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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Jie Chen Wenbin Liao Du Wen Jianqiang Li Fangzhong Wang College of Computer Science and Software Engineering Shenzhen University China National Engineering Laboratory for Big Data System Computing Technology Shenzhen University China Laboratory of Synthetic Microbiology School of Chemical Engineering & Technology Tianjin University China

The annotation of Open Reading Frames (ORFs) is a crucial step in gene annotation, as it precisely delineates the specific regions of expressed genes. However, small Open Reading Frames (smORFs), in comparison to ORFs, are shorter in length, exhibit lower expression abundance, and are more challenging to predict. Particularly in the presence of noise in prokaryotic data and limited availability of positive sample data, the difficulty of prediction is amplified. Therefore, it is necessary to study smORF prediction methods. However, current machine learning models use limited data for modeling and overlook the existence of undiscovered positive samples within the negative samples. Additionally, they do not incorporate prior knowledge that can be calibrated to enhance the 3-nt periodicity. This work utilizes a multimodal VAE for data dimensionality reduction and employs a GAN to generate latent vectors for data augmentation. It incorporates PU learning to leverage unknown samples and combines Riboseq data from experiments with and without antibiotic treatment. Additionally, an adversarial training mechanism is employed to enhance the model’s robustness.

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Generalization-Enhanced Code Vulnerability Detection via Multi-Task Instruction Fine-Tuning

arXiv

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arXiv 2024年

作者： Du, Xiaohu Wen, Ming Zhu, Jiahao Xie, Zifan Ji, Bin Liu, Huijun Shi, Xuanhua Jin, Hai School of Cyber Science and Engineering Huazhong University of Science and Technology China School of Computer Science and Technology Huazhong University of Science and Technology China College of Computer National University of Defense Technology China National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab HUST Wuhan430074 China Hubei Engineering Research Center on Big Data Security Hubei Key Laboratory of Distributed System Security HUST Wuhan430074 China JinYinHu Laboratory Wuhan430077 China Cluster and Grid Computing Lab HUST Wuhan430074 China

Code Pre-trained Models (CodePTMs) based vulnerability detection have achieved promising results over recent years. However, these models struggle to generalize as they typically learn superficial mapping from source code to labels instead of understanding the root causes of code vulnerabilities, resulting in poor performance in real-world scenarios beyond the training instances. To tackle this challenge, we introduce VulLLM, a novel framework that integrates multi-task learning with Large Language Models (LLMs) to effectively mine deep-seated vulnerability features. Specifically, we construct two auxiliary tasks beyond the vulnerability detection task. First, we utilize the vulnerability patches to construct a vulnerability localization task. Second, based on the vulnerability features extracted from patches, we leverage GPT-4 to construct a vulnerability interpretation task. VulLLM innovatively augments vulnerability classification by leveraging generative LLMs to understand complex vulnerability patterns, thus compelling the model to capture the root causes of vulnerabilities rather than overfitting to spurious features of a single task. The experiments conducted on six large datasets demonstrate that VulLLM surpasses seven state-of-the-art models in terms of effectiveness, generalization, and robustness. © 2024, CC BY.

关键词： Large datasets

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RAHP: A Redundancy-aware Accelerator for High-performance Hypergraph Neural Network

RAHP: A Redundancy-aware Accelerator for High-performance Hy...

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IEEE/ACM International Symposium on Microarchitecture (MICRO)

作者： Hui Yu Yu Zhang Ligang He Yingqi Zhao Xintao Li Ruida Xin Jin Zhao Xiaofei Liao Haikun Liu Bingsheng He Hai Jin 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 Wuhan China Department of Computer Science University of Warwick United Kingdom National University of Singapore Singapore

ISBN: (数字)9798350350579

ISBN: (纸本)9798350350586

Hypergraph Neural Network (HyperGNN) has emerged as a potent methodology for dissecting intricate multilateral connections among various entities. Current software/hardware solutions leverage a sequential execution model that relies on hyperedge and vertex indices for conducting standard matrix operations for HyperGNN inference. Yet, they are impeded by the dual challenges of redundant computation and irregular memory access overheads. This is primarily due to the frequent and repetitive access and updating of a number of feature vectors corresponding to the same hyperedges and vertices. To address these challenges, we propose the first redundancy-aware accelerator, RAHP, which enables high performance execution of HyperGNN inference. Specifically, we present a redundancy-aware asynchronous execution approach into the accelerator design for HyperGNN to reduce redundant computations and off-chip memory accesses. To unveil opportunities for data reuse and unlock the parallelism that existing HyperGNN solutions fail to capture, it prioritizes vertices with the highest degree as roots, prefetching other vertices along the hypergraph structure to capture the common vertices among multiple hyperedges, and synchronizing the computations of hyperedges and vertices in real-time. By such means, this facilitates the concurrent processing of relevant hyperedge and vertex computations of the common vertices along the hypergraph topology, resulting in smaller redundant computations overhead. Furthermore, by efficiently caching intermediate results of the common vertices, it curtails memory traffic and off-chip communications. To fully harness the performance potential of our proposed approach in the accelerator, RAHP incorporates a topology-driven data loading mechanism to minimize off-chip memory accesses on the fly. It is also endowed with an adaptive data synchronization scheme to mitigate the effects of conflicting updates of both hyperedges and vertices. Moreover, RAHP emplo

关键词： Computational modeling Neural networks Memory management Loading Energy conservation Vectors Software Topology Synchronization Standards

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SharDAG: Scaling DAG-Based Blockchains Via Adaptive Sharding

SharDAG: Scaling DAG-Based Blockchains Via Adaptive Sharding

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International Conference on data engineering

作者： Feng Cheng Jiang Xiao Cunyang Liu Shijie Zhang Yifan Zhou Bo Li Baochun Li Hai Jin 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 Hong Kong University of Science and Technology Hong Kong University of Toronto Canada

ISBN: (数字)9798350317152

ISBN: (纸本)9798350317169

Directed Acyclic Graph (DAG)-based blockchain (a.k.a distributed ledger) has become prevalent for supporting highly concurrent applications. Its inherent parallel data structure accelerates block generation significantly, shifting the bottleneck from performance to storage scalability. An intuitive solution is to apply state sharding that divides the entire ledger (i.e., transactions and states) into multiple shards. While each node only stores proportional transactions, it suffers from the challenges of storing and ensuring the processing consistency of cross-shard transactions. In this paper, we propose SharDAG, a new mechanism that leverages adaptive sharding for DAG-based blockchains to achieve high performance and strong consistency. The key idea of SharDAG is to exploit unique characteristics - silent assets - and design a lightweight processing mechanism based on avatar account caching. Furthermore, we design a Byzantine resilient cross-shard verification mechanism with a theoretically optimal number of participating nodes, which guarantees the consistency and security of avatar account aggregation. Our comprehensive evaluations on real-world workloads demonstrate that SharDAG presents up to 3.8 x throughput improvement compared to the state-of-the-art and reduces the storage overhead of cross-shard transactions.

关键词： Sharding Directed acyclic graph Distributed ledger Avatars Scalability Receivers Throughput

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Comprehensive Architecture Search for Deep Graph Neural Networks

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IEEE Transactions on big data 2025年

作者： Dong, Yukang Pan, Fanxing Gui, Yi Jiang, Wenbin Wan, Yao Zheng, Ran Jin, Hai National Engineering Research Center for Big Data Technology Huazhong University of Science and Technology Wuhan430074 China Huazhong University of Science and Technology Service Computing Technology and System Laboratory Wuhan430074 China Huazhong University of Science and Technology Cluster and Grid Computing Laboratory Wuhan430074 China Huazhong University of Science and Technology School of Computer Science and Technology Wuhan430074 China Zhejiang Lab Hangzhou311121 China

In recent years, Neural Architecture Search (NAS) has emerged as a promising approach for automatically discovering superior model architectures for deep Graph Neural Networks (GNNs). Different methods have paid attention to different types of search spaces. However, due to the time-consuming nature of training deep GNNs, existing NAS methods often fail to explore diverse search spaces sufficiently, which constrains their effectiveness. To crack this hard nut, we propose CAS-DGNN, a novel comprehensive architecture search method for deep GNNs. It encompasses four kinds of search spaces that are the composition of aggregate and update operators, different types of aggregate operators, residual connections, and hyper-parameters. To meet the needs of such a complex situation, a phased and hybrid search strategy is proposed to accommodate the diverse characteristics of different search spaces. Specifically, we divide the search process into four phases, utilizing evolutionary algorithms and Bayesian optimization. Meanwhile, we design two distinct search methods for residual connections (All-connected search and Initial Residual search) to streamline the search space, which enhances the scalability of CAS-DGNN. The experimental results show that CAS-DGNN achieves higher accuracy with competitive search costs across ten public datasets compared to existing methods. © 2015 IEEE.

关键词： Neural network models

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ECLIPSE: Expunging Clean-label Indiscriminate Poisons via Sparse Diffusion Purification

arXiv

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arXiv 2024年

作者： Wang, Xianlong Hu, Shengshan Zhang, Yechao Zhou, Ziqi Zhang, Leo Yu Xu, Peng Wan, Wei Jin, Hai National Engineering Research Center for Big Data Technology and System China Services Computing Technology and System Lab China Cluster and Grid Computing Lab China Hubei Engineering Research Center on Big Data Security China Hubei Key Laboratory of Distributed System Security China School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan430074 China School of Computer Science and Technology Huazhong University of Science and Technology Wuhan430074 China School of Information and Communication Technology Griffith University SouthportQLD4215 Australia

Clean-label indiscriminate poisoning attacks add invisible perturbations to correctly labeled training images, thus dramatically reducing the generalization capability of the victim models. Recently, defense mechanisms such as adversarial training, image transformation techniques, and image purification have been proposed. However, these schemes are either susceptible to adaptive attacks, built on unrealistic assumptions, or only effective against specific poison types, limiting their universal applicability. In this research, we propose a more universally effective, practical, and robust defense scheme called ECLIPSE. We first investigate the impact of Gaussian noise on the poisons and theoretically prove that any kind of poison will be largely assimilated when imposing sufficient random noise. In light of this, we assume the victim has access to an extremely limited number of clean images (a more practical scene) and subsequently enlarge this sparse set for training a denoising probabilistic model (a universal denoising tool). We then introduce Gaussian noise to absorb the poisons and apply the model for denoising, resulting in a roughly purified dataset. Finally, to address the trade-off of the inconsistency in the assimilation sensitivity of different poisons by Gaussian noise, we propose a lightweight corruption compensation module to effectively eliminate residual poisons, providing a more universal defense approach. Extensive experiments demonstrate that our defense approach outperforms 10 state-of-the-art defenses. We also propose an adaptive attack against ECLIPSE and verify the robustness of our defense scheme. Our code is available at https://***/CGCL-codes/ECLIPSE. Copyright © 2024, The Authors. All rights reserved.

关键词： Deep neural networks

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Personalized Federated Learning with Multiple Classifier Aggregation

SSRN

引用

SSRN 2024年

作者： Zheng, Shaifeng Zhu, Qingling Lin, Qiuzhen Liu, Songbai Wong, Ka-Chun Li, Jianqiang College of Computer Science and Software Engineering Shenzhen University Shenzhen China National Engineering Laboratory for Big Data System Computing Technology Shenzhen University China Department of Computer Science City University of Hong Kong Hong Kong

Personalized federated learning (PFL) has garnered attention due to its capability to address statistical heterogeneity among clients. Typically, prevailing PFL methods aggregate a single global model for personalization, which may be inadequate for clients with diverse data distributions. Furthermore, in the local update, each private dataset is used to optimize the model independently, which increases the risk of overfitting the current data distribution and losing previously acquired knowledge, resulting in knowledge forgetting. In this study, personalized federated learning with multiple classifier aggregation is proposed. The method involves splitting the client model into its head and base, then optimizing them respectively using an alternating optimization strategy that first optimizes the head and then the base. Initially, to address the suboptimal model problem, the proposed approach aggregates multiple classifiers using data distribution and employs knowledge distillation to impart positive and negative classifier knowledge for learning the most suitable personalized model head. Additionally, to mitigate knowledge forgetting, a learnable personalization layer is introduced, and hidden loss is utilized to learn the knowledge of the global base and prevent overfitting of the model base. Empirical results demonstrate that the proposed method achieves competitive performance across various benchmarks, outperforming the majority of state-of-the-art PFL algorithms. The source code is publicly available at \href{https://***/xiaye-maker/FedMCA}{https://***/xiaye-maker/FedMCA} © 2024, The Authors. All rights reserved.

关键词： Aggregates

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GraphInstruct: Empowering Large Language Models with Graph Understanding and Reasoning Capability

arXiv

引用

arXiv 2024年

作者： Luo, Zihan Song, Xiran Huang, Hong Lian, Jianxun Zhang, Chenhao Jiang, Jinqi Xie, Xing Huazhong University of Science and Technology Wuhan China Microsoft Research Asia Beijing China The National Engineering Research Center for Big Data Technology and System Service Computing Technology and Systems Laboratory Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology China

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://***/CGCL-codes/GraphInstruct. Copyright © 2024, The Authors. All rights reserved.

关键词： Computational linguistics

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FuzzyTrack: User Adaptive Cervical Spine Motion Prediction with Earable Inertial Sensing

引用

IEEE Transactions on Fuzzy systems 2024年

作者： Luo, Chengwen Li, Yaxue Chen, Gecheng Li, Xing Zhang, Jin Wei, Bo Li, Jianqiang Shenzhen University National Engineering Laboratory for Big Data System Computing Technology China Dongguan University of Technology School of Electrical Engineering & Intelligentization Guangdong Dongguan523808 China Northeastern University China State Key Laboratory of Synthetical Automation for Process Industries Liaoning Shenyang110819 China Newcastle University United Kingdom

The widespread use of electronic devices has contributed to an increase in poor posture, particularly when it comes to the cervical spine, leading to various cervical vertebral pain disorders. In this paper, we focus on accurately monitoring the motion status of the cervical spine using the accelerometers and gyroscope sensors embedded in earphones. Our aim is to gain a better understanding of cervical spine health. To address the individual differences among subjects, we introduce fuzzy rules to the Re-ISDA method, proposing a novel approach known as FuzRe-ISDA. Unlike traditional domain adaptation methods, the FuzRe-ISDA method offers flexibility in adjusting the contribution from different source domains. It takes into account the collective impact of multiple models on predicting new user behavior. Moreover, this method can quickly adapt to new users without requiring extensive datasets. Experimental results demonstrate that our FuzRe-ISDA approach outperforms popular domain adaptation methods in terms of accuracy when predicting cervical motion. This highlights the effectiveness of our approach in addressing individual differences and improving the reliability of cervical spine motion prediction. © 1993-2012 IEEE.

关键词： Fuzzy rules

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An Elite Archive-Assisted Multi-Objective Evolutionary Algorithm for mRNA Design

An Elite Archive-Assisted Multi-Objective Evolutionary Algor...

引用

Congress on Evolutionary Computation

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

ISBN: (数字)9798350308365

ISBN: (纸本)9798350308372

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.

关键词： Measurement Design methodology Evolutionary computation Search problems Linear programming Stability analysis Vaccines

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