ppxscal/embedding_network huggingface dataset:
Analysis of Interhelical Angle and Sequential Distance in Proteins
Authors: Sangyoon Lee
Venue: Proceedings of the international conference on Computational Science and Its Applications, Part II (2008)

This paper presents the results and discussion of statistical analysis of helix-helix interactions in proteins in terms of interhelical angle and sequential distance. The protein data includes 1290 high-resolution globular protein structures with less than 20 percent homology. We first define possible cases of interactions between helices and identify protein pairs that satisfy the conditions for each case. Two cases of helix-helix interactions are investigated using six parameters that can be obtained by considering the interactions as rigid-body motions. The computational results show that orientational preferences in helix packing are dominated by interactions between helices that are proximal in sequence. This bias is described with a univariate probability density function that depends only on the sequential distance between interacting helices. We also compute bivariate probability densities that depend on both interhelical orientation and sequential distance. The dominance of certain preferred orientations and sequential distance values in this bivariate distribution are also observed. Angle preferences persist even when the bivariate distribution is normalized by the univariate distribution. This statistical analysis provides quantitative probability distributions from which statistical potentials for secondary structure assembly can be derived.
A Glance on Current XML Twig Pattern Matching Algorithms
Authors: Duy-Bo Dao, Jinli Cao
Venue: Proceedings of the international conference on Computational Science and Its Applications, Part II (2008)

Extensible Markup Language (XML) has become a de facto standard for information representation and exchange over the Internet. The core operation of XML Query Processing is twig pattern matching, that is, finding in an XML document tree D all matches of a given twig query Q. Modern twig query matching algorithms often first decompose individual path matches and then merge them to form twig matches. In this paper, we review and evaluate two current efficient algorithms, namely HolisticTwigStack and TwigList. The HolisticTwigStack algorithm, which based on TwigStack, a notable and effective algorithm, uses a stack structure to avoid the storage of intermediate matches and the process of merging matches, whereas the TwigList algorithm use simple lists. Our analysis on experimental results show that the advantages and disadvantages of both HolisticTwigStack and TwigList for efficient XML Twig Pattern Matching in term of processing time and memory usage.
Baseline Results for the ImageCLEF 2007 Medical Automatic Annotation Task Using Global Image Features
Authors: Mark O. Güld, Thomas M. Deserno
Venue: Advances in Multilingual and Multimodal Information Retrieval: 8th Workshop of the Cross-Language Evaluation Forum, CLEF 2007, Budapest, Hungary, September 19-21, 2007, Revised Selected Papers (2008)

This paper provides baseline results for the medical automatic annotation task of CLEF 2007 by applying the image retrieval in medical applications (IRMA)-based algorithms previously used in 2005 and 2006, with identical parameterization. Three classifiers based on global image features are combined within a nearest neighbor (NN) approach: texture histograms and two distance measures, which are applied on down-scaled versions of the original images and model common variabilities in the image data. According to the evaluation scheme introduced in 2007, which uses the hierarchical structure of the coding scheme for the categorization, the baseline classifier yields scores of 51.29 and 52.54 when reporting full codes for 1-NN and 5-NN, respectively. This corresponds to error rates of 20.0% and 18.0% (rank 18 among 68 runs), respectively. Improvements via addressing the code hierarchy were not obtained. However, comparing the baseline results yields that the 2007 task was slightly easier than the previous ones.
Coherent Synchronization of a Chaotic Communication System Based on a QAM-4 Transmitter
Authors: Roxana Burghelea, Jean Philippe Mangeot, Frédéric Launay, Patrick Coirault, Safwan Assad
Venue: Proceedings of the 3rd international conference on Image and Signal Processing (2008)

Remarkable research efforts have been invested in recent years on the chaotic communications schemes. In this paper we propose a modulation technique based on QAM-4 (Quadrature Amplitude Modulation). The data is split into I and Q channels. Each channel is spread by chaotic sequences generated over a fixed time interval by a specific digital chaotic system. There are two principal advantages of introducing the chaos in a communication scheme. The first is that it allows signals to be transmitted in a secure way, so that the signal could be perceived as a noise for a potential intruder. Secondly, the spread-spectrum characteristics of the signal improve the noise rejection propreties. A new coherent receiver structure is presented to synchronize each channel. Simulation results are presented to show the effectiveness of the proposed scheme.
Updates and Asynchronous Communication in Trusted Computing Systems
Authors: Jose Carlos Brustoloni, David Kyle
Venue: Proceedings of the 2008 The 28th International Conference on Distributed Computing Systems (2008)

Software-based usage controls typically are vulnerable to attacks. Trusted Platform Modules (TPMs) can enable much more robust controls. However, as conventionally understood, TPM-secured systems may not support software updates or asynchronous communication. We contribute techniques that overcome these limitations, enabling updates, secure transmission of usage-controlled files via email orremovable disks, and secure use of such files on low-cost commercially available computers. We implemented the proposed scheme on Linux and report on its performance.
Identifying user behavior in online social networks
Authors: Marcelo Maia, Jussara Almeida, Virgílio Almeida
Venue: Proceedings of the 1st Workshop on Social Network Systems (2008)

Online social networks pose an interesting problem: how to best characterize the different classes of user behavior. Traditionally, user behavior characterization methods, based on user individual features, are not appropriate for online networking sites. In these environments, users interact with the site and with other users through a series of multiple interfaces that let them to upload and view content, choose friends, rank favorite content, subscribe to users and do many other interactions. Different interaction patterns can be observed for different groups of users. In this paper, we propose a methodology for characterizing and identifying user behaviors in online social networks. First, we crawled data from YouTube and used a clustering algorithm to group users that share similar behavioral pattern. Next, we have shown that attributes that stem from the user social interactions, in contrast to attributes relative to each individual user, are good discriminators and allow the identification of relevant user behaviors. Finally, we present and discuss experimental results of the use of proposed methodology. A set of useful profiles, derived from the analysis of the YouTube sample is presented. The identification of different classes of user behavior has the potential to improve, for instance, recommendation systems for advertisements in online social networks.
Technical communique: Robust quantized feedback stabilization of linear systems
Authors: M. L. Corradini, G. Orlando
Venue: Automatica (Journal of IFAC) (2008)

This paper investigates the feedback stabilization problem for SISO linear uncertain control systems with saturating quantized measurements. In the fixed quantization sensitivity framework, we propose a time varying control law able to effectively account for the presence of saturation, which is often the main source of instability, designed using sliding mode techniques. Such controller is proved able to stabilize the plant both in the presence and in the absence of quantization.
The Perceived Impact of Mobile Sales Force Automation Systems on Salespeople's Performance
Authors: Eusebio Scornavacca, Adam Sutherland
Venue: Proceedings of the 2008 7th International Conference on Mobile Business (2008)

Research on the use of mobile applications by the sales force has increased over the past couple of years, however, little is still known about the impact of these solutions on the sales people’s performance. This paper explores the perceived impact of mobile sales force automation (mSFA) on sales people’s performance. The findings indicate that salespeople and management share different perceptions in regards to the extent that mSFA could improve individual performance. The paper concludes with a summary of the findings and recommendations for future research.
A (somewhat) new solution to the variable binding problem
Authors: Leon Barrett, Jerome Feldman, Liam Mac Dermed
Venue: Neural Computation (2008)

To perform automatic, unconscious inference, the human brain must solve the binding problem by correctly grouping properties with objects. Temporal binding models like SHRUTI already suggest much of how this might be done in a connectionist and localist way by using temporal synchrony. We propose a set of alternatives to temporal synchrony mechanisms that instead use short signatures. This serves two functions: it allows us to explore an additional biologically plausible alternative, and it allows us to extend and improve the capabilities of these models. These extensions model the human ability to both perform unification and handle multiple instantiations of logical terms. To verify our model's feasibility, we simulate it with a computer system modeling simple, neuron-like computations.
Efficient Public Key Encryption with Keyword Search Schemes from Pairings
Authors: Chunxiang Gu, Yuefei Zhu, Heng Pan
Venue: Information Security and Cryptology: Third SKLOIS Conference, Inscrypt 2007, Xining, China, August 31 - September 5, 2007, Revised Selected Papers (2007)

Public key encryption with keyword search (PEKS) scheme to enable one to search encrypted keywords without compromising the security of the original data. In this paper, we propose a new PEKS scheme based on bilinear pairings. The scheme is computationally consistent. There is no pairing operation involved in the encryption procedure and so our new PEKS scheme is more efficient than the scheme of Boneh et.al. in [1]. Then, we provide further discussions on removing secure channel from PEKS, and present an efficient secure channel free PEKS scheme. Our two new schemes can be proved secure in the random oracle model, under the appropriate computational assumptions.
Parameter uniform numerical methods for singularly perturbed elliptic problems with parabolic boundary layers
Authors: E. O'Riordan, G. I. Shishkin
Venue: Applied Numerical Mathematics (2008)

Parameter-uniform numerical methods for a singularly perturbed elliptic problem with parabolic boundary layers in the solution are analyzed. A priori parameter explicit bounds on the solution and its derivatives are obtained using a suitable decomposition of the solution into regular and layer components. Based on this decomposition a numerical method is constructed and analyzed.
Language evolution from a simulation perspective: on the coevolution of compositionality and regularity
Authors: William S-Y. Wang
Venue:  (2007)

The thesis presents a multi-agent computational model to explore a key question in language emergence, i.e., whether syntactic abilities result from innate, species-specific competences, or they evolve from domain-general abilities through gradual adaptations. The model simulates a process of coevolutionary emergence of two linguistic universals (compositionality, in the form of lexical items; and regularity, in the form of constitute word orders) in human language, i.e., the acquisition and conventionalization of these features coevolve during the transition from a holistic signaling system to a compositional language. It also traces a "bottom-up" process of syntactic development, i.e., agents, by reiterating local orders between two lexical items, can gradually form global order(s) to regulate multiple lexical items in sentences. These results suggest that compositionality, regularity, and correlated linguistic abilities could have emerged as a result of some domain-general abilities, such as pattern extraction and sequential learning. In addition to individual learning mechanisms, the thesis further explores the effects of cultural transmission, social and semantic structures on language evolution. First, it simulates some major forms of cultural transmission, and discusses the role of conventionalization during horizontal transmission in language evolution. Second, it traces the emergence and maintenance of language in some stable social structures, and explores the role of popular agents in language evolution, the relationship between mutual understanding and social hierarchy, and the effect of exoteric communications on the convergence of communal languages. Finally, it studies language maintenance given different semantic spaces, and illustrates that the semantic structure may cause bias in the constituent word order, which can help to predict the word order bias in human languages. These explorations examine the role of self-organization in language evolution, provide some reconsideration on the bottleneck effect during cultural transmission, and shed light on the study of the social structure effects on language evolution.
Pilot study: application of constructive theory to educational software architecture
Authors: Sarah Irvine Belson
Venue:  (2008)

The premise of this study was that educational software products should be evaluated not just on content, but also on software design. Criteria was established that was based on sound Constructive theory, by key Constructive theorists, and their individual different outlooks on Constructivism, and the Criteria was used to evaluate the products software design for Constructivism. Software products were evaluated on the established Constructive Criteria, and Content Analysis methodology was used to determine the extent that the Criteria was applied to the software design in each product researched. A model of Criteria was established, and the software products were analyzed, with the emphasis on evaluating software design not on, "what student learn," but, on "how they learn." Constructivism was the preferred theory that was most applicable to educational software because of its open ended, interactive, self learning, features that used progression, real world, and discovery as some of its qualities that were conducive to learning, and sustained the test of time. The Products although representing a small sample of educational software products, were however, representative in observing the presence of Criteria found in each Product. The results of the Content Analysis strongly indicated that software design is often neglected when software products are developed. The disparity found was, the software developers did not understand sound educational theory, while educators could not evaluate software design, and they were focused on content, the lesson plans to be covered. The study also indicated a need for basic Constructive Criteria that is easy to understand and evaluate for both educators and developers.
A Simple Reduction Analysis and Algorithm Using Rough Sets
Authors: Ning Xu, Yun Zhang, Yongquan Yu
Venue: Proceedings of the international conference on Rough Sets and Intelligent Systems Paradigms (2007)

Indiscernibility relation and attribute reduction criteria are the important concepts in rough sets, also are the important base for further researching on attribute reduction. By analyzing the set theory background of indiscernibility and the reduction theory, it can be seen that an information system has the similar characteristics relative to a relation database table and can be analyzed using its data table structure. Combining the structure information of the system with the rough sets reduction theory, a simple reduction analysis can be completed and get useful reduction information. Such as whether a system has redundant attributes or not and how many attributes are need by the system to maintaining its classes, etc. The analysis is realized by a simple algorithm: PARA, the algorithm together with an effective heuristics algorithm can decide an area of the minimum reduct. It greatly reduces the searching area of finding minimum reduct and can play some role in high-dimensionality reduction. A given example shows the algorithm.
Industrializing Data Mining, Challenges and Perspectives
Authors: Françoise Fogelman-Soulié
Venue: Proceedings of the 2008 European Conference on Machine Learning and Knowledge Discovery in Databases - Part I (2008)

Business Intelligence is a very active sector in all industrial domains. Classical techniques (reporting and Olap), mainly concerned with presenting data, are already widely deployed. Meanwhile, Data Mining has long been used in companies as a nichetechnique, reserved for experts only and for very specific problems (credit scoring, fraud detection for example). But with the increasing availability of large data volumes (in particular, but not only, from theWeb), companies are more and more turning to data mining to provide them with high added-value predictive analytics. However producing models in large numbers, making use of large data volumes in an industrial context can only happen if solutions to challenges, both theoretic and operational, are found: we need algorithms which can be used to produce models when datasets have thousands of variables and millions of observations; we need to learn how to run and control the correct execution of hundreds of models; we need ways to automate the data mining process.I will present these constraints in industrial contexts and show how KXEN has exploited theoretical results (coming from Vladimir Vapnik's work) to provide answers to the above-mentioned challenges. I will give a few examples of real-life applications and will conclude with some remarks on the future of data mining in the industrial domain.
A global joint model for semantic role labeling
Authors: Kristina Toutanova, Aria Haghighi, Christopher D. Manning
Venue: Computational Linguistics (2008)

We present a model for semantic role labeling that effectively captures the linguistic intuition that a semantic argument frame is a joint structure, with strong dependencies among the arguments. We show how to incorporate these strong dependencies in a statistical joint model with a rich set of features over multiple argument phrases. The proposed model substantially outperforms a similar state-of-the-art local model that does not include dependencies among different arguments. We evaluate the gains from incorporating this joint information on the Propbank corpus, when using correct syntactic parse trees as input, and when using automatically derived parse trees. The gains amount to 24.1% error reduction on all arguments and 36.8% on core arguments for gold-standard parse trees on Propbank. For automatic parse trees, the error reductions are 8.3% and 10.3% on all and core arguments, respectively. We also present results on the CoNLL 2005 shared task data set. Additionally, we explore considering multiple syntactic analyses to cope with parser noise and uncertainty.
Modeling the World from Internet Photo Collections
Authors: Noah Snavely, Steven M. Seitz, Richard Szeliski
Venue: International Journal of Computer Vision (2008)

There are billions of photographs on the Internet, comprising the largest and most diverse photo collection ever assembled. How can computer vision researchers exploit this imagery? This paper explores this question from the standpoint of 3D scene modeling and visualization. We present structure-from-motion and image-based rendering algorithms that operate on hundreds of images downloaded as a result of keyword-based image search queries like "Notre Dame" or "Trevi Fountain." This approach, which we call Photo Tourism, has enabled reconstructions of numerous well-known world sites. This paper presents these algorithms and results as a first step towards 3D modeling of the world's well-photographed sites, cities, and landscapes from Internet imagery, and discusses key open problems and challenges for the research community.
Free-Space Interconnects for High-Performance Optoelectronic Switching
Authors: Peter S. Guilfoyle, John M. Hessenbruch, Richard V. Stone
Venue: Computer (1998)

Two architectures have been developed that use and demonstrate free-space optical interconnects for digital logic: a high-performance optoelectronic computing module and a second-generation digital opto-electronic computer.
Combining Biometric Authentication with Privacy-Enhancing Technologies
Authors: Konstantin Hyppönen, Marko Hassinen, Elena Trichina
Venue: Proceedings of the 1st international conference on Trusted Computing and Trust in Information Technologies: Trusted Computing - Challenges and Applications (2008)

Although state of public research in privacy-enhancing technologies (PET) is reasonably good, they are not yet widely used in common electronic documents. We argue that low acceptance of PET is due to a large gap between ordinary paper-based documents and new e-ID schemes. We show how to make the gap narrower by introducing a mobile electronic identity tool with privacy-preserving biometric authentication scheme.
Expressions of Empathy in ECAs
Authors: Radoslaw Niewiadomski, Magalie Ochs, Catherine Pelachaud
Venue: Proceedings of the 8th international conference on Intelligent Virtual Agents (2008)

Recent research has shown that empathic virtual agents enable to improve human-machine interaction. Virtual agent's expressions of empathy are generally fixed intuitively and are not evaluated. In this paper, we propose a novel approach for the expressions of empathy using complex facial expressions like superposition and masking. An evaluation study have been conducted in order to identify the most appropriate way to express empathy. According to the evaluation results people find more suitable facial expressions that contain elements of emotion of empathy. In particular, complex facial expressions seem to be a good approach to express empathy.
Image Quality Assessment and Equipment Optimisation with Automated Phantom Evaluation in Full Field Digital Mammography (FFDM)
Authors: Nadia Oberhofer, Nicoletta Paruccini, Ehrenfried Moroder
Venue: Proceedings of the 9th international workshop on Digital Mammography (2008)

The work investigates the feasibility of using a commercial software performing automatic threshold-detail-image analysis for absolute image quality evaluation (phantom CDMAM ver. 4.0 + CDMAM Analyser ver. 1.1).The software proposes an overall image quality index IQFinv. The quantities IQFinv, contrast-to-noise-ratio (CNR), threshold contrast and average glandular dose (AGD) are studied for a wide range of exposure settings in three full field digital mammographic units of different manufacturers. IQFinv correlates linearly with CNR and exhibits a better correlation to threshold contrast than CNR itself in all units, turning out to be a reliable parameter for image quality assessment.At comparable AGD and exposure settings, all systems exhibit equivalent image quality. Using the automatic exposure control (AEC) all units achieve, for thin and medium breasts, a higher image quality than requested by the European Guidelines, whereas only in one unit the image quality remains above the desired level for thick breasts.