ppxscal/embedding_network huggingface dataset:
Classification of 3d Protein based on Structure Information Feature
Authors: Chenyang Cui, Zhen Liu
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

In molecular biology, classification of 3D protein structures is a very important topic. In this paper, from the view of geometry, we propose one kind of feature called SID ( I D , Structure Information Dimension) for describing 3D protein structures in order to perform similarity search and classification. The goal of the approach is to reduce the 3D protein structures matching problem to the comparison of the probability distribution. Experimental results show the proposed approach is effective to pre-classification of 3d proteins, and needs less computation and storage cost comparing to the existing methods, the proposed feature of 3d protein is invariant to the translation, rotation and scale of 3d protein structures.
A dynamic object manipulation approach to dynamic biped locomotion
Authors: Borhan Beigzadeh, Majid Nili Ahmadabadi, Ali Meghdari, Adel Akbarimajd
Venue: Robotics and Autonomous Systems (2008)

In this paper, we aim at an integrated approach to Dynamic Biped Walking (DBW) and Dynamic Object Manipulation (DOM) at an abstract level. To this end, we offer a unified and abstract concept with a dual interpretation as a DOM and as a DBW system. We validate the proposed approach by using a set of simulations on an illustrative case study and show how it can be used in modeling as well as design of planning and control algorithms for DOM and DBW systems. In the case study, we describe the proposed approach and show its dual interpretation by identifying the relations between 2D dynamic object manipulation of a disc using two planar manipulators and 2D dynamic object locomotion of lower part of a biped robot. More specifically, having obtained the equations of DOM, we change the boundary conditions of the problem in such a way that both radius and mass of the disc tend to infinity. Simultaneously, both size and mass of the manipulators' base, i.e. the planet earth, tend to some values in the order of human body mass and dimension. Regarding these changes, we can transform DOM into DBW and vice versa. To test the proposed approach, a simple control strategy is introduced to handle impact between the manipulators (legs) and the object (the earth). In addition, a motion planning system is designed in such a way that the manipulators (legs) catch and throw the manipulated object (the earth) in appropriate configurations.
Faster algorithms for construction of recovery trees enhancing QoP and QoS
Authors: Weiyi Zhang, Guoliang Xue, Jian Tang, Krishnaiyan Thulasiraman
Venue: IEEE/ACM Transactions on Networking (TON) (2008)

Médard et al. proposed an elegant recovery scheme (known as the MFBG scheme) using red/blue recovery trees for multicast path protection against single link or node failures. Xue et al. extended the MFBG scheme and introduced the concept of quality of protection (QoP) as a metric for multifailure recovery capabilities of single failure recovery schemes. They also presented polynomial time algorithms to construct recovery trees with good QoP and quality of service (QoS). In this paper, we present faster algorithms for constructing recovery trees with good QoP and QoS performance. For QoP enhancement, our O(n + m) time algorithm has comparable performance with the previously best O(n2(n + m)) time algorithm, where and denote the number of nodes and the number of links in the network, respectively. For cost reduction, our O(n + m) time algorithms have comparable performance with the previously best O(n2(n + m)) time algorithms. For bottleneck bandwidth maximization, our O(mlog n) time algorithms improve the previously best O(nm) time algorithms. Simulation results show that our algorithms significantly outperform previously known algorithms in terms of running time, with comparable QoP or QoS performance.
Blood Hemolysis of Implantable Artificial Lung
Authors: Gi-Beum Kim, Mun-Yong Lee, Seol-Hee Jeon, Md. Mizanur Rahman, Min-Ho Kim, Seong-Jong Kim, In-Shick Kim, Jin-Shang Kim, Hyung-Sub Kang, Chul-Un Hong
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

The purpose of this study was to investigate the effect of multiple mechanical forces in hemolysis for usage as intravascular lung assist device. Specific attention was focused on the effect of membrane vibration. The results of experimental, PZT materials were used as an exciting system to improve efficiency of blood suitability of hollow fiber membrane for development of new intravascular lung assist device.
Sites of flux: imagining space in the dance-architectures of The Changing Room and Sea Unsea
Authors: Mette Ramsgard Thomsen
Venue: Personal and Ubiquitous Computing (2008)

This paper presents the conceptualization of an event space of interaction. Referring to enchantment as a means of describing an indeterminate and evolving state of interaction, where the meaning of the interactive object or environment remains open ended and exploratory, this paper explores how contemporary architectural concepts of space and inhabitation can allow for a new framing of interactive experiences. Presenting the two dance-architectures The Changing Room and Sea Unsea as case studies, the paper seeks to demonstrate challenges to the way space and place are understood in Human---Computer Interaction.
Sheaf tools for encryption
Authors: Elena Sendroiu
Venue: Proceedings of the 9th WSEAS International Conference on Systems (2005)

This paper proposes the use of sheaf theory in security encryption in parallel and distributed computing systems. So, we exploit the architecture of distributed computing systems. In particular, we are using a general notion of sheaf as a functor on a category with a Grothendieck topology, i.e. a site. Sheaf properties give data reconstitution. This can be used in distributed encryption and authentication. In particular, our sheaf definitions provide computation tools to accomplish these goals, hence we have made optimal procedures for construction and validation of sheaves. Thereafter, we describe an encryption algorithm and an authentication method by sheaves. Moreover, we have introduced a new notion in sheaf theory on a site, family for matching, in order to simplify the sheaf definition more. This has given us the possibility to construct an optimal encryption algorithm by sheaves. In addition, the generated matching family, from a family for matching, is used to verify data integrity.
Transient flow around an impulsively started cylinder using a dynamic mesh method
Authors: L. Q. Wang, Z. F. Li, D. Z. Wu, Z. R. Hao
Venue: International Journal of Computational Fluid Dynamics (2007)

The finite volume method (FVM) with a dynamic mesh method (DMM) to deal with the moving boundary was applied to the simulation of two-dimensional incompressible viscous flow past a circular cylinder that is impulsively started into rotation and translation. The non-dimensional rotating to translating speed ratio α is varied from 0.28 to 2.07, with the Reynolds number being 200 for the range of α. The computation covers a period, during which the cylinder translates seven times its diameter. The current scheme handles the impulsively moving boundary directly by DMM, which is implemented using both mesh deforming and local remeshing. The instantaneous asymmetrical flow configurations for various α are presented and compared with the experimental visualizations. Quantitatively, the velocity distributions with drag and lift coefficients are also compared with the experimental and numerical results. Results show that the flow is strongly influenced by the rotation. Comparisons are found to be satisfactory.
Delay-dependent fault detection and diagnosis using B-spline neural networks and nonlinear filters for time-delay stochastic systems
Authors: Tao Li, Yang Yi, Lei Guo, Hong Wang
Venue: Neural Computing and Applications (2008)

A new fault detection and diagnosis (FDD) scheme is studied in this paper for the continuous-time stochastic dynamic systems with time delays, where the available information for the FDD is the input and the measured output probability density functions (PDFs) of the system. The square-root B-spline neural networks is used to formulate the output PDFs with the dynamic weightings. As a result, the concerned FDD problem can be transformed into a robust FDD problem subjected to a continuous time uncertain nonlinear system with time delays. Delay-dependent criteria to detect and diagnose the system fault are provided by using linear matrix inequality (LMI) techniques. It is shown that this new criterion can provide higher sensitivity performance than the existing result. Simulations are given to demonstrate the efficiency of the proposed approach.
An adaptive ghost fluid finite volume method for compressible gas-water simulations
Authors: Chunwu Wang, Huazhong Tang, Tiegang Liu
Venue: Journal of Computational Physics (2008)

An adaptive ghost fluid finite volume method is developed for one- and two-dimensional compressible multi-medium flows in this work. It couples the real ghost fluid method (GFM) [C.W. Wang, T.G. Liu, B.C. Khoo, A real-ghost fluid method for the simulation of multi-medium compressible flow, SIAM J. Sci. Comput. 28 (2006) 278-302] and the adaptive moving mesh method [H.Z. Tang, T. Tang. Moving mesh methods for one- and two-dimensional hyperbolic conservation laws, SIAM J. Numer. Anal. 41 (2003) 487-515; H.Z. Tang, T. Tang, P.W. Zhang, An adaptive mesh redistribution method for non-linear Hamilton-Jacobi equations in two- and three-dimensions, J. Comput. Phys. 188 (2003) 543-572], and thus combines their advantages. This work shows that the local mesh clustering in the vicinity of the material interface can effectively reduce both numerical and conservative errors caused by the GFM around the material interface and other discontinuities. Besides the improvement of flow field resolution, the adaptive GFM also largely increases the computational efficiency. Several numerical experiments are conducted to demonstrate robustness and efficiency of the current method. They include several 1D and 2D gas-water flow problems, involving a large density gradient at the material interface and strong shock-interface interactions. The results show that our algorithm can capture the shock waves and the material interface accurately, and is stable and robust even for solutions with large density and pressure gradients.
An extended Crank-Nicholson method and its applications in the solution of partial differential equations: 1-D and 3-D conduction equations
Authors: Nikos E. Mastorakis
Venue: Proceedings of the 10th WSEAS International Conference on APPLIED MATHEMATICS (2006)

In this paper, an extention of the Crank-Nicholson method for solving parabolic equations is launched. The method uses finite differences. For the derivative of the variable of time, we use central difference at 4 points (instead of 2 points of the classical Crank-Nicholson method), while for the second-order derivatives of the other spatial variables we use lagrangian interpolation at 4 points of the central differences at 5 points (instead of lagrangian interpolation at 2 points of the central differences at 3 points of the classical Crank-Nicholson method). The method is illustrated below.
Algorithms for Storytelling
Authors: Deept Kumar, Naren Ramakrishnan, Richard F. Helm, Malcolm Potts
Venue: IEEE Transactions on Knowledge and Data Engineering (2008)

We formulate a new data mining problem called storytelling as a generalization of redescription mining. In traditional redescription mining, we are given a set of objects and a collection of subsets defined over these objects. The goal is to view the set system as a vocabulary and identify two expressions in this vocabulary that induce the same set of objects. Storytelling, on the other hand, aims to explicitly relate object sets that are disjoint (and hence, maximally dissimilar) by finding a chain of (approximate) redescriptions between the sets. This problem finds applications in bioinformatics, for instance, where the biologist is trying to relate a set of genes expressed in one experiment to another set, implicated in a different pathway. We outline an efficient storytelling implementation that embeds the CARTwheels redescription mining algorithm in an A* search procedure, using the former to supply next move operators on search branches to the latter. This approach is practical and effective for mining large datasets and, at the same time, exploits the structure of partitions imposed by the given vocabulary. Three application case studies are presented: a study of word overlaps in large English dictionaries, exploring connections between genesets in a bioinformatics dataset, and relating publications in the PubMed index of abstracts.
Context-aware role-based access control in pervasive computing systems
Authors: Devdatta Kulkarni, Anand Tripathi
Venue: Proceedings of the 13th ACM symposium on Access control models and technologies (2008)

In this paper we present a context-aware RBAC (CARBAC) model for pervasive computing applications. The design of this model has been guided by the context-based access control requirements of such applications. These requirements are related to users' memberships in roles, permission executions by role members, and context-based dynamic integration of services in the environment with an application. Context information is used in role admission policies, in policies related to permission executions by role members, and in policies related to accessing of dynamically interfaced services by role members. The dynamic nature of context information requires model-level support for revocations of role memberships and permission activations when certain context conditions fail to hold. Based on this model we present a programming framework for building context-aware applications, providing mechanisms for specifying and enforcing context-based access control requirements.
Analysis of MR Images Deformed by Magnetic Implants
Authors: K. Bartusek, Z. Smekal, E. Gescheidtova
Venue: Proceedings of the Third International Conference on Systems (2008)

Electrically and magnetically conducting materials found in the human body cause major deformations in images obtained by magnetic resonance imaging (MRI). To study the deformations and to develop new MR methods with these deformations suppressed, a method for measuring magnetic susceptibility has been designed for samples that do not produce MR signals. In the paper, a method is described for processing the phase image being measured, in order to greatly eliminate systematic errors in the MR measurement of magnetic susceptibility and to calculate it.
Fast distributed scheduling via primal-dual
Authors: Alessandro Panconesi, Mauro Sozio
Venue: Proceedings of the twentieth annual symposium on Parallelism in algorithms and architectures (2008)

In this paper we give an efficient distributed algorithm computing approximate solutions to a very general, and classical, scheduling problem. The approximation guarantee is within a constant factor of the optimum. By "efficient", we mean that the number of communication rounds is poly-logarithmic in the size of the input. In the problem, we have a bipartite graph with computing agents on one side and resources on the other. Agents that share a resource can communicate in one time step. Each agent has a list of jobs, each with its own length and profit, to be executed on a neighbouring resource within a given time-window. Resources can execute non preemptively only one job at a time. The goal is to maximize the profit of the jobs that are scheduled. It is well known that this problem is NP-hard. A very interesting feature of our algorithm is that it is derived in a systematic manner from a primal-dual algorithm.
Generating fuzzy rules from training instances for fuzzy classification systems
Authors: Shyi-Ming Chen, Fu-Ming Tsai
Venue: Expert Systems with Applications: An International Journal (2008)

In recent years, many methods have been proposed to generate fuzzy rules from training instances for handling the Iris data classification problem. In this paper, we present a new method to generate fuzzy rules from training instances for dealing with the Iris data classification problem based on the attribute threshold value @a, the classification threshold value @b and the level threshold value @c, where @a@?[0,1], @b@?[0,1] and @c@?[0,1]. The proposed method gets a higher average classification accuracy rate than the existing methods.
WEIRD testbeds with fixed and mobile WiMAX technology for user applications, telemedicine and monitoring of impervious areas
Authors: Silvano Mignanti, Mario Castellano, Mariarita Spada, Paulo Simoes, Gabriele Tamea, Antonio Cimmino, Pedro Miguel Neves, Ilaria Marchetti, Fausto Andreotti, Giada Landi, Kostas Pentikousis
Venue: Proceedings of the 4th International Conference on Testbeds and research infrastructures for the development of networks & communities (2008)

Wireless Metropolitan Area Networks based on IEEE 802.16d/e standards are soon to be deployed in several countries. However, there is lack of published literature with results from actual testbeds. This paper introduces the work done in the EU Sixth Framework Programme Project WEIRD to design and set up WiMAX testbeds in four EU countries. We describe the methodlogy followed, detail our implementation and present results from the testbeds, as deployed in the first phase of WEIRD. The testbeds are used to demonstrate how WiMAX technology can be used to extend the connectivity of the pan-European data communications network (GEANT2) to isolated and impervious areas and, furthermore, to assure end-to-end quality of service to novel applications.
Chinese Human Genetic Resources Sharing Service Infrastructure
Authors: Ma Liguang, Cao Yanrong, He Jianbang
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

This paper described the architecture construction of National Infrastructure Program for Chinese Human Genetic Resources Sharing System (NIPCGR). In particular, the framework of system and critical technology was introduced. Some issues about the resources sharing service environment were also discussed. According to the data description criteria, the data and information of Chinese human genetic resources was collected, standardized and integrated with the sharing platform. The sharing mechanism and data security technology were implemented with software and hardware medium. At last, the web-based resource sharing service was provided to the people with mutual-mode for international, national, regional, organizations or individuals who are interested in.
Quantum-mechanical effects in nanometer scale MuGFETs
Authors: Se Re Na Yun, Chong Gun Yu, Jong Tae Park, Jean Pierre Colinge
Venue: Microelectronic Engineering (2008)

Solving the Poisson and Schrodinger equations self-consistently in two dimensions reveals quantum-mechanical effects that influence the electron concentration, the threshold voltage and the subthreshold slope of MuGFETs. The average electron concentration needed to reach the threshold voltage depends on the gate configuration and on the device geometry. The dependence of the energy of the subbands on the different gate configurations is studied, and the relation between threshold voltage and the lowest subband energy is investigated. Due to a dynamic threshold voltage effect, the drain current is lower in the quantum-based drain current model than in classical simulations. This dynamic increase of threshold voltage is due to an increase of the subband energy with the electron concentration. This effect degrades the subthreshold slope. It is observed in non-symmetrical devices (FinFET, tri-gate), but not in symmetrical structures (GAA). This gives symmetrical devices like GAA nanowires an intrinsic advantage compared to the other types of devices.
SIGWEB annual report
Authors: Ethan V. Munson
Venue: ACM SIGWEB Newsletter (2008)

I want to take a few moments to bring you up-to-date on the state of SIGWEB. I'll be making a formal report to the membership at our annual meeting on June 19 in Pittsburgh, USA, which will be during the Hypertext 2008 conference, and also right at the end of the JCDL 2008 conference.
Real-time motion planning for robot manipulators in unknown environments using infrared sensors
Authors: Shuguo Wang, Jin Bao, Yili Fu
Venue: Robotica (2007)

This paper deals with sensor-based motion planning method for a robot arm manipulator operating among unknown obstacles of arbitrary shape. It can be applied to online collision avoidance with no prior knowledge of the obstacles. Infrared sensors are used to build a description of the robot's surroundings. This approach is based on the configuration space but the construction of the C-obstacle surface is avoided. The point automation is confined on some planes with square grids in the C-space. A path-searching algorithm based on square grids is used to guide the automation maneuvering around the C-obstacles on the selected planes. To avoid the construction of the C-obstacle surface, the robot geometry model is expanded, and the static collision detection method is used. Hence, the computation time is reduced and the algorithm can work in real time. The effectiveness of the proposed method is verified by a series of experiments.
PSTN migration using IMS
Authors: Susan A. White, Mark M. Clougherty
Venue: Bell Labs Technical Journal (2008)

The IP Multimedia System (IMS) is being adopted globally as the standard architecture for next-generation voice and multimedia services. As a result, many operators plan to use IMS and its inherent benefits for public switched telephone network (PSTN) migration, with a goal of eventual elimination of the traditional PSTN. Initial IMS deployments utilize a Telecommunication and Internet converged Services and Protocols for Advanced Networking (TISPAN) IMS-based PSTN emulation subsystem (PES) architecture in which H.248 is used as the control protocol in the access node and is converted to Session Initiation Protocol (SIP) in the IMS core. However, as the adoption of IMS increases and standards become more mature, many operators plan to eliminate H.248 interim architectures and evolve to a more efficient and scaleable SIP-based end-to-end solution. There are several architectural choices the operator has to make in planning the migration to IMS. First, a customer premises equipment (CPE)-based, network-based, or mixed approach can be adopted for PSTN migration. Second, for network-based PSTN migration, the PSTN line termination can be standalone in a line access gateway (LAG) or integrated into a next-generation multi-service access node (MSAN). In addition, there are implementation choices related to the type of SIP endpoint and services supported. This paper will address these architectural and implementation options and describe associated service examples. &copy; 2008 Alcatel-Lucent.