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Greedily assemble tandem repeats for next generation sequences 贪婪地为下一代序列组装串联重复序列
Pub Date : 2019-11-08 DOI: 10.1504/ijhpcn.2019.103536
Yongqing Jiang, Jinhua Lu, Jingyu Hou, Wanlei Zhou
Eukaryotic genomes contain high volumes of intronic and intergenic regions in which repetitive sequences are abundant. These repetitive sequences represent challenges in genomic assignment of short read sequences generated through next generation sequencing and are often excluded in analysis losing invaluable genomic information. Here we present a method, known as tandem repeat assembler (TRA), for the assembly of repetitive sequences by constructing contigs directly from paired-end reads. Using an experimentally acquired data set for human chromosome 14, tandem repeats >200 bp were assembled. Alignment of the contigs to the human genome reference (GRCh38) revealed that 84.3% of tandem repetitive regions were correctly covered. For tandem repeats, this method outperformed state-of-the-art assemblers by generating correct N50 of contigs up to 512 bp.
真核生物基因组包含大量的内含子和基因间区域,其中重复序列丰富。这些重复序列对通过下一代测序产生的短读序列的基因组分配提出了挑战,并且经常被排除在分析之外,失去了宝贵的基因组信息。在这里,我们提出了一种称为串联重复组装(TRA)的方法,通过直接从成对末端读取构建contigs来组装重复序列。利用实验获得的人类14号染色体数据集,组装了>200 bp的串联重复序列。与人类基因组参考序列(GRCh38)比对显示,84.3%的串联重复区域被正确覆盖。对于串联重复序列,该方法通过生成高达512 bp的正确N50来优于最先进的组装器。
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引用次数: 0
Generic data storage-based dynamic mobile app for standardised electronic health records database 基于通用数据存储的标准化电子健康记录数据库动态移动应用程序
Pub Date : 2019-11-08 DOI: 10.1504/ijhpcn.2019.10025212
Shivani Batra, Shelly Sachdeva, S. Bhalla
Standardisation plays an important role in making healthcare application worldwide adaptable. It uses archetypes for semantic interoperability. In addition to the interoperability, a mechanism to handle future evolution is the primary concern for market sustainability. An application should possess dynamism in terms of the front end (user interface) as well as the back end (database) to build a future proof system. Current research aims to extend the functionality of prior work on HEALTHSURANCE with a search efficient generic storage and validation support. At application level, graphical user interface is dynamically built using knowledge provided by standards in terms of archetypes. At the database level, generic storage structure is provided with improved searching capabilities to support faster access, to capture dynamic knowledge evolution and to handle sparseness. A standardised format and content helps to uplift the credibility of data and maintains a uniform and specific set of constraints used to evaluate user's health. Architecture proposed in current research enables implementation of mobile app based on an archetype paradigm that can avoid reimplementation of the systems, supports migrating databases and allows the creation of future-proof systems.
标准化在使全球医疗保健应用具有适应性方面发挥着重要作用。它使用原型实现语义互操作性。除了互操作性之外,处理未来演变的机制是市场可持续性的主要关注点。应用程序应该在前端(用户界面)和后端(数据库)方面具有动态性,以构建面向未来的系统。目前的研究旨在通过搜索高效的通用存储和验证支持来扩展HEALTHSURANCE先前工作的功能。在应用程序级别,图形用户界面是使用标准根据原型提供的知识动态构建的。在数据库级别,通用存储结构提供了改进的搜索功能,以支持更快的访问、捕捉动态知识演变和处理稀疏性。标准化的格式和内容有助于提高数据的可信度,并保持用于评估用户健康的一套统一和特定的约束条件。当前研究中提出的架构使基于原型范例的移动应用程序的实现能够避免系统的重新实现,支持迁移数据库并允许创建面向未来的系统。
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引用次数: 1
Selection of effective probes for an individual to identify P300 signal generated from P300 BCI speller 为个人选择有效的探针来识别P300 BCI拼写器产生的P300信号
Pub Date : 2019-11-08 DOI: 10.1504/ijhpcn.2019.10025210
Weilun Wang, G. Chakraborty
P300 is a strong event related potential (ERP) generated in the brain and observed on the scalp when an unusual event happens. To decipher P300 signal, we have to use the property of P300 to distinguish P300 signal from non-P300 signal. In this work, we used data collected from P300 BCI Speller with 128 probes. Conventional BCI speller uses eight probes at pre-defined locations on the skull. Though P300 is strong in the parietal region of the brain, location of the strongest signal varies from person to person. The idea is that, if we optimise probe locations for an individual, we could reduce the number of probes required. In fact, the process mode for the raw brain wave signals also will affect the classification accuracy. We designed an algorithm to analyse the raw signals. We achieved over 81% classification accuracy on average with only three probes from only one target stimulus and one non-target stimulus.
P300是一种强烈的事件相关电位(ERP),当不寻常的事件发生时,在大脑中产生并在头皮上观察到。为了破译P300信号,我们必须利用P300的特性来区分P300信号和非P300信号。在这项工作中,我们使用了128个探针从P300 BCI拼写器收集的数据。传统的脑机接口拼写器在颅骨上预定的位置使用8个探针。虽然P300在大脑的顶叶区域很强,但最强信号的位置因人而异。这个想法是,如果我们为个体优化探针位置,我们就可以减少所需的探针数量。事实上,原始脑电波信号的处理方式也会影响分类的准确性。我们设计了一个算法来分析原始信号。我们仅从一个目标刺激和一个非目标刺激中使用三次探针,平均达到81%以上的分类准确率。
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引用次数: 2
A novel ECC-based lightweight authentication protocol for internet of things devices 一种新的基于ecc的物联网设备轻量级认证协议
Pub Date : 2019-11-08 DOI: 10.1504/ijhpcn.2019.10025215
A. Tewari, B. Gupta
In spite of being a promising technology which will make our lives a lot easier we cannot be oblivious to the fact IoT is not safe from online threat and attacks. Thus, along with the growth of IoT we also need to work on its aspects. Taking into account the limited resources that these devices have it is important that the security mechanisms should also be less complex and do not hinder the actual functionality of the device. In this paper, we propose an ECC based lightweight authentication for IoT devices which deploy RFID tags at the physical layer. ECC is a very efficient public key cryptography mechanism as it provides privacy and security with less computation overhead. We also present a security and performance analysis to verify the strength of our proposed approach. We have verified the security and authentication session execution of our protocol using the Promela model and SPIN tool.
尽管物联网是一项很有前途的技术,它将使我们的生活变得更加轻松,但我们不能忽视这样一个事实,即物联网在面对在线威胁和攻击时并不安全。因此,随着物联网的发展,我们还需要在其各个方面开展工作。考虑到这些设备拥有的有限资源,重要的是安全机制也应该不那么复杂,并且不妨碍设备的实际功能。在本文中,我们提出了一种基于ECC的轻量级认证,用于在物理层部署RFID标签的物联网设备。ECC是一种非常有效的公钥加密机制,它以较少的计算开销提供了隐私和安全性。我们还提出了安全性和性能分析,以验证我们提出的方法的强度。我们已经使用Promela模型和SPIN工具验证了协议的安全性和身份验证会话执行。
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引用次数: 14
Fault-tolerant flexible lossless cluster compression method for monitoring data in smart grid 智能电网监控数据容错柔性无损聚类压缩方法
Pub Date : 2019-11-08 DOI: 10.1504/ijhpcn.2019.10025204
Zhijian Qu, Hanling Wang, Xiang Peng, Ge Chen
Big data in smart grid dispatch monitoring systems is susceptible to interference from processing delays and slow response times. Hence, a new fault-tolerant flexible lossless cluster compression method is proposed. This paper presents the Five-tuples (S, D, O, T, M) model, and builds a monitoring data processing platform based on hive. By deploying the dispatch host and monitoring servers under the cloud computing environment, where data nodes are respectively transformed by Deflate, Gzip, BZip2 and LZO lossless compression method. Taking the power dispatch automation system of Long-hai line as example, experimental results show that the cluster lossless compression ratio of BZip2 is greater than 81%; when data records reach twelve million, the compression ratio can be further improved to certain extent by using RCFile storage hive format, which has significant flexible features. Therefore, the new method proposed in this paper can improve the flexibility and fault-tolerant ability of big monitoring data processing in smart grid.
智能电网调度监控系统中的大数据容易受到处理延迟和响应时间过慢的干扰。为此,提出了一种新的容错柔性无损聚类压缩方法。本文提出了五元组(S, D, O, T, M)模型,构建了一个基于hive的监测数据处理平台。通过在云计算环境下部署调度主机和监控服务器,其中数据节点分别采用Deflate、Gzip、BZip2和LZO无损压缩方法进行转换。以陇海线路电力调度自动化系统为例,实验结果表明,BZip2的聚类无损压缩率大于81%;当数据记录达到1200万条时,采用RCFile存储hive格式可以在一定程度上进一步提高压缩比,具有显著的灵活性。因此,本文提出的新方法可以提高智能电网大监测数据处理的灵活性和容错能力。
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引用次数: 0
An efficient approach to optimise I/O cost in data-intensive applications using inverted indexes on HDFS splits 在数据密集型应用程序中使用HDFS拆分上的倒排索引来优化I/O成本的有效方法
Pub Date : 2019-11-08 DOI: 10.1504/ijhpcn.2019.10025211
N. K. Seera, S. Taruna
Hadoop is prominent for its distributed file system (HDFS) and scalability. Hadoop MapReduce framework is extensively used in big data analytics and business-intelligence applications. The analytic queries executed by these applications often include multiple ad hoc queries and aggregate queries with some selection predicates. The cost of executing these queries grows incredibly as the size of dataset grows. The most effective strategy to improve query performance in such applications is to process only relevant data keeping irrelevant data aside, which can be done using index structures. This paper is an attempt to improve query performance by avoiding full scans on data files. The algorithms used in this paper create inverted indexes on HDFS input splits. We show how query processing in MR jobs can benefit in terms of performance by employing these custom inverted indexes. The experiments demonstrate that queries executed using indexed data execute 1.5x faster than the traditional queries.
Hadoop以其分布式文件系统(HDFS)和可扩展性而闻名。Hadoop MapReduce框架广泛应用于大数据分析和商业智能应用。这些应用程序执行的分析查询通常包括多个特别查询和带有一些选择谓词的聚合查询。随着数据集规模的增长,执行这些查询的成本会难以置信地增长。在这类应用程序中提高查询性能的最有效策略是只处理相关数据,而不处理无关数据,这可以使用索引结构来实现。本文试图通过避免对数据文件进行完全扫描来提高查询性能。本文使用的算法在HDFS输入分割上创建倒排索引。我们将展示MR作业中的查询处理如何通过使用这些自定义倒排索引来提高性能。实验表明,使用索引数据执行的查询比传统查询快1.5倍。
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引用次数: 1
Combined bit map representation and its applications to query processing of resource description framework on GPU 结合位图表示及其在GPU资源描述框架查询处理中的应用
Pub Date : 2019-11-08 DOI: 10.1504/ijhpcn.2019.10025206
C. Phongpensri, Chidchanok Choksuchat
Resource description framework (RDF) is a common representation in semantic web context, including the web data sources and their relations in the URI form. With the growth of data accessible on the Internet, the RDF data currently contains millions of relations. Thus, answering a semantic query requires going through large amounts of data relations, which is time consuming. In this work, we present a representation framework, combined bit map representation (CBM), which compactly represents RDF data while helping speed up semantic query processing using graphics processing units (GPUs). Since GPUs have limited memory size, without compaction the RDF data cannot be entirely stored in the GPU memory; the CBM structure enables more RDF data to reside in the GPU memory. Since GPUs have many processing elements, their parallel use speeds up RDF query processing. The experimental results show that the proposed representation can reduce the size of RDF data by 70%. Furthermore, the search time on this representation using the GPU is 60% faster than with conventional implementation.
资源描述框架(RDF)是语义web上下文中的一种通用表示,它以URI的形式将web数据源及其关系包括在内。随着Internet上可访问数据的增长,RDF数据目前包含数百万个关系。因此,回答语义查询需要遍历大量的数据关系,这非常耗时。在这项工作中,我们提出了一个表示框架,组合位图表示(CBM),它紧凑地表示RDF数据,同时帮助加速使用图形处理单元(gpu)的语义查询处理。由于GPU有有限的内存大小,没有压缩RDF数据不能完全存储在GPU内存中;CBM结构允许更多的RDF数据驻留在GPU内存中。由于gpu有许多处理元素,它们的并行使用加速了RDF查询处理。实验结果表明,该方法可以将RDF数据的大小减少70%。此外,使用GPU对这种表示的搜索时间比传统实现快60%。
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引用次数: 0
Outlier detection of time series with a novel hybrid method in cloud computing 云计算中一种新型混合方法的时间序列异常点检测
Pub Date : 2019-09-19 DOI: 10.1504/ijhpcn.2019.102350
Qi Liu, Zhen Wang, Xiaodong Liu, N. Linge
In the wake of the developments in science and technology, cloud computing has obtained more attention in different fields. Meanwhile, outlier detection for data mining in cloud computing is playing significant role in different research domains and massive research works have been devoted to outlier detection. However, the existing available methods require lengthy computation time. Therefore, the improved algorithm of outlier detection, which has higher performance to detect outliers, is presented. In this paper, the proposed method, which is an improved spectral clustering algorithm (SKM++), is fit for handling outliers. Then, pruning data can reduce computational complexity and combine distance-based method Manhattan distance (distm) to obtain outlier score. Finally, the method confirms the outlier by extreme analysis. This paper validates the presented method by experiments with real collected data by sensors and comparison against the existing approaches. The experimental results show that our proposed method outperforms the existing.
随着科学技术的发展,云计算在各个领域得到了越来越多的关注。与此同时,云计算数据挖掘中的离群点检测在不同的研究领域发挥着重要作用,对离群点检测进行了大量的研究工作。然而,现有的方法需要较长的计算时间。因此,本文提出了一种改进的离群点检测算法,该算法具有更高的离群点检测性能。本文提出的方法是一种改进的谱聚类算法(skm++),适合处理异常点。然后,对数据进行剪枝可以降低计算复杂度,并结合基于距离的曼哈顿距离(distm)方法得到离群值。最后,通过极值分析确定异常值。本文通过传感器实测数据的实验和与现有方法的比较,验证了所提方法的有效性。实验结果表明,本文提出的方法优于现有的方法。
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引用次数: 1
Sparse reconstruction of piezoelectric signal for phased array structural health monitoring 相控阵结构健康监测中压电信号的稀疏重构
Pub Date : 2019-09-19 DOI: 10.1504/ijhpcn.2019.102354
Yajie Sun, Feihong Gu, S. Ji
Structural health monitoring technology has been widely used in the detection and identification of plate structure damage. Ultrasonic phased array technology has become an important method for structural health monitoring because of its flexible beam scanning and strong focusing performance. However, a large number of phased array signals will be produced, which leads to difficulty in storing, transmitting and processing. Therefore, under the condition of the signal being sparse, compressive sensing theory can make signal acquisition with much lower sampling rate than traditional Nyquist sampling theorem. Firstly, the sparse orthogonal transformation is used to make the sparse representation. Then, the measurement matrix is used for the projection observation. Besides, the reconstruction algorithm is used for sparse reconstruction. In this paper, the experimental verification of the antirust aluminium plate material is carried out. The experiment shows that the proposed method is useful for reconstructing the signal of phased array structure health monitoring.
结构健康监测技术已广泛应用于板结构损伤的检测与识别。超声相控阵技术以其波束扫描灵活、聚焦性能强等优点,已成为结构健康监测的重要手段。但是会产生大量相控阵信号,给存储、传输和处理带来困难。因此,在信号稀疏的情况下,压缩感知理论能够以比传统奈奎斯特采样定理低得多的采样率进行信号采集。首先,利用稀疏正交变换进行稀疏表示。然后,利用测量矩阵进行投影观测。此外,重构算法用于稀疏重构。本文对防锈铝板材料进行了实验验证。实验表明,该方法可用于相控阵结构健康监测信号的重构。
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引用次数: 2
FollowMe: a mobile crowd sensing platform for spatial-temporal data sharing FollowMe:移动人群感知平台,实现时空数据共享
Pub Date : 2019-09-19 DOI: 10.1504/ijhpcn.2019.102347
Mingzhong Wang
Mobile crowd sensing becomes a promising solution for massive data collection with the public participation. Besides the challenges of user incentives, and diversified data sources and quality, the requirement of sharing spatial-temporal data drives the privacy concerns of contributors as one of the top priorities in the design and implementation of a sound crowdsourcing platform. In this paper, FollowMe is introduced as a use case of mobile crowd sensing platform to explain possible design guidelines and solutions to address these challenges. The incentive mechanisms are discussed according to both the quantity and quality of users' contributions. Then, a k-anonymity based solution is applied to protect contributors' privacy in both scenarios of trustworthy and untrustworthy crowdsourcers. Thereafter, a reputation-based filtering solution is proposed to detect fake or malicious reports, and finally a density-based clustering algorithm is introduced to find hotspots which can help the prediction of future events. Although FollowMe is designed for a virtual world of the popular mobile game Pokemon Go, the solutions and discussions are supposed to be applicable to more complex applications sharing spatial-temporal data about users.
在公众参与下,移动人群感知成为海量数据收集的一个很有前景的解决方案。除了用户激励、多样化的数据来源和质量的挑战之外,共享时空数据的要求推动了贡献者的隐私问题,这是设计和实施一个健全的众包平台的首要任务之一。本文介绍了FollowMe作为移动人群传感平台的一个用例,以解释可能的设计指南和解决这些挑战的解决方案。根据用户贡献的数量和质量,讨论了激励机制。然后,在可信众包和不可信众包两种情况下,应用基于k-匿名的解决方案来保护贡献者的隐私。然后,提出了一种基于声誉的过滤方案来检测虚假或恶意报告,最后引入了一种基于密度的聚类算法来发现热点,从而有助于预测未来事件。虽然FollowMe是为流行的手机游戏Pokemon Go的虚拟世界设计的,但解决方案和讨论应该适用于更复杂的应用程序,共享用户的时空数据。
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引用次数: 2
期刊
Int. J. High Perform. Comput. Netw.
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