ppxscal/embedding_network huggingface dataset:
Exploiting homogeneity in protein sequence clusters for construction of protein family hierarchies
Authors: Chien-Yu Chen, Wen-Chin Chung, Chung-Tsai Su
Venue: Pattern Recognition (2006)

In the field of proteomics, protein hierarchies based on sequence analysis have been extensively applied to automate the annotations of new proteins and facilitate the discovery and analysis of protein families. However, the presence of ambiguous similarities in large databases increases the difficulty of delivering protein family hierarchies with favorable sensitivity and specificity. This work develops the HomoClust algorithm that exploits the homogeneity of protein sequences in generating protein family hierarchies. HomoClust improves the clustering quality of traditional hierarchical clustering algorithms by adopting different clustering mechanisms for different levels of sequence similarity. With considering homogeneity detection during clustering process, HomoClust increases the sensitivity of protein clusters without a drop in high specificity.
QuickSteps to Winning Business Presentations, 1 edition
Authors: Carole Boggs Matthews, Martin Matthews
Venue:  (2006)

A hands-on, visual guide to mastering business presentation skills With its clear explanations and illustrative graphics, QuickSteps to Winning Business Presentations is the fastest, easiest way to achieve professional business presentation skills using Microsoft PowerPoint. Learn how to conceptualize presentations, gather and prepare materials from a variety of sources, and adapt presentations to different types of audiences and situations, including Web delivery. Step-by-step instructions on using PowerPoint’s versatile features, such as animation, sound, graphics, and video, are also included. In no time, you will dramatically improve your presentation skills.
Induced uncertain linguistic OWA operators applied to group decision making
Authors: Zeshui Xu
Venue: Information Fusion (2006)

The ordered weighted averaging (OWA) operator was developed by Yager [IEEE Trans. Syst., Man, Cybernet. 18 (1998) 183]. Later, Yager and Filev [IEEE Trans. Syst., Man, Cybernet.--Part B 29 (1999) 141] introduced a more general class of OWA operators called the induced ordered weighted averaging (IOWA) operators, which take as their argument pairs, called OWA pairs, in which one component is used to induce an ordering over the second components which are exact numerical values and then aggregated. The aim of this paper is to develop some induced uncertain linguistic OWA (IULOWA) operators, in which the second components are uncertain linguistic variables. Some desirable properties of the IULOWA operators are studied, and then, the IULOWA operators are applied to group decision making with uncertain linguistic information.
Disturbing the Dyson conjecture, in a generally GOOD way
Authors: Andrew V. Sills
Venue: Journal of Combinatorial Theory Series A (2006)

Dyson's celebrated constant term conjecture [F.J. Dyson, Statistical theory of the energy levels of complex systems I, J. Math. Phys. 3 (1962) 140-156] states that the constant term in the expansion of Π1 ≤ i ≠ j ≤ n(1 - xi/xj)aj is the multinomial coefficient (a1 + a2 + ... + an)!/(a1!a2! ... an!). The definitive proof was given by I.J. Good [I.J. Good, Short proof of a conjecture of Dyson, J. Math. Phys. 11 (1970) 1884]. Later, Andrews extended Dyson's conjecture to a q-analog [G.E. Andrews, Problems and prospects for basic hypergeometric functions, in: R. Askey (Ed.), The Theory and Application of Special Functions, Academic Press, New York, 1975, pp. 191-224]. In this paper, closed form expressions are given for the coefficients of several other terms in the Dyson product, and are proved using an extension of Good's idea. Also, conjectures for the corresponding q-analogs are supplied. Finally, perturbed versions of the q-Dixon summation formula are presented.
Linux System Programming: Talking Directly to the Kernel and C Library
Authors: Robert Love
Venue:  (2007)

This book is about writing software that makes the most effective use of the system you're running on -- code that interfaces directly with the kernel and core system libraries, including the shell, text editor, compiler, debugger, core utilities, and system daemons. The majority of both Unix and Linux code is still written at the system level, and Linux System Programming focuses on everything above the kernel, where applications such as Apache, bash, cp, vim, Emacs, gcc, gdb, glibc, ls, mv, and X exist. Written primarily for engineers looking to program (better) at the low level, this book is an ideal teaching tool for any programmer. Even with the trend toward high-level development, either through web software (such as PHP) or managed code (C#), someone still has to write the PHP interpreter and the C# virtual machine. Linux System Programming gives you an understanding of core internals that makes for better code, no matter where it appears in the stack. Debugging high-level code often requires you to understand the system calls and kernel behavior of your operating system, too. Key topics include: An overview of Linux, the kernel, the C library, and the C compilerReading from and writing to files, along with other basic file I/O operations, including how the Linux kernel implements and manages file I/OBuffer size management, including the Standard I/O libraryAdvanced I/O interfaces, memory mappings, and optimization techniquesThe family of system calls for basic process managementAdvanced process management, including real-time processesFile and directories-creating, moving, copying, deleting, and managing themMemory management -- interfaces for allocating memory, managing the memory you have, and optimizing your memory accessSignals and their role on a Unix system, plus basic and advanced signal interfacesTime, sleeping, and clock management, starting with the basics and continuing through POSIX clocks and high resolution timers With Linux System Programming, you will be able to take an in-depth look at Linux from both a theoretical and an applied perspective as you cover a wide range of programming topics.
Software spotlight focus on protecting data with DESlock
Authors: Gilbert Held
Venue: International Journal of Network Management (2007)

Data protection is similar in some respects to the weather. A lot of people may talk about it, but not many persons actually try to change things for the better. Perhaps part of the problem associated with the use of encryption software that limits its use is the need to remember a series of additional passwords and the consequence associated with forgetting these passwords. Fortunately, the proliferation of USB storage devices enables software developers to use this near-ubiquitous hardware device to facilitate software operations. One such product that employs a USB storage device to facilitate the encryption of data is DESlock+, a feature-rich Windows data encryption utility program from Data Encryption Systems Ltd. of Somerset, UK, which is the focus of this column.
A genetic algorithm and a particle swarm optimizer hybridized with Nelder-Mead simplex search
Authors: Shu-Kai S. Fan, Yun-Chia Liang, Erwie Zahara
Venue: Computers and Industrial Engineering (2006)

This paper integrates Nelder-Mead simplex search method (NM) with genetic algorithm (GA) and particle swarm optimization (PSO), respectively, in an attempt to locate the global optimal solutions for the nonlinear continuous variable functions mainly focusing on response surface methodology (RSM). Both the hybrid NM-GA and NM-PSO algorithms incorporate concepts from the NM, GA or PSO, which are readily to implement in practice and the computation of functional derivatives is not necessary. The hybrid methods were first illustrated through four test functions from the RSM literature and were compared with original NM, GA and PSO algorithms. In each test scheme, the effectiveness, efficiency and robustness of these methods were evaluated via associated performance statistics, and the proposed hybrid approaches prove to be very suitable for solving the optimization problems of RSM-type. The hybrid methods were then tested by ten difficult nonlinear continuous functions and were compared with the best known heuristics in the literature. The results show that both hybrid algorithms were able to reach the global optimum in all runs within a comparably computational expense.
Photometric Stereo with General, Unknown Lighting
Authors: Ronen Basri, David Jacobs, Ira Kemelmacher
Venue: International Journal of Computer Vision (2007)

Work on photometric stereo has shown how to recover the shape and reflectance properties of an object using multiple images taken with a fixed viewpoint and variable lighting conditions. This work has primarily relied on known lighting conditions or the presence of a single point source of light in each image. In this paper we show how to perform photometric stereo assuming that all lights in a scene are distant from the object but otherwise unconstrained. Lighting in each image may be an unknown and may include arbitrary combination of diffuse, point and extended sources. Our work is based on recent results showing that for Lambertian objects, general lighting conditions can be represented using low order spherical harmonics. Using this representation we can recover shape by performing a simple optimization in a low-dimensional space. We also analyze the shape ambiguities that arise in such a representation. We demonstrate our method by reconstructing the shape of objects from images obtained under a variety of lightings. We further compare the reconstructed shapes against shapes obtained with a laser scanner.
Locally linear metric adaptation with application to semi-supervised clustering and image retrieval
Authors: Hong Chang, Dit-Yan Yeung
Venue: Pattern Recognition (2006)

Many computer vision and pattern recognition algorithms are very sensitive to the choice of an appropriate distance metric. Some recent research sought to address a variant of the conventional clustering problem called semi-supervised clustering, which performs clustering in the presence of some background knowledge or supervisory information expressed as pairwise similarity or dissimilarity constraints. However, existing metric learning methods for semi-supervised clustering mostly perform global metric learning through a linear transformation. In this paper, we propose a new metric learning method that performs nonlinear transformation globally but linear transformation locally. In particular, we formulate the learning problem as an optimization problem and present three methods for solving it. Through some toy data sets, we show empirically that our locally linear metric adaptation (LLMA) method can handle some difficult cases that cannot be handled satisfactorily by previous methods. We also demonstrate the effectiveness of our method on some UCI data sets. Besides applying LLMA to semi-supervised clustering, we have also used it to improve the performance of content-based image retrieval systems through metric learning. Experimental results based on two real-world image databases show that LLMA significantly outperforms other methods in boosting the image retrieval performance.
The rate of convergence for the cyclic projections algorithm II: norms of nonlinear operators
Authors: Frank Deutsch, Hein Hundal
Venue: Journal of Approximation Theory (2006)

The rate of convergence for the cyclic projections algorithm onto an intersection of finitely many closed convex sets in a Hilbert space is investigated. Recently we showed that this rate could be described in terms of the "angles" between the convex sets involved. Here we show that these angles may often be described in terms of the "norms" of certain nonlinear operators, and hence obtain an alternate way of computing this rate of convergence.
Chris Crawford on Interactive Storytelling (New Riders Games)
Authors: Chris Crawford
Venue:  (2004)

As a game designer or new media storyteller, you know that the story is everything. However, figuring out how to tell it interactively-and in a way that keeps your audience coming back for more-can be challenging. Here to help you out (and to open your mind to ever more creative ways of producing those stories) is the man who created the cult publication The Art of Computer Game Design and who has devoted much of his career to that very topic: Chris Crawford. To highlight the path for future gains in the quest for a truly interactive story, Chris provides a solid sampling of what doesn't work, contrasting unsuccessful methodologies with those that hold promise for the future. Throughout you'll find examples of contemporary games that rely on different technologies-and learn the storytelling lessons to be garnered from each of the past methodologies. Within the context of interactive storytelling, Chris explores ways of providing conflict and challenge, the difference between low- and high-interactivity designs, the necessity to move beyond purely visual thinking (so that the player is engaged on multiple levels), and more.
Multiscale diffusion Monte Carlo simulation of epitaxial growth
Authors: Chuan-Chih Chou, Michael L. Falk
Venue: Journal of Computational Physics (2006)

We present an accelerated kinetic Monte Carlo (KMC) simulation algorithm for molecular beam epitaxial growth during step flow. The acceleration is achieved by allowing adatoms far from the step edges to execute larger jumps with correspondingly reduced rates. The computational complexities of a number of different algorithmic implementations are analyzed and compared. The scaling of the accelerated algorithms are verified by test runs performed on a one-dimensional model. Both performance and accuracy are evaluated. One to two orders of magnitude increases of efficiency are achieved while preserving physical accuracy.
Semantic role labeling of nominalized predicates in Chinese
Authors: Nianwen Xue
Venue: Proceedings of the main conference on Human Language Technology Conference of the North American Chapter of the Association of Computational Linguistics (2006)

Recent work on semantic role labeling (SRL) has focused almost exclusively on the analysis of the predicate-argument structure of verbs, largely due to the lack of human-annotated resources for other types of predicates that can serve as training and test data for the semantic role labeling systems. However, it is well-known that verbs are not the only type of predicates that can take arguments. Most notably, nouns that are nominalized forms of verbs and relational nouns generally are also considered to have their own predicate-argument structure. In this paper we report results of SRL experiments on nominalized predicates in Chinese, using a newly completed corpus, the Chinese Nombank. We also discuss the impact of using publicly available manually annotated verb data to improve the SRL accuracy of nouns, exploiting a widely-held assumption that verbs and their nominalizations share the same predicate-argument structure. Finally, we discuss the results of applying reranking techniques to improve SRL accuracy for nominalized predicates, which showed insignificant improvement.
Grid harvest service: a performance system of grid computing
Authors: Ming Wu, Xian-He Sun
Venue: Journal of Parallel and Distributed Computing (2006)

Conventional performance evaluation mechanisms focus on dedicated systems. Grid computing infrastructure, on the other hand, is a shared collaborative environment constructed on virtual organizations. Each organization has its own resource management policy and usage pattern. The non-dedicated characteristic of Grid computing prevents the leverage of conventional performance evaluation systems. In this study, we introduce the grid harvest service (GHS) performance evaluation and task scheduling system for solving large-scale applications in a shared environment. GHS is based on a novel performance prediction model and a set of task scheduling algorithms. GHS supports three classes of task scheduling, single task, parallel processing and meta-task. Experimental results show that GHS provides a satisfactory solution for performance prediction and task scheduling of large applications and has a real potential.
Declarative failure recovery for sensor networks
Authors: Ramakrishna Gummadi, Nupur Kothari, Todd Millstein, Ramesh Govindan
Venue: Proceedings of the 6th international conference on Aspect-oriented software development (2007)

Wireless sensor networks consist of a system of distributed sensors embedded in the physical world, and promise to allow observation of previously unobservable phenomena. Since they are exposed to unpredictable environments, sensor-network applications must handle a wide variety of faults: software errors, node and link failures, and network partitions. The code to manually detect and recover from faults crosscuts the entire application, is tedious to implement correctly and efficiently, and is fragile in the face of program modifications. We investigate language support for modularly managing faults. Our insight is that such support can be naturally provided as an extension to existing "macroprogramming" systems for sensor networks. In such a system, a programmer describes a sensor network application as a centralized program; a compiler then produces equivalent node-level programs. We describe a simple checkpoint API for macroprograms, which can be automatically implemented in a distributed fashion across the network. We also describe declarative annotations that allow programmers to specify checkpointing strategies at a higher level of abstraction. We have implemented our approach in the Kairos macroprogramming system. Experiments show it to improve application availability by an order of magnitude and incur low messaging overhead.
Beginning Mobile Phone Game Programming
Authors: Michael Morrison
Venue:  (2004)

Build several fully functional games as well as a game engine to use for programming cell phone and mobile games with Beginning Mobile Phone Game Programming! The included CD provides the tool, code and graphics necessary to complete all exercises covered in the chapters. Beginning Cell Phone Game Programming demystifies wireless game programming by providing clear, practical lessons using the J2ME Game API. You will learn how to use the most popular mobile programming language, Java, to build compact games that can run on any Java-enabled device, including mobile phones, pagers and handheld computers. You will also learn to add a splash screen, create a demo mode, keep track of high scores, and test, debug, and deploy your games.Topics covered include: How to construct a game engine to drive mobile games. How to use Java 2 Micro Edition (J2ME) and the Java Game API to get the most performance out of your mobile games. How to implement sprite animation and control interactions among moving sprites. How to play sound effects and music in mobile games. How to take advantage of wireless networks to build mobile multiplayer games. How to design and develop a variety of different games spanning several video games genres. 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
Beginning Illustration and Storyboarding for Games (Premier Press Game Development (Paperback))
Authors: Les Pardew
Venue:  (2004)

Coverage includes- In 1987, Les Pardew started his career by creating the animation for Magic Johnson Fast Break Basketball on the Commodore 64. He soon found that he loved working on games and has been in the industry ever since. His work encompasses more than 100 video game titles, including some major titles such as Super Star Wars, NCAA Basketball, Starcraft: Brood War, James Bond 007, Robin Hood: Prince of Thieves, and CyberTiger. He currently serves as President of Alpine Studios, which he founded with Ross Wolfley in the fall of 2000. Alpine Studios is a game development company focusing on family-friendly games. Alpine Studios' products include Kublox, Combat Medic, Motocross Mania 2, and Ford Truck Mania. Les is also the author of Game Art for Teens. The only book to specifically address illustration and storyboarding for games. Full of illustrations and step-by-step projects. Offers real-world instruction for game concept art development. Also touches on basic art skill development. Comes complete with Q&As, extensice end-of-chapter exercises, projects, and a CD to reinforce self-practice and learning.
A study of identical twins' palmprints for personal verification
Authors: Adams Wai-Kin Kong, David Zhang, Guangming Lu
Venue: Pattern Recognition (2006)

Automatic biometric systems based on human characteristics for personal identification have attracted great attention. Their performance highly depends on the distinctive information in the biometrics. Identical twins having the closest genetics-based relationship are expected to have maximum similarity in their biometrics. Classifying identical twins is a challenging problem for some automatic biometric systems. Palmprint has been studied for personal identification for over seven years. Most of the previous research concentrates on algorithm development. In this paper, we systemically examine palmprints from the same DNA for automatic personal identification and to uncover the genetically related palmprint features. The experimental results show that the three principal lines and some portions of weak lines are genetically related features but our palms still contain rich genetically unrelated features for classifying identical twins.
A proof of the q, t-square conjecture
Authors: Mahir Can, Nicholas Loehr
Venue: Journal of Combinatorial Theory Series A (2006)

We prove a combinatorial formula conjectured by Loehr and Warrington for the coefficient of the sign character in ∇ (pn). Here ∇ denotes the Bergeron-Garsia nabla operator, and pn is a power-sum symmetric function. The combinatorial formula enumerates lattice paths in an n × n square according to two suitable statistics.
JBoss at Work: A Practical Guide
Authors: Tom Marrs, Scott Davis
Venue:  (2005)

Consisting of a number of well-known open source products, JBoss is more a family of interrelated services than a single monolithic application. But, as with any tool that's as feature-rich as JBoss, there are number of pitfalls and complexities, too. Most developers struggle with the same issues when deploying J2EE applications on JBoss: they have trouble getting the many J2EE and JBoss deployment descriptors to work together; they have difficulty finding out how to get started; their projects don't have a packaging and deployment strategy that grows with the application; or, they find the Class Loaders confusing and don't know how to use them, which can cause problems.JBoss at Work: A Practical Guide helps developers overcome these challenges. As you work through the book, you'll build a project using extensive code examples. You'll delve into all the major facets of J2EE application deployment on JBoss, including JSPs, Servlets, EJBs, JMS, JNDI, web services, JavaMail, JDBC, and Hibernate. With the help of this book, you'll:Implement a full J2EE application and deploy it on JBossDiscover how to use the latest features of JBoss 4 and J2EE 1.4, including J2EE-compliant web servicesMaster J2EE application deployment on JBoss with EARs, WARs, and EJB JARsUnderstand the core J2EE deployment descriptors and how they integrate with JBoss-specific descriptorsBase your security strategy on JAASWritten for Java developers who want to use JBoss on their projects, the book covers the gamut of deploying J2EE technologies on JBoss, providing a brief survey of each subject aimed at the working professional with limited time.If you're one of the legions of developers who have decided to give JBoss a try, then JBoss at Work: A Practical Guide is your next logical purchase. It'll show you in plain language how to use the fastest growing open source tool in the industry today. If you've worked with JBoss before, this book will get you up to speed on JBoss 4, JBoss WS (web services), and Hibernate 3.