ppxscal/embedding_network huggingface dataset:
Sequence kernels for predicting protein essentiality
Authors: Cyril Allauzen, Mehryar Mohri, Ameet Talwalkar
Venue: Proceedings of the 25th international conference on Machine learning (2008)

The problem of identifying the minimal gene set required to sustain life is of crucial importance in understanding cellular mechanisms and designing therapeutic drugs. This work describes several kernel-based solutions for predicting essential genes that outperform existing models while using less training data. Our first solution is based on a semi-manually designed kernel derived from the Pfam database, which includes several Pfam domains. We then present novel and general domain-based sequence kernels that capture sequence similarity with respect to several domains made of large sets of protein sequences. We show how to deal with the large size of the problem -- several thousands of domains with individual domains sometimes containing thousands of sequences -- by representing and efficiently computing these kernels using automata. We report results of extensive experiments demonstrating that they compare favorably with the Pfam kernel in predicting protein essentiality, while requiring no manual tuning.
Electrochemistry on microcircuits. I: Copper microelectrodes in oxalic acid media
Authors: C. Gabrielli, L. Beitone, C. Mace, E. Ostermann, H. Perrot
Venue: Microelectronic Engineering (2008)

Microelectrode size and connections are the two main limitations to conceive microelectrode arrays with a micrometric scale to study the electrochemical phenomena involved in the damascene process. A new chip consisting of an array of microelectrodes realized in an industrial CMOS process addresses these issues. This new fabrication technique for the realization of copper microelectrode arrays was reported. The design and the manufacturing of this device were aimed at studying the behaviour of copper by electrochemical measurements at small scale in media of interest for the microelectronic industry. In this paper, the design and the manufacturing of microelectrode array composed of copper electrode couples of various geometries were described. An advanced photolithography technique developed for the semiconductor industry was used to fabricate them. The tools permitting their characterization are also presented in order to study the wet processes involved in the damascene process by various electrochemical techniques, namely voltammetry and electrochemical impedance measurements.
Resource space model, OWL and database: Mapping and integration
Authors: Hai Zhuge, Yunpeng Xing, Peng Shi
Venue: ACM Transactions on Internet Technology (TOIT) (2008)

Semantics exhibits diversity in the real world, mental abstraction world, document world, and machine world. Studying mappings between different forms of semantics helps unveil the uniformity in the diversity. This article investigates the mappings between three typical semantic models: the Web ontology language (OWL), relational database model, and resource space model (a classification-based semantic model). By establishing mappings between the semantic primitives of the three models, we study the mapping from OWL description onto resource space and analyze the normal forms of the generated resource space. Mapping back from resource space onto OWL description is then discussed. Further, we investigate the mapping between OWL description and relational database, as well as the mapping between relational database and resource space. Normal forms of the generated relational tables are analyzed. To support advanced applications on the future Web, we suggest integrating the resource space, OWL, and databases to form a powerful semantic platform that enables different semantic models to enhance each other.
Super-diffusive behavior of mobile nodes from GPS traces
Authors: Sungwon Kim, Chul-Ho Lee, Do Young Eun
Venue: ACM SIGMOBILE Mobile Computing and Communications Review (2008)

Mobility is the most important factor in mobile adhoc networks (MANETs) and delay-tolerant networks (DTNs). Mobility models that fail to capture real movement pattern of mobile nodes will result in misleading guidelines on the design of new protocols and their performance evaluations and thus prevent us from making judicious decisions.
Learning (k,l)-contextual tree languages for information extraction from web pages
Authors: Stefan Raeymaekers, Maurice Bruynooghe, Jan Bussche
Venue: Machine Learning (2008)

This paper introduces a novel method for learning a wrapper for extraction of information from web pages, based upon (k,l)-contextual tree languages. It also introduces a method to learn good values of k and l based on a few positive and negative examples. Finally, it describes how the algorithm can be integrated in a tool for information extraction.
A quadrature-based third-order moment method for dilute gas-particle flows
Authors: R. O. Fox
Venue: Journal of Computational Physics (2008)

Dilute gas-particle flows can be described by a kinetic equation containing terms for spatial transport, gravity, fluid drag, and particle-particle collisions. However, the direct numerical solution of the kinetic equation is intractable for most applications due to the large number of independent variables. A useful alternative is to reformulate the problem in terms of the moments of the velocity distribution function. Closure of the moment equations is challenging for flows away from the equilibrium (Maxwellian) limit. In this work, a quadrature-based third-order moment closure is derived that can be applied to gas-particle flows at any Knudsen number. A key component of quadrature-based closures is the moment-inversion algorithm used to find the weights and abscissas. A robust inversion procedure is proposed for moments up to third order, and tested for three example applications (Riemann shock problem, impinging jets, and vertical channel flow). Extension of the moment-inversion algorithm to fifth (or higher) order is possible, but left to future work. The spatial fluxes in the moment equations are treated using a kinetic description and hence a gradient-diffusion model is not used to close the fluxes. Because the quadrature-based moment method employs the moment transport equations directly instead of a discretized form of the Boltzmann equation, the mass, momentum and energy are conserved for arbitrary Knudsen number (including the Euler limit). While developed here for dilute gas-particle flows, quadrature-based moment methods can, in principle, be applied to any application that can be modeled by a kinetic equation (e.g., thermal and non-isothermal flows currently treated using lattice Boltzmann methods), and examples are given from the literature.
A Node Self Similarity Approach for Interoperability Testing of Ad Hoc Routing Protocols
Authors: Stephane Maag, Cyril Grepet
Venue: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications - Workshops (2008)

Interoperability testing for ad hoc routing protocols is crucial to the reliability of wireless mobile ad hoc networks. Nevertheless, most of the works in this area are devoted to simulations analyzing the performance of such protocols without taking into account their formal requirements and specifications. Our works deal with formal methods to test the interoperability of a MANET routing protocol, DSR. From previous works, many inconclusive verdicts were obtained on some test cases. To reduce them, a node self-similarity approach is presented in that paper.
Characterization of PIR detector for monitoring occupancy patterns and functional health status of elderly people living alone at home
Authors: Alka R. Kaushik, B. G. Celler
Venue: Technology and Health Care (2007)

Changes in the behavioral activity of elderly people living alone at home may be an indicator for the assessment of their functional health status. In this paper, we evaluate the characteristics of a pyro-electric infrared detector (PIRD) to identify any section of the room where detector will fail to respond and assess the number of detectors required to identify the movements of the occupant reliably. The experimental results suggest that the PIRD output decreases very sharply from 1 V at 3 m to 0.2 V at 5 m and is below 0.5 V for hand movements at detection angle of <20&deg; and >50&deg;. Hence, spatial sensitivity of PIRD is non-uniform at different distances for different walking speeds. If a detector is used in a room of dimension half the maximum range of the PIRD, there exist dead points where detection sensitivity is low giving rise to false alarms. Hence, a single detector installed in a room fails to respond to small movements in the extended range. Four detectors at each corner of the room help to increase the sensitivity of the detection whereby even small movements such as reading a book, telephonic conversation etc. can be identified.
A Cryptology Course at Bletchley Park
Authors: Robert Lewand
Venue: Cryptologia (2007)

Each summer since 2004, an intensive course in cryptology has been offered to college and university teachers at Bletchley Park under the auspices of the National Science Foundation's Chautauqua Short Course Program. This article provides an overview of the Chautauqua Program and describes the Bletchley Park course.
Enabling resource-awareness for in-network data processing in wireless sensor networks
Authors: Uwe Röhm, Mohamed Medhat Gaber, Quincy Tse
Venue: Proceedings of the nineteenth conference on Australasian database - Volume 75 (2008)

The next-generation of wireless sensor platforms allows for more advanced in-network data processing. The central challenge remains energy and communication efficiency. This paper presents a resource-awareness framework for wireless sensor networks that allows in-network data processing to adapt to changing resource levels such as battery power or available memory. We have implemented the proposed framework as part of a query processing system for the Sun SPOT sensor network platform. As a case study, we have applied the framework to the query processor's on-line data clustering algorithm, making it resource-aware. In an experimental study, we demonstrate how communication costs can be significantly reduced by de-coupling clustering and data communication. The results also show the effectiveness of the resource-aware clustering algorithm: It can keep a constant memory footprint for only a marginal acceptable error in result accuracy.
Reusable object-oriented solutions for numerical simulation of PDEs in a high performance environment
Authors: Andrea Lani, Tiago Quintino, Dries Kimpe, Herman Deconinck, Stefan Vandewalle, Stefaan Poedts
Venue: Scientific Programming (2006)

Object-oriented platforms developed for the numerical solution of PDEs must combine flexibility and reusability, in order to ease the integration of new functionalities and algorithms. While designing similar frameworks, a built-in support for high performance should be provided and enforced transparently, especially in parallel simulations. The paper presents solutions developed to effectively tackle these and other more specific problems (data handling and storage, implementation of physical models and numerical methods) that have arisen in the development of COOLFluiD, an environment for PDE solvers. Particular attention is devoted to describe a data storage facility, highly suitable for both serial and parallel computing, and to discuss the application of two design patterns, Perspective and Method-Command-Strategy, that support extensibility and run-time flexibility in the implementation of physical models and generic numerical algorithms respectively.
Finding calendar-based periodic patterns
Authors: Anjana Kakoti Mahanta, Fokrul Alom Mazarbhuiya, Hemanta K. Baruah
Venue: Pattern Recognition Letters (2008)

Mining patterns in a market-basket dataset is a well-stated problem. There are a number of approaches to deal with this problem. Different types of patterns may be present in a dataset. An interesting one is patterns that hold seasonally, which are called calendar-based patterns. Earlier methods require periods to be specified by the user. We present here a method which is able to extract different types of periodic patterns that may exist in a temporal market-basket dataset and it is not needed for the user to specify the periods in advance. We consider the time-stamps as a hierarchical data structure and then extract different types of patterns. The algorithm can detect both wholly and partially periodic patterns. Although we have applied our approach to market-basket dataset, the approach can be used for any event related dataset where the events are associated with time intervals.
A Novel Image Text Extraction Method Based on K-Means Clustering
Authors: Yan Song, Anan Liu, Lin Pang, Shouxun Lin, Yongdong Zhang, Sheng Tang
Venue: Proceedings of the Seventh IEEE/ACIS International Conference on Computer and Information Science (icis 2008) (2008)

Texts in web pages, images and videos contain important clues for information indexing and retrieval. Most existing text extraction methods depend on the language type and text appearance. In this paper, a novel and universal method of image text extraction is proposed. A coarse-to-fine text location method is implemented. Firstly, a multi-scale approach is adopted to locate texts with different font sizes. Secondly, projection profiles are used in location refinement step. Color-based k-means clustering is adopted in text segmentation. Compared to grayscale image which is used in most existing methods, color image is more suitable for segmentation based on clustering. It treats corner-points, edge-points and other points equally so that it solves the problem of handling multilingual text. It is demonstrated in experimental results that best performance is obtained when k is 3. Comparative experimental results on a large number of images show that our method is accurate and robust in various conditions.
Bonding wire characterization using automatic deformability measurement
Authors: C. J. Hang, I. Lum, J. Lee, M. Mayer, C. Q. Wang, Y. Zhou, S. J. Hong, S. M. Lee
Venue: Microelectronic Engineering (2008)

A promising way to control underpad chip damage in IC packaging caused by wire bonding forces would be to use new wire chemistries that produce softer free-air balls (FABs). The number of new wire types that can be tested is limited by the available resources. The conventional FAB hardness characterization method is the microindentation test, a labour intensive and off-line task requiring cross-sectioning of a large number of samples. To accelerate FAB hardness characterization, an innovative on-line method is studied and presented here, enabling the fast comparison of different wire types. Collection of data from an instrumented wire bonder allows comparison of the deformability, i.e. the average amount of FAB deformation under a defined load. Increased deformability implies a softer FAB. The influences have been studied of changes in capillary, bonding substrate metallization and substrate temperature on the results obtained. It is found that these influences need to be held constant during a comparison study.
Thar's gold in them thar constructs
Authors: Henri Barki
Venue: ACM SIGMIS Database (2008)

Conceptualization and measurement of constructs provide many opportunities for contributing to information systems research and practice by providing a better understanding and explanation of interesting and important phenomena. To assist researchers in such endeavors, this paper describes four approaches to construct conceptualization and illustrates them with examples from past research. The paper also suggests directions for future research by identifying examples of constructs that stand to benefit from the application of the four approaches.
Inexact quasi-Newton global convergent method for solving constrained nonsmooth equations
Authors: M. J. smietanski
Venue: International Journal of Computer Mathematics (2007)

In this work we introduce a new method for solving nonsmooth equations with simple constraints. The method is based on the inexact and quasi-Newton approaches with backtracking strategy. Some conditions are given that ensure global superlinear convergence to a solution of the equation. We also propose a nonmonotone algorithm scheme. Both versions of the algorithm were constructed for Lipschitz continuous equations.
Mechanism of silica precipitation by lowering pH in chemi-thermomechanical pulping black liquors
Authors: Muhammad Ikram Aujla, Ishtiaq-Ur-Rehman Ishtiaq-Ur-Rehman, Asad Javaid
Venue: Proceedings of the 1st WSEAS International Conference on Computational Chemistry (2007)

Black liquor is a complex colloidal system obtained by chemical pulping process. It comprises of lignin, nearly 50% of the total organic and Silica approx. 2-3% (OD basis) of the total inorganic components. Black liquor is fed to chemical recovery plant where silica causes scales in the channels and concentrators. Mechanism of silica precipitation, from black liquor, by lowering pH has been investigated in this research. Lowering of pH results in charge neutralization, affecting the precipitation of silica molecules. Silica starts agglomeration at pH 10. At lower pH levels, in the presence of other salts, small colonies of silica start precipitating. Large colonies, rich in silica are obtained at pH 9.8. Below this pH precipitation of lignin is increased. It is evident that the pH values at which silica precipitates (9.8) almost quantitatively, is close to the pH value at which lignin starts precipitating, however, maximum desilication can be achieved at pH 9.8.
An Efficient Tree Structure for Delay Sensitive Data Gathering in Wireless Sensor Networks
Authors: Soonmok Kwon, Jeong-gyu Kim, Cheeha Kim
Venue: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications - Workshops (2008)

It is important to design an energy efficient data gathering tree structure for wireless sensor networks. As for the energy efficiency, network’s overall energy consumption and pernode fairness have been studied. Note that the minimum degree spanning tree (MDST) is optimal in the sense of per-node fairness. We believe that the per-node fairness is of practical interest and that the delay bound associated with it must be investigated. Unfortunately, no such efforts have been made so far.In this paper, we propose a tree structure, called the DBMDST, which modifies MDST to reduce the height and extend its degree. With the DB-MDST, the near optimal delay bound (i.e., comparable to the one obtained using the shortest path tree) can be achieved at the cost of as much energy as consumed by the MDST while it cannot be achieved with the MDST. Simulation results support the claim stated.
Interference evaluation for a cellular system based on OFDMA
Authors: Cristiano Monti, Romeo Giuliano, Franco Mazzenga, Pierpaolo Loreti
Venue: Proceedings of the 2nd international conference on Mobile multimedia communications (2006)

Orthogonal multiple access/multiplexing (OFDMA/OFDM) techniques represent the radio interface technologies for the next generation broadband access networks. WiMAX system adopts them for point-to-multipoint transmission. In a typical cell radius deployment of one to tree kilometers, WiMAX systems can be expected to deliver capacity of up to 40 Mbps. However the co-channel interference due to cell frequency reuse can lead to decreasing performance. In particular, throughput and BER can get worse drastically. In this paper we deal the evaluation of interference in a WiMax cellular system. Analysis is carried out using a semi-analytical approach based on a general expression of the SINR accounting for multipath, frequency and time offsets between the reference terminal and the interfering devices. Performance have been obtained under different operating modes of the OFDMA/OFDM cellular network that is synchronous and asynchronous BSs.
The relationship between land surface temperature and NDVI with remote sensing: application to Shanghai Landsat 7 ETM+ data
Authors: W. Yue, W. Tan
Venue: International Journal of Remote Sensing (2007)

The relationship between land surface temperature (LST) and Normalized Difference Vegetation Index (NDVI) associated with urban land-use type and land-use pattern is discussed in the City of Shanghai, China using data collected by the Enhanced Thematic Mapper Plus (ETM+) and aerial photographic remote sensing system. There is an apparent correlation between LST and NDVI from the visual interpretation of LST and NDVI contrasts. Mean LST and NDVI values associated with different land-use types are significantly different. Multiple comparisons of mean LST and NDVI values associated with pairings of each land-use type are also shown to be significantly different. The result of a regressive analysis shows an inverse correlation relationship between LST and NDVI within all land-use polygons, the same to each land-use type, but correlation coefficients associated with land-use types are different. An analysis on the relationship between LST, NDVI and Shannon Diversity Index (SHDI) shows a positive correlation between LST and SHDI and a negative correlation between NDVI and SHDI. According to the above results, LST, SHDI and NDVI can be considered to be three basic indices to study the urban ecological environment and to contribute to further validation of the applicability of relatively low cost, moderate spatial resolution satellite imagery in evaluating environmental impacts of urban land function zoning, then to examine the impact of urban land-use on the urban environment in Shanghai City. This provides an effective tool in evaluating the environmental influences of zoning in urban ecosystems with remote sensing and geographical information systems.
Applying CDMA technique to network-on-chip
Authors: Xin Wang, Tapani Ahonen, Jari Nurmi
Venue: IEEE Transactions on Very Large Scale Integration (VLSI) Systems (2007)

The issues of applying the code-division multiple access (CDMA) technique to an on-chip packet switched communication network are discussed in this paper. A packet switched network-on-chip (NoC) that applies the CDMA technique is realized in register-transfer level (RTL) using VHDL. The realized CDMA NoC supports the globally-asynchronous locally-synchronous (GALS) communication scheme by applying both synchronous and asynchronous designs. In a packet switched NoC, which applies a point-to-point connection scheme, e.g., a ring topology NoC, data transfer latency varies largely if the packets are transferred to different destinations or to the same destination through different routes in the network. The CDMA NoC can eliminate the data transfer latency variations by sharing the data communication media among multiple users concurrently. A six-node GALS CDMA on-chip network is modeled and simulated. The characteristics of the CDMA NoC are examined by comparing them with the characteristics of an on-chip bidirectional ring topology network. The simulation results reveal that the data transfer latency in the CDMA NoC is a constant value for a certain length of packet and is equivalent to the best case data transfer latency in the bidirectional ring network when data path width is set to 32 bits.