ppxscal/embedding_network huggingface dataset:
Meeting report: The Institute for Genomic Research&#x002F;Wellcome Trust Conference: Genomes 2004 14&ndash;17 April 2004, The Wellcome Trust Conference Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK: Features - The Institute for Genomic Research&#x002F;Wellcome Trust Conference: Genomes 2004. The Wellcome Trust Conference Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Authors: Jo Wixon
Venue: Comparative and Functional Genomics (2004)

This conference brought the microbial genomics community together to share their most up-to-the-minute achievements, so much so that several talks cannot be covered here, as the work discussed has not yet been published. This meeting report has details of a cross-section of the talks from the sessions on &lsquo;Genome analysis and comparative genomics&rsquo;, &lsquo;Computational genomics&rsquo; and &lsquo;Functional genomics&rsquo;, ranging from studies on complex environmental samples, to specific pathogenic bacteria, to yeasts. Copyright &copy; 2004 John Wiley & Sons, Ltd. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Quasi-Monte Carlo algorithms for diffusion equations in high dimensions
Authors: G. Venkiteswaran, M. Junk
Venue: Mathematics and Computers in Simulation (2005)

Diffusion equation posed on a high dimensional space may occur as a sub-problem in advection-diffusion problems (see [G. Venkiteswaran, M. Junk, A QMC approach for high dimensional Fokker-Planck equations modelling polymeric liquids, Math. Comput. Simul. 68 (2005) 43-56.] for a specific application). Although the transport part can be dealt with the method of characteristics, the efficient simulation of diffusion in high dimensions is a challenging task. The traditional Monte Carlo method (MC) applied to diffusion problems converges and is N^-^1^/^2 accurate, where N is the number of particles. It is well known that for integration, quasi-Monte Carlo (QMC) outperforms Monte Carlo in the sense that one can achieve N^-^1 convergence, up to a logarithmic factor. This is our starting point to develop methods based on Lecot's approach [C. Lecot, F.E. Khettabi, Quasi-Monte Carlo simulation of diffusion, Journal of Complexity 15 (1999) 342-359.], which are applicable in high dimensions, with a hope to achieve better speed of convergence. Through a number of numerical experiments we observe that some of the QMC methods not only generalize to high dimensions but also show faster convergence in the results and thus, slightly outperform standard MC.
On solving univariate sparse polynomials in logarithmic time
Authors: J. Maurice Rojas, Yinyu Ye
Venue: Journal of Complexity (2005)

Let f be a degree D univariate polynomial with real coefficients and exactly m monomial terms. We show that in the special case m = 3 we can approximate within ε all the roots of f in the interval [0,R] using just O(log(D)log(D log R/ε)) arithmetic operations. In particular, we can count the number of roots in any bounded interval using just O(log2 D) arithmetic operations. Our speed-ups are significant and near-optimal: The asymptotically sharpest previous complexity upper bounds for both problems were super-linear in D, while our algorithm has complexity close to the respective complexity lower bounds. We also discuss conditions under which our algorithms can be extended to general m, and a connection to a real analogue of Smale's 17th Problem.
Book review: MS-DOS User's Guide, Special Ed. by David W. Solomon, Caroline M. Halliday, David D. Busch, & Timothy S. Stanley (Que Corporation, 1989)
Venue: ACM SIGSMALL/PC Notes (1990)

All MS-DOS users can find an abundance of helpful and often needed information in the MS-DOS User's Guide. This is a very complete guide to MS-DOS and PC-DOS versions 3 and 4. References are made to versions 1 and 2 of the operating system, however the emphasis of book is on versions 3 (with more attention to version 3.3) and 4. The guide does not include references to the DEBUG or LINK commands. Also, the guide does not try to explain GW-BASIC nor any other application software. This is a book about the operating system for operating system users, i.e. all users. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Numerical error in an ethics course
Authors: M. Dee Medley
Venue: Journal of Computing Sciences in Colleges (2004)

This paper describes methods for adding numerical error experimentation to an upper level course in ethics and professionalism in Computer Science. The purpose is to enhance the students' understanding of the potential harmful effects of programs with faults.
Bandwidth optimization by reliable-path determination in Mobile Ad-Hoc Networks
Authors: Sriram Raghavan, Srikanth Akkiraju, Santhosh Sridhar
Venue: Proceedings of the 3rd international conference on Mobile and ubiquitous multimedia (2004)

A Mobile Ad Hoc Network is typically characterized by two sets of nodes, one set being more stationary than the other. It is observed that identifying this set of relatively stationary nodes critically facilitates the dual purpose of reducing the routing overhead and providing larger data bandwidth. It is therefore both interesting and expedient to study the behavior of a typical Mobile Ad Hoc Network and identify the sub-graph which can impact these improvements where the application demands are high. It is particularly enlightening when scaled to a larger network, as one of the substantial factors affecting cost in an Ad Hoc network is the routing overhead. In this paper, a method is proposed to determine, dynamically, the most reliable path for routing in a Mobile Ad Hoc scenario and ensure that packets are routed along that path to guarantee enhanced data traffic routed per unit time owing to savings from route-discovery and to decrease normalized routing overhead. The Mobile Ad Hoc Network is modeled as a graph with the mobile units denoting the nodes of the graph and the set of reachable units as its neighbors and identifying the weakly connected sub-dominion of that graph, which is the most reliable path for routing. The proposed algorithm recognizes those set of weakly connected nodes which are relatively more stable when compared to the other nodes hence requiring less routing and thus resulting in more number of data packets and ensuring better bandwidth utilization. Our algorithm proposes and confirms the dual betterments namely improvement in the utilization of bandwidth and reduction in the normalized routing overhead in any given network scenario.
Journey of enlightenment: the evolution of development at Microsoft
Authors: Eric Brechner
Venue: Proceedings of the 27th international conference on Software engineering (2005)

Like many software companies, Microsoft has been doing distributed application development for many years. However, recent changes in the market have altered the rules, both in terms of customer expectations and programming models for ubiquitous interconnected smart devices. These changes have provoked two dramatic shifts in the way we develop software. The first is the creation and use of the .NET Framework as a simple, secure, and robust platform for device-independent software development, data manipulation, and communications. The second is an agile yet highly disciplined approach to designing, testing, implementing, and verifying our software which presumes all bugs are unacceptable and must be found and fixed early before they impact internal groups, external partners, and eventually our customers. This paper discusses the nature and impact of these two dramatic shifts to the development practices at Microsoft.
SVL: Storage Virtualization Engine Leveraging DBMS Technology
Authors: Lin Qiao, Balakrishna R. Iyer, Divyakant Agrawal, Amr El Abbadi
Venue: Proceedings of the 21st International Conference on Data Engineering (2005)

The demands on storage systems are increasingly requiring expressiveness, fault-tolerance, security, distribution, etc. Such functionalities have been traditionally provided by DBMS. We propose a storage management system, SVL, that leverages DBMS technology. The primary problem in block storage management is block virtualization which is essentially an abstraction layer that separates the user view of storage from the implementation of storage. Storage virtualization standardizes storage management in a heterogeneous storage and/or host environment, and plays a crucial role in enhancing storage functionality and utilization. Currently specialized hardware or microcode based solutions are popular for implementing block storage management systems, commonly referred to as disk controllers. We demonstrate how to take a general purpose commercial RDBMS, rather than a specialized solution, to support block storage management. We exploit the simple semantics of storage management systems to streamline database performance and thus attain acceptability from a storage point of view. This work promises to pave the way for diverse and innovative industrial applications of database management systems.
Coloring face hypergraphs on surfaces
Authors: Zdeněk Dvořák, Daniel Král, Riste Škrekovski
Venue: European Journal of Combinatorics (2005)

The face hypergraph of a graph G embedded on a surface has the same vertex set as G and its edges are the sets of vertices forming faces of G. A hypergraph is k-choosable if for each assignment of lists of colors of sizes k to its vertices, there is a coloring of the vertices from these lists avoiding a monochromatic edge.We prove that the face hypergraph of the triangulation of a surface of Euler genus g is O(3√g)- choosable. This bound matches a previously known lower bound of order Ω(3√g). If each face of the graph is incident with at least r distinct vertices, then the face hypergraph is also O(r√g)-choosable. Note that colorings of face hypergraphs for r = 2 correspond to usual vertex colorings and the upper bound O(√g) thus follows from Heawood's formula. Separate results for small genera are presented: the bound 3 for triangulations of the surface of Euler genus g = 3 and the bound ⌈7 + √36g + 49/6⌉ for surfaces of Euler genus g ≥ 3. Our results dominate the previously known bounds for all genera except for g = 4, 7, 8, 9, 14.
Tactile Semiotics: The Meanings of Touch Explored with Low-Tech Prototypes
Authors: Simone Gumtau
Venue: Proceedings of the First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (2005)

In this paper I will describe the term Tactile Semiotics ¿ the meanings we ascribe to different types of haptic sensations. When designing devices for haptic communication or haptic input devices for HCI, it makes sense firstly to look to psychophysics as an informant. However, to gain insight into tactility as both experience and meaning, it may also be beneficial to look at the cultural and social context of touch. Also, I will explain how it is possible to explore this field with the help of low-tech prototypes and methodologies more common in art and design.
Automated OSCAR Testing with Linux-VServers
Authors: Fernando Laudares Camargos, Benoit des Ligneris
Venue: Proceedings of the 19th International Symposium on High Performance Computing Systems and Applications (2005)

The testing process of a complex program managed with a version system and developed by a large team of international developers is a very lengthy and demanding task. In this paper, we present an automated testing infrastructure for OSCAR that rely on the virtualization of Linux computers. The virtualization layer is provided by the Linux-VServer project. The current design and implementation of the testing program will be presented from a developer point of view. Tests that can be made with the current implementation will be detailed as well as tests that can not be made given our technical choices.
Multimodal presentation method for a dance training system
Authors: Akio Nakamura, Sou Tabata, Tomoya Ueda, Shinichiro Kiyofuji, Yoshinori Kuno
Venue: CHI '05 extended abstracts on Human factors in computing systems (2005)

This paper presents a multimodal information presentation method for a basic dance training system. The system targets on beginners and enables them to learn basics of dances easily. One of the most effective ways of learning dances is to watch a video showing the performance of dance masters. However, some information cannot be conveyed well through video. One is the translational motion, especially that in the depth direction. We cannot tell exactly how far does the dancers move forward or backward. Another is the timing information. Although we can tell how to move our arms or legs from video, it is difficult to know when to start moving them. We solve the first issue by introducing an image display on a mobile robot. We can learn the amount of translation just by following the robot. We introduce active devices for the second issue. The active devices are composed of some vibro-motors and are developed to direct action-starting cues with vibration. Experimental results show the effectiveness of our multimodal information presentation method.
Link analysis ranking: algorithms, theory, and experiments
Authors: Allan Borodin, Gareth O. Roberts, Jeffrey S. Rosenthal, Panayiotis Tsaparas
Venue: ACM Transactions on Internet Technology (TOIT) (2005)

The explosive growth and the widespread accessibility of the Web has led to a surge of research activity in the area of information retrieval on the World Wide Web. The seminal papers of Kleinberg [1998, 1999] and Brin and Page [1998] introduced Link Analysis Ranking, where hyperlink structures are used to determine the relative authority of a Web page and produce improved algorithms for the ranking of Web search results. In this article we work within the hubs and authorities framework defined by Kleinberg and we propose new families of algorithms. Two of the algorithms we propose use a Bayesian approach, as opposed to the usual algebraic and graph theoretic approaches. We also introduce a theoretical framework for the study of Link Analysis Ranking algorithms. The framework allows for the definition of specific properties of Link Analysis Ranking algorithms, as well as for comparing different algorithms. We study the properties of the algorithms that we define, and we provide an axiomatic characterization of the INDEGREE heuristic which ranks each node according to the number of incoming links. We conclude the article with an extensive experimental evaluation. We study the quality of the algorithms, and we examine how different structures in the graphs affect their performance.
Efficient Factorization of the Joint-Space Inertia Matrix for Branched Kinematic Trees
Authors: Roy Featherstone
Venue: International Journal of Robotics Research (2005)

This paper describes new factorization algorithms that exploit branch-induced sparsity in the joint-space inertia matrix (JSIM) of a kinematic tree. It also presents new formulae that show how the cost of calculating and factorizing the JSIM vary with the topology of the tree. These formulae show that the cost of calculating forward dynamics for a branched tree can be considerably less than the cost for an unbranched tree of the same size. Branches can also reduce complexity; some examples are presented of kinematic trees for which the complexity of calculating and factorizing the JSIM are less than O(n2) and O(n3) , respectively. Finally, a cost comparison is made between an O(n) algorithm and an O(n3) algorithm, the latter incorporating one of the new factorization algorithms. It is shown that the O(n3) algorithm is only 15% slower than the O(n) algorithm when applied to a 30-degrees-of-freedom humanoid, but is 2.6 times slower when applied to an equivalent unbranched chain. This is due mainly to the O(n3) algorithm running about 2.2 times faster on the humanoid than on the chain.
BASIC for numerical quadrature
Authors: David K. Kahaner
Venue: ACM SIGNUM Newsletter (1981)

Although I have been involved in the development of programs for numerical evaluation of integrals for a number of years, it was only recently that I became aware of the importance of providing such tools in BASIC. I admit to having had a built-in predjudice against people using BASIC. To me it seemed that these people were either solving trivial problems, or were too lazy to learn FORTRAN. But in the last year or so, I have been made aware that BASIC is very much an alive language with sophisticated scientific users. The growth in popularity of the microcomputer is partly responsible for this. At NBS I also see many more scientists who are not as computer oriented as those I met at Los Alamos and this has some effect too. In this talk I would like to describe a few important quadrature techniques that are essential to have and how they can be best implemented in BASIC. This seems to me a rather neglected area. There may be a few odd bits of software around in BASIC, but most are not what I would call state-of-the-art. If I am wrong about this I would be happy to be corrected. We could publish a bibliography of such programs here in the SIGNUM Newsletter. In the first section, as a convenience to those of us who are not very familiar with the language, I outline several of the differences with FORTRAN.
On Plug-ins and Extensible Architectures
Authors: Dorian Birsan
Venue: Queue (2005)

Extensible application architectures such as Eclipse offer many advantages, but one must be careful to avoid "plug-in hell." In a world of increasingly complex computing requirements, we as software developers are continually searching for that ultimate, universal architecture that allows us to productively develop high-quality applications. This quest has led to the adoption of many new abstractions and tools. Some of the most promising recent developments are the new pure plug-in architectures.
Existence of periodic solutions in neutral state-dependent delays equations and models
Authors: Zhihui Yang, Jinde Cao
Venue: Journal of Computational and Applied Mathematics (2005)

Sufficient conditions are obtained for the existence of positive periodic solutions of neutral equations with state-dependent delays. The proof is based on the theory of coincidence degree. The existence results are applied to equations of population dynamics.
Book review: Annual Review of Computer Science. Ed. by J. F. Traub (Annual Reviews Inc.)
Venue: Issue 110 (October 1989) (1989)

Preparing a review of a field as vast as Computer Science on annual basis is not an easy job. A common problem with such reviews is that the material presented in them lacks the cohesion associated with a book and look more like just a binding of articles. In this regard the Editorial Board of the Annual Review has done a great job by not only selecting papers on active research topics but also presenting them in a book-like manner to provide the reader with an ease of reading.
Transposition of the cocitation method with a view to classifying web pages
Authors: Camille Prime-Claverie, Michael Beigbeder, Thierry Lafouge
Venue: Journal of the American Society for Information Science and Technology (2004)

The Web is a huge source of information, and one of the main problems facing users is finding documents which correspond to their requirements. Apart from the problem of thematic relevance, the documents retrieved by search engines do not always meet the users' expectations. The document may be too general, or conversely too specialized, or of a different type from what the user is looking for, and so forth. We think that adding metadata to pages can considerably improve the process of searching for information on the Web. This article presents a possible typology for Web sites and pages, as well as a method for propagating metadata values, based on the study of the Web graph and more specifically the method of cocitation in this graph.
Recurrence analysis for effective array prefetching in Java: Research Articles
Authors: Brendon Cahoon, Kathryn S. McKinley
Venue: Concurrency and Computation: Practice Experience (2005)

Java is an attractive choice for numerical, as well as other, algorithms due to the software engineering benefits of object-oriented programming. Because numerical programs often use large arrays that do not fit in the cache, they suffer from poor memory performance. To hide memory latency, we describe a new unified compile-time analysis for software prefetching arrays and linked structures in Java. Our previous work used data-flow analysis to discover linked data structure accesses. We generalize our prior approach to identify loop induction variables as well, which we call recurrence analysis. Our algorithm schedules prefetches for all array references that contain induction variables. We evaluate our technique using a simulator of an out-of-order superscalar processor running a set of array-based Java programs. Across all of our programs, prefetching reduces execution time by a geometric mean of 23&percnt;, and the largest improvement is 58&percnt;. We also evaluate prefetching on a PowerPC processor, and we show that prefetching reduces execution time by a geometric mean of 17&percnt;. Because our analysis is much simpler and quicker than previous techniques, it is suitable for including in a just-in-time compiler. Traditional software prefetching algorithms for C and Fortran use locality analysis and sophisticated loop transformations. We further show that the additional loop transformations and careful scheduling of prefetches from previous work are not always necessary for modern architectures and Java programs. Copyright &copy; 2005 John Wiley & Sons, Ltd.
Coming soon
Authors: Newton Lee
Venue: Computers in Entertainment (CIE) (2005)

Technology Induced Change in Film/Television Distribution High Performance Data Recording Architecture and High Definition Video Mobile Digital Rights Management for Multimedia The Universal Preservation Format: A Recommended Practice for Archiving Media and Electronic Records Design vs. Content: A Survey of Ten Popular Web Sites That Made Emotional Connections with the User Agents Based Modelling for a Peer-to-Peer MMOG Architecture A RIO-like Technique for Interactivity Loss Avoidance in Fast-Paced Multiplayer Online Games: A Preliminary Study Portholes and Planes: Faster Dynamic Evaluation of Potentially Visible Sets and more...
An Approach for the Unified Time Management Mechanism for HLA
Authors: Jiung-Yao Huang, Ming-Chih Tung, Lin Hui, Ming-Che Lee
Venue: Simulation (2005)

The High Level Architecture (HLA) is the IEEE 1516 standard to model and design a distributive simulation environment. It establishes a common distributed simulation framework, which facilitates the interoperability and reuse of simulation components. However, some HLA services are very low level and difficult to use, especially when a simulation is designed with a particular time synchronization mechanism. This article describes an agent interface, called Smart Time Management (STM). The capabilities of the STM include the following: taking over the event's time-stamp tagging work, maintaining a lookahead value, and unifying different time advance approaches provided by the HLA runtime infrastructure. In addition, it adopts the time warp mechanism for optimistic simulation. In conclusion, the STM presents a unified and scalable middle layer to allow the user to construct an HLA federation with a unanimous Time Management interface when solving the synchronization issue.