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EPiK-a Workflow for Electron Tomography in Kepler

Procedia computer science 2014年 20卷 2295-2305页

作者： Ruijuan Chen Xiaohua Wan Ilkay Altintas Jianwu Wang Daniel Crawl Sébastien Phan Albert Lawrence Mark Ellisman National Center for Microscopy and Imaging Research University of California San Diego La Jolla CA USA. Key Lab of Intelligent Information Processing and Advanced Computing Research Lab Institute of Computing Technology Chinese Academy of Sciences Beijing China. San Diego Supercomputer Center University of California San Diego La Jolla CA USA.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility.

关键词： EPiK Electron Tomography Kepler Scientific workflows TxBR

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Fractal and complex network analyses of protein molecular dynamics

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Physica A: Statistical Mechanics and its Applications 2014年 416卷 21-32页

作者： Yuan-Wu Zhou Jin-Long Liu Zu-Guo Yu Zhi-Qin Zhao Vo Anh Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 China Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China Civil Construction Engineering Department Guangxi University of Science and Technology Liuzhou 545006 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia

Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuation analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h ( q ) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h ( 2 ) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H ≈ 0.5 indicating the absence of long-range correlation). The degree distributions of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h ( 2 ) of MF-DFA on the time series, exponent λ of the exponential degree distribution and fractal dimension d B of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between 〈 h ( 2 ) 〉 (from MF-DFA on time series) and 〈 d B 〉 of the converted HVGs for different energy, pressure and volume.

关键词： Protein molecular dynamics Multifractal detrended fluctuation analysis Horizontal visibility graph Fractal analysis Degree distribution

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Failure Handling of E-Business Services in an Extensible Constraint Service Model

Failure Handling of E-Business Services in an Extensible Con...

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2013 IEEE 4th International Conference on Software Engineering and Service Science

作者： Ruoyu Chen Lejian Liao Zhi Fang Beijing Engineering Research Centre of High Volume Language Information Processing & Cloud Computing Applications Beijing Key Laboratory of Intelligent Information TechnologySchool of Computer ScienceBeijing Institute of Technology

ISBN: (纸本)9781467349994

Failure handling of business transactions is essential in E-Business *** paper extends the service process specification proposed in a contract-centered constraint-based service modelling framework with failure handling *** failure in process model,generalized failure such as QoS violation can be modelled in *** semantics for failure handling in E-Business services as well as policies are discussed via a state transition system.A virtual machine is built for contracting and executing of services under this framework.

关键词： Services service Failure Handling of E-Business Services in an Extensible Constraint Service Model

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ProvenanceLens: Service provenance management in the cloud

ProvenanceLens: Service provenance management in the cloud

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International Conference on Collaborative computing: Networking, Applications and Worksharing (CollaborateCom)

作者： Tao Li Ling Liu Xiaolong Zhang Kai Xu Chao Yang Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System School of Computer Wuhan University of Science and Technology School of Computer Science. Georgia Institute of Technology Atlanta GA USA Computer Science and Information Engineering Hubei University Wuhan China

ISBN: (纸本)9781479953288

Service provenance can be defined as a profile of service execution history. Queries of service provenance data can answer questions such as when and by whom a server is invoked? which services operate on this data? What might be the root cause for the service failure? Most of the organizations today collect and manage their own service provenance in order to trace service execution failures, locate service bottlenecks, guide resource allocation, detect and prevent abnormal behaviors. As services become ubiquitous, there is an increasing demand for proving service provenance management as a service. This paper describes ProvenanceLens, a two-tier service provenance management framework. The top tier is the service provenance capturing and storage subsystem and the next tier provides analysis and inference capabilities of service provenance data, which are value-added functionality for service health diagnosis and remedy. Both tiers are built based on the service provenance data model, an essential and core component of ProvenanceLens, which categorizes all service provenance data into three broad categories: basic provenance, composite provenance and application provenance. In addition, ProvenanceLens provides a suite of basic provenance operations, such as select, trace, aggregate. The basic provenance data is collected through a light-weight service provenance capturing subsystem that monitors service execution workflows, collects service profiling data, encapsulates service invocation dependencies. The composite and application provenance data are aggregated through a selection of provenance operations. We demonstrate the effectiveness of ProvenanceLens using a real world educational service currently in operation for a dozen universities in China.

关键词： Silicon Analytical models Data models Computational modeling

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Attribute reduction based on approximation dependency degree

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Journal of Computers (Finland) 2013年第4期8卷 920-928页

作者： Li, Min Deng, ShaoBo Feng, Shengzhong Fan, Jianping NanChang Institute of Technology Nanchang Jiangxi 330099 China Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen Guangdong 518055 China Key laboratory of intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100080 China

Attribute reduction is one of the core research content of Rough sets theory. Many existing algorithms mainly are aimed at the reduction of consistency decision table, and very little work has been done for attribute reduction aimed at inconsistency decision table. In fact, the methods finding Pawlak reduction from consistent decision table are not suitable for inconsistency decision table. In this paper, we introduce the approximation dependency reduction modal and present the Quick Attribution Reduction based on Approximation Dependency Degree (Quick-ARADD), which can retain the original boundary region and the original positive region unchanged, and keep the approximation accuracy unchanged for all decision equivalence classes (the partition of universe on decision attributes) of a decision table. Theoretical analysis and experimental results show that the Quick-ARADD algorithm is effective and feasible. © 2013 ACADEMY PUBLISHER.

关键词： Decision tables

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Attribute granulation based on attribute discernibility and AP algorithm

Journal of Software

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Journal of Software 2013年第4期8卷 834-841页

作者： Zhu, Hong Ding, Shifei Zhao, Han Bao, Lina School of Computer Science and Technology China University of Mining and Technology Xuzhou 221116 China School of Medical Information Xuzhou Medical College Xuzhou 221000 China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China

For high dimensional data, the redundant attributes of samplers will not only increase the complexity of the calculation, but also affect the accuracy of final result. The existing attribute reduction methods are encountering bottleneck problem of timeliness and spatiality. In order to looking for a relatively coarse attributes granularity of problem solving, this paper proposes an efficient attribute granulation method to remove redundancy attribute. The method calculates the similarity of attributes according attribute discernibility first, and then clusters attributes into several group through affinity propagation clustering algorithm. At last, representative attributes are produced through some algorithms to form a coarser attribute granularity. Experimental results show that the attribute granulation method based on affinity propagation clustering algorithm(AGAP) method is a more efficient algorithm than traditional attribute reduction algorithm(AR). © 2013 ACADEMY PUBLISHER.

关键词： Granulation

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Fractal and multifractal properties of a family of fractal networks

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Journal of Statistical Mechanics: Theory and Experiment 2014年第2期2014卷

作者： Li, Bao-Gen Yu, Zu-Guo Zhou, Yu Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan HUNAN 411105 China School of Mathematical Sciences Queensland University of Technology Brisbane GPO Box 2434 Q4001 Australia

In this work, we study the fractal and multifractal properties of a family of fractal networks introduced by Gallos et al (2007 Proc. Nat. Acad. Sci. USA 104 7746). In this fractal network model, there is a parameter e which is between 0 and 1, and allows for tuning the level of fractality in the network. Here we examine the multifractal behavior of these networks, the dependence relationship of the fractal dimension and the multifractal parameters on parameter e. First, we find that the empirical fractal dimensions of these networks obtained by our program coincide with the theoretical formula given by Song et al (2006 Nature Phys. 2 275). Then from the shape of the τ(q) and D(q) curves, we find the existence of multifractality in these networks. Last, we find that there exists a linear relationship between the average information dimension D(1) and the parameter e. © 2014 IOP Publishing Ltd and SISSA Medialab srl.

关键词： network dynamics networks random graphs

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Time evolving graphical password for securing mobile devices 13

Time evolving graphical password for securing mobile devices

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8th ACM SIGSAC Symposium on information, Computer and Communications Security, ASIA CCS 2013

作者： Wang, Zhan Jing, Jiwu Li, Liang State Key Laboratory of Information Security Institute of Information Engineering Chinese Academy of Sciences Beijing 100093 China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China

ISBN: (纸本)9781450317672

Increasingly widespread use of mobile devices for processing monetary transactions and accessing business secrets has created a great demand on securing mobile devices. Poorly designed authentication mechanisms (e.g., screen lock and SIM card lock) on mobile devices either make users feel a hassle to lock the devices, or are vulnerable to attacks, such as shoulder surfing and smudge attack. In this paper, we propose a new login option for unlocking mobile devices called Time-Evolving Graphical Password (TEGP), which improves the strength of the password gradually over time by evolving the distortion degree of the images in the challenge portfolio without changing the pass images. By taking advantage of the extraordinary human ability to recall images, TEGP authenticates users by asking them to recognize the pass images which are transformed from the images uploaded by the user at registration. To achieve desired security and remain the usability, we present two metrics, information Retention Rate (IRR) and Password Diversity Score (PDS), to advise the selection and distortion of the pass images and decoy images. Our experimental results show the memorability from the perspective of users, and the ability of TEGP to defend against various attacks. © 2013 ACM.

关键词： Edge detection

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Dynamic description logic based semantics web service composition

Dynamic description logic based semantics web service compos...

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9th International Conference on Semantics, Knowledge and Grids, SKG 2013

作者： Zhang, Jianhua Wang, Wenjie Shi, Zhongzhi Tian, Dongping Yue, Jinpeng Zhang, Bo Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China

ISBN: (纸本)9781479930128

Web service composition is one of the fundamental technologies in implementing Service Oriented Architecture (SOA) based applications. Description Logic based Web service composition can easily express the static knowledge, however it is lack the dynamic knowledge support. Dynamic Description Logic extends from Description Logic and it can represent both static and dynamic knowledge. In this paper, we propose a Web service composition method base on AI planning which introduce the action dimension to the Web service composition. Finally, we give a simple example to show the algorithm's validity. © 2013 IEEE.

关键词： Computer circuits

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Semantic separator learning and its applications in unsupervised Chinese text parsing

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Frontiers of Computer Science 2013年第1期7卷 55-68页

作者： Yuming WU Xiaodong LUO Zhen YANG Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China Graduate University of the Chinese Academy of Sciences Beijing 100049 China China Telecom Corporation Limited Shanghai Branch Shanghai 200120 China Shanghai Research Institute of China Telecom Corporation Limited Shanghai 200120 China

Grammar learning has been a bottleneck problem for a long time. In this paper, we propose a method of seman- tic separator learning, a special case of grammar learning. The method is based on the hypothesis that some classes of words, called semantic separators, split a sentence into sev- eral constituents. The semantic separators are represented by words together with their part-of-speech tags and other infor- mation so that rich semantic information can be involved. In the method, we first identify the semantic separators with the help of noun phrase boundaries, called subseparators. Next, the argument classes of the separators are learned from cor- pus by generalizing argument instances in a hypernym space. Finally, in order to evaluate the learned semantic separators, we use them in unsupervised Chinese text parsing. The exper- iments on a manually labeled test set show that the proposed method outperforms previous methods of unsupervised text parsing.

关键词： semantic separator separator learning unsuper vised text parsing

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