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13th IEEE Congress on Evolutionary Computation, CEC 2024

作者： Hong, Wenjing Chen, Cheng Zhu, Zexuan Tang, Ke Shenzhen University National Engineering Laboratory for Big Data System Computing Technology Shenzhen China Research Institute of Trustworthy Autonomous Systems Southern University of Science and Technology Shenzhen China Southern University of Science and Technology Department of Computer Science and Engineering Shenzhen China

ISBN: (纸本)9798350308365

Messenger RNA (mRNA) vaccines have emerged as highly effective strategies in the prophylaxis and treatment of diseases. mRNA design, a key to the success of mRNA vaccines, in-volves finding optimal codons and increasing secondary structure stability to lengthen mRNA half-life, ultimately enhancing protein expression. Despite receiving widespread attention, most methods primarily rely on manual design, which is time-consuming and labor-intensive. While optimization approaches can alleviate this issue, existing methods still exhibit critical limitations caused by conflicts between codon usage and mRNA structural stability, compounded by the vast design space of mRNA resulting from the presence of synonymous codons. In this paper, a novel multi-objective evolutionary optimization-based mRNA design method is proposed. We first formulate the mRNA design problem as a multi-objective optimization problem and then develop an Elite Archive-Assisted Multi-Objective Evolutionary algorithm for mRNA Design, namely EAA-MOED, by incorporating a novel elite archive-assisted method into a weighted optimization framework to improve search efficiency. Experimental studies, involving two state-of-the-art mRNA design methods and five well-known MOEAs, show the competitiveness of the proposed EAA-MOED in mRNA design. © 2024 IEEE.

关键词： Vaccines

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On the Effectiveness of Function-Level Vulnerability Detectors for Inter-Procedural Vulnerabilities 24

On the Effectiveness of Function-Level Vulnerability Detecto...

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44th ACM/IEEE International Conference on Software engineering, ICSE 2024

作者： Li, Zhen Wang, Ning Zou, Deqing Li, Yating Zhang, Ruqian Xu, Shouhuai Zhang, Chao Jin, Hai Hubei Key Laboratory of Distributed System Security Hubei Engineering Research Center on Big Data Security Cluster and Grid Computing Lab National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Hong Kong Jin YinHu Laboratory Wuhan China School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan China University of Colorado Colorado Springs Department of Computer Science Colorado Springs Colorado United States Institute for Network Sciences and Cyberspace Tsinghua University Beijing China School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China

ISBN: (纸本)9798400702174

Software vulnerabilities are a major cyber threat and it is important to detect them. One important approach to detecting vulnerabilities is to use deep learning while treating a program function as a whole, known as function-level vulnerability detectors. However, the limitation of this approach is not understood. In this paper, we investigate its limitation in detecting one class of vulnerabilities known as inter-procedural vulnerabilities, where the to-be-patched statements and the vulnerability-triggering statements belong to different functions. For this purpose, we create the first Inter -Procedural Vulnerability dataset (InterPVD) based on C/C++ open-source software, and we propose a tool dubbed VulTrigger for identifying vulnerability-triggering statements across functions. Experimental results show that VulTrigger can effectively identify vulnerability-triggering statements and inter-procedural vulnerabilities. Our findings include: (i) inter-procedural vulnerabilities are prevalent with an average of 2.8 inter-procedural layers;and (ii) function-level vulner-ability detectors are much less effective in detecting to-be-patched functions of inter-procedural vulnerabilities than detecting their counterparts of intra-procedural vulnerabilities. © 2024 ACM.

关键词： Open source software

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xGCN: An Extreme Graph Convolutional Network for Large-scale Social Link Prediction 23

xGCN: An Extreme Graph Convolutional Network for Large-scale...

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2023 World Wide Web Conference, WWW 2023

作者： Song, Xiran Lian, Jianxun Huang, Hong Luo, Zihan Zhou, Wei Lin, Xue Wu, Mingqi Li, Chaozhuo Xie, Xing Jin, Hai Huazhong University of Science and Technology Wuhan China Microsoft Research Asia Beijing China Microsoft Gaming Redmond United States 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 China

ISBN: (纸本)9781450394161

Graph neural networks (GNNs) have seen widespread usage across multiple real-world applications, yet in transductive learning, they still face challenges in accuracy, efficiency, and scalability, due to the extensive number of trainable parameters in the embedding table and the paradigm of stacking neighborhood aggregations. This paper presents a novel model called xGCN for large-scale network embedding, which is a practical solution for link predictions. xGCN addresses these issues by encoding graph-structure data in an extreme convolutional manner, and has the potential to push the performance of network embedding-based link predictions to a new record. Specifically, instead of assigning each node with a directly learnable embedding vector, xGCN regards node embeddings as static features. It uses a propagation operation to smooth node embeddings and relies on a Refinement neural Network (RefNet) to transform the coarse embeddings derived from the unsupervised propagation into new ones that optimize a training objective. The output of RefNet, which are well-refined embeddings, will replace the original node embeddings. This process is repeated iteratively until the model converges to a satisfying status. Experiments on three social network datasets with link prediction tasks show that xGCN not only achieves the best accuracy compared with a series of competitive baselines but also is highly efficient and scalable. © 2023 ACM.

关键词： Graph neural networks

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Intersecting-boundary-sensitive fingerprinting for tampering detection of DNN models 24

Intersecting-boundary-sensitive fingerprinting for tampering...

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Proceedings of the 41st International Conference on Machine Learning

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

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.

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ChestBox: Enabling Fast State Sharing for Stateful Serverless computing with State Functions

IEEE Transactions on Sustainable Computing

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IEEE Transactions on Sustainable computing 2024年第03期10卷 491-502页

作者： Zhang, Xinmin Wu, Song Gu, Lin He, Qiang Jin, Hai Huazhong University of Science and Technology 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 Wuhan Hubei430074 China

This paper presents ChestBox, a novel approach that utilizes state functions to facilitate low-latency state sharing for stateful serverless computing. When an application function needs to share a state, the state function creates a memory space with Linux's shared memory object to store the state. Other application functions can then read the state directly from the shared memory. ChestBox enables fast state sharing that avoids excessive memory overhead without compromising on-demand resource allocation compared to existing solutions. This effectively reduces the energy consumption of serverless computing and promotes sustainable computing. The implementation of ChestBox on Apache OpenWhisk unearths two major implementation challenges, which we address with respective optimization techniques, i.e., state function channel and state swapping. The evaluation of ChestBox with four real-world applications shows that compared with the state-of-The-Art approach, it can reduce state-sharing latency by up to 99.71%, while reducing execution costs by 24.59% and storage costs by 99.76%. © 2016 IEEE.

关键词： Storage allocation (computer)

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Can Language Models Serve as Temporal Knowledge Bases?

Can Language Models Serve as Temporal Knowledge Bases?

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2022 Findings of the Association for Computational Linguistics: EMNLP 2022

作者： Zhao, Ruilin Zhao, Feng Xu, Guandong Zhang, Sixiao 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 China Data Science and Machine Intelligence Lab University of Technology Sydney Sydney Australia

Recent progress regarding the use of language models (LMs) as knowledge bases (KBs) has shown that language models can act as structured knowledge bases for storing relational facts. However, most existing works only considered the LM-as-KB paradigm in a static setting, which ignores the analysis of temporal dynamics of world knowledge. Furthermore, a basic function of KBs, i.e., the ability to store conflicting information (i.e., 1-N, N-1 and N-M relations), is underexplored. In this paper, we formulate two practical requirements for treating LMs as temporal KBs: (i) the capacity to store temporally-scoped knowledge that contains conflicting information and (ii) the ability to use stored knowledge for temporally-scoped knowledge queries. We introduce a new dataset called LAMA-TK which is aimed at probing temporally-scoped knowledge, and investigate the two above requirements to explore the LM-as-KB paradigm in the temporal domain. On the one hand, experiments show that LMs can memorize millions of temporally-scoped facts with relatively high accuracy and transfer stored knowledge to temporal knowledge queries, thereby expanding the LM-as-KB paradigm to the temporal domain. On the other hand, we show that memorizing conflicting information, which has been neglected by previous works, is still challenging for LMs and hinders the memorization of other unrelated one-to-one relationships. © 2022 Association for Computational Linguistics.

关键词： Computational linguistics

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LOPO: An Out-of-order Layer Pulling Orchestration Strategy for Fast Microservice Startup 42

LOPO: An Out-of-order Layer Pulling Orchestration Strategy f...

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42nd IEEE International Conference on Computer Communications, INFOCOM 2023

作者： Gu, Lin Huang, Junhao Huang, Shaoxing Zeng, Deze Li, Bo Jin, Hai Huazhong University of Science and Technology 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 Wuhan China China University of Geosciences School of Computer Science Wuhan China Hong Kong University of Science and Technology Department of Computer Science and Engineering Hong Kong

ISBN: (纸本)9798350334142

Container based microservices have been widely applied to promote the cloud elasticity. The mainstream Docker containers are structured in layers, which are organized in stack with bottom-up dependency. To start a microservice, the required layers are pulled from a remote registry and stored on its host server, following the layer dependency order. This incurs long microservice startup time and hinders the performance efficiency. In this paper, we discover that, for the first time, the layer pulling order can be adjusted to accelerate the microservice startup. Specifically, we address the problem on microservice layer pulling orchestration for startup time minimization and prove it as NP-hard. We propose a Longest-chain based Out-of-order layer Pulling Orchestration (LOPO) strategy with low computational complexity and guaranteed approximation ratio. Through extensive real-world trace driven experiments, we verify the efficiency of our LOPO and demonstrate that it reduces the microservice startup time by 22.71% on average in comparison with state-of-the-art solutions. © 2023 IEEE.

关键词： Containers

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AegonKV: a high bandwidth, low tail latency, and low storage cost KV-separated LSM store with SmartSSD-based GC offloading 25

AegonKV: a high bandwidth, low tail latency, and low storage...

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Proceedings of the 23rd USENIX Conference on File and Storage Technologies

作者： Zhuohui Duan Hao Feng Haikun Liu Xiaofei Liao Hai Jin Bangyu Li 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

ISBN: (纸本)9781939133458

The key-value separation is renowned for its significant mitigation of the write amplification inherent in traditional LSM trees. However, KV separation potentially increases performance overhead in the management of Value region, especially for garbage collection (GC) operation that is used to reduce the redundant space occupation. In response, many efforts have been made to optimize the GC mechanism for KV separation. However, our analysis indicates that such solution based on trade-offs between CPU and I/O overheads cannot simultaneously satisfy the three requirements of KV separated systems in terms of throughput, tail latency, and space usage. This limitation hinders their real-world *** this paper, we introduce AegonKV, a "three-birds-one-stone" solution that comprehensively enhances the throughput, tail latency, and space usage of KV separated systems. AegonKV first proposes a SmartSSD-based GC offloading mechanism to enable asynchronous GC operations without competing with LSM read/write for bandwidth or CPU. AegonKV leverages offload-friendly data structures and hardware/ software execution logic to address the challenges of GC offloading. Experiments demonstrate that AegonKV achieves the largest throughput improvement of 1.28-3.3 times, a significant reduction of 37%-66% in tail latency, and 15%-85% in space overhead compared to existing KV separated systems.

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Proceedings of the 60th Annual ACM/IEEE Design Automation Conference

作者： Jin Zhao Yu Zhang Jian Cheng Yiyang Wu Chuyue Ye Hui Yu Zhiying Huang Hai Jin Xiaofei Liao Lin Gu Haikun Liu National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab Huazhong University of Science and Technology Wuhan China and Zhejiang-HUST Joint Research Center for Graph Processing Zhejiang Lab Hangzhou China National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab Huazhong University of Science and Technology Wuhan China

ISBN: (纸本)9798350323481

Temporal graph processing is used to handle the snapshots of the temporal graph, which concerns changes in graph over time. Although several software/hardware solutions have been designed for efficient temporal graph processing, they still suffer from serious irregular data access due to the uncoordinated graph traversal. To overcome these limitations, this paper proposes SaGraph, a domain-specific hardware accelerator to support the efficient processing of temporal graph. Specifically, temporal graph processing shows strong data access similarity, i.e., most graph accesses of the processing of different snapshots are the same and usually refer to a small fraction of vertices. SaGraph can dynamically coordinate the graph traversals and adaptively cache the vertex states to fully exploit the data access similarity for smaller data access overhead. We implemented and evaluated SaGraph on a Xilinx Alveo U280 FPGA card. Compared with the cutting-edge software and hardware solutions, SaGraph achieves 8.5×-157.3×, 4.2×-16.1× speedups and 34.7×-423.6×, 5.3×-14.7× energy savings, respectively.

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MSE-CapsPPISP: Spatial Hierarchical Protein-Protein Interaction Sites Prediction Using Squeeze-and-Excitation Capsule Networks

MSE-CapsPPISP: Spatial Hierarchical Protein-Protein Interact...

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2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

作者： Lv, Weipeng Jiang, Changkun Li, Jianqiang Shenzhen University College of Computer Science and Software Engineering National Engineering Laboratory for Big Data System Computing Technology Shenzhen China

ISBN: (纸本)9781665468190

The discovery of protein-protein interaction sites (PPIs) is vital for exploring the principle of PPI and understanding the nature of life activities. Developing computational approaches to predict PPIs can effectively compensate for the shortcomings of biological experiments, which are mostly time-consuming and vulnerable to noise. In recent years, deep learning has been used to develop PPIs prediction models. Most of them consider the contextual information of the target amino acid residues and use a local protein sequence to represent the targets. However, the traditional deep-learning techniques, e.g., deep neural networks (DNNs) and convolutional neural networks (CNNs), disregard the important spatial hierarchies contained in the features of protein sequences, leading to their failure to effectively distinguish the interaction sites from different residue regions. In this work, we design MSE-CapsPPISP, a new deep-learning model to address the PPIs prediction with spatial hierarchies. The key idea of MSE-CapsPPISP is to take into account the hierarchical relationships between the features of protein sequences. We characterize the hierarchical relationships by designing a tailored Capsule Network (CapsNet) model, which is a novel type of neural network with vector neurons. Moreover, to make the network representation more robust, MSE-CapsPPISP uses multi-scale CNNs to extract multi-scale features of protein sequences and Squeeze-and-Excitation blocks to recalibrate the features. The validation results show that our MSE-CapsPPISP outperforms the baseline CNNs-based architecture DeepPPISP and other competing schemes in the PPIs prediction task. © 2022 IEEE.

关键词： Forecasting

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