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Unraveling the 3D Genome Architecture in Plants:Present and Future

Molecular Plant 2020年第12期13卷 1676-1693页

作者： Weizhi Ouyang Dan Xiong Guoliang Li Xingwang Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data 3D Genomics Research CenterHuazhong Agricultural UniversityWuhan 430070China

The eukaryotic genome has a hierarchicalthree-dimensional(3D)organization with functional implications for DNA replication,DNA repair,and transcriptional *** the past decade,scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C,ChlA-PET,and ***,we systematically review current understanding of chromatin organization in plants at multiple *** also discuss the emerging opinions and concepts in 3D genome research,focusing on state-of-the-art 3D genome techniques,RNA-chromatin interactions,liquid-liquid phase separation,and dynamic chromatin *** propose the application of single-cell/single-molecule multi-omics,multiway(DNA-DNA,DNA-RNA,and RNA-RNA interactions)chromatin conformation capturing methods,and proximity ligation-independent 3D genome-mapping technologies to explore chromatin organization structure and function in *** methods could reveal the spatial interactions between trait-related SNPs and their target genes at various spatiotemporal resolutions,and elucidate the molecular mecha-nisms of the interactions among DNA elements,RNA molecules,and protein factors during the formation of key traits in plants.

关键词： 3D genomic methods plant 3D genome dynamic chromatin organization liquid-liquid phase separation RNA-chromatin interaction

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An Efficient Graph Accelerator with Distributed On-Chip Memory Hierarchy 22nd

An Efficient Graph Accelerator with Distributed On-Chip Mem...

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22nd International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2022

作者： Zheng, Ran Jiang, Yingxin Wang, Yibo Su, Yongbo Zheng, Long Yao, Pengcheng Liao, Xiaofei 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 Zhejiang Lab Hangzhou311121 China

ISBN: (纸本)9783031226762

Graph processing has evolved and expanded swiftly with artificial intelligence and big data technology. High-Bandwidth Memory (HBM), which delivers terabyte-level memory bandwidth, has opened up new development possibilities for FPGA-based graph accelerators. However, despite the tremendous expansion of underlying hardware capabilities, existing graph accelerators have not benefited too much. In this paper, we observe that the uniformed on-chip memory hierarchy is the key to the low scalability of existing graph accelerators. We present a novel graph accelerator with a distributed on-chip memory hierarchy called GraphS. The on-chip memory of GraphS is divided into numerous tiny blocks, each of which is assigned to only one Processing Element (PE). Different PEs are connected through a scalable network-on-chip (NoC). For realistic graphs with power-law properties, a degree-aware preprocessing method is designed to balance the workload among different PEs. Our results with various graph algorithms demonstrate that GraphS can outperform state-of-the-art ForeGraph by up to 21.84 ×. © 2023, Springer Nature Switzerland AG.

关键词： Network-on-chip

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Reveal training performance mystery between Tensor Flow and PyTorch in the single GPU environment

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Science China(Information Sciences) 2022年第1期65卷 147-163页

作者： Hulin DAI Xuan PENG Xuanhua SHI Ligang HE Qian XIONG Hai JIN National Engineering Research Center for Big Data Technology and System Service Computing Technology and System LabSchool of Computer Science and Technology Huazhong University of Science and Technology Department of Computer Science University of Warwick

Deep learning has gained tremendous success in various fields while training deep neural networks(DNNs) is very compute-intensive, which results in numerous deep learning frameworks that aim to offer better usability and higher performance to deep learning practitioners. Tensor Flow and Py Torch are the two most popular frameworks. Tensor Flow is more promising within the industry context, while Py Torch is more appealing in academia. However, these two frameworks differ much owing to the opposite design philosophy:static vs dynamic computation graph. Tensor Flow is regarded as being more performance-friendly as it has more opportunities to perform optimizations with the full view of the computation graph. However, there are also claims that Py Torch is faster than Tensor Flow sometimes, which confuses the end-users on the choice between them. In this paper, we carry out the analytical and experimental analysis to unravel the mystery of comparison in training speed on single-GPU between Tensor Flow and Py Torch. To ensure that our investigation is as comprehensive as possible, we carefully select seven popular neural networks, which cover computer vision, speech recognition, and natural language processing(NLP). The contributions of this work are two-fold. First, we conduct the detailed benchmarking experiments on Tensor Flow and Py Torch and analyze the reasons for their performance difference. This work provides the guidance for the end-users to choose between these two frameworks. Second, we identify some key factors that affect the performance,which can direct the end-users to write their models more efficiently.

关键词： deep learning performance comparison TensorFlow PyTorch

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Towards Effective and Efficient Error Handling Code Fuzzing Based on Software Fault Injection 31

Towards Effective and Efficient Error Handling Code Fuzzing ...

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31st IEEE International Conference on Software Analysis, Evolution and Reengineering, SANER 2024

作者： Chen, Kang Wen, Ming Jia, Haoxiang Wu, Rongxin Jin, Hai Wuhan430074 China Jin YinHu Laboratory Wuhan430074 China School of Informatics Xiamen University Xiamen361005 China School of Computer Science and Technology HUST Wuhan430074 China National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab China Hubei Engineering Research Center on Big Data Security Hubei Key Laboratory of Distributed System Security China Cluster and Grid Computing Lab China

ISBN: (纸本)9798350330663

Software systems often encounter various errors or exceptions in practice, and thus proper error handling code is essential to ensure the reliability of software systems. Unfortunately, error handling code is often bug-prone, while sufficiently testing them is challenging as such code often cannot be triggered under normal conditions. Motivated by this, recent studies have proposed to leverage software fault injection (SFI) based fuzzing to discover potential bugs in complicated error handling code. Despite the promising results achieved, their effectiveness and efficiency are still compromised in practice due to the huge search space of error sites, inadequate fuzzing guidance, and the overhead induced by context-sensitive SFI. To achieve effective and efficient testing of error handling code, this study presents AFL-FI, which first utilizes a similarity-based method to identify suspicious error sites, and then incorporates the idea of error site coverage to guide the fuzzing process. Finally, the design of lightweight context-sensitive SFI enables AFL-FI to execute test cases efficiently. We evaluate AFL-FI on eight large-scale open-source projects, and the results show that it can outperform existing state-of-the-art fuzzing tools significantly in terms of branch code coverage. More importantly, AFL-FI has discovered 13 previously unknown bugs, and all of them have been confirmed while 12 of them have been fixed. Besides, our evaluation also demonstrates that all the key designs of AFL-F I are effective that contribute significantly to its overall performance. © 2024 IEEE.

关键词： Errors

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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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Secure Channel Free ID-Based Searchable Encryption for Peer-to-Peer Group

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Journal of Computer Science & technology 2016年第5期31卷 1012-1027页

作者： Xiao-Fen Wang Yi Mu Rongmao Chen Xiao-Song Zhang College of Computer Science and Engineering University of Electronic Science and Technology of China Chengdu 611731 China Big Data Research Center University of Electronic Science and Technology of China Chengdu 611731 China School of Computing and Information Technology University of Wollongong Wollongong NSW 2500 Australia College of Computer National University of Defense Technology Changsha 410073 China

data sharing and searching are important functionalities in cloud storage. In this paper, we show how to securely and flexibly search and share cloud data among a group of users without a group manager. We formalize a novel cryptosystem： secure channel free searchable encryption in a peer-to-peer group, which features with the secure cloud data sharing and searching for group members in an identity-based setting. Our scheme allows group members to join or leave the group dynamically. We present two schemes： basic scheme and enhanced scheme. We formally prove that our basic scheme achieves consistency and indistinguishability against the chosen keyword and ciphertext attack and the outsider＇s keyword guessing attack, respectively. An enhanced scheme is also proposed to achieve forward secrecy, which allows to revoke user search right over the former shared data.

关键词： searchable encryption forward secrecy data sharing peer-to-peer group

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Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 573-588页

作者： Yan Zhang Jingwen Zhang Wei Zhang Mohan Wang Shuangqi Wang Yao Xu Lun Zhao Xingwang Li Guoliang Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data 3D Genomics Research CenterHuazhong Agricultural UniversityWuhan 430070China

Studies on the lung cancer genome are indispensable for developing a cure for lung ***-genome resequencing,genome-wide association studies,and transcriptome sequencing have greatly improved our understanding of the cancer ***,dysregulation of longrange chromatin interactions in lung cancer remains poorly *** better understand the three-dimensional(3D)genomic interaction features of the lung cancer genome,we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II(RNAPII),CCCTC-binding factor(CTCF),enhancer of zeste homolog 2(EZH2),and histone 3 lysine 27 trimethylation(H3K27me3)using long-read chromatin interaction analysis by paired-end tag sequencing(ChIA-PET).Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes,either through loops or domains,and their distributions along the genome were distinct from and complementary to those associated with ***-related genes were highly enriched with chromatin interactions,and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes,such as additional repressive interactions on FOXO4 and promoter–promoter interactions between NF1 and *** of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes,suggesting that chromatin interactions are essential for proper expression of lung cancer-related *** findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.

关键词： Lung cancer 3D genome ChIA-PET Chromatin interaction Dysregulation

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Channel Capacity and Power Allocation of MIMO Visible Light Communication system

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China Communications 2023年第2期20卷 122-138页

作者： Shuai Ma Ruixin Yang Guanjie Zhang Hang Li Wen Cao Linqiong Jia Yanyu Zhang Shiyin Li Peng Cheng Laboratory Shenzhen 518055China School of Information and Control Engineering China University of Mining and TechnologyXuzhou 221116China Shenzhen Research Institute of Big Data Shenzhen 518172China School of Electronics and Control Engineering Chang’an UniversityXi’an 710064China School of Electronic and Optical Engineering Nanjing University of Science and TechnologyNanjing 210094China National Digital Switching System Engineering&Technological Research Center Zhengzhou 450000China

In this paper,the channel capacity of the multiple-input multiple-output(MIMO)visible light communication(VLC)system is investigated under the peak,average optical and electrical power *** the channel capacity of MIMO VLC is shown to be a mixed integer programming *** address this open problem,we propose an inexact gradient projection method to find the channel capacity-achieving discrete input distribution and the channel capacity of MIMO *** we derive both upper and lower bounds of the capacity of MIMO VLC with the closed-form ***,by considering practical discrete constellation inputs,we develop the optimal power allocation scheme to maximize transmission rate of MIMO VLC *** results show that more discrete points are needed to achieve the channel capacity as SNR *** the upper and lower bounds of channel capacity are tight at low SNR *** addition,comparing the equal power allocation,the proposed power allocation scheme can significantly increase the rate for the low-order modulation inputs.

关键词： visible light communication MIMO discrete constellation inputs power allocation

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Accumulative Time Based Ranking Method to Reputation Evaluation in Information Networks

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Journal of Computer Science & technology 2022年第4期37卷 960-974页

作者： Hao Liao Qi-Xin Liu Ze-Cheng Huang Ke-Zhong Lu Chi Ho Yeung Yi-Cheng Zhang National Engineering Laboratory on Big Data System Computing Technology College of Computer Science and SoftwareEngineeringShenzhen UniversityShenzhen 518060China Guangdong Province Key Laboratory of Popular High Performance Computers Shenzhen UniversityShenzhen 518060China Guangdong Province Engineering Center of China-Made High Performance Data Computing System College of ComputerScience and Software EngineeringShenzhen UniversityShenzhen 518060China Institute of Big Data Intelligent Management and Decision Shenzhen UniversityShenzhen 518060China Department of Science and Environmental Studies The Education University of Hong KongHong Kong 999077China Department of Physics University of FribourgFribourg 1700Switzerland

Due to over-abundant information on the Web, information filtering becomes a key task for online users to obtain relevant suggestions and how to extract the most related item is always a key topic for researchers in various fields. In this paper, we adopt tools used to analyze complex networks to evaluate user reputation and item quality. In our proposed Accumulative Time Based Ranking (ATR) algorithm, we take into account the growth record of the network to identify the evolution of the reputation of users and the quality of items, by incorporating two behavior weighting factors which can capture the hidden facts on reputation and quality dynamics for each user and item respectively. Our proposed ATR algorithm mainly combines the iterative approach to rank user reputation and item quality with temporal dependence compared with other reputation evaluation methods. We show that our algorithm outperforms other benchmark ranking algorithms in terms of precision and robustness on empirical datasets from various online retailers and the citation datasets among research publications. Therefore, our proposed method has the capability to effectively evaluate user reputation and item quality.

关键词： temporal network behavior dynamics reputation evaluation ranking algorithm

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GradSA: Gradient Sparsification and Accumulation for Communication-Efficient Distributed Deep Learning 15th

GradSA: Gradient Sparsification and Accumulation for Communi...

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15th International Conference on Green, Pervasive, and Cloud Computing, GPC 2020

作者： Liu, Bo Jiang, Wenbin Zhao, Shaofeng Jin, Hai He, Bingsheng National Engineering Research Center for Big Data Technology and System Service Computing Technology and System Lab Cluster and Grid Computing Lab Huazhong University of Science and Technology Wuhan China Wuhan National Laboratory for Optoelectronics Key Laboratory of Information Storage System Engineering Research Center of Data Storage Systems and Technology Huazhong University of Science and Technology Wuhan China Library Henan University of Economics and Law Zhengzhou China Department of Computer Science School of Computing National University of Singapore Singapore Singapore

ISBN: (纸本)9783030642426

Large-scale distributed deep learning is of great importance in various applications. For distributed training, the inter-node gradient communication often becomes the performance bottleneck. Gradient sparsification has been proposed to reduce the communication overhead. However, the sparsification only arbitrarily selects a small fraction of gradients, while the efficiency of selection dimension has been overlooked. Furthermore, gradient staleness is inevitable after applying the sparsification which will ultimately lead to model divergence. In this paper, we propose a staleness-compensated sparse stochastic gradient descent algorithm, GradSA, to improve the training efficiency. Layer-level gradients are sparsified to reduce the communication overhead, which conform to the characteristics of the network structure, and historical accumulation of the approximated gradients is utilized to speed up convergence. We demonstrate the model convergence acceleration and the efficiency of our layer-level selection over existing state-of-the-art works, such as DGC, TernGrad, and 8-Bit quantization. © 2020, Springer Nature Switzerland AG.

关键词： Efficiency

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