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4th International Conference on Algorithms, Computing and Artificial Intelligence, ACAI 2021

作者： Wan, Qian Wei, Luona Chen, Xinhai Liu, Jie Science and Technology on Parallel and Distributed Processing Laboratory National University of Defense Technology Hunan Changsha China College of Systems Engineering National University of Defense Technology Hunan Changsha China Laboratory of Software Engineering for Complex Systems National University of Defense Technology Hunan Changsha China

ISBN: (纸本)9781450385053

Fully capturing contextual information and analyzing the association between entity semantics and type is helpful for joint extraction task: 1) The context can reflect the part of speech and semantics of entity. 2) The entity type is closely related to the relation between entities. Previous research used to simply embed the contextual information into shallow layer of the model, ignoring the association between entity semantics and type. In this paper, we propose a graph network with full-information modeling to explicitly model different-level information in the text. The contextual information of entity is dynamically embedded in each span representation to improve the reasoning ability. To capture the fine-grained association between the semantics and type of entity, the graph network uses the feature of entity types to generate edge information between different nodes. Experimental results show that our model outperforms previous models on the CoNLL04 dataset and obtains competitive results on the SciERC dataset in both entity recognition and relation extraction. Extensive additional experiments further verify the effectiveness of the model. © 2021 ACM.

关键词： Natural language processing systems

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P-refined RBF-FD solution of a poisson problem 6

P-refined RBF-FD solution of a poisson problem

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6th International Conference on Smart and Sustainable Technologies, SpliTech 2021

作者： Jancic, Mitja Slak, Jure Kosec, Gregor 'Jožef Stefan' International Postgraduate School Jamova cesta 39 Ljubljana1000 Slovenia 'Jožef Stefan' Institute Parallel and Distributed Systems Laboratory Jamova cesta 39 Ljubljana1000 Slovenia

ISBN: (纸本)9789532901122

Local meshless methods obtain higher convergence rates when RBF approximations are augmented with monomials up to a given order. If the order of the approximation method is spatially variable, the numerical solution is said to be p-refined. In this work, we employ RBF-FD approximation method with polyharmonic splines augmented with monomials and study the numerical properties of p-refined solutions, such as convergence orders and execution time. To fully exploit the refinement advantages, the numerical performance is studied on a Poisson problem with a strong source within the domain. © 2021 University of Split, FESB.

关键词： Finite difference method

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Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis

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EuPA Open Proteomics 2014年 5卷 21-31页

作者： Quandt, Andreas Espona, Lucia Balasko, Akos Weisser, Hendrik Brusniak, Mi-Youn Kunszt, Peter Aebersold, Ruedi Malmström, Lars Department of Biology Institute of Molecular Systems Biology ETH Zurich Switzerland SyBIT SystemsX.ch Switzerland MTA SZTAKI Laboratory of Parallel and Distributed Systems Budapest Hungary Institute for Systems Biology Seattle United States S3IT University of Zurich Switzerland Faculty of Science University of Zurich Switzerland

Tandem mass spectrometry and sequence database searching are widely used in proteomics to identify peptides in complex mixtures. Here we present a benchmark study in which a pool of 20,103 synthetic peptides was measured and the resulting data set was analyzed using around 1800 different software and parameter set combinations. The results indicate a strong relationship between the performance of an analysis workflow and the applied parameter settings. We present and discuss strategies to optimize parameter settings in order to significantly increase the number of correctly assigned fragment ion spectra and to make the analysis method robust. © 2014 The Authors.

关键词： Classical database search Data analysis Mass spectrometry Search engine Synthetic peptides

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A hybrid RBF-FD and WLS mesh-free strong-form approximation method 7

A hybrid RBF-FD and WLS mesh-free strong-form approximation ...

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7th International Conference on Smart and Sustainable Technologies, SpliTech 2022

作者： Jancic, Mitja Kosec, Gregor JoÅ½ef Stefan Institute Parallel and Distributed Systems Laboratory Jamova cesta 39 Ljubljana1000 Slovenia JoÅ½ef Stefan International Postgraduate School Jamova cesta 39 Ljubljana1000 Slovenia

ISBN: (纸本)9789532901160

Since the advent of mesh-free methods as a tool for the numerical analysis of systems of Partial Differential Equations (PDEs), many variants of differential operator approximation have been proposed. In this work, we propose a local mesh-free strong-form method that combines the stability of Radial Basis Function-Generated Finite Differences (RBF-FD) with the computational effectiveness of Diffuse Approximation Method (DAM), forming a so-called hybrid method. To demonstrate the advantages of a hybrid method, we evaluate its computational complexity and accuracy of the obtained numerical solution by solving a two-dimensional Poisson problem with an exponentially strong source in the computational domain. Finally, we employ the hybrid method to solve a three-dimensional Boussinesq's problem on an isotropic half-space and show that the implementation overhead can be justified. © 2022 University of Split, FESB.

关键词： Mesh generation

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Efficient and available in-memory KV-store with hybrid erasure coding and replication 16

Efficient and available in-memory KV-store with hybrid erasu...

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Proceedings of the 14th Usenix Conference on File and Storage Technologies

作者： Heng Zhang Mingkai Dong Haibo Chen Shanghai Key Laboratory of Scalable Computing and Systems Institute of Parallel and Distributed Systems Shanghai Jiao Tong University

ISBN: (纸本)9781931971287

In-memory key/value store (KV-store) is a key building block for many systems like databases and large websites. Two key requirements for such systems are efficiency and availability, which demand a KV-store to continuously handle millions of requests per second. A common approach to availability is using replication such as primary-backup (PBR), which, however, requires M + 1 times memory to tolerate M failures. This renders scarce memory unable to handle useful user *** paper makes the first case of building highly available in-memory KV-store by integrating erasure coding to achieve memory efficiency, while not notably degrading performance. A main challenge is that an in-memory KV-store has much scattered metadata. A single KV put may cause excessive coding operations and parity updates due to numerous small updates to metadata. Our approach, namely Cocytus, addresses this challenge by using a hybrid scheme that leverages PBR for small-sized and scattered data (e.g., metadata and key), while only applying erasure coding to relatively large data (e.g., value). To mitigate well-known issues like lengthy recovery of erasure coding, Cocytus uses an online recovery scheme by leveraging the replicated metadata information to continuously serving KV requests. We have applied Cocytus to Memcached. Evaluation using YCSB with different KV configurations shows that Cocytus incurs low overhead for latency and throughput, can tolerate node failures with fast online recovery, yet saves 33% to 46% memory compared to PBR when tolerating two failures.

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A dynamic virtual fragmentation method for query recovery optimization

A dynamic virtual fragmentation method for query recovery op...

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Computer Science Society (SCCC) International Conference Chilean FLAGGED

作者： J.A. Vazquez Parallel and Distributed Systems Laboratory Research Computer Center National Petroleum Institute of Mexico Mexico

The time consumed during the execution of queries in a parallel and distributed environment is highly affected by the form in which the tables comprising a database have been fragmented. The classical methods of fragmentation in a distributed database system helps, to a great extent, to make the information retrieval faster and with smaller calculation efforts. This is particularly true for applications where the specifications are well known in advance at the time of the creation of the tables that compose the database, which in some form or other influenced the design and the definition of the type of fragmentation and their distribution on different sites of processing. Nevertheless, the above characteristics cannot be used in applications where the distributed management cannot do inferences that help it to know in what sites the data with the characteristics the user is looking for are located. Under these conditions the time and amount of work used by the participants in the query solution can be highly increased. In this paper the dynamic virtual fragmentation method is presented. The method works as an alternative way that allows us to diminish response time consumed by queries using horizontal fragmented tables. The proposed method has been proven and implemented in a database parallel server running on a shared nothing supercomputer.

关键词： Optimization methods distributed databases Information retrieval Partitioning algorithms Laboratories Concurrent computing distributed computing Augmented virtuality Delay Supercomputers

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Fused Data Structures for Handling Multiple Faults in distributed systems

Fused Data Structures for Handling Multiple Faults in Distri...

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International Conference on distributed Computing systems

作者： Bharath Balasubramanian Vijay K. Garg Parallel and Distributed Systems Laboratory Department of Electrical and Computer Engineering University of Texas Austin USA

The paper describes a technique to correct crash faults in large data structures hosted on distributed servers, based on the concept of fused backups. The prevalent solution to this problem is replication. To correct f crash faults among n distinct data structures, replication requires nf additional replicas. If each of the primaries contains O(m) nodes of O(s) size each, this translates to O(nmsf) total backup space. Our technique uses a combination of erasure correcting codes and selective replication to correct f crash faults using just f additional backups consuming O(msf) total backup space, while incurring minimal overhead during normal operation. Since the data is maintained in the coded form, recovery is costly as compared to replication. However, in a system with infrequent faults, the savings in space outweighs the cost of recovery. We explore the theory and algorithms for these fused backups and provide a library of such backups for all the data structures in the Java 6 Collection framework. Our experimental evaluation confirms that fused backups are space-efficient as compared to replication (almost n times), while they cause very little overhead for updates. Many real world distributed systems such as Amazon's Dynamo data store use replication to achieve reliability. An alternate, fusion-based design can result in significant savings in space as well as other resources such as power.

关键词： Servers Computer crashes Indexes Arrays Fault tolerance Fault tolerant systems

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Maintaining Consistency Properties of Grid Workflows in Collaborative Editing systems

Maintaining Consistency Properties of Grid Workflows in Coll...

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International Conference on Grid and Cooperative Computing (GCC)

作者： Gergely Sipos Péter Kacsuk Parallel and Distributed Systems Laboratory MTA SZTAKI Hungarian Academy of Sciences (ATOMKI) Budapest Hungary

Real-time collaborative editing systems allow a group of users to view and edit the same item at the same time from geographically dispersed sites. Consistency maintenance in the face of concurrent accesses to shared entities is one of the core issues in the design of these systems. The paper introduces a locking based approach that grid application developer environments can apply to protect the consistency properties of workflows during collaborative editing scenarios. We developed two pessimistic locking algorithms to assure that under no circumstances can application developers break the acyclic criteria of workflow graphs or add invalid edges to them. We prove that the algorithms result consistent graphs, moreover, do not result the cancellation of any userpsilas editing transaction. We see that the second, improved algorithm gives much better performance in terms of number of concurrent users that can work on a graph.

关键词： Collaborative work Partitioning algorithms International collaboration Concurrent computing distributed computing Grid computing Laboratories Real time systems Protection Collaborative software

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Secure and Efficient Runtime Environment for Smart Contracts on JointCloud

Secure and Efficient Runtime Environment for Smart Contracts...

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IEEE International Conference on Joint Cloud Computing (JCC)

作者： Yuhao Xue Dong Du Lei Zhang Yubin Xia Institude of Parallel and Distributed Systems Shanghai Jiao Tong University China Nanhu Laboratory China

Many cloud providers, including Amazon, Google, Microsoft, and Alibaba Cloud, offer support for blockchain cloud services that rely on a runtime environment, such as the Ethereum Virtual Machine (EVM), to execute smart contracts and ensure consistency between participants. However, existing runtime systems suffer from two main limitations. Firstly, traditional runtime systems like EVM cannot guarantee privacy protection as all the data uploaded to the blockchain is visible to all participants. This restricts the use of blockchain in limited scenarios. Secondly, each computation on the runtime system must be synchronized to all nodes in the network, resulting in a significant increase in computational overhead, which can be challenging to implement for more complex applications. One approach to address these limitations is to utilize Trusted Execution Environments (TEE) for blockchain runtime, which can provide privacy protection and mitigate redundant synchronization operations. However, using TEE for blockchain may significantly increase cloud costs. To overcome these challenges, this paper proposes PL-EVM, a new runtime environment for smart contracts that utilizes jointcloud. PL-EVM achieves high-security guarantees by using TEE to protect privacy-sensitive data and incorporates dynamic migration and splitting mechanisms to achieve high efficiency and low costs. Our evaluation results show that PL-EVM can improve performance and reduce costs by 4% to 32.22%.

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Efficient distributed Secure Memory with Migratable Merkle Tree

Efficient Distributed Secure Memory with Migratable Merkle T...

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IEEE Symposium on High-Performance Computer Architecture

作者： Erhu Feng Dong Du Yubin Xia Haibo Chen Institute of Parallel and Distributed Systems Shanghai Jiao Tong University Shanghai Artificial Intelligence Laboratory

Hardware-assisted enclaves with memory encryption have been widely adopted in the prevailing architectures, e.g., Intel SGX/TDX, AMD SEV, ARM CCA, etc. However, existing enclave designs fall short in supporting efficient cooperation among cross-node enclaves (i.e., multi-machines) because the range of hardware memory protection is within a single node. A naive approach is to leverage cryptography at the application level and transfer data between nodes through secure channels (e.g., SSL). However, it incurs orders of magnitude costs due to expensive encryption/decryption, especially for distributed applications with large data transfer, e.g., MapReduce and graph computing. A secure and efficient mechanism of distributed secure memory is necessary but still *** paper proposes Migratable Merkle Tree (MMT), a design enabling efficient distributed secure memory to support distributed confidential computing. MMT sets up an integrity forest for distributed memory on multiple nodes. It allows an enclave to securely delegate an MMT closure, which contains both data and metadata of a subtree, to a remote enclave. By reusing the memory encryption mechanisms of existing enclaves, our design achieves secure data transfer without software re-encryption. We have implemented a prototype of MMT and a trusted firmware for management, and further applied MMT to real-world distributed applications. The evaluation results show that compared with existing systems using the AES-NI instruction, MMT can achieve up to 13x speedup on data transferring, and gain 12%~58% improvement on the end-to-end performance of MapReduce and PageRank.

关键词： Protocols Program processors Memory management Prototypes Metadata Data transfer Software

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