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A hybrid memory architecture supporting fine-grained data migration

Frontiers of computer science 2024年第2期18卷 31-41页

作者： Ye CHI Jianhui YUE Xiaofei LIAO Haikun LIU Hai JIN National Engineering Research Center for Big Data Technology and System Services Computing Technology and System LabCluster and Grid Computing LabSchool of Computer Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Department of Computer Science Michigan Technological UniversityMichigan 49931USA

Hybrid memory systems composed of dynamic random access memory(DRAM)and Non-volatile memory(NVM)often exploit page migration technologies to fully take the advantages of different memory *** previous proposals usually migrate data at a granularity of 4 KB pages,and thus waste memory bandwidth and DRAM *** this paper,we propose Mocha,a non-hierarchical architecture that organizes DRAM and NVM in a flat address space physically,but manages them in a cache/memory *** the commercial NVM device-Intel Optane DC Persistent Memory Modules(DCPMM)actually access the physical media at a granularity of 256 bytes(an Optane block),we manage the DRAM cache at the 256-byte size to adapt to this feature of *** design not only enables fine-grained data migration and management for the DRAM cache,but also avoids write amplification for Intel Optane *** also create an Indirect Address Cache(IAC)in Hybrid Memory Controller(HMC)and propose a reverse address mapping table in the DRAM to speed up address translation and cache ***,we exploit a utility-based caching mechanism to filter cold blocks in the NVM,and further improve the efficiency of the DRAM *** implement Mocha in an architectural *** results show that Mocha can improve application performance by 8.2%on average(up to 24.6%),reduce 6.9%energy consumption and 25.9%data migration traffic on average,compared with a typical hybrid memory architecture-HSCC.

关键词： non-volatile memory hybrid memory system data migration fine-grained caching

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Age-of-Information-Aware Federated Learning

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Journal of computer science & Technology 2024年第3期39卷 637-653页

作者：徐殷肖明军吴晨吴杰周津锐孙贺 Student Member CCF 1.School of Computer Science and TechnologyUniversity of Science and Technology of ChinaHefei 230026China Suzhou Institute for Advanced Research University of Science and Technology of ChinaSuzhou 215123China School of Data Science University of Science and Technology of ChinaHefei 230026China Department of Computer and Information Sciences Temple UniversityPhiladelphiaPA 19122U.S.A. CCF IEEE

Federated learning(FL)is an emerging privacy-preserving distributed computing paradigm,enabling numerous clients to collaboratively train machine learning models without the necessity of transmitting clients’private datasets to the central *** most existing research where the local datasets of clients are assumed to be unchanged over time throughout the whole FL process,our study addresses such scenarios in this paper where clients’datasets need to be updated periodically,and the server can incentivize clients to employ as fresh as possible datasets for local model *** primary objective is to design a client selection strategy to minimize the loss of the global model for FL loss within a constrained *** this end,we introduce the concept of“Age of Information”(AoI)to quantitatively assess the freshness of local datasets and conduct a theoretical analysis of the convergence bound in our AoI-aware FL *** on the convergence bound,we further formulate our problem as a restless multi-armed bandit(RMAB)***,we relax the RMAB problem and apply the Lagrangian Dual approach to decouple it into multiple ***,we propose a Whittle’s Index Based Client Selection(WICS)algorithm to determine the set of selected *** addition,comprehensive simulations substantiate that the proposed algorithm can effectively reduce training loss and enhance the learning accuracy compared with some state-of-the-art methods.

关键词： federated learning Age of Information restless multi-armed bandit Whittle’s index

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Leveraging user-item interactions and hotel characteristics for hotel recommendations in Indonesia with graph neural networks 9th

Leveraging user-item interactions and hotel characteristics ...

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9th International Conference on computer science and Computational Intelligence, ICCSCI 2024

作者： Panarto, Francis Alexander Phanghegar, Tyrone Matthew Gunardi, Vincent Cenggoro, Tjeng Wawan Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

Travelers usually check information about the destination before they decide to go. However, sometimes the information is too much to handle and causes confusion. A filtering mechanism is needed to help them make their choices. The solution is to implement a recommendation system;some common techniques that are used for this are Collaborative Filtering and content-based filtering, but both techniques have their flaws. Therefore, we propose a solution to combine those two methods through Graph Neural Network architectures to help fix their flaws. The proposed method will be used for recommending hotels in Indonesia using the HotelRec dataset as the base dataset and hotel features acquired from the TripAdvisor API. We use several GNN architectures, such as GCN, LightGCN, GraphSAGE, and GAT, to implement our approach. Then, we compare it to several baseline models, such as SVD and NeuMF, which are common baselines in recommendation systems. The performance of these models is calculated based on three metrics: HitRate@K, NDCG@K, and Recall@K. Based on the result of this experiment, we found that incorporating hotel features into the learning process of the model, accompanied by user-item interactions, boosted the model's performance by at least 20% in all metrics, especially in datasets with a smaller number of interactions. © 2024 The Authors.

关键词： Collaborative filtering

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data Mining and Bioinformatics Approaches to Elucidate Bacterial Communities in the Extreme Environment

Data Mining and Bioinformatics Approaches to Elucidate Bacte...

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2023 International Conference on Informatics, Multimedia, Cyber and Information Systems, ICIMCIS 2023

作者： Trinugroho, Joko Pebrianto Hidayat, Alam Ahmad Nirwantono, Rudi Asadi, Faisal Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University School of Computer Science Bioinformatics and Data Science Research Center Mathematics Department Jakarta11480 Indonesia Bina Nusantara University Faculty of Engineering Bioinformatics and Data Science Research Center Biotechnology Department Jakarta11480 Indonesia Bina Nusantara University School of Computer Science Bioinformatics and Data Science Research Center Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350307306

Bacteria are microscopic organisms that can be found in many environments. They are abundant and have many roles in our life. Studying bacteria is essential so that we can identify the bacteria that are needed for many industrial applications. However, the main problem is that majority of the bacteria are unculturable, hampering the exploration of bacteria from different environments. Metagenomics approach which employs Next Generation Sequencing technology could help study bacteria by utilizing 16S rRNA marker gene. This study aims to demonstrate data mining and bioinformatics approaches to analyze 16S rRNA sequencing data. The raw sequencing data of 16S rRNA was collected from biological database. Then, the data were trimmed, denoised, and clustered to generate Amplicon Sequence Variants (ASVs). Diversity (alpha and beta) and taxonomic analyses were then conducted to elucidate the bacterial diversity and taxonomic profile of ASVs. The results of this work showed that Shannon and PD indices in China's hot spring were higher than Singapore and the USA. Furthermore, a significant difference was observed in the PD index. The unweighted UniFrac distance also showed there was a significant difference of the bacterial communities between the three locations. In addition, the taxonomic investigation unveiled prevalent bacterial groups in the ecosystem, namely Proteobacteria, Chloroflexi, Cyanobacteria, and Crenarchaeota. The research outcomes have the potential to serve as a foundational resource for subsequent bacterial metagenomic research, particularly the hot spring environment. © 2023 IEEE.

关键词： Bacteria

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P3DC:Reducing DRAM Cache Hit Latency by Hybrid Mappings

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Journal of computer science & Technology 2024年第6期39卷 1341-1360页

作者： Ye Chi Ren-Tong Guo Xiao-Fei Liao Hai-Kun Liu Jianhui Yue National Engineering Research Center for Big Data Technology and System Wuhan 430074China Services Computing Technology and System Laboratory Wuhan 430074China Cluster and Grid Computing Laboratory Wuhan 430074China School of Computer Science and Technology Huazhong University of Science and TechnologyWuhan 430074China School of Big Data and Internet Shenzhen Technology UniversityShenzhen 518118China Department of Computer Science Michigan Technological UniversityHoughton 49931-1295U.S.A.

Die-stacked dynamic random access memory(DRAM)caches are increasingly advocated to bridge the performance gap between the on-chip cache and the main *** fully realize their potential,it is essential to improve DRAM cache hit rate and lower its cache hit *** order to take advantage of the high hit-rate of set-association and the low hit latency of direct-mapping at the same time,we propose a partial direct-mapped die-stacked DRAM cache called *** design is motivated by a key observation,i.e.,applying a unified mapping policy to different types of blocks cannot achieve a high cache hit rate and low hit latency *** address this problem,P3DC classifies data blocks into leading blocks and following blocks,and places them at static positions and dynamic positions,respectively,in a unified set-associative *** also propose a replacement policy to balance the miss penalty and the temporal locality of different *** addition,P3DC provides a policy to mitigate cache thrashing due to block type *** results demonstrate that P3DC can reduce the cache hit latency by 20.5%while achieving a similar cache hit rate compared with typical set-associative caches.P3DC improves the instructions per cycle(IPC)by up to 66%(12%on average)compared with the state-of-the-art direct-mapped cache—BEAR,and by up to 19%(6%on average)compared with the tag-data decoupled set-associative cache—DEC-A8.

关键词： die-stacked dynamic random access memory(DRAM) cache set-associative direct-mapped hit latency

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Soft-GNN:towards robust graph neural networks via self-adaptive data utilization

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Frontiers of computer science 2025年第4期19卷 1-12页

作者： Yao WU Hong HUANG Yu SONG Hai JIN National Engineering Research Center for Big Data Technology and System Service Computing Technology and System LabCluster and Grid Computing LabSchool of Computer Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China College of Information and Communication National University of Defense TechnologyWuhan 430019China Department of Computer Science and Operations Research Universitéde MontréalMontreal H3C 3J7Canada

Graph neural networks(GNNs)have gained traction and have been applied to various graph-based data analysis tasks due to their high ***,a major concern is their robustness,particularly when faced with graph data that has been deliberately or accidentally polluted with *** presents a challenge in learning robust GNNs under noisy *** address this issue,we propose a novel framework called Soft-GNN,which mitigates the influence of label noise by adapting the data utilized in *** approach employs a dynamic data utilization strategy that estimates adaptive weights based on prediction deviation,local deviation,and global *** better utilizing significant training samples and reducing the impact of label noise through dynamic data selection,GNNs are trained to be more *** evaluate the performance,robustness,generality,and complexity of our model on five real-world datasets,and our experimental results demonstrate the superiority of our approach over existing methods.

关键词： graph neural networks node classification label noise robustness

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A Hybrid CNN-SVM Approach for Malaria in Blood Cell Detection 2

A Hybrid CNN-SVM Approach for Malaria in Blood Cell Detectio...

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2nd International Conference on Software Engineering and Information Technology, ICoSEIT 2024

作者： Karnyoto, Andrea Stevens Isnan, Mahmud Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia

ISBN: (纸本)9798350317503

There is still a severe malaria problem worldwide, particularly in regions with limited access to diagnostic tools. It is crucial to develop a system for detecting malaria in blood cells. This paper presents a hybrid Convolutional Neural Network (CNN), and as a classifier, we use a Support Vector Machine (SVM) framework for the automated detection of malaria parasites in blood cell images. The proposed system leverages the strengths of CNNs in feature extraction and representation learning from images, combined with the discriminative power of SVMs for classification. Initially, CNN extracts intricate features from blood cell images, capturing essential patterns indicative of malaria infection. Subsequently, the extracted features are used to train an SVM classifier, enabling accurate discrimination between parasitized and uninfected blood cells. Experimental dataset evaluations were obtained from the Lister Hill National center for Biomedical Communications website of the National Library of Medicine. The proposed model achieves a better f1-score, outperforming individual CNN or SVM models, around 0.015 compared to individual CNN models and 0.27 compared to individual SVM models. This hybrid CNN-SVM methodology offers a promising solution for accurately and efficiently detecting malaria parasites in blood cell images. © 2024 IEEE.

关键词： Support vector machines

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Implementation of Fine-Tuned BERT for Enzyme Classification Based on Gene Ontology 11

Implementation of Fine-Tuned BERT for Enzyme Classification ...

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11th International Conference on Advanced Informatics: Concept, Theory and Application, ICAICTA 2024

作者： Henry, Matthew Martianus Kenneth, Christian Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia

ISBN: (纸本)9798331520311

Enzymes are biocatalysts with vital roles in biological functions and many industrial applications. Diverse enzymes are classified using Enzyme Commission (EC) nomenclature, making differentiation challenging. On the other hand, another biological information, gene ontology (GO), can describe the biological aspects of enzymes, covering related biological processes (BP), molecular functions (MF), and their locations within cells (CC). This study proposes a novel EC class and subclass classification of enzymes within the ontology subclass based on their GO semantics using a Bidirectional Encoder Representation of Transformer (BERT). The BERT model is first fine-tuned using the preprocessed GO term name and definition, with the enzymes in each ontology class (BP, MF, or CC) are also divided based on how the GO assigned, either through manual annotation (NONIEA) or electronically inferred (IEA). BERT successfully obtained 0.93, 0.60, 0.99, 0.90, 0.40, and 0.35 F1 scores during fine-tuning for BP IEA, BP NONIEA, MF IEA, MF NONIEA, CC IEA, and CC NONIEA, respectively. On the test set, the fine-tuned BERT significantly outperformed GOntoSim, a framework to calculate semantic similarity based on classical information theory, in EC class classification across all metrics with less inference time in all ontology subclass. Expanded further to the EC subclass, BERT can classify the enzyme on the EC subclass level in BP IEA and MF IEA ontology subclass. However, longer epochs are needed in fine-tuning. This result shows that the names and definitions of GO terms are distinguishable features in classifying enzymes as an alternative to the information content approach. © 2024 IEEE.

关键词： Gene Ontology

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Aggregating Structural Features for Computational Analysis of Mutations in BRCT Domains of BRCA1 Protein

Aggregating Structural Features for Computational Analysis o...

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2023 International Conference on Informatics, Multimedia, Cyber and Information Systems, ICIMCIS 2023

作者： Hidayat, Alam Ahmad Nirwantono, Rudi Isnan, Mahmud Trinugroho, Joko Pebrianto Pardamean, Bens Bina Nusantara University School of Computer Science Bioinformatics and Data Science Research Center Mathematics Department Jakarta11480 Indonesia Bina Nusantara University Faculty of Engineering Bioinformatics and Data Science Research Center Biotechnology Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Binus Graduate Program Bioinformatics and Data Science Research Center Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350307306

Understanding the mechanistic interpretability of mutation effects in a protein can help predict the clinical implications of the genetic variants. Hence, computational variant effect predictions that involve protein structural features of the protein mutations might be suitable in this case. In this work, we focus on BRCT domains of BRCA1 gene that is widely studied in breast cancer studies. We retrieved 88 selected missense variants found in BRCT domains annotated in both ClinVar and gnomAD databases. To computationally characterize the pathogenic property of the mutations we used two types of features extracted from protein structures: a change in free Gibbs energy and a set of features derived from molecular dynamics simulations of each mutant. Using a dimensional reduction and Gaussian mixture model (GMM)-based clustering we demonstrate that the variants are segregated into two regions that may correspond to their pathogenic status. This method can be a potential computational pipeline for providing the preliminary mechanistic interpretation of mutation effects in terms of their thermodynamic and structural features. © 2023 IEEE.

关键词： Proteins

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SAND: semi-automated adaptive network defense via programmable rule generation and deployment

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science China(Information sciences) 2022年第7期65卷 121-138页

作者： Haoyu CHEN Deqing ZOU Hai JIN Shouhuai XU Bin YUAN National Engineering Research Center for Big Data Technology and System Services Computing Technology and System LabCluster and Grid Computing Lab School of Computer Science and TechnologyHuazhong University of Science and Technology National Engineering Research Center for Big Data Technology and System Services Computing Technology and System LabHubei Engineering Research Center on Big Data Security School of Cyber Science and EngineeringHuazhong University of Science and Technology Department of Computer Science University of Colorado at Colorado Springs

Cyber security is dynamic as defenders often need to adapt their defense postures. The state-ofthe-art is that the adaptation of network defense is done manually(i.e., tedious and error-prone). The ideal solution is to automate adaptive network defense, which is however a difficult problem. As a first step towards automation, we propose investigating how to attain semi-automated adaptive network defense(SAND). We propose an approach extending the architecture of software-defined networking, which is centered on providing defenders with the capability to program the generation and deployment of dynamic defense rules enforced by network defense tools. We present the design and implementation of SAND, as well as the evaluation of the prototype implementation. Experimental results show that SAND can achieve agile and effective dynamic adaptations of defense rules(less than 15 ms on average for each operation), while only incurring a small performance overhead.

关键词： network defense adaptive defense automated defense programmable defense security services software-defined networking security management

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