ppxscal/embedding_network huggingface dataset:
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates
Authors: Matan Ninio, Eyal Privman, Tal Pupko, Nir Friedman
Venue: Bioinformatics (2007)

Distance-based methods for phylogeny reconstruction are the fastest and easiest to use, and their popularity is accordingly high. They are also the only known methods that can cope with huge datasets of thousands of sequences. These methods rely on evolutionary distance estimation and are sensitive to errors in such estimations. In this study, a novel Bayesian method for estimation of evolutionary distances is developed. The proposed method enables the use of a sophisticated evolutionary model that better accounts for among-site rate variation (ASRV), thereby improving the accuracy of distance estimation. Rate variations are estimated within a Bayesian framework by extracting information from the entire dataset of sequences, unlike standard methods that can only use one pair of sequences at a time. We compare the accuracy of a cascade of distance estimation methods, starting from commonly used methods and moving towards the more sophisticated novel method. Simulation studies show significant improvements in the accuracy of distance estimation by the novel method over the commonly used ones. We demonstrate the effect of the improved accuracy on tree reconstruction using both real and simulated protein sequence alignments. An implementation of this method is available as part of the SEMPHY package. Contact: talp@tau.ac.il
A geometric approach to non-parametric density estimation
Authors: Matthew Browne
Venue: Pattern Recognition (2007)

A novel non-parametric density estimator is developed based on geometric principles. A penalised centroidal Voronoi tessellation forms the basis of the estimator, which allows the data to self-organise in order to minimise estimate bias and variance. This approach is a marked departure from usual methods based on local averaging, and has the advantage of being naturally adaptive to local sample density (scale-invariance). The estimator does not require the introduction of a plug-in kernel, thus avoiding assumptions of symmetricity and morphology. A numerical experiment is conducted to illustrate the behaviour of the estimator, and it's characteristics are discussed.
Tangible play: research and design for tangible and tabletop games
Authors: Elise van den Hoven, Ali Mazalek
Venue: Proceedings of the 12th international conference on Intelligent user interfaces (2007)

This workshop addresses questions related to the areas of tangible interaction, game design and emerging technologies for tangible and tabletop games. We bring together researchers and practitioners from diverse fields related to these topics, such as HCI, computer science, interaction design and game design. We seek collaborative ways to move forward the field of tangible and tabletop games.
O'Leary Series: Microsoft PowerPoint 2003 Introductory, 1 edition
Authors: Timothy J. O'Leary, Linda I. O'Leary
Venue:  (2004)

The goal of the O’Leary Series is to give students a basic understanding of computing concepts and to build the skills necessary to ensure that information technology is an advantage in whatever career they choose in life. The O’Leary Microsoft Office 2003 texts are crafted to be the true step-by-step way for students to develop Microsoft Office application skills. The text design emphasizes step-by-step instructions with full screen captures that illustrate the results of each step performed. Each Tutorial (chapter) combines conceptual coverage with detailed software-specific instructions. A running case that is featured in each tutorial highlights the real-world applications of each software program and leads students step-by-step from problem to solution.Table of contentsTutorial 1: Creating a Presentation Tutorial 2: Modifying and Refining a PresentationWorking Together: Copying, Embedding and Linking Between Applications Tutorial 3: Using Advanced Presentation Features Tutorial 4: Creating a Presentation for a Kiosk and the Web Working Together 2: Reviewing, Embedding, and Broadcasting a Presentation
Information Architecture for the World Wide Web
Authors: Peter Morville, Louis Rosenfeld
Venue:  (2006)

The post-Ajaxian Web 2.0 world of wikis, folksonomies, and mashups makes well-planned information architecture even more essential. How do you present large volumes of information to people who need to find what they're looking for quickly? This classic primer shows information architects, designers, and web site developers how to build large-scale and maintainable web sites that are appealing and easy to navigate.The new edition is thoroughly updated to address emerging technologies -- with recent examples, new scenarios, and information on best practices -- while maintaining its focus on fundamentals. With topics that range from aesthetics to mechanics, Information Architecture for the World Wide Web explains how to create interfaces that users can understand right away. Inside, you'll find:An overview of information architecture for both newcomers and experienced practitionersThe fundamental components of an architecture, illustrating the interconnected nature of these systems. Updated, with updates for tagging, folksonomies, social classification, and guided navigationTools, techniques, and methods that take you from research to strategy and design to implementation. This edition discusses blueprints, wireframes and the role of diagrams in the design phaseA series of short essays that provide practical tips and philosophical advice for those who work on information architectureThe business context of practicing and promoting information architecture, including recent lessons on how to handle enterprise architectureCase studies on the evolution of two large and very different information architectures, illustrating best practices along the wayHow do you document the rich interfaces of web applications? How do you design for multiple platforms and mobile devices? With emphasis on goals and approaches over tactics or technologies, this enormously popular book gives you knowledge about information architecture with a framework that allows you to learn new approaches -- and unlearn outmoded ones.
Multivariate image similarity in the compressed domain using statistical graph matching
Authors: Ch. Theoharatos, V. K. Pothos, N. A. Laskaris, G. Economou, S. Fotopoulos
Venue: Pattern Recognition (2006)

We address the problem of image similarity in the compressed domain, using a multivariate statistical test for comparing color distributions. Our approach is based on the multivariate Wald-Wolfowitz test, a nonparametric test that assesses the commonality between two different sets of multivariate observations. Using some pre-selected feature attributes, the similarity measure provides a comprehensive estimate of the match between different images based on graph theory and the notion of minimal spanning tree (MST). Feature extraction is directly provided from the JPEG discrete cosine transform (DCT) domain, without involving full decompression or inverse DCT. Based on the zig-zag scheme, a novel selection technique is introduced that guarantees image's enhanced invariance to geometric transformations. To demonstrate the performance of the proposed method, the application on a diverse collection of images has been systematically studied in a query-by-example image retrieval task. Experimental results show that a powerful measure of similarity between compressed images can emerge from the statistical comparison of their pattern representations.
URICA: Usage-awaRe Interactive Content Adaptation for mobile devices
Authors: Iqbal Mohomed, Jim Chengming Cai, Eyal de Lara
Venue: Proceedings of the 1st ACM SIGOPS/EuroSys European Conference on Computer Systems 2006 (2006)

Usage-awaRe Interactive Content Adaptation (URICA) is an automatic technique that adapts content for display on mobile devices based on usage semantics. URICA allows users who are unsatisfied with the system's adaptation decision to take control of the adaptation process and make changes until the content is suitably adapted for their purposes. The successful adaptation is recorded and used in making future adaptation decisions. To validate URICA, we implemented a prototype system called Chameleon that performs fidelity adaptation on web images. We conducted a user study in which participants used Chameleon to browse image-rich web pages on bandwidth-limited cellular links and used the collected traces to evaluate our system. We show that Chameleon reduces the latency for browsing web content by up to 65% and reduces bandwidth consumption by up to 80%. Chameleon also allows users to exchange bandwidth consumption for user interaction based on their personal preferences.
Information Trapping: Real-Time Research on the Web
Authors: Tara Calishain
Venue:  (2006)

How many times have you run a Google search that resulted in thousands of results? With over 8 billion pages online and more posted every day, the Web more than likely contains the information you're looking for - if only you could find it. In Information Trapping: Real-Time Research on the Web, Internet-search-engine expert Tara Calishain makes researching more efficient and rewarding for anyone for whom the Web is an indispensable tool - academics, journalists, scientists, and professionals, as well as bloggers, genealogists, and hobbyists. She does so by teaching the latest techniques for building automated information-gathering systems. As an alternative to the typical one-time search for information, Tara demonstrates how readers can use RSS feeds, page monitoring tools, and other software to set up information streams of many different data types - from text to multimedia to conversations - for capture and review.
Modeling and analysis of biological processes by mem(brane) calculi and systems
Authors: Nadia Busi, Claudio Zandron
Venue: Proceedings of the 38th conference on Winter simulation (2006)

In recent years, the modeling and analysis techniques developed in the area of formal languages and of concurrent process calculi have been successfully applied to the field of Systems Biology. In this setting, Brane Calculi and Membrane Systems are two of the most prominent approaches for the modeling of the behaviour of biological membranes. Membrane Systems have been introduced by Gh. P&acaron;un as a class of distributed parallel computing devices of a biochemical type, while Brane Calculi are a family of process calculi, based on a set of biologically inspired primitives of membrane interaction. In this paper we model the behaviour of a biological process - namely, the LDL Cholesterol Degradation Pathway - in both Brane Calculi and Membrane Systems. We also provide a brief discussion on the application of analysis techniques to this case study.
Fingerprint matching using ridges
Authors: Jianjiang Feng, Zhengyu Ouyang, Anni Cai
Venue: Pattern Recognition (2006)

Traditionally, fingerprint matching is minutia-based, which establishes the minutiae correspondences between two fingerprints. In this paper, a novel fingerprint matching algorithm is presented, which establishes both the ridge correspondences and the minutia correspondences between two fingerprints. First N initial substructure (including a minutia and adjacent ridges) pairs are found by a novel alignment method. Based on each of these substructure pairs, ridge matching is performed by incrementally matching ridges and minutiae, and then a matching score is computed. The maximum one of the N scores is used as the final matching score of two fingerprints. Preliminary results on FVC2002 databases show that ridge matching approach performs comparably with the minutia-based one.
Capabilities of outlier detection schemes in large datasets, framework and methodologies
Authors: Jian Tang, Zhixiang Chen, Ada Waichee Fu, David W. Cheung
Venue: Knowledge and Information Systems (2006)

Outlier detection is concerned with discovering exceptional behaviors of objects. Its theoretical principle and practical implementation lay a foundation for some important applications such as credit card fraud detection, discovering criminal behaviors in e-commerce, discovering computer intrusion, etc. In this paper, we first present a unified model for several existing outlier detection schemes, and propose a compatibility theory, which establishes a framework for describing the capabilities for various outlier formulation schemes in terms of matching users'intuitions. Under this framework, we show that the density-based scheme is more powerful than the distance-based scheme when a dataset contains patterns with diverse characteristics. The density-based scheme, however, is less effective when the patterns are of comparable densities with the outliers. We then introduce a connectivity-based scheme that improves the effectiveness of the density-based scheme when a pattern itself is of similar density as an outlier. We compare density-based and connectivity-based schemes in terms of their strengths and weaknesses, and demonstrate applications with different features where each of them is more effective than the other. Finally, connectivity-based and density-based schemes are comparatively evaluated on both real-life and synthetic datasets in terms of recall, precision, rank power and implementation-free metrics.
On models, modelling and the distinctive nature of model-based reasoning
Venue: AI Communications (1999)

What are models and how is the relatively new technology of Model-Based Reasoning different from conventional modelling in science and engineering? These questions are explored in this paper by examining the fundamental nature of models. We explore model characteristics, different classes of model and various dimensions of the modelling space. Our analysis puts models into a general framework from which emerges the interesting case of qualitative models. Inevitably, such a broad treatment must be a personal view but the objective is to draw attention to key issues. Our aim is to increase understanding of the modelling process and clarify the options available for model builders. We argue that the technology known as Model-Based Reasoning, which uses explicit, executable models is a powerful and widely applicable approach that has much potential for managing the complexity encountered in many application domains. The advantages of the method include an emphasis on principled model design, the ability to guarantee completeness of the solutions and powerful reuse and automation opportunities.
Adobe Photoshop Master Class: Maggie Taylor's Landscape of Dreams (Adobe Master Class)
Authors: Amy Standen
Venue:  (2005)

Maggie Taylor's digital photo collages have been described as a contemporary exploration of the Surrealist world view. In Taylor's strange, parallel universe, birds ride bicycles, ideas materialize in the shape of clouds, and wings sprout from the backs of prim Victorian women. Starting with objects that she finds on eBay, in flea markets, and in her own surroundings, Taylor then uses her ï¾ flatbed scanner, Adobe Photoshop, and an Iris printer, to produce images of surprising beauty and emotional impact. ï¾ Adobe Photoshop Master Class: Maggie Taylor's Landscape of Dreams offers a close and richly illustrated examination of Taylor's practice, tracing her images from inspiration through execution. Taylor explains her influences, both in art and in her own life, and takes the reader inside the making of some of her intriguing, painterly work. Along the way, we hear from respected artists and critics familiar with Taylor's work, and from the artist herself, in conversation with the author. ï¾ Illustrated with more than 65 color plates, Landscape of Dreams is essential reading (and viewing) for all those interested in applying technology to a creative personal vision. 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
A fluid-structure interaction method with solid-rigid contact for heart valve dynamics
Authors: R. van Loon, P. D. Anderson, F. N. van de Vosse
Venue: Journal of Computational Physics (2006)

A computational method is proposed for problems where fluid-structure interaction is combined with solid-rigid contact. This combination is particularly important for the dynamics and impact of heart valves. The Navier-Stokes equation in an Eulerian setting is coupled to a Neo-Hookean solid model using a Lagrangian description. A fictitious domain method extended with a local mesh adaptation algorithm provides the required flexibility with respect to the motion and deformation of the valve. In addition, it ensures the solids ability of sustaining pressures present in the fluid. Making use of the fact that the fluid and solid mesh are not required to be connected conformingly, it is shown that the model can be extended with a contact algorithm without introducing meshing complications near the contact surfaces.
Wi-Fi Hotspots: Setting Up Public Wireless Internet Access (Networking Technology)
Authors: Eric Geier
Venue:  (2006)

Wi-Fi HotspotsSetting Up Public Wireless Internet AccessInstalling and operating a Wi-Fi hotspot allows you to attract customers and differentiate your business. Deploying even a small wireless network has proven to be a difficult task for the average consumer, however. With this book as your guide, you can painlessly figure out the requirements for your Wi-Fi hotspot, how to properly set it up, how to operate it, and how to optimize it for the needs and security of your customers.Wi-Fi Hotspots helps you throughout the entire process of setting up a hotspot to offer free or fee-based Internet access to the general public: Understand the benefits to your business of hosting a hotspot Decide what type of hotspot you should implement Examine what equipment is best suited for your hotspot Follow step-by-step procedures for setting up your hotspot Get the word out about your hotspot availability Ensure your hotspot is not used improperly Evaluate Wi-Fi security concerns Fix common problems hotspot users face Increase the coverage area of your Wi-Fi hotspotWhether you are a small business owner looking to attract customers and distinguish your business or you are an IT professional at a larger organization looking to establish hotspot connectivity, this book provides you with everything you need to know in order to provide public wireless Internet access.Eric Geier is a computing and wireless networking author and consultant. For several years, he's be employed with Wireless-Nets, Ltd., a consulting firm focusing on the implementation of wireless mobile solutions and training.Eric is a Certified Wireless Network Administrator (CWNA). He is an author and contributor of several books and eLearning (CBT) courses. He is a regular contributor at Wi-FiPlanet.com.For more information about Eric Geier, visit his website at http://www.egeier.comCompanion CD-ROMThe companion CD-ROM contains two software utilities, ZoneCD and NetStumbler, to help you implement and manage your Wi-Fi hotspot.This book is part of the Networking Technology Series fromCisco Press®, which offers networking professionals valuable information for constructing efficient networks, understanding new technologies, and building successful careers.Category: Wireless NetworkingCovers: Wi-Fi Hotspots
iPod Book: Doing Cool Stuff with the iPod and the iTunes Music Store, The (2nd Edition)
Authors: Scott Kelby
Venue:  (2005)

There are basically two kinds of iPod books: (1) The "tell me all about it" kind, which includes in-depth discussions on compression algorithms, debates about analog vs. digital equalizers; and tutorials on how to export your playlist in Unicode format. (2) There's this book. It's not a "tell me all about it" book, it's a "show me how to do it" book.Award-winning author Scott Kelby shows you step-by-step how it's all done, using the same casual, plain-English style that has made him one of the world's best-selling technology authors. You'll learn how to do only the most important, most requested, and just plain cool things you're going to want to do with your iPodï¾so you can start having fun with it today. Right now!Each page covers just one topic, complete with full color photos, making it easy to find just what you're looking for fast. Plus, it shows you how to get the most from the iTunes Music Store, how to integrate your iPod into your car, which iPod accessories are hot, how to use photos with your iPod, and everything you need to know about the latest addition to the iPod family, the new iPod Nano! It's all hereï¾in the only book of its kindï¾and you're gonna love it!
Your UNIX: The Ultimate Guide, 2 edition
Authors: Sumitabha Das
Venue:  (2005)

Your UNIX: The Ultimate Guide is both an outstanding pedagogical tool and an exhaustive reference. It is the ideal text for any Unix course. It can also be used for any introductory programming course that includes Unix and for advanced courses such as those on Operating Systems and System Administration. Excellent pedagogy is implemented throughout. Real-world examples make it easier for students to grasp concepts while chapters on advanced material take more experienced students beyond the basics. Over nine hundred exercises and self-test questions allow students to test and reinforce their understanding of material at different levels. This book also features coverage of Linux, where Linux differs from UNIX. Table of contents1 Introducing UNIX2 Becoming Familiar with UNIX Commands3 The File System4 File Attributes5 The vi/vim Editor6 The GNU emacs Editor7 The Shell8 The Process9 The Shell - Customizing the Environment10 Simple Filters11 Filters Using Regular Expressions - grep and sed12 Filtering and Programming with awk13 Shell Programming14 Networking Tools15 perl - The Master Manipulator16 Program Development Tools17 Systems Programming I - Files18 Systems Programming II - Process Control19 System AdministrationAppendix A The C Shell - Programming ConstructsAppendix B The Korn and Bash Shells - Exclusive Programming ConstructsAppendix C vi/vim and emacs Command ReferenceAppendix D The Regular Expression SupersetAppendix E The HOWTOAppendix F The ASCII Character SetAppendix G GlossaryAppendix H Solutions to Self-Test Questions 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
Passenger travel behavior model in railway network simulation
Authors: Ting Li, Eric van Heck, Peter Vervest, Jasper Voskuilen, Freek Hofker, Fred Jansma
Venue: Proceedings of the 38th conference on Winter simulation (2006)

Transportation planners and public transport operators alike have become increasingly aware of the need to diffuse the concentration of the peak period travel. Differentiated pricing is one possible method to even out the demand and reduce peak load requirement. An evaluation of the potential effectiveness of strategies directed to flatten the demand distribution requires an understanding of the underlying factors that drive travel behavior (e.g., time-shifting, route change, mode change) with regard to price and service. In this paper, we present a Passenger Railway Network Simulation model with the intention of linking supply and demand. The objective is to evaluate the differentiated pricing impact on the passenger travel behavior, and consequently on the overall network performance, both financially and operationally. This paper focuses on the design and modeling approach of the Travel Behavior Model.