ppxscal/embedding_network huggingface dataset:
PairProSVM: Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM
Authors: Man-Wai Mak, Jian Guo, Sun-Yuan Kung
Venue: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (2008)

The subcellular locations of proteins are important functional annotations. An effective and reliable subcellular localization method is necessary for proteomics research. This paper introduces a new method---PairProSVM---to automatically predict the subcellular locations of proteins. The profiles of all protein sequences in the training set are constructed by PSI-BLAST and the pairwise profile-alignment scores are used to form feature vectors for training a support vector machine (SVM) classifier. It was found that PairProSVM outperforms the methods that are based on sequence alignment and amino-acid compositions even if most of the homologous sequences have been removed. This paper also demonstrates that the performance of PairProSVM is sensitive (and somewhat proportional) to the degree of its kernel matrix meeting the Mercer's condition. PairProSVM was evaluated on Reinhardt and Hubbard's, Huang and Li's, and Gardy et al.'s protein datasets. The overall accuracies on these three datasets reach 99.3\\%, 76.5\\%, and 91.9\\%, respectively, which are higher than or comparable to those obtained by sequence alignment and by the methods compared in this paper.
Implementing an e-Government Observatory for Rural SMEs
Authors: Nikos Manouselis, Kostas Kastrantas, Argiris Tzikopoulos, Constantina Costopoulou, Alexander Sideridis
Venue: Proceedings of the 1st world summit on The Knowledge Society: Emerging Technologies and Information Systems for the Knowledge Society (2008)

ICT training activities for rural areas can be complemented by online points of reference that SMEs can access to find relevant information and educational resources. To this direction, we present the design and implementation of the Rural-eGov Observatory, which aims to serve as an online reference point for SMEs in five European regions. The Observatory collects, describes and categorizes training resources and e-government services that may prove useful to rural SMEs.
Teaching of English to Hearing Impaired Individuals Whose Mother Language Is the Sign Language
Authors: Athanasios Drigas, Dimitris Kouremenos, John Vrettaros
Venue: Proceedings of the 1st world summit on The Knowledge Society: Emerging Technologies and Information Systems for the Knowledge Society (2008)

The teaching of the English language as a second language to deaf and hearing impaired individuals, whose mother language is the sign language, through the prism of the project `Dedalos', is the main topic of this article. More particularly, a special e-learning platform was developed, which incorporated special pedagogic methods of distant linguistic training as well as innovative and high-quality educational e-content, suitably adapted to the needs of hearing impaired people through the use of contemporary animation and digital video technologies. In addition, audits and evaluation tests were incorporated within the platform, in order to assess and evaluate the linguistic skills of the hearing impaired students and the educational e-content was divided into various levels according to the educational level of each e-student. Both the evaluation process and the setting of the e-content to the appropriate level are achieved through the use of an intelligent taxonomy system.
Cognitive and Semantic Perspectives of Token Representation in Diagrams
Authors: Rossano Barone, Peter C. Cheng
Venue: Proceedings of the 5th international conference on Diagrammatic Representation and Inference (2008)

The article considers a perspective on token representation in diagrams and its relation to other properties typical of diagrammatic external representations (ERs). We distinguish between direct and indirect cognitive modes of token reference based on whether a referential attribute of ER tokens, represented by a cognitive system, is used as a surrogate for represented tokens. We then consider how this characterization sheds light on particular cognitive properties of representing objects and relations in diagrams and diagrammatic kinds of engagement with sentential classes of ER.
A Spatial Equational Logic for the Applied Π-Calculus
Authors: Étienne Lozes, Jules Villard
Venue: Proceedings of the 19th international conference on Concurrency Theory (2008)

Spatial logics have been proposed to reason locally and modularly on algebraic models of distributed systems. In this paper we define the spatial equational logic A&Pi; L whose models are processes of the applied &Pi; -calculus. This extension of the &Pi; -calculus allows term manipulation and records communications as active substitutions in a frame, thus augmenting the underlying predefined equational theory. Our logic allows one to reason locally either on frames or on processes, thanks to static and dynamic spatial operators. We study the logical equivalences induced by various relevant fragments of A&Pi; L, and show in particular that the whole logic induces a coarser equivalence than structural congruence. We give characteristic formulae for some of these equivalences and for static equivalence. Going further into the exploration of A&Pi; L's expressivity, we also show that it can eliminate standard term quantification.
New Critical Analysis on Global Convergence of Recurrent Neural Networks with Projection Mappings
Authors: Chen Qiao, Zong-Ben Xu
Venue: Proceedings of the 4th international symposium on Neural Networks: Advances in Neural Networks, Part III (2007)

In this paper, we present the general analysis of global convergence for the recurrent neural networks (RNNs) with projection mappings in the critical case that M(L,Γ), a matrix related with the weight matrix W and the activation mapping of the networks, is nonnegative for a positive diagonal matrix Γ. In contrast to the existing conclusion such as in [1], the present critical stability results do not require the condition that ΓW must be symmetric and can be applied to the general projection mappings other than nearest point projection mappings. An example has also been shown that the theoretical results obtained in the present paper have explicitly practical application.
Adoption of High Impact Governmental eServices: Seduce or Enforce?
Authors: Rex Arendsen, Tom M. Engers, Wim Schurink
Venue: Proceedings of the 7th international conference on Electronic Government (2008)

The adoption of high impact governmental e-services is not obvious. Especially small and medium sized companies hesitate to invest and adopt. Non-adoption endangers the realization of the 25% reduction objective within the EU's Lisbon Agenda of the administrative burden of businesses by 2012. On the other hand governmental organisations gain from the use of these e-services. In several cases this is the underlying argument behind the legal enforcement of the use of governmental e-services. In the study reported in this paper we answer the question which factors influence the adoption of these high impact governmental e-services. The designed research model has been tested in an empirical business-to-government context. In contrast to several business-to-business studies we found that especially organisational readiness is a hampering factor for the adoption of these governmental high impact e-services. These findings question the effectiveness of governmental enforcement strategies.
Supporting Effective Monitoring and Knowledge Building in Online Collaborative Learning Systems
Authors: Santi Caballé, Angel A. Juan, Fatos Xhafa
Venue: Proceedings of the 1st world summit on The Knowledge Society: Emerging Technologies and Information Systems for the Knowledge Society (2008)

This paper aims to report on an experience of using an innovative groupware tool to support real, collaborative learning. We base the success of on-line collaborative learning on extracting relevant knowledge from interaction data analysis in order to provide learners and instructors with efficient awareness, feedback, and monitoring as regards individual and group performance and collaboration. Monitoring is especially important for online instructors since they can use this valuable provision of information as a meta cognitive tool for regulating the collaborative learning process more conveniently and provide adequate support when needed. In addition, learning and knowledge building may be greatly enhanced by presenting selected knowledge to learners as for their particular skills exhibited during interaction, such as the impact and effectiveness of their contributions. Indeed, by letting learners be aware of both their own and others' progress in the process of knowledge building may promote learners' participation and boost group performance. The ultimate goal of this paper is to provide a model to achieve a more effective support and assessment of the collaborative process while enhancing and improving the learning experience. To validate this study, a real online learning environment is employed to support asynchronous collaborative activities.
Defunctionalized interpreters for programming languages
Authors: Olivier Danvy
Venue: Proceeding of the 13th ACM SIGPLAN international conference on Functional programming (2008)

This document illustrates how functional implementations of formal semantics (structural operational semantics, reduction semantics, small-step and big-step abstract machines, natural semantics, and denotational semantics) can be transformed into each other. These transformations were foreshadowed by Reynolds in "Definitional Interpreters for Higher-Order Programming Languages" for functional implementations of denotational semantics, natural semantics, and big-step abstract machines using closure conversion, CPS transformation, and defunctionalization. Over the last few years, the author and his students have further observed that functional implementations of small-step and of big-step abstract machines are related using fusion by fixed-point promotion and that functional implementations of reduction semantics and of small-step abstract machines are related using refocusing and transition compression. It furthermore appears that functional implementations of structural operational semantics and of reduction semantics are related as well, also using CPS transformation and defunctionalization. This further relation provides an element of answer to Felleisen's conjecture that any structural operational semantics can be expressed as a reduction semantics: for deterministic languages, a reduction semantics is a structural operational semantics in continuation style, where the reduction context is a defunctionalized continuation. As the defunctionalized counterpart of the continuation of a one-step reduction function, a reduction context represents the rest of the reduction, just as an evaluation context represents the rest of the evaluation since it is the defunctionalized counterpart of the continuation of an evaluation function.
2D Articulated Body Tracking with Self-occultations Handling
Authors: Eric Para, Olivier Bernier, Catherine Achard
Venue: Proceedings of the 5th international conference on Articulated Motion and Deformable Objects (2008)

Recently many methods for human articulated body tracking were proposed in the literature. These techniques are often computationally intensive and cannot be used for Human-Computer Interface. We propose in this article a real-time algorithm for upper body tracking with occultation handling. The tracking is based on an articulated body model, also used to automatically initialize the target. After an independent search of the most likely positions of each limb, a dynamic programming algorithm is used to find the best configuration according to the links between limbs. The self-occultations between the limbs are directly taken into account by the tracking algorithm and results show the interest of the proposed approach.
Uncertainty quantification and grid-based geometrical computations for turbulent fluid mixing
Authors: Jean Nicolas Pestieau
Venue:  (2007)

There are two major parts to this thesis, both involving averaged quantities in turbulent fluid mixing. In the first part we consider the chaotic flow of a Richtmyer-Meshkov instability resulting from a shock passing through a density discontinuity. From a Bayesan uncertainty quantification framework, we use high-resolution simulations to propose convergence rates for the numerical solution and the solution error of this chaotic flow in a perturbed circular (2D) geometry. After suitable averaging procedures we obtain stable statistics in homogeneous regions for several flow quantities, including the single-phase densities and wave positions. In the second part we turn our attention to the problem of validating a general closure by Glimm et al. for compressible multi-species, multi-phase flow models. More specifically, we discuss a grid-based algorithm we have implemented in the hydrodynamics front-tracking code FronTier that collects simulation data more accurately. This tool was devised to improve the data analysis of averaged quantities in 3D planar Rayleigh-Taylor simulations, a crucial component to the validation of the nonlinear interfacial terms that define the closures. Our method is conservative in nature as it uses the exact (up to modeling assumptions) volume fractions of irregular cells cut by the interface. We discuss at length the geometrical formulas used in our algorithm. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Automating Experiments Using Semantic Data on a Bioinformatics Grid
Authors: Chris Wroe, Carole Goble, Mark Greenwood, Phillip Lord, Simon Miles, Juri Papay, Terry Payne, Luc Moreau
Venue: IEEE Intelligent Systems (2004)

myGrid assists bioinformaticians in designing and executing in silico experiments using the Grid's resources. In myGrid, much of this experimental design has been encoded as workflows. Workflows must be represented at tiered levels of detail to ensure that they can respond to changes in service availability, be customized to services in different locations, and be shared with others to varying degrees. The authors have developed workflow templates in which classes of services are composed, and a resolution mechanism by which these classes are instantiated. The specification of service classes and their resolution depends on seven kinds of service metadata. Functionally equivalent services vary widely in implementation. The authors describe workflow harmonization in which the workflow is modified to accommodate variations between substituted services. Finally, they examine the role of scientist and automated process in resolution and harmonization and discuss scope for further automation.
A Novel CDS-Based Reputation Monitoring System for Wireless Sensor Networks
Authors: Avinash Srinivasan, Feng Li, Jie Wu
Venue: Proceedings of the 2008 The 28th International Conference on Distributed Computing Systems Workshops (2008)

Reputation and Trust-based Monitoring Systems (RTMSs) have provided a ubiquitous framework for secure Wireless Sensor Network (WSN) computing. Employing sensors for neighborhood monitoring, which is secondary to their intended duties, depletes valuable and scarce resources which is counter-productive in WSNs. In this paper, we propose a novel, Connected Dominating Set (CDS)-based reputation monitoring system. Our model is the first attempt to employ a CDS-based monitoring backbone to securely aggregate the reputation of sensors without subjecting them to energy depletion or reputation pollution attacks encountered in existing reputation monitoring systems. Secure and certificateless node mobility and robustness to node replication and ID spoofing attacks are two vital by-products of our model. We confirm the performance of our model via simulation studies.
Evaluation of 3D Breast Surface Reconstruction Accuracy Using Non-contact Scanner Images: A Phantom Study
Authors: Cuiping Zhang, Predrag R. Bakic, Shugao Xia, Fengshan Liu, Andrew D. Maidment
Venue: Proceedings of the 9th international workshop on Digital Mammography (2008)

Analysis of the breast surface deformation during mammographic compression will provide insight into breast tissue elastic properties. Our long term goal is to accurately estimate physical properties of breast tissue for the purpose of realistic deformation simulation. As a first step, we analyzed the acquisition accuracy of the reconstructed breast phantom surface using a non-contact laser scanner. The effect of the acquisition angle and the presence of the transparent compression plate covering the phantom were considered. Comparing 48 phantom surfaces, each reconstructed from 4 scanner images acquired at different positions, we observed an average acquisition error of 1.94 mm for images without the compression plate; the average acquisition error for images with the compression plate was 3.26 mm. Performance of two observers showed little variation.
Algorithms for data placement, reconfiguration and monitoring in storage networks
Authors: Samir Khuller
Venue:  (2007)

In this thesis we address three problems related to self-management of storage networks - data placement, data reconfiguration and data monitoring. Examples of such storage networks include centrally managed systems like Storage Area Networks and Network Attached Storage devices, or even highly distributed systems like a P2P network or a Sensor Network. One of the crucial functions of a storage system is that of deciding the placement of data within the system. This data placement is dependent on the demand pattern for the data and subject to constraints of the storage system. For instance, if a particular data item is very popular the storage system might want to host it on a disk with high bandwidth or make multiple copies of the item. We present new results for some of these data placement problems. As the demand pattern changes over time, the storage system will have to modify its placement accordingly. Such a modification in placement will typically involve movement of data items from one set of disks to another or changing the number of copies of a data item in the system. For such a modification to be effective, it should be computed and applied quickly since the system is running inefficiently during this reconfiguration. We propose new schemes to reconfigure the data placement to deal with changing demand. To re-compute data placement periodically and to reconfigure the data placement, we need to continuously track of the demand distribution in the storage system and also be able to answer aggregate queries about the demand distribution. The data monitoring portion of the thesis deals with such problems that arise in the context of distributed data management applications. A monitoring system for such a scenario would need to process large amounts of data from a widely distributed set of data sources. The thesis presents new schemes that improve communication-efficiency of existing methods that address these problems.
Timed Modeling of Web Services Composition for Automatic Testing
Authors: Mounir Lallali, Fatiha Zaidi, Ana Cavalli
Venue: Proceedings of the 2007 Third International IEEE Conference on Signal-Image Technologies and Internet-Based System (2007)

This paper presents the modeling of BPEL (timed) constructs by using a new formalism WS-TEFSM (Web Service Timed Extended Finite State Machine). A formal mapping of all BPEL constructs is proposed as well as a model that corresponds to the BPEL Web services composition. The WS-TEFSM formalism allows to deal with timing constraints, data variables, clocks and priority on transitions. To perform the transformation, we define a renaming function and an asynchronous product of all partial machine corresponding to the BPEL process sub-activities. This model is enriched by the addition of priorities on transitions, which permit to handle the termination of the BPEL process and its sub-activities, and by global variables, which are used in the management of events and faults. This transformation step is essential to ensure the test of Web services. A rigorous approach is crucial as we have to deal with complex systems that manage distribution, low-coupled nature and asynchronous behaviors.
Application of Local Activity Theory of Cellular Neural Network to the Chen's System
Authors: Danling Wang, Lequan Min, Yu Ji
Venue: Proceedings of the 5th international symposium on Neural Networks: Advances in Neural Networks, Part II (2008)

The local activity theory introduced by Chua has provided a new tool for studying the complexity of high dimensional coupled nonlinear differential systems, in particular for reaction- diffusion cellular neural networks(R-D CNNs). In this paper some criteria for the local activity theory range from one-port to three-port cellular neural network cells with three local state variables are applied to Chen's system. Numerical simulations show that the dynamic behaviors of the Chen's CNN with one,two or three ports have the similar characteristics.
FA2BOUG-A FORTRAN 90 code to compute Bouguer gravity anomalies from gridded free-air anomalies: Application to the Atlantic-Mediterranean transition zone
Authors: J. Fullea, M. Ferníndez, H. Zeyen
Venue: Computers Geosciences (2008)

In this paper we present a computer program written in FORTRAN 90 specifically designed to determine the Bouguer anomaly from publicly available global gridded free-air anomaly and elevation database sets. FA2BOUG computes the complete Bouguer correction (i.e. Bullard A, B and C corrections) for both land and sea points in several spatial domains according to the distance between the topography and the calculation point. In each zone a different algorithm is used. In a distant zone we consider the harmonic spherical expansion of the potential of each right rectangular prism representing an elevation grid point. In an intermediate zone we compute the gravitational attraction produced by each prism using the analytic formula. Finally, an inner zone contribution is divided into two parts: a flat-topped prism with a height equal to the elevation of the calculation point, and four quadrants of a conic prism sloping continuously from each square of the inner zone to the calculation point. The program has been applied to the Atlantic-Mediterranean transition zone to obtain a complete Bouguer anomaly map of the area, integrating available onshore Bouguer anomaly with satellite-derived free-air anomaly data. Positive Bouguer anomalies are found in the Atlantic oceanic domain (240-300mGal), central and eastern Alboran Basin (40-160mGal) and SW Iberian Peninsula (>40mGal). Major negative Bouguer anomalies are located beneath the west Alboran Basin (
An Implementation Infrastructure for Server-Passive Timed-Release Cryptography
Authors: Konstantinos Chalkias, Foteini Baldimtsi, Dimitrios Hristu-Varsakelis, George Stephanides
Venue: Proceedings of the 2008 The Fourth International Conference on Information Assurance and Security (2008)

As online transactions become increasingly practical, a broad range of industrial and e-government applications have emerged which depend on time-based protection of confidential data. Despite theoretical progress in timed-release cryptography (TRC), there is still no implementation infrastructure that takes advantage of the latest TRC algorithms. The purpose of this paper is to propose such an infrastructure for pairing-based timed-release cryptography (PB-TRC) systems. Our model uses key generation centers (KGCs) which publish decryption keys periodically, and satisfies the security requirements of modern third party-based TRC schemes. Our approach combines the best features of existing models into a generic and complete infrastructure which is to support TRC. It is also "lighter" in terms of complexity and communication, and is as effective (in terms of security and related properties) as the TRC protocol it is used with.