ppxscal/embedding_network huggingface dataset:
A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes
Authors: Antonina Andreeva, Henning Tidow
Venue: Bioinformatics (2008)

Summary: We report a previously uncharacterized CHHC Zn-finger domain identified in spliceosomal U11-48K proteins, tRNA methyl-transferases TRM13 and gametocyte specific factors. We show that this domain behaves as an independent folding unit and that it stoichiometrically binds zinc in a one-to-one ratio. Based on the conserved sequence features we predict that this domain may function as a RNA recognition and binding module. Contact: tony@mrc-lmb.cam.ac.uk Supplementary information: Supplementary data are available on Bioinformatics online.
Bayesian survival analysis in genetic association studies
Authors: Ioanna Tachmazidou, Toby Andrew, Claudio J. Verzilli, Michael R. Johnson, Maria De Iorio
Venue: Bioinformatics (2008)

Motivation: Large-scale genetic association studies are carried out with the hope of discovering single nucleotide polymorphisms involved in the etiology of complex diseases. There are several existing methods in the literature for performing this kind of analysis for case-control studies, but less work has been done for prospective cohort studies. We present a Bayesian method for linking markers to censored survival outcome by clustering haplotypes using gene trees. Coalescent-based approaches are promising for LD mapping, as the coalescent offers a good approximation to the evolutionary history of mutations. Results: We compare the performance of the proposed method in simulation studies to the univariate Cox regression and to dimension reduction methods, and we observe that it performs similarly in localizing the causal site, while offering a clear advantage in terms of false positive associations. Moreover, it offers computational advantages. Applying our method to a real prospective study, we observe potential association between candidate ABC transporter genes and epilepsy treatment outcomes. Availability: R codes are available upon request. Contact: ioanna.tachmazidou@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Multilayer perceptron neural networks with novel unsupervised training method for numerical solution of the partial differential equations
Authors: Yazdan Shirvany, Mohsen Hayati, Rostam Moradian
Venue: Applied Soft Computing (2009)

In this paper by using MultiLayer Perceptron and Radial Basis Function (RBF) neural networks, a novel method for solving both kinds of differential equation, ordinary and partial differential equation, is presented. From the differential equation and its boundary conditions, the energy function of the network is prepared which is used in the unsupervised training method to update the network parameters. This method was implemented to solve the nonlinear Schrodinger equation in hydrogen atom and triangle-shaped quantum well. Comparison of this method results with analytical solution and two well-known numerical methods, Runge-kutta and finite element, shows the efficiency of Neural Networks with high accuracy, fast convergence and low use of memory for solving the differential equations.
Unsupervised retrieval of attack profiles in collaborative recommender systems
Authors: Kenneth Bryan, Michael O'Mahony, Pádraig Cunningham
Venue: Proceedings of the 2008 ACM conference on Recommender systems (2008)

Trust, reputation and recommendation are key components of successful e-commerce systems. However, e-commerce systems are also vulnerable in this respect because there are opportunities for sellers to gain advantage through manipulation of reputation and recommendation. One such vulnerability is the use of fraudulent user profiles to boost (or damage) the ratings of items in an online recommender system. In this paper we cast this problem as a problem of detecting anomalous structure in network analysis and propose a novel mechanism for detecting this anomalous structure. We present an evaluation that shows that this approach is effective at uncovering the types of recommender systems attack described in the literature.
Item pricing for revenue maximization
Authors: Maria-Florina Balcan, Avrim Blum, Yishay Mansour
Venue: ACM SIGecom Exchanges (2008)

In this note we report recent results on item pricing for revenue maximization in the presence of buyers with complex, unknown preferences. We focus on two important classes of settings: buyers with general valuations for the case of items in unlimited supply, and buyers with subadditive valuations for the case of items in limited supply.
A high-performance dual-wizard infrastructure for designing speech, pen, and multimodal interfaces
Authors: Phil Cohen, Colin Swindells, Sharon Oviatt, Alex Arthur
Venue: Proceedings of the 10th international conference on Multimodal interfaces (2008)

The present paper reports on the design and performance of a novel dual-Wizard simulation infrastructure that has been used effectively to prototype next-generation adaptive and implicit multimodal interfaces for collaborative groupwork. This high-fidelity simulation infrastructure builds on past development of single-wizard simulation tools for multiparty multimodal interactions involving speech, pen, and visual input [1]. In the new infrastructure, a dual-wizard simulation environment was developed that supports (1) real-time tracking, analysis, and system adaptivity to a user's speech and pen paralinguistic signal features (e.g., speech amplitude, pen pressure), as well as the semantic content of their input. This simulation also supports (2) transparent user training to adapt their speech and pen signal features in a manner that enhances the reliability of system functioning, i.e., the design of mutually-adaptive interfaces. To accomplish these objectives, this new environment also is capable of handling (3) dynamic streaming digital pen input. We illustrate the performance of the simulation infrastructure during longitudinal empirical research in which a user-adaptive interface was designed for implicit system engagement based exclusively on users' speech amplitude and pen pressure [2]. While using this dual-wizard simulation method, the wizards responded successfully to over 3,000 user inputs with 95-98% accuracy and a joint wizard response time of less than 1.0 second during speech interactions and 1.65 seconds during pen interactions. Furthermore, the interactions they handled involved naturalistic multiparty meeting data in which high school students were engaged in peer tutoring, and all participants believed they were interacting with a fully functional system. This type of simulation capability enables a new level of flexibility and sophistication in multimodal interface design, including the development of implicit multimodal interfaces that place minimal cognitive load on users during mobile, educational, and other applications.
PRIMO - Towards Privacy Aware Image Sharing
Authors: Thorben Burghardt, Andreas Walter, Erik Buchmann, Klemens Böhm
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 03 (2008)

A growing number of users in Web 2.0 based social network sites and photo sharing portals upload millions of images per day. In many cases, this leads to serious privacy threats. The images reveal not only the personal relationships and attitudes of the uploader, but of other persons displayed in the images as well. In this paper, we propose the PRIMO system architecture for privacy-aware image sharing. Our approach is based on semantic annotations, face recognition and user-defined privacy rules. PRIMO connects to many social network sites and photo sharing portals via the OpenSocial API and proprietary interfaces.
The use of mobile phones by older adults: a Malaysian study
Authors: Hazrina Hassan, Mohd Hairul Nizam Md Nasir
Venue: Issue 92 (September 2008) (2008)

Mobile phone has become essential parts of personal and business life. The recent growth of mobile phone usage is an observable fact that crosses all age and gender boundaries. It can potentially play a significant role in assisting older people in many ways especially in terms of maintaining social relationship, providing sense of safety and accessibility. However, older people seem to be a neglected user group in the design of mobile phone devices and services. Hence, this paper attempts to report the issues which are related with the design of mobile devices and services for older people aged 56 years old and over in Malaysia. The findings may serve as a reference to mobile device manufacturers and service providers when designing mobile devices and services for older Malaysians. This research uses a survey instrument to gather data from older peoples across all the states in Malaysia with the total of 176 older peoples responded. The questionnaires were mainly distributed to older persons who use mobile phones independently in their daily routines
Interfaces with the ineffable: Meeting aesthetic experience on its own terms
Authors: Kirsten Boehner, Phoebe Sengers, Simeon Warner
Venue: ACM Transactions on Computer-Human Interaction (TOCHI) (2008)

A variety of approaches have emerged in HCI that grapple with the ineffable, ill-defined, and idiosyncratic nature of aesthetic experience. The most straightforward approach is to transform the ineffable aspects of these experiences into precise representations, producing systems that are well-defined and testable but may miss the fullness of the experienced phenomenon. But without formal models and codified methods, how can we design and evaluate for a phenomenon we aren't sure can be adequately captured&quest; In this article, we present a case study of a system for reflection and awareness of emotional presence that was, in a sense, lived into being. Through system design, use, and evaluation we recount how the system evolved into something that enhanced rather than impoverished the sympathetic awareness of another. In discussing the strategies and results of the case study, we examine what it means for the HCI community to not only design for aesthetic experiences but also bring aesthetics into the practice of HCI.
PID control of MIMO process based on rank niching genetic algorithm
Authors: L. V. Arruda, M. C. Swiech, M. R. Delgado, F. Neves-Jr
Venue: Applied Intelligence (2008)

Non-linear multiple-input multiple-output (MIMO) processes which are common in industrial plants are characterized by significant interactions and non- linearities among their variables. Thus, tuning several controllers in complex industrial plants is a challenge for process engineers and operators. An approach for adjusting the parameters of n proportional---integral---derivative (PID) controllers based on multiobjective optimization and genetic algorithms (GA) is presented in this paper. A modified genetic algorithm with elitist model and niching method is developed to guarantee a set of solutions (set of PID parameters) with different tradeoffs regarding the multiple requirements of the control performance. Experiments considering a fluid catalytic cracking (FCC) unit, under PI and dynamic matrix control (DMC) are carried out in order to evaluate the proposed method. The results show that the proposed approach is an alternative to classical techniques as Ziegler---Nichols rules and others.
UFO: a resilient layered routing architecture
Authors: Yaping Zhu, Andy Bavier, Nick Feamster, Sampath Rangarajan, Jennifer Rexford
Venue: ACM SIGCOMM Computer Communication Review (2008)

Conventional wisdom has held that routing protocols cannot achieve both scalability and high availability. Despite scaling relatively well, today's Internet routing system does not react quickly to changing network conditions (e.g., link failures or excessive congestion). Overlay networks, on the other hand, can respond quickly to changing network conditions, but their reliance on aggressive probing does not scale to large topologies. The paper presents a layered routing architecture called UFO (Underlay Fused with Overlays), which achieves the best of both worlds by having the "underlay" provide explicit notification about network conditions to help improve the efficiency and scalability of routing overlays.
ArchIS: an XML-based approach to transaction-time temporal database systems
Authors: Fusheng Wang, Carlo Zaniolo, Xin Zhou
Venue: The VLDB Journal &mdash; The International Journal on Very Large Data Bases (2008)

Effective support for temporal applications by database systems represents an important technical objective that is difficult to achieve since it requires an integrated solution for several problems, including (i) expressive temporal representations and data models, (ii) powerful languages for temporal queries and snapshot queries, (iii) indexing, clustering and query optimization techniques for managing temporal information efficiently, and (iv) architectures that bring together the different pieces of enabling technology into a robust system. In this paper, we present the ArchIS system that achieves these objectives by supporting a temporally grouped data model on top of RDBMS. ArchIS' architecture uses (a) XML to support temporally grouped (virtual) representations of the database history, (b) XQuery to express powerful temporal queries on such views, (c) temporal clustering and indexing techniques for managing the actual historical data in a relational database, and (d) SQL/XML for executing the queries on the XML views as equivalent queries on the relational database. The performance studies presented in the paper show that ArchIS is quite effective at storing and retrieving under complex query conditions the transaction-time history of relational databases, and can also assure excellent storage efficiency by providing compression as an option. This approach achieves full-functionality transaction-time databases without requiring temporal extensions in XML or database standards, and provides critical support to emerging application areas such as RFID.
A methodology for rapid illumination-invariant face recognition using image processing filters
Authors: Ognjen Arandjelović, Roberto Cipolla
Venue: Computer Vision and Image Understanding (2009)

Achieving illumination invariance in the presence of large pose changes remains one of the most challenging aspects of automatic face recognition from low resolution imagery. In this paper, we propose a novel recognition methodology for their robust and efficient matching. The framework is based on outputs of simple image processing filters that compete with unprocessed greyscale input to yield a single matching score between two individuals. Specifically, we show how the discrepancy of the illumination conditions between query input and training (gallery) data set can be estimated implicitly and used to weight the contributions of the two competing representations. The weighting parameters are representation-specific (i.e. filter-specific), but not gallery-specific. Thus, the computationally demanding, learning stage of our algorithm is offline-based and needs to be performed only once, making the added online overhead minimal. Finally, we describe an extensive empirical evaluation of the proposed method in both a video and still image-based setup performed on five databases, totalling 333 individuals, over 1660 video sequences and 650 still images, containing extreme variation in illumination, pose and head motion. On this challenging data set our algorithm consistently demonstrated a dramatic performance improvement over traditional filtering approaches. We demonstrate a reduction of 50-75% in recognition error rates, the best performing method-filter combination correctly recognizing 97% of the individuals.
Positive solutions for a class of boundary-value problem with integral boundary conditions in Banach spaces
Authors: Meiqiang Feng, Dehong Ji, Weigao Ge
Venue: Journal of Computational and Applied Mathematics (2008)

This paper investigates the existence and multiplicity of positive solutions for a class of nonlinear boundary-value problem of second-order differential equations with integral boundary conditions in ordered Banach spaces. The arguments are based upon a specially constructed cone and the fixed point theory in a cone for strict set contraction operators. The nonexistence of a positive solution is also studied.
Optimum groundwater locations in the northern United Arab Emirates
Authors: E. Ghoneim
Venue: International Journal of Remote Sensing (2008)

Due to the increase in urban and agricultural activities in arid regions, the exploration of new locations of possible groundwater discharge and accumulation is required to augment the limited water resources. In order to locate such discharge areas, it is necessary first to identify zones of high recharge potentials. In such an arid region, like the northern United Arab Emirates (UAE), one of the ways to predict areas of potential groundwater recharge is by understanding the hydrological response of its drainage basins to rainfall events. Due to the scarcity of basic hydrological data, a hydrological model driven mainly by information on the physiographic characteristics, drainage network properties (generated from DEM), and surface cover distribution (generated from satellite images) was used to comprehend the dynamics of surface runoff through hydrographs, and hence water loss in the study area. Results show that the northern UAE is drained by 48 drainage basins emerging from the Oman Mountains. Two-thirds of these basins drain easterly toward the Gulf of Oman, and one-third drain westerly toward the Arabian Gulf. These basins are found to be structurally controlled by three major fault trends, which are the NE trend (Dibba zone), NW trend (Ham Zone), and WNW trend (Hatta zone). The hydrological response of a basin is correlated with its morphological characteristics. Based on these characteristics, and through the application of a cluster analysis, it was feasible to classify the largest basins in the region into four groundwater potentiality groups in accordance with the magnitude of their peak discharges. From this study, it became evident that the downstream area of the two major basins of Ar-Rafiah and Limhah, and their vicinities are the most probable sites for groundwater accumulation. The drainage systems of these two basins, especially those controlled by major fault lines, play a vital role in transmitting surface-subsurface rainwater from the Oman Mountains, the recharge zone, into the western desert plain, the discharge zone, where freshwater accumulates underground. The study also revealed that a large volume of groundwater is dissipated into the sea along the eastern coast. A detailed examination of MODIS thermal data supports this by revealing cool surface anomalies issuing from the mountain range toward both the western desert plain and the Gulf of Oman following major rainfall events. Thus, the technique used facilitates the prediction of new locations of optimum groundwater resources in the northern UAE. Such a technique could be adopted, with appropriate modifications, elsewhere in arid regions, where groundwater is restricted and subject to greater complexity.
Implementing the extended return statement for Ada 2005
Authors: S. Tucker Taft
Venue: Proceedings of the 2008 ACM annual international conference on SIGAda annual international conference (2008)

Ada 2005 adds an important capability to the language by allowing the construction and return of an object of a limited type by a function. New syntax for an extended return statement was added to enhance this capability further. This capability to return newly constructed objects of a limited type from a function, when combined with the additional capability to use aggregates to construct objects of a limited type, goes a long way to making use of limited types far more friendly and effective. Although the extended return statement and the associated ability to construct and return objects of a limited type brings new power to Ada, it also brings new choices and challenges to the Ada compiler implementor, when trying to decide how best to implement this feature. This presentation will review some of these alternatives, and present a high-level description of one particular approach based on the notion of an object creation context (OCC) which is designed to minimize the complexity of the generated code while providing an efficient and flexible implementation.
Support for seamless data exchanges between web services through information mapping analysis using kernel methods
Authors: Buhwan Jeong, Daewon Lee, Jaewook Lee, Hyunbo Cho
Venue: Expert Systems with Applications: An International Journal (2009)

A challenging issue to web services interoperability is seamless data exchanges between web services to be composed. A solution to this problem is to establish semantic mappings from an information item to another. To do that, we present an approximate information mapping analysis. We propose a kernel-based structural similarity measure for XML documents. Simulation results with industrial XML data show that the proposed kernel-based measure outperforms other existing methods.
TSV constraints related to temperature excursion, pressure during molding, materials used and handling loads
Authors: Tomasz Fa&#x0142;at, Kazimierz Friedel, Norman Marenco, Stephan Warnat
Venue: Microsystem Technologies (2008)

The current paper focuses on several mechanical aspects of a waferlevel packaging approach using a direct face-to-face Chip-to-Wafer (C2W) bonding of a MEMS device on an ASIC substrate wafer. Requirements of minimized inherent stress from packaging and good decoupling from forces applied in manufacturing and application are discussed with particular attention to the presence of through-silicon vias (TSV) in the substrate wafer. The paper deals with FEM analysis of temperature excursion, pressure during molding, materials used and handling load influence on mechanical stress within the TSV system and on wafer level, which can be large enough to disintegrate the system.