold2(AF2)is an artificial intelligence(AI)system developed by DeepMind that can predict three-dimensional(3D)structures of proteins from amino acid sequences with atomic-level *** structure prediction is one of the most challenging problems in computational biology and chemistry,and has puzzled scientists for 50 *** advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much *** release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community,especially in the fields of biology and ***2 is thought to have a significant impact on structural biology and research areas that need protein structure information,such as drug discovery,protein design,prediction of protein function,et *** the time is not long since AF2 was developed,there are already quite a few application studies of AF2 in the fields of biology and medicine,with many of them having preliminarily proved the potential of *** better understand AF2 and promote its applications,we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success,and particularly focus on reviewing its applications in the fields of biology and *** of current AF2 prediction will also be discussed.

关键词： system fields Fold

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Task Separation and Knowledge Sharing for Class Incremental Learning 5

Task Separation and Knowledge Sharing for Class Incremental ...

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5th International Conference on Intelligent computing and Human-Computer Interaction, ICHCI 2024

作者： Zhang, Jiali Qiao, Xiaoyan School of Computer Science and Technology Shandong Technology and Business University Yantai Key Laboratory of Big Data Modeling and Intelligent Computing Immersion Technology and Evaluation Shandong Engineering Research Center Shandong Yantai China School of Mathematics and Information Science Shandong Technology and Business University Yantai Key Laboratory of Big Data Modeling and Intelligent Computing Immersion Technology and Evaluation Shandong Engineering Research Center Shandong Yantai China

ISBN: (纸本)9798350368284

Methods based on dynamically expanding architectures can effectively mitigate catastrophic forgetting in class incremental learning (CIL), but they often overlook information sharing and integration between subnetworks, leading to performance degradation and increased parameter count and memory consumption as the network expands. To address these complex issues, we introduce a new method called Task Separation and Knowledge Sharing (TSKS), which transfers knowledge at both the logical and feature levels through Hybrid Knowledge Distillation (HKD). In logical distillation, we combine Global Knowledge Distillation (GKD) and Task Knowledge Distillation (TKD) to establish connections between tasks. To prevent the model from favoring new classes, we design an Attention- Based Feature Fusion (ABFF) mechanism to capture important features. Additionally, we introduce a Soft-Margin Auxiliary Loss (SMAL) to help the model learn new concepts. Extensive experiments show that TSKS outperforms existing models on CIFAR100 and ImageNet100, regardless of whether memory samples are used. Notably, TSKS demonstrates superior performance in memory-free settings, indicating a reduced reliance on rehearsal memory. © 2024 IEEE.

关键词： Adversarial machine learning

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A Graph with Adaptive AdjacencyMatrix for Relation Extraction

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Computers, Materials & Continua 2024年第9期80卷 4129-4147页

作者： Run Yang YanpingChen Jiaxin Yan Yongbin Qin Engineering Research Center of Text Computing&Cognitive Intelligence Ministry of EducationGuizhou UniversityGuiyang550025China State Key Laboratory of Public Big Data Guizhou UniversityGuiyang550025China College of Computer Science and Technology Guizhou UniversityGuiyang550025China

The relation is a semantic expression relevant to two named entities in a *** a sentence usually contains several named entities,it is essential to learn a structured sentence representation that encodes dependency information specific to the two named *** related work,graph convolutional neural networks are widely adopted to learn semantic dependencies,where a dependency tree initializes the adjacency ***,this approach has two main ***,parsing a sentence heavily relies on external toolkits,which can be ***,the dependency tree only encodes the syntactical structure of a sentence,which may not align with the relational semantic *** this paper,we propose an automatic graph learningmethod to autonomously learn a sentence’s structural *** of using a fixed adjacency matrix initialized by a dependency tree,we introduce an Adaptive Adjacency Matrix to encode the semantic dependency between *** elements of thismatrix are dynamically learned during the training process and optimized by task-relevant learning objectives,enabling the construction of task-relevant semantic dependencies within a *** model demonstrates superior performance on the TACRED and SemEval 2010 datasets,surpassing previous works by 1.3%and 0.8%,*** experimental results show that our model excels in the relation extraction task,outperforming prior models.

关键词： Relation extraction graph convolutional neural network adaptive adjacency matrix

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Towards High-throughput and Low-latency Billion-scale Vector Search via CPU/GPU Collaborative Filtering and Re-ranking 23

Towards High-throughput and Low-latency Billion-scale Vector...

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23rd USENIX Conference on File and Storage Technologies, FAST 2025

作者： Tian, Bing Liu, Haikun Tang, Yuhang Xiao, Shihai Duan, Zhuohui Liao, Xiaofei Jin, Hai Zhang, Xuecang Zhu, Junhua Zhang, Yu National Engineering Research Center for Big Data Technology and System Service Computing Technology and System Lab/Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology China Huawei Technologies Co. Ltd. China

ISBN: (纸本)9781939133458

Approximate nearest neighbor search (ANNS) has emerged as a crucial component of database and AI infrastructure. Ever-increasing vector datasets pose significant challenges in terms of performance, cost, and accuracy for ANNS services. None of modern ANNS systems can address these issues simultaneously. In this paper, we present FusionANNS, a high-throughput, low-latency, cost-efficient, and high-accuracy ANNS system for billion-scale datasets using SSDs and only one entry-level GPU. The key idea of FusionANNS lies in CPU/GPU collaborative filtering and re-ranking mechanisms, which significantly reduce I/O operations across CPUs, GPU, and SSDs to break through the I/O performance bottleneck. Specifically, we propose three novel designs: (1) multi-tiered indexing to avoid data swapping between CPUs and GPU, (2) heuristic re-ranking to eliminate unnecessary I/Os and computations while guaranteeing high accuracy, and (3) redundant-aware I/O deduplication to further improve I/O efficiency. We implement FusionANNS and compare it with the state-of-the-art SSD-based ANNS system-SPANN and GPU-accelerated in-memory ANNS system-RUMMY. Experimental results show that FusionANNS achieves 1) 9.4-13.1× higher query per second (QPS) and 5.7-8.8× higher cost efficiency compared with SPANN;2) and 2-4.9× higher QPS and 2.3-6.8× higher cost efficiency compared with RUMMY, while guaranteeing low latency and high accuracy. © 2025 FAST. All Rights Reserved.

关键词： Collaborative filtering

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IGED:Towards Intelligent DDoS Detection Model Using Improved Generalized Entropy and DNN

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Computers, Materials & Continua 2024年第8期80卷 1851-1866页

作者： Yanhua Liu Yuting Han HuiChen Baokang Zhao XiaofengWang Ximeng Liu College of Computer and Data Science Fuzhou UniversityFuzhou350108China Engineering Research Center of Big Data Intelligence Ministry of EducationFuzhou350108China Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou UniversityFuzhou350108China College of Computer National University of Defense TechnologyChangsha410073China

As the scale of the networks continually expands,the detection of distributed denial of service(DDoS)attacks has become increasingly *** propose an intelligent detection model named IGED by using improved generalized entropy and deep neural network(DNN).The initial detection is based on improved generalized entropy to filter out as much normal traffic as possible,thereby reducing data *** the fine detection is based on DNN to perform precise DDoS detection on the filtered suspicious traffic,enhancing the neural network’s generalization *** results show that the proposed method can efficiently distinguish normal traffic from DDoS *** with the benchmark methods,our method reaches 99.9%on low-rate DDoS(LDDoS),flooded DDoS and CICDDoS2019 datasets in terms of both accuracy and efficiency in identifying attack flows while reducing the time by 17%,31%and 8%.

关键词： DDoS real-time improved generalized entropy DNN

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On the Security of Smart Home Systems:A Survey

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Journal of Computer Science & technology 2023年第2期38卷 228-247页

作者：袁斌万俊吴宇晗邹德清金海 School of Cyber Science and Engineering Huazhong University of Science and TechnologyWuhan 430074China Hubei Key Laboratory of Distributed System Security Huazhong University of Science and Technology Wuhan 430074China Hubei Engineering Research Center on Big Data Security Huazhong University of Science and Technology Wuhan 430074China National Engineering Research Center for Big Data Technology and System Huazhong University of Science and TechnologyWuhan 430074China Services Computing Technology and System Lab Huazhong University of Science and TechnologyWuhan 430074China Shenzhen Huazhong University of Science and Technology Research Institute Shenzhen 518057China School of Computer Science and Technology Huazhong University of Science and TechnologyWuhan 430074China Cluster and Grid Computing Lab Huazhong University of Science and TechnologyWuhan 430074China

Among the plethora of IoT(Internet of Things)applications,the smart home is one of the ***,the rapid development of the smart home has also made smart home systems a target for ***,researchers have made many efforts to investigate and enhance the security of smart home *** a more secure smart home ecosystem,we present a detailed literature review on the security of smart home ***,we categorize smart home systems’security issues into the platform,device,and communication *** exploring the research and specific issues in each of these security areas,we summarize the root causes of the security flaws in today's smart home systems,which include the heterogeneity of internal components of the systems,vendors'customization,the lack of clear responsibility boundaries and the absence of standard security ***,to better understand the security of smart home systems and potentially provide better protection for smart home systems,we propose research directions,including automated vulnerability mining,vigorous security checking,and data-driven security analysis.

关键词： IoT(Internet of Things) smart home IoT security smart home security

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FedRKG: A Privacy-Preserving Federated Recommendation Framework via Knowledge Graph Enhancement 18th

FedRKG: A Privacy-Preserving Federated Recommendation Framew...

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18th International Conference on Green, Pervasive, and Cloud computing, GPC 2023

作者： Yao, Dezhong Liu, Tongtong Cao, Qi Jin, Hai National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan430074 China School of Computing Science University of Glasgow Glasgow United Kingdom

ISBN: (纸本)9789819998951

Federated Learning (FL) has emerged as a promising approach for preserving data privacy in recommendation systems by training models locally. Recently, Graph Neural Networks (GNN) have gained popularity in recommendation tasks due to their ability to capture high-order interactions between users and items. However, privacy concerns prevent the global sharing of the entire user-item graph. To address this limitation, some methods create pseudo-interacted items or users in the graph to compensate for missing information for each client. Unfortunately, these methods introduce random noise and raise privacy concerns. In this paper, we propose FedRKG, a novel federated recommendation system, where a global knowledge graph (KG) is constructed and maintained on the server using publicly available item information, enabling higher-order user-item interactions. On the client side, a relation-aware GNN model leverages diverse KG relationships. To protect local interaction items and obscure gradients, we employ pseudo-labeling and Local Differential Privacy (LDP). Extensive experiments conducted on three real-world datasets demonstrate the competitive performance of our approach compared to centralized algorithms while ensuring privacy preservation. Moreover, FedRKG achieves an average accuracy improvement of 4% compared to existing federated learning baselines. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd 2024.

关键词： Recommender systems

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Image Denoising Method Based on Channel Compression and Split-Attention Mechanism 5

Image Denoising Method Based on Channel Compression and Spli...

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5th International Conference on Computer Engineering and Intelligent Control, ICCEIC 2024

作者： Sun, Hao Qiao, Xiaoyan School of Computer Science and Technology Shandong Technology and Business University Technology and Evaluation Shandong Engineering Research Center Yantai Key Laboratory of Big Data Modeling and Intelligent Computing Immersion Shandong Yantai China

ISBN: (纸本)9798331507992

In the image restoration task, how to make full use of spatial and channel feature information to improve the reconstruction quality of the model without significantly increasing the computational complexity is an important research issue. To address this challenge, this paper proposes a CS module (Channel Compression and Split-Attention) specifically for optimizing image denoising tasks. The module first compresses the features through a preliminary convolution operation, then introduces the split attention convolution mechanism to split the features by channel and dynamically weight them, thereby enhancing the model's adaptive attention to different feature channels and improving feature expression capabilities. Through experiments on multiple image denoising datasets, the results show that the CS module significantly improves the image reconstruction quality, especially in terms of peak signal-to-noise ratio (PSNR). At the same time, the introduction of the CS module does not lead to a significant increase in computational complexity, maintaining a high computational efficiency, which verifies the practicality and superiority of the module in image denoising tasks. © 2024 IEEE.

关键词： Restoration

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Intersecting-Boundary-Sensitive Fingerprinting for Tampering Detection of DNN Models 41

Intersecting-Boundary-Sensitive Fingerprinting for Tampering...

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41st International Conference on Machine Learning, ICML 2024

作者： Bai, Xiaofan He, Chaoxiang Ma, Xiaojing Zhu, Bin Benjamin Jin, Hai School of Cyber Science and Engineering Huazhong University of Science and Technology China National Engineering Research Center for Big Data Technology and System China Services Computing Technology and System Lab China Hubei Engineering Research Center on Big Data Security China Hubei Key Laboratory of Distributed System Security China Microsoft United States School of Computer Science and Technology Huazhong University of Science and Technology China Cluster and Grid Computing Lab China

Cloud-based AI services offer numerous benefits but also introduce vulnerabilities, allowing for tampering with deployed DNN models, ranging from injecting malicious behaviors to reducing computing resources. Fingerprint samples are generated to query models to detect such tampering. In this paper, we present Intersecting-Boundary-Sensitive Fingerprinting (IBSF), a novel method for black-box integrity verification of DNN models using only top-1 labels. Recognizing that tampering with a model alters its decision boundary, IBSF crafts fingerprint samples from normal samples by maximizing the partial Shannon entropy of a selected subset of categories to position the fingerprint samples near decision boundaries where the categories in the subset intersect. These fingerprint samples are almost indistinguishable from their source samples. We theoretically establish and confirm experimentally that these fingerprint samples' expected sensitivity to tampering increases with the cardinality of the subset. Extensive evaluation demonstrates that IBSF surpasses existing state-of-the-art fingerprinting methods, particularly with larger subset cardinality, establishing its state-of-the-art performance in black-box tampering detection using only top-1 labels. The IBSF code is available at: https://***/CGCL-codes/IBSF. Copyright 2024 by the author(s)

关键词： HTTP

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CDA-GNN: A Chain-driven Accelerator for Efficient Asynchronous Graph Neural Network 24

CDA-GNN: A Chain-driven Accelerator for Efficient Asynchrono...

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61st ACM/IEEE Design Automation Conference, DAC 2024

作者： Yu, Hui Zhang, Yu He, Ligang He, Donghao Li, Qikun Zhao, Jin Liao, Xiaofei Jin, Hai Gu, Lin Liu, Haikun National Engineering Research Center for Big Data Technology and System Service Computing Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology China Department of Computer Science University of Warwick United Kingdom

ISBN: (纸本)9798400706011

Asynchronous Graph Neural Network (AGNN) has attracted much research attention because it enables faster convergence speed than the synchronous GNN. However, existing software/hardware solutions suffer from redundant computation overhead and excessive off-chip communications for AGNN due to irregular state propagations along the dependency chains between vertices. This paper proposes a chain-driven asynchronous accelerator, CDA-GNN, for efficient AGNN inference. Specifically, CDA-GNN proposes a chain-driven asynchronous execution approach into novel accelerator design to regularize the vertex state propagations for fewer redundant computations and off-chip communications and also designs a chain-aware data caching method to improve data locality for AGNN. We have implemented and evaluated CDA-GNN on a Xilinx Alveo U280 FPGA card. Compared with the cutting-edge software solutions (i.e., Dorylus and AMP) and hardware solutions (i.e., BlockGNN and FlowGNN), CDA-GNN improves the performance of AGNN inference by an average of 1,173x, 182.4x, 10.2x, and 7.9x and saves energy by 2,241x, 242.2x, 12.4x, and 8.9x, respectively. © 2024 Copyright is held by the owner/author(s). Publication rights licensed to ACM.

关键词： Graph neural networks

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