ppxscal/embedding_network huggingface dataset:
An analytical pipeline for genomic representations used for cytosine methylation studies
Authors: Reid F. Thompson, Mark Reimers, Batbayar Khulan, Mathieu Gissot, Todd A. Richmond, Quan Chen, Xin Zheng, Kami Kim, John M. Greally
Venue: Bioinformatics (2008)

Motivation: Representations of the genome can be generated by the selection of a subpopulation of restriction fragments using ligation-mediated PCR. Such representations form the basis for a number of high-throughput assays, including the HELP assay to study cytosine methylation. We find that HELP data analysis is complicated not only by PCR amplification heterogeneity but also by a complex and variable distribution of cytosine methylation. To address this, we created an analytical pipeline and novel normalization approach that improves concordance between microarray-derived data and single locus validation results, demonstrating the value of the analytical approach. A major influence on the PCR amplification is the size of the restriction fragment, requiring a quantile normalization approach that reduces the influence of fragment length on signal intensity. Here we describe all of the components of the pipeline, which can also be applied to data derived from other assays based on genomic representations. Contact: jgreally@aecom.yu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Point/Counterpoint
Authors: Ed Weller, David Card, Bill Curtis, Bob Raczynski
Venue: IEEE Software (2008)

"Point Argument: Applying SPC to Software Development: Where and Why," by Ed Weller and David Card. Statistical Process Control focuses on key subprocesses in the overall software development process. Under the right conditions, SPC is another useful tool in our toolkit. "Counterpoint Argument: Software Data Violate SPC's Underlying Assumptions," by Bob Raczynski and Bill Curtis. Software tasks are an intermingled mix of skill levels, component complexities, and project conditions that severely diminish the power of SPC techniques such as control charts. This department is part of a special issue on quantitative project management.
Conditional spectral moments in matching pursuit based on the chirplet elementary function
Authors: S. Ghofrani, D. C. McLernon, A. Ayatollahi
Venue: Digital Signal Processing (2008)

In this paper, we derive closed form formulae for the first- and the second-order conditional spectral moments, which are generalizations of the concept of instantaneous frequency (IF) and instantaneous bandwidth (IB). We prove that for the matching pursuit (MP) distribution, based on the chirplet elementary function, the first-order conditional spectral moment or the IF is guaranteed to be real valued and the IB is always positive. In addition, not only is the second-order conditional spectral moment positive but so also are all even higher-order conditional spectral moments. These new properties are shown to be additional reasons for using the MP decomposition. We also compare the chirplet and Gaussian atoms, because both always give positive values for the Wigner-Ville distribution (WVD), and therefore the MP distribution is also always positive. We show that when the chirplet atom is used, the MP distribution has superior resolution and the convergence is faster when compared with the Gaussian atom. Finally, as the MP algorithm is computationally demanding, we study how to overcome this limitation when using the chirplet atom.
Approach to microsystem design
Authors: Miroslav Husak, Jiri Jakovenko, Pavel Kulha
Venue: Proceedings of the 4th WSEAS International Conference on Telecommunications and Informatics (2005)

Microsystems concentrate all progressive element and technologies of microelectronics. The paper describes the approach to the design of a simple microsystem structure on the one side and smart microsystems on the second side. There is proposed a concept of models on the different levels in the paper. The design of microsystems is a complex of various energy domains. Electrical models are solved using tools for solving electrical circuits. The equivalence of parameters between electrical and mechanical domains is very often used in the design of a simple structure. The highest level creates the system models, in the lowest level there is the physical model and material models. Analytical and numerical models are very often used. SUN workstation and PC network as hardware are used. Professional software tools (Cadence, Spice, CoventorWare) serve for microsystem design. Some design examples are presented in the paper.
Using synchronic and diachronic relations for summarizing multiple documents describing evolving events
Authors: Stergos D. Afantenos, Vangelis Karkaletsis, Panagiotis Stamatopoulos, Constantin Halatsis
Venue: Journal of Intelligent Information Systems (2008)

In this paper we present a fresh look at the problem of summarizing evolving events from multiple sources. After a discussion concerning the nature of evolving events we introduce a distinction between linearly and non-linearly evolving events. We present then a general methodology for the automatic creation of summaries from evolving events. At its heart lie the notions of Synchronic and Diachronic cross-document Relations (SDRs), whose aim is the identification of similarities and differences between sources, from a synchronical and diachronical perspective. SDRs do not connect documents or textual elements found therein, but structures one might call messages. Applying this methodology will yield a set of messages and relations, SDRs, connecting them, that is a graph which we call grid. We will show how such a grid can be considered as the starting point of a Natural Language Generation System. The methodology is evaluated in two case-studies, one for linearly evolving events (descriptions of football matches) and another one for non-linearly evolving events (terrorist incidents involving hostages). In both cases we evaluate the results produced by our computational systems.
Using the Conceptual Cohesion of Classes for Fault Prediction in Object-Oriented Systems
Authors: Andrian Marcus, Denys Poshyvanyk, Rudolf Ferenc
Venue: IEEE Transactions on Software Engineering (2008)

High cohesion is a desirable property of software, as it positively impacts understanding, reuse, and maintenance. Currently proposed measures for cohesion in Object-Oriented (OO) software reflect particular interpretations of cohesion and capture different aspects of cohesion. The paper proposes a new measure for the cohesion of classes in an OO software system, based on the analysis of the unstructured information embedded in the source code, such as comments and identifiers. The measure, named the Conceptual Cohesion of Classes (C3), is inspired from the mechanisms used to measure textual coherence in cognitive psychology and computational linguistics. The paper presents the principles and the technology that stand behind the C3 measure. A large case study on three open source software systems is presented, which compares the new measure with an extensive set of existing metrics and uses them to construct models that predict software faults. The case study shows that the novel measure captures different aspects of class cohesion compared to any of the existing cohesion measures. In addition, combining C3 with existing structural cohesion metrics proves to be a better predictor of faulty classes when compared to different combinations of structural cohesion metrics.
A sufficient condition for bipartite graphs to be type one
Authors: Baogang Xu
Venue: Journal of Graph Theory (1998)

The total chromatic number &chi;T(G) of graph G is the least number of colors assigned to V(G) &cup; E(G) such that no adjacent or incident elements receive the same color. In this article, we give a sufficient condition for a bipartite graph G to have &chi;T(G) = &Delta;(G) + 1. &copy; 1998 John Wiley Sons, Inc. J. Graph Theory 29: 133137, 1998
Report on the 9th International Workshop on Web Information and Data Management (WIDM 2007)
Authors: Irini Fundulaki, Neoklis Polyzotis
Venue: ACM SIGIR Forum (2008)

The 9th ACM International Workshop on Web Information and Data Management (WIDM 2007) was held in Lisbon, Portugal, in conjunction with the 16th International Conference on Information and Knowledge Management (CIKM), on November 9, 2007.
Dublin Core-Based Metadata Extracting Algorithm from RDF-Based Information Elements
Authors: HongBin Wang, DaXin Liu, Wei Sun
Venue: Proceedings of the First International Workshop on Knowledge Discovery and Data Mining (2008)

The Semantic Web and Semantic Web technologies offer us a new approach to managing information and processes, the fundamental principle of which is the creation and use of semantic metadata. A Dublin Corebased metadata extracting algorithm from RDF-based information elements is proposed in this paper. The rule library is designed in the paper after introducing the semantic rules. The system named IDPMS (Integration Design Platform Management System) based on the above-mentioned algorithm is developed, which can perform automatic Dublin Core-based metadata extracting algorithm from information elements which is described by RDF documents. The Dublin Core-based metadata extracting algorithm from RDF-based information elements is described in this paper. The experiment is analyzed in the end. Keywords: Metadata, Dublin Core, information elements, Semantic Web
No Stress Tech Guide To OpenOffice.org Writer 2
Authors: Indera Murphy
Venue:  (2007)

This workbook is for anyone that wants to learn OpenOffice.org Writer version 2. If you are looking for step-by-step instructions to help you master the word processor in OpenOffice.org, this is the book that you have been looking for. There are time saving tips, advice and humor to help you learn the advanced concepts, which will enhance your word processing knowledge. The No Stress Tech Guide To OpenOffice.org Writer 2 will lead the novice and intermediate user through the features of Writer, which will take your skills to the next level. After completing the exercises in this workbook, you will be an advanced user.
Enhanced MIMO wireless video communication using multiple-description coding
Authors: Milos Tesanovic, David Bull, Angela Doufexi, Andrew Nix
Venue: Image Communication (2008)

Significant enhancements in spectral efficiency and error-resilience must be obtained from emerging wireless video systems if high-quality multimedia transmission is to become cost-effective. MIMO (multiple-input-multiple-output) technology promises to deliver the sustainable high transmission quality required for such applications. MIMO is a generic technology which, depending on the actual architecture deployed and the channel conditions encountered, produces variable error conditions. In particular, the way these errors interact with the transmitted data will depend on both the data source and the coding mechanism employed. In this context, this paper focuses on the interactions when MIMO systems are used to transmit compressed video. In terms of multimedia transmission, spatial multiplexing (SM) has often been proposed as the most suitable MIMO technique. Most SM-based video transport schemes focus on the advantages of multiplexing gain, which are achieved at the expense of relatively high SNR values. This paper proposes the use of multiple-description video coding (MDC) as a means of emulating the spatial diversity lacking in SM systems, to provide a new class of wireless video transmission algorithm. Singular value decomposition (SVD) is employed to create orthogonal sub-channels which provide an efficient means of mapping video content to the wireless channels. Extensive simulations demonstrate the effectiveness of MDC as a video decomposition which couples well with the underpinning SVD architecture. In addition, resource allocation in MIMO-SVD systems is examined in the context of transmitted video quality, and further enhancements have been achieved for low SNR values. Results indicate improvements in average PSNR of the decoded test sequences of around 5-7dB, compared to standard, single-description video transmission. This is further enhanced by an additional 2-3dB in the case of channels with low SNR values through the use of unequal power allocation. This approach is particularly well suited to MDC. The results presented are supported by significant enhancements in subjective quality and form the basis of a strong case in favour of MDC-based MIMO systems.
Guaranteed approach with the farthest of the runaways
Authors: I. I. Shevchenko
Venue: Automation and Remote Control (2008)

Games of the family {¿ N } N¿2 are formulated and studied with the application of generalized Isaacs's approach. The game ¿ N is a simplest model of the counteraction of one persecutor P and coalition N of E N runaways for the case when the payoff is the distance up to the coalition of E N equal to the Euclidean distance between P and the farthest from the runaways; P is in command of the termination moment. Moreover, an approach within the limits of which in games with a smooth terminal payoff are generated strategies prescribing players' motions in the directions of local gradients of the payoff is described. The approach is used for constructing pursuit strategies in games in which smooth approximations of the maximum of Euclidean distances up to the runaways are in place of payoffs. Pursuit strategies prescribing the motion in the direction of the farthest of the runaways are studied. A numerical simulation of the development of the games ¿2 and ¿3 is conducted in using different strategies by the players.
Wireless ad hoc VoIP
Authors: Patrick Stuedi, Gustavo Alonso
Venue: Proceedings of the 2007 Workshop on Middleware for next-generation converged networks and applications (2007)

VoIP is one of the traditional application scenarios for Mobile Ad Hoc Networks (MANETs) in settings such as emergency response. Ideally, VoIP would be transparent to the network type such that users would not have to worry whether their machine is currently part of a MANET or attached to the Internet. However, setting up a VoIP session using the Session Initiation Protocol (SIP) is difficult in MANETs since SIP relies on centralized components. In this paper, we show that the goal of transparent VoIP, for both isolated and Internet connected MANETs, can be achieved using SIPHoc, a SIP middleware for MANETs. We further discuss the deployment on laptops and iPAQ handhelds, and we look at various SIP interoperability issues.
A novel lossless data compression scheme based on the error correcting Hamming codes
Authors: Hussein Al-Bahadili
Venue: Computers Mathematics with Applications (2008)

This paper introduces a novel lossless binary data compression scheme that is based on the error correcting Hamming codes, namely the HCDC scheme. In this scheme, the binary sequence to be compressed is divided into blocks of n bits length. To utilize the Hamming codes, the block is considered as a Hamming codeword that consists of p parity bits and d data bits (n=d+p). Then each block is tested to find if it is a valid or a non-valid Hamming codeword. For a valid block, only the d data bits preceded by 1 are written to the compressed file, while for a non-valid block all n bits preceded by 0 are written to the compressed file. These additional 1 and 0 bits are used to distinguish the valid and the non-valid blocks during the decompression process. An analytical formula is derived for computing the compression ratio as a function of block size, and fraction of valid data blocks in the sequence. The performance of the HCDC scheme is analyzed, and the results obtained are presented in tables and graphs. Finally, conclusions and recommendations for future works are pointed out.
Traffic capacity of multi-cell WLANS
Authors: Thomas Bonald, Ali Ibrahim, James Roberts
Venue: Proceedings of the 2008 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2008)

Performance of WLANs has been extensively studied during the past few years. While the focus has mostly been on isolated cells, the coverage of WLANs is in practice most often realised through several cells. Cells using the same frequency channel typically interact through the exclusion region enforced by the RTS/CTS mechanism prior to the transmission of any packet. In this paper, we investigate the impact of this interaction on the overall network capacity under realistic dynamic traffic conditions. Specifically, we represent each cell as a queue and derive the stability condition of the corresponding coupled queuing system. This condition is then used to calculate the network capacity. To gain insight into the particular nature of interference in multi-cell WLANs, we apply our model to a number of simple network topologies and explicitly derive the capacity in several cases. The results notably show that the capacity gain obtained by using M frequency channels can grow significantly faster than M, the rate one might intuitively expect. In addition to stability results, we present an approximate model to derive the impact of network load on the mean transfer rate seen by the users.
A solution of missile-aircraft pursuit-evasion differential games in medium range
Authors: Fumiaki Imado, Takeshi Kuroda
Venue: Proceedings of the 10th WSEAS International Conference on APPLIED MATHEMATICS (2006)

This paper shows a method to obtain the exact solution for a missile and an aircraft differential games which minimizes and maximizes the essential pay-off of the problem: the miss distance, without employing any linearized approximation. For this purpose, we introduced the concept of energy maneuverability. Once the families of optimal terminal surfaces are obtained, the proposed method can solve mini-max solutions under several vehicle's acceleration constraints. Although it is impossible to obtain the solution in real time, however, if the results are incorporated into the missile guidance system as a knowledge base, the performance will be fairly improved.
Capture-avoiding substitution as a nominal algebra
Authors: Murdoch J. Gabbay, Aad Mathijssen
Venue: Formal Aspects of Computing (2008)

Substitution is fundamental to the theory of logic and computation. Is substitution something that we define on syntax on a case-by-case basis, or can we turn the idea of substitution into a mathematical object? We give axioms for substitution and prove them sound and complete with respect to a canonical model. As corollaries we obtain a useful conservativity result, and prove that equality-up-to-substitution is a decidable relation on terms. These results involve subtle use of techniques both from rewriting and algebra. A special feature of our method is the use of nominal techniques. These give us access to a stronger assertion language, which includes so-called &#x2018;freshness&#x2019; or &#x2018;capture-avoidance&#x2019; conditions. This means that the sense in which we axiomatise substitution (and prove soundness and completeness) is particularly strong, while remaining quite general.
Visual door detection integrating appearance and shape cues
Authors: A. C. Murillo, J. Košecká, J. J. Guerrero, C. Sagüés
Venue: Robotics and Autonomous Systems (2008)

An important component of human-robot interaction is the capability to associate semantic concepts with encountered locations and objects. This functionality is essential for visually guided navigation as well as location and object recognition. In this paper we focus on the problem of door detection using visual information only. Doors are frequently encountered in structured man-made environments and function as transitions between different places. We adopt a probabilistic approach for door detection, by defining the likelihood of various features for generated door hypotheses. Differing from previous approaches, the proposed model captures both the shape and appearance of the door. This is learned from a few training examples, exploiting additional assumptions about the structure of indoor environments. After the learning stage, we describe a hypothesis generation process and several approaches to evaluate the likelihood of the generated hypotheses. The approach is tested on numerous examples of indoor environment. It shows a good performance provided that the door extent in the images is sufficiently large and well supported by low level feature measurements.
Transceiver Technologies for Impulse Radio Ultra Wideband (IR UWB) Wireless Systems
Authors: Hong Nie, Zhizhang (David) Chen
Venue: Proceedings of the Communication Networks and Services Research Conference (2008)

Ultra Wideband (UWB) systems are wireless systems which transmit signals across a much wider frequency spectrum than conventional wireless systems.
Automating Contract Negotiation
Authors: John Debenham, Elaine Lawrence
Venue: Proceedings of the Fifth International Conference on Information Technology: New Generations (2008)

The automation of contract negotiation requires intelligent agents that can assimilate and use real-time information flows wisely. Electronic markets are information-rich with access to the Internet and the World Wide Web. A new breed of "information-based'' agents are founded on concepts from information theory, and are designed to operate with information flows of varying and questionable integrity. These agents are part of a larger project that aims to make informed automated trading in applications such as eProcurement a reality.
Inter-consortia battles in mobile payments standardisation
Authors: Andriew S. Lim
Venue: Electronic Commerce Research and Applications (2008)

Mobile payments can be seen as an innovation service offered by key players from the financial and mobile communication industries. Many believe that standards ensure the success of mobile payments. However, actors with heterogeneous interests cause the complexity in standards-setting process and, therefore, the absence of standards for mobile payments. Various groups have been formed to generate standardised solutions for mobile payments. This paper describes and analyses the role of these groups and how they influence the development of mobile payments. Five consortia are explored in min-case analysis. They are the Mobile Payment Forum, the Mobey Forum, Simpay, PayCircle, and the European Committee for Banking Standards. The existence of these consortia has instigated inter-consortia competition. As a result, there are three types of mobile payments developments identified: bank-account based, telecommunications companies billing-based, and credit-card based. The implications of the developments are discussed with the help of interpretive theory.
Worst-Case Execution Time - A Tool Provider's Perspective
Authors: Christian Ferdinand, Reinhold Heckmann
Venue: Proceedings of the 2008 11th IEEE Symposium on Object Oriented Real-Time Distributed Computing (2008)

This paper describes the structure of a tool to predict safe and tight upper bounds of the worst-case execution time (WCET) of tasks running on embedded processors and the use of a WCET tool in an industrial context. We describe common obstacles in the initial use of a WCET tool and consider the integration with scheduling analysis and model-based design tools.
Extending boundary-scan to perform a memory built-in self-test
Authors: Henning Bahr, Gordon Russell, Yajian Li
Venue: Proceedings of the 9th International Conference on Circuits (2005)

We present a novel test architecture which combines IEEE 1149.1 Boundary-Scan with a Memory Built-In Self-Test. The TDI pin is used for serially shifting in the test data into a test data register which is connected to the memory. The finite state machine of the TAP controller performs the memory test algorithm. The test response is shifted out via the TDO pin for off-chip analyses. The test architecture offers small area overhead, acceptable test time, increased flexibility and analysis capabilities while maintaining compliance to the Boundary-Scan standard.