ppxscal/embedding_network huggingface dataset:
Sequence Ontology annotation guide: Conference Papers
Authors: Karen Eilbeck, Suzanna E. Lewis
Venue: Comparative and Functional Genomics (2004)

This Sequence Ontology (SO)[13] aims to unify the way in which we describe sequence annotations, by providing a controlled vocabulary of terms and the relationships between them. Using SO terms to label the parts of sequence annotations greatly facilitates downstream analyses of their contents, as it ensures that annotations produced by different groups conform to a single standard. This greatly facilitates analyses of annotation contents and characteristics, e.g. comparisons of UTRs, alternative splicing, etc. Because SO also specifies the relationships between features, e.g. part&lowbar;of, kind&lowbar;of, annotations described with SO terms are also better substrates for validation and visualization software.This document provides a step-by-step guide to producing a SO compliant file describing a sequence annotation. We illustrate this by using an annotated gene as an example. First we show where the terms needed to describe the gene's features are located in SO and their relationships to one another. We then show line by line how to format the file to construct a SO compliant annotation of this gene. Copyright &copy; 2005 John Wiley & Sons, Ltd.
Abstract interdomain security assertions: a basis for extra-grid virtual organizations
Authors: B. E. Carpenter, P. A. Janson
Venue: IBM Systems Journal (2004)

One significant challenge in building grids between organizations with heterogeneous security systems is the need to express and enforce security policies that specify the users in one organization (the source domain) who are allowed to access the resources in another organization (the target domain). This requires linking the syntax and semantics of security assertions referring to users and their attributes in the source domain to those referring to resources in the target domain. This paper suggests some basic requirements for solving this problem, in particular, an abstract form of interdomain security assertion (IDSA) relying, for instance, on globally meaningful URIs (Uniform Resource Identifiers) to refer to users, resources, and their attributes. This canonical abstract form of IDSA is, however, used strictly for assertion mapping purposes. It may--but need not-- be visible in any concrete security assertion syntax in any domain. The paper further suggests different scenarios in which URIs for users, resources, and attributes defined in one domain can be mapped to semantically meaningful references--with varying degrees of granularity and accountability--in another domain where they would otherwise be meaningless.
An entry of Ramanujan on hypergeometric series in his notebooks
Authors: K. Srinivasa Rao, G. Vanden Berghe, C. Krattenthaler
Venue: Journal of Computational and Applied Mathematics (2005)

Example 7, after Entry 43, in Chapter XII of the first Notebook of Srinivasa Ramanujan is proved and, more generally, a summation theorem for 3F2(a,a,x; 1+a, 1+a+N; 1), where N is a nonnegative integer, is derived.
SonicTexting
Authors: Michal Rinott
Venue: CHI '05 extended abstracts on Human factors in computing systems (2005)

SonicTexting is a system for inputting text -- 'texting' -- using gestures and sound. As in musical instruments and everyday mechanical objects, sound in SonicTexting is synchronous and responsive to actions. SonicTexting explores people's hand-ear coordination and demonstrates the use of informative digital sound. It proposes that through touch and sound, a functional activity like text entry can become an experience on the borders between performing a task, playing an instrument and playing a game.
A survey of nucleotide cyclases in Actinobacteria: unique domain organization and expansion of the class III cyclase family in Mycobacterium tuberculosis: Primary Research Papers
Authors: Avinash R. Shenoy, K. Sivakumar, A. Krupa, N. Srinivasan, Sandhya S. Visweswariah
Venue: Comparative and Functional Genomics (2004)

Cyclic nucleotides are well-known second messengers involved in the regulation of important metabolic pathways or virulence factors. There are six different classes of nucleotide cyclases that can accomplish the task of generating cAMP, and four of these are restricted to the prokaryotes. The role of cAMP has been implicated in the virulence and regulation of secondary metabolites in the phylum Actinobacteria, which contains important pathogens, such as Mycobacterium tuberculosis, M. leprae, M. bovis and Corynebacterium, and industrial organisms from the genus Streptomyces. We have analysed the actinobacterial genome sequences found in current databases for the presence of different classes of nucleotide cyclases, and find that only class III cyclases are present in these organisms. Importantly, prominent members such as M. tuberculosis and M. leprae have 17 and 4 class III cyclases, respectively, encoded in their genomes, some of which display interesting domain fusions seen for the first time. In addition, a pseudogene corresponding to a cyclase from M. avium has been identified as the only cyclase pseudogene in M. tuberculosis and M. bovis. The Corynebacterium and Streptomyces genomes encode only a single adenylyl cyclase each, both of which have corresponding orthologues in M. tuberculosis. A clustering of the cyclase domains in Actinobacteria reveals the presence of typical eukaryote-like, fungi-like and other bacteria-like class III cyclase sequences within this phylum, suggesting that these proteins may have significant roles to play in this important group of organisms. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Computing the Grundy sequences for octal games
Authors: Jason Catterton
Venue: Journal of Computing Sciences in Colleges (2005)

Two player games, such as Nim and Kayles, in which players can remove a number of stones and leave a certain number of piles of stones afterwards, are octal if and only if you can leave at most two piles. The rules for an octal game may be encoded as a decimal, 0.d1d2d3...dn where di signifies how many piles you can leave after taking i stones. The digit di is formed as a sum of the powers of two with the exponent indicating a valid number of piles to leave. For example, if you can remove i stones and leave 0 or 1 piles then di will be 1(20) + 1(21) + 0(22). The encoding of the rules for Kayles is 0.77 because you can take one or two stones and leave 0, 1, or 2 piles after a move.
Discovering Operational Signatures with Time Constraints from a Discrete Event Sequence
Authors: Philippe Bouche, Marc Le Goc
Venue: Proceedings of the Fourth International Conference on Hybrid Intelligent Systems (2004)

This paper aims at showing a method to discover signatures (or models of chronicles) from a discrete event sequence (alarms) generated by a Monitoring Cognitive Agent (MCA). When the counting process of the events generated by a couple (Process, MCA) behaves like a Poisson process, this couple can be considered as stochastic discrete event generator SDEG_{(Pr, MCA)} and modeled as a superposition of Poisson and an homogeneous discrete time Markov chain. The 'BJT' algorithm uses these two representations in order to help in the discovering of signatures. The results obtained on an industrial process monitored with a Sachem system have been validated by Experts, confirming so the relevance of the approach within an industrial frame.
IATAC: a smart predictor to turn-off L2 cache lines
Authors: Jaume Abella, Antonio González, Xavier Vera, Michael F. P. O'Boyle
Venue: ACM Transactions on Architecture and Code Optimization (TACO) (2005)

As technology evolves, power dissipation increases and cooling systems become more complex and expensive. There are two main sources of power dissipation in a processor: dynamic power and leakage. Dynamic power has been the most significant factor, but leakage will become increasingly significant in future. It is predicted that leakage will shortly be the most significant cost as it grows at about a 5&times; rate per generation. Thus, reducing leakage is essential for future processor design. Since large caches occupy most of the area, they are one of the leakiest structures in the chip and hence, a main source of energy consumption for future processors.This paper introduces IATAC (inter-access time per access count), a new hardware technique to reduce cache leakage for L2 caches. IATAC dynamically adapts the cache size to the program requirements turning off cache lines whose content is not likely to be reused. Our evaluation shows that this approach outperforms all previous state-of-the-art techniques. IATAC turns off 65&percnt; of the cache lines across different L2 cache configurations with a very small performance degradation of around 2&percnt;.
An adaptive rate-control streaming mechanism with optimal buffer utilization
Authors: Shu-Ching Chen, Mei-Ling Shyu, Irina Gray, Hongli Luo
Venue: Journal of Systems and Software (2005)

In this paper, an end-to-end real-time adaptive protocol for multimedia transmission is presented. The bandwidth is dynamically allocated according to the network status, and the client buffer occupancy and playback requirement. The transmission rate is determined by the quadratic probing algorithm that can obtain the maximal utilization of the client buffer and minimal occupation of the network bandwidth. It is also coupled with a congestion control mechanism that can effectively decrease the packet loss rate during network congestion. We investigate the performance of our quadratic probing algorithm in different congestion levels under both the local area net (LAN) and Internet environments. Performance analysis reveals that our approach is more robust in avoiding overflows and underflows in different network congestion levels, and adapting to the changing network delays. Comparisons are made with the fixed rate approach and the rate by playback requirement approach. The experimental results show that our proposed real-time protocol with the rate adjusting quadratic probing algorithm is efficient in utilizing the network resources and decreasing the packet loss ratios.
ERP-system: marketing analysis module
Authors: Tzanko Golemanov, Emilia Golemanova
Venue: Proceedings of the 5th international conference on Computer systems and technologies (2004)

This paper substantiates the necessity of ERP-systems' use in the trade-oriented companies. The main requirements of a marketing analysis software module are defined. The basic characteristics and functionality of the Registry_M module during its implementation at a company dealing with automobile spare parts import and trade are discussed.
Operation Tables for Scheduling in the Presence of Incomplete Bypassing
Authors: Aviral Shrivastava, Eugene Earlie, Nikil Dutt, Alex Nicolau
Venue: Proceedings of the international conference on Hardware/Software Codesign and System Synthesis: 2004 (2004)

Register bypassing is a powerful and widely used feature in modern processors to eliminate certain data hazards. Although complete bypassing is ideal for performance, bypassing has significant impact on cycle time, area, and power consumption of the processor. Due to the strict constraints on performance, cost and power consumption in embedded processors, architects need to evaluate and implement incomplete register bypassing mechanisms. However traditional data hazard detection and/or avoidance techniques used in retargetable schedulers break down in the presence of incomplete bypassing. In this paper, we present the concept of Operation Tables, which can be used to detect data hazards, even in the presence of incomplete bypassing. Furthermore our technique integrates the detection of both data, as well as resource hazards, and can be easily employed in a compiler to generate better schedules. Our experimental results on the popular Intel XScale embedded processor platform show that even with a simple intra-basic block scheduling technique, we achieve upto 20% performance improvement over fully optimized GCC generated code on embedded applications from the MiBench suite.
Aspect-oriented programming and modular reasoning
Authors: Gregor Kiczales, Mira Mezini
Venue: Proceedings of the 27th international conference on Software engineering (2005)

Aspects cut new interfaces through the primary decomposition of a system. This implies that in the presence of aspects, the complete interface of a module can only be determined once the complete configuration of modules in the system is known. While this may seem anti-modular, it is an inherent property of crosscutting concerns, and using aspect-oriented programming enables modular reasoning in the presence of such concerns.
Generic programming for high-performance scientific applications: Research Articles
Authors: Lie-Quan Lee, Andrew Lumsdaine
Venue: Concurrency and Computation: Practice Experience (2005)

We present case studies that apply generic programming to the development of high-performance parallel code for solving two archetypal partial differential equations (PDEs). We examine the overall structure of the example scientific codes and consider their generic implementation. With a generic approach it is a straightforward matter to reuse software components from different sources; implementations with components from the Iterative Template Library (ITL), the Matrix Template Library (MTL), Blitz++, A++&sol;P++, and Fortran BLAS are presented. Our newly developed Generic Message Passing library is used for communication. We compare the generic implementations with equivalent implementations developed with alternative libraries and languages and discuss performance as well as software engineering issues. Copyright &copy; 2005 John Wiley & Sons, Ltd.
A genetic integrated fuzzy classifier
Authors: Vito Di Gesù, Giosuè Lo Bosco
Venue: Pattern Recognition Letters (2005)

This paper introduces a new classifier, that is based on fuzzy-integration schemes controlled by a genetic optimisation procedure. Two different types of integration are proposed here, and are validated by experiments on real data sets of biological cells. The performance of our classifier is tested against a feed-forward neural network and a Support Vector Machine. Results show the good performance and robustness of the integrated classifier strategies.
Computing Machinery and Emergence: The Aesthetics and Metaphysics of Video Games
Authors: Jon Cogburn, Mark Silcox
Venue: Minds and Machines (2005)

We build on some of Daniel Dennett's ideas about predictive indispensability to characterize properties of video games discernable by people as computationally emergent if, and only if: (1) they can be instantiated by a computing machine, and (2) there is no algorithm for detecting instantiations of them. We then use this conception of emergence to provide support to the aesthetic ideas of Stanley Fish and to illuminate some aspects of the Chomskyan program in cognitive science.
Probabilistic information retrieval model for a dependency structured indexing system
Authors: Changki Lee, Gary Geunbae Lee
Venue: Information Processing and Management: an International Journal (2005)

Most previous information retrieval (IR) models assume that terms of queries and documents are statistically independent from each other. However, conditional independence assumption is obviously and openly understood to be wrong, so we present a new method of incorporating term dependence into a probabilistic retrieval model by adapting a dependency structured indexing system using a dependency parse tree and Chow Expansion to compensate the weakness of the assumption. In this paper, we describe a theoretic process to apply the Chow Expansion to the general probabilistic models and the state-of-the-art 2-Poisson model. Through experiments on document collections in English and Korean, we demonstrate that the incorporation of term dependences using Chow Expansion contributes to the improvement of performance in probabilistic IR systems.
A data distributed parallel algorithm for nonrigid image registration
Authors: Fumihiko Ino, Kanrou Ooyama, Kenichi Hagihara
Venue: Parallel Computing (2005)

Image registration is a technique for defining a geometric relationship between each point in images. This paper presents a data distributed parallel algorithm that is capable of aligning large-scale three-dimensional (3-D) images of deformable objects. The novelty of our algorithm is to overcome the limitations on the memory space as well as the execution time. In order to enable this, our algorithm incorporates data distribution, data-parallel processing, and load balancing techniques into Schnabel's registration algorithm that realizes robust and efficient alignment based on information theory and adaptive mesh refinement. We also present some experimental results obtained on a 128-CPU cluster of PCs interconnected by Myrinet and Fast Ethernet switches. The results show that our algorithm requires less amount of memory resources, so that aligns datasets up to 1024x1024x590 voxel images with reducing the execution time from hours to minutes, a clinically compatible time.
Call for papers
Authors: Newton Lee
Venue: Computers in Entertainment (CIE) (2005)

The ACM Computers in Entertainment online magazine (http://www.acmcie.org) covers a wide range of theoretical and practical computer applications in the field of entertainment. It features video interviews of leading professionals. It publishes high-quality papers on the latest development in software, hardware, and business policies that improve existing mainstream entertainment and that create new genres of entertainment. Topics of interest include but are not limited to: animation, animatronics, digital asset management, digital cinema, digital rights management, games, interactive television, Internet, movies, music, performing arts, robotics, toys, and virtual reality. The magazine welcomes submissions of articles from scholars and professionals involved in all aspects of entertainment technology.
Exploiting an Infrastructure IP to Reduce the Costs of Memory Diagnosis Costs in SoCs
Authors: P. Bernardi, M. Grosso, M. Rebaudengo, M. Sonza Reorda
Venue: Proceedings of the 10th IEEE European Symposium on Test (2005)

Discriminating between good and faulty chips is often not enough during IC manufacturing phases, where a complete understanding about failure mechanisms is required to ramp up production yield. When considering embedded memories, information about the whole set of faults needs to be extracted from the IC and processed: this asks for solutions supporting high data volume transfer. We propose an embedded architecture allowing efficient diagnosis of SoCs containing several BISTed memory cores, which minimizes ATE memory requirements for pattern storage and drastically speeds up the complete diagnostic procedure. Experimental results highlight the convenience of the approach with respect to alternative ATE driven procedures, while resorting to negligible area overhead.
Image Based High Realistic Visual Pattern Effect Achieving Method
Authors: Yinfei Pan, Duanqing Xu, Chun Chen, Ying Zhang
Venue: Proceedings of the Third International Conference on Image and Graphics (2004)

This study is to meet the demands of high realistic and efficient pattern application in textile CAD systems. A method to achieve photo effect by changing patterns in real scenes was given out. According to the scene surface texture trend, the area of the scene surface, which needs to obtain the pattern effect, was divided into control meshes. A mesh division and adjusting idea was developed. A vector operation based texture mapping counterpoint pixels attainting algorithm was presented, which could embody texture distortion demands. In order to achieve the immersion authenticity, a mapping pixelsý brightness value synthesis method was put forward, which inherited the surface material characteristics. The validity of the method was confirmed by citing some typical examples. The method can create high realistic visual pattern effect. In the same time, its computational cost is relatively low and will have high efficiency. It is also convenient to implement.
Combining Local and Global Features for Image Segmentation Using Iterative Classification and Region Merging
Authors: Qiyao Yu, David A. Clausi
Venue: Proceedings of the 2nd Canadian conference on Computer and Robot Vision (2005)

In MRF based unsupervised segmentation, the MRF model parameters are typically estimated globally. Those global statistics sometimes are far from accurate for local areas if the image is highly non-stationary, and hence will generate false boundaries. The problem cannot be solved if local statistics are not considered. This work incorporates the local feature of edge strength in the MRF energy function, and segmentation is obtained by reducing the energy function using iterative classification and region merging.
Exploring the foundation of genomics: a Northern blot reference set for the comparative analysis of transcript profiling technologies: Research Papers
Authors: Danielle Kemmer, Margareta Faxén, Emily Hodges, Jonathan Lim, Elena Herzog, Elsebrit Ljungström, Anders Lundmark, Mary K. Olsen, Raf Podowski, Erik L. L. Sonnhammer, Peter Nilsson, Mark Reimers, Boris Lenhard, Steven L. Roberds, Claes Wahlestedt, Christer Höög, Pankaj Agarwal, Wyeth W. Wasserman
Venue: Comparative and Functional Genomics (2004)

In this paper we aim to create a reference data collection of Northern blot results and demonstrate how such a collection can enable a quantitative comparison of modern expression profiling techniques, a central component of functional genomics studies. Historically, Northern blots were the de facto standard for determining RNA transcript levels. However, driven by the demand for analysis of large sets of genes in parallel, high-throughput methods, such as microarrays, dominate modern profiling efforts. To facilitate assessment of these methods, in comparison to Northern blots, we created a database of published Northern results obtained with a standardized commercial multiple tissue blot (dbMTN). In order to demonstrate the utility of the dbMTN collection for technology comparison, we also generated expression profiles for genes across a set of human tissues, using multiple profiling techniques. No method produced profiles that were strongly correlated with the Northern blot data. The highest correlations to the Northern blot data were determined with microarrays for the subset of genes observed to be specifically expressed in a single tissue in the Northern analyses. The database and expression profiling data are available via the project website (). We believe that emphasis on multi-technique validation of expression profiles is justified, as the correlation results between platforms are not encouraging on the whole. Supplementary material for this article can be found at: Copyright &copy; 2005 John Wiley & Sons, Ltd.
Review of "Testing Embedded Software by Bart Broekman and Edwin Notenboom"; Addison Wesley.; 2003
Authors: Mordechai Ben-Menachem
Venue: ACM SIGSOFT Software Engineering Notes (2005)

This book discusses testing of software and software-rich systems; particularly those that are embedded in larger Hardware/Software systems. On the other hand, to describe it another way, this book is one of those books that make writing book reviews really fun and worthwhile. (If that sounds like I like the book, you are right!) I have looked at just about every testing book to come out since Glenford Myers' 'The Art of Software Testing' in 1979 (I have most of them, too; having caught acute bibliophilia at an early age). This is clearly one of the better ones in quite a while; at least since Boris Beizer, and that is saying a lot.