ppxscal/embedding_network huggingface dataset:
Phylogenetic reconstruction from non-genomic data
Authors: José C. Clemente, Kenji Satou, Gabriel Valiente
Venue: Bioinformatics (2007)

Motivation: Recent results related to horizontal gene transfer suggest that phylogenetic reconstruction cannot be determined conclusively from sequence data, resulting in a shift from approaches based on polymorphism information in DNA or protein sequence to studies aimed at understanding the evolution of complete biological processes. The increasing amount of available information on metabolic pathways for several species makes it of greater relevance to understand the similarities and differences among such pathways. These similarities can then be used to infer phylogenetic trees not based exclusively in sequence data, therefore avoiding the previously mentioned problems. Results: In this article, we present a method to assess the structural similarity of metabolic pathways for several organisms. Our algorithms work by using one of the three possible enzyme similarity measures (hierarchical, information content, gene ontology), and one of the two clustering methods (neighbor-joining, unweighted pair group method with arithmetic mean), to produce a phylogenetic tree both in Newick and graphic format. The web server implementing our algorithms is optimized to answer queries in linear time. Availability: The software is available for free public use on a web server, at the address http://www.jaist.ac.jp/~clemente/cgi-bin/phylo.pl. It is available on demand in source code form for research use to educational institutions, non-profit research institutes, government research laboratories and individuals, for non-exclusive use, without the right of the licensee to further redistribute the source code. Contact:valiente@lsi.upc.edu; clemente@jaist.ac.jp
Clustering aggregation
Authors: Aristides Gionis, Heikki Mannila, Panayiotis Tsaparas
Venue: ACM Transactions on Knowledge Discovery from Data (TKDD) (2007)

We consider the following problem: given a set of clusterings, find a single clustering that agrees as much as possible with the input clusterings. This problem, clustering aggregation, appears naturally in various contexts. For example, clustering categorical data is an instance of the clustering aggregation problem; each categorical attribute can be viewed as a clustering of the input rows where rows are grouped together if they take the same value on that attribute. Clustering aggregation can also be used as a metaclustering method to improve the robustness of clustering by combining the output of multiple algorithms. Furthermore, the problem formulation does not require a priori information about the number of clusters; it is naturally determined by the optimization function. In this article, we give a formal statement of the clustering aggregation problem, and we propose a number of algorithms. Our algorithms make use of the connection between clustering aggregation and the problem of correlation clustering. Although the problems we consider are NP-hard, for several of our methods, we provide theoretical guarantees on the quality of the solutions. Our work provides the best deterministic approximation algorithm for the variation of the correlation clustering problem we consider. We also show how sampling can be used to scale the algorithms for large datasets. We give an extensive empirical evaluation demonstrating the usefulness of the problem and of the solutions.
B-rep SE: simplicially enhanced boundary representation
Authors: Michael Freytag, Vadim Shapiro
Venue: Proceedings of the ninth ACM symposium on Solid modeling and applications (2004)

Boundary representation (B-rep) is a popular representation scheme for mechanical objects due to its ability to accurately represent piecewise smooth surfaces bounding solids. However, non-trivial topology and geometry of the surface patches hinder point generation, classification, searching, and other algorithms. We propose a new hybrid representation that addresses these shortcomings by imposing on the boundary representation an additional simplicial structure. The simplicial structure applies a triangle-mesh metaphor to the usual boundary representation, allowing access to points on the exact solid boundary or its many approximations. The resulting simplicially enhanced boundary representation (B-rep SE) simplifies and accelerates the usual boundary representation queries. We discuss full implementation of B-rep SE with the Parasolid kernel and demonstrate the advantages of B-rep SE in applications that integrate and visualize arbitrary fields on a solid's boundary.
Simultaneous alignment and annotation of cis-regulatory regions
Authors: Abha Singh Bais, Steffen Grossmann, Martin Vingron
Venue: Bioinformatics (2007)

Motivation: Current methods that annotate conserved transcription factor binding sites in an alignment of two regulatory regions perform the alignment and annotation step separately and combine the results in the end. If the site descriptions are weak or the sequence similarity is low, the local gap structure of the alignment poses a problem in detecting the conserved sites. It is therefore desirable to have an approach that is able to simultaneously consider the alignment as well as possibly matching site locations. Results: With SimAnn we have developed a tool that serves exactly this purpose. By combining the annotation step and the alignment of the two sequences into one algorithm, it detects conserved sites more clearly. It has the additional advantage that all parameters are calculated based on statistical considerations. This allows for its successful application with any binding site model of interest. We present the algorithm and the approach for parameter selection and compare its performance with that of other, non-simultaneous methods on both simulated and real data. Availability: A command-line based C++ implementation of SimAnn is available from the authors upon request. In addition, we provide Perl scripts for calculating the input parameters based on statistical considerations. Contact: bais@molgen.mpg.de
MCSA/MCSE Managing and Maintaining a Windows Server 2003 Environment Exam Cram 2 (Exam Cram 70-292)
Authors: Bruce Parrish, Kirk Hausman, Ed Tittel
Venue:  (2003)

Your resource to upgrading your MCSE or MCSA Certification to Windows Sever 2003!Join the ranks of readers who have trusted Exam Cram 2 to their certification preparation needs! The MCSA/MCSE Managing and Maintaining a Windows Server 2003 Environment Exam Cram 2 is focused on what you need to know to pass the 70-292 upgrade exam for Windows Server 2003. The Exam Cram 2 Method of Study provides you with a concise method to learn the exam topics. The book includes tips, exam notes, acronyms and memory joggers in order to help you pass the exam.Included in the MCSA/MCSE Managing and Maintaining a Windows Server 2003 Environment Exam Cram 2: A tear-out "Cram Sheet" for last minute test preparation. Two complete practice exams and answer keys with key explanations. The PrepLogic Practice Tests, test engine to simulate the testing environment and test your knowledge.Trust in the series that has helped many others achieve certification success - Exam Cram 2.
Mechanizing and Improving Dependency Pairs
Authors: Jürgen Giesl, René Thiemann, Peter Schneider-Kamp, Stephan Falke
Venue: Journal of Automated Reasoning (2006)

The dependency pair technique is a powerful method for automated termination and innermost termination proofs of term rewrite systems (TRSs). For any TRS, it generates inequality constraints that have to be satisfied by well-founded orders. We improve the dependency pair technique by considerably reducing the number of constraints produced for (innermost) termination proofs. Moreover, we extend transformation techniques to manipulate dependency pairs that simplify (innermost) termination proofs significantly. To fully mechanize the approach, we show how transformations and the search for suitable orders can be mechanized efficiently. We implemented our results in the automated termination prover AProVE and evaluated them on large collections of examples.
Business process transformation patterns & the business process transformation wizard
Authors: Bala Ramachandran, Kaori Fujiwara, Makoto Kano, Akio Koide, Jay Benayon
Venue: Proceedings of the 38th conference on Winter simulation (2006)

In spite of many advances in business process simulation technologies, their adoption by the business analyst community has been primarily limited to specialists. We propose a Business Process Transformation Wizard as a capability to bridge this gap. This enables analysts to explore different business process transformation options using Business Process Transformation patterns and analyze their performance using quantitative technologies. In this paper, we explain the approach encapsulated in the BPT Wizard and illustrate it with an example.
Modeling semiconductor tools for small lotsize FAB simulations
Authors: Kilian Schmidt, Jörg Weigang, Oliver Rose
Venue: Proceedings of the 38th conference on Winter simulation (2006)

Short cycle times are critical to the success of semiconductor manufacturing. The addition of more and more mask layers leads to higher raw process times and makes short cycle times an increasingly challenging task. One cycle time reduction possibility semiconductor manufacturers now look at is lotsize reduction. A reduction in lotsize transfers directly into lower raw process times. Modeling and simulation are key to assess opportunities and risks of such an approach. This paper looks at the implications that follow from small lotsizes for tool models used for the assessment.
Document zone content classification and its performance evaluation
Authors: Yalin Wang, Ihsin T. Phillips, Robert M. Haralick
Venue: Pattern Recognition (2006)

This paper describes an algorithm for the determination of zone content type of a given zone within a document image. We take a statistical based approach and represent each zone with 25 dimensional feature vectors. An optimized decision tree classifier is used to classify each zone into one of nine zone content classes. A performance evaluation protocol is proposed. The training and testing data sets include a total of 24,177 zones from the University of Washington English Document Image database III. The algorithm accuracy is 98.45% with a mean false alarm rate of 0.50%.
Introduction To UNIX, 1 edition
Authors: Kate Wrightson, Joe Merlino
Venue:  (2002)

Introduction to UNIX has been carefully developed to meet the needs of students at the college/university level. Most other UNIX books published today are designed for the working professional. This book was written for students taking an introductory course in a UNIX based computer class. Both majors and non-majors may take this course; as there is no prior knowledge of UNIX required. Upon completion of this course, students will be able to manage most common activities in a UNIX shell account, use standard applications in an X-Windows environment and will have had some introduction to standard UNIX system administration.Table of contentsPart I – UNIX BasicsChapter 1 – What is UNIX?Chapter 2 – Basic UNIX ConceptsChapter 3 – Understanding UNIX CommandsChapter 4 – The File SystemChapter 5 – Jobs and ProcessesChapter 6 – Using the ShellPart II – Working with UNIXChapter 7 – The vi EditorChapter 8 – Other Text EditorsChapter 9 – Internet ApplicationsChapter 10 – Networking IChapter 11 – Networking IIPart III – Shell ProgrammingChapter 12 – Shell Programming IChapter 13 – Shell Programming IIChapter 14 – Shell Programming IIIChapter 15 – Shell Programming IVPart IV – System AdministrationChapter 16 – Basic System Administration IChapter 17 – Basic System Administration IIChapter 18 – X WindowsChapter 19 – Running ServersPart V - AppendicesAppendix A: UNIX Command CompendiumAppendix B: GlossaryAppendix C: Common Configuration FilesAppendix D: Internet Resources
Convex combinations of long memory estimates from different sampling rates
Authors: Leonardo R. Souza, Jeremy Smith, Reinaldo C. Souza
Venue: Computational Statistics (2006)

This paper investigates convex combinations of long memory estimates from both the original and sub-sampled data. Sub-sampling is carried out by decreasing the sampling rate, which leaves the long memory parameter unchanged. Any convex combination of these sub-sample estimates requires a preliminary correction for the bias observed at lower sampling rates, reported by Souza and Smith (2002). Through Monte Carlo simulations, we investigate the bias and the standard deviation of the combined estimates, as well as the root mean squared error (RMSE). Combining estimates can significantly lower the RMSE of a standard estimator (by about 30% on average for ARFIMA (0, d, 0) series), at the cost of inducing some bias.
Residual distribution schemes for advection and advection-diffusion problems on quadrilateral cells
Authors: P. De Palma, G. Pascazio, D. T. Rubino, M. Napolitano
Venue: Journal of Computational Physics (2006)

This paper provides a study of some difficulties arising when extending residual distribution schemes for scalar advection and advection-diffusion problems from triangular grids to quadrilateral ones. The Fourier and truncation error analyses on a structured mesh are employed and a generalized modified wavenumber is defined, which provides a general framework for the multidimensional analysis and comparison of different schemes. It is shown that, for the advection equation, linearity preserving schemes for quadrilaterals provide lower dissipation with respect to their triangle-based counterparts and very low or no damping for high frequency Fourier modes on structured grids; therefore, they require an additional artificial dissipation term for damping marginally stable modes in order to be employed with success for pure advection problems. In the case of advection-diffusion problems, a hybrid approach using an upwind residual distribution scheme for the convective fluctuation and any other scheme for the diffusion term is only first-order accurate. On the other hand, distributing the entire residual by an upwind scheme provides second-order accuracy; however, such an approach is unstable for diffusion dominated problems, since residual distribution schemes are characterized by undamped modes associated with the discretization of the diffusive fluctuation. The present analysis allows one to determine the conditions for a stable hybrid approach to be second-order accurate and to design an optimal scheme having minimum dispersion error on a nine-point stencil. Well-documented testcases for advection and advection-diffusion problems are used to compare the accuracy properties of several schemes.
Secrets of Podcasting, Second Edition: Audio Blogging for the Masses (2nd Edition) (Secrets of...)
Authors: Bart G. Farkas
Venue:  (2006)

Whether you want to create your own podcasts or just would like to locate and then listen to audio programs on your portable player, this is the book for you. In Secrets of Podcasting, Second Edition,author Bart G. Farkas provides real-world guidance and advice on how to: Download and enjoy podcasts with any MP3 player Create a script and set the structure and flow of your audio or video podcast Choose the right equipment-including the right microphone, headphones, and even preamp Use a digital recording device instead of your PC or Mac Pick audio editing and recording software Legally play music in your podcast or vodcast Distribute your podcast or vodcast
Modeling of autonomous problem solving process by dynamic construction of task models in multiple tasks environment
Authors: Yu Ohigashi, Takashi Omori
Venue: Neural Networks (2006)

Traditional reinforcement learning (RL) supposes a complex but single task to be solved. When a RL agent faces a task similar to a learned one, the agent must relearn the task from the beginning because it doesn't reuse the past learned results. This is the problem of quick action learning, which is the foundation of decision making in the real world. In this paper, we suppose agents that can solve a set of tasks similar to each other in a multiple tasks environment, where we encounter various problems one after another, and propose a technique of action learning that can quickly solve similar tasks by reusing previously learned knowledge. In our method, a model-based RL uses a task model constructed by combining primitive local predictors for predicting task and environmental dynamics. To evaluate the proposed method, we performed a computer simulation using a simple ping-pong game with variations.
Errurs: seeing double
Authors: Gerald M. Weinberg
Venue: ACM SIGDOC Asterisk Journal of Computer Documentation (1978)

Today, dear subject, I will subject you to the subject of <u>heteronyms</u>.
Exploring gene causal interactions using an enhanced constraint-based method
Authors: Xintao Wu, Yong Ye
Venue: Pattern Recognition (2006)

DNA microarray provides a powerful basis for analysis of gene expression. Bayesian networks, which are based on directed acyclic graphs (DAGs) and can provide models of causal influence, have been investigated for gene regulatory networks. The difficulty with this technique is that learning the Bayesian network structure is an NP-hard problem, as the number of DAGs is superexponential in the number of genes, and an exhaustive search is intractable. In this paper, we propose an enhanced constraint-based approach for causal structure learning. We integrate with graphical Gaussian modeling and use its independence graph as an input of our constraint-based causal learning method. We also present graphical decomposition techniques to further improve the performance. Our enhanced method makes it feasible to explore causal interactions among genes interactively. We have tested our methodology using two microarray data sets. The results show that the technique is both effective and efficient in exploring causal structures from microarray data.
When humans need humans: The lack of use of computer-based ICT in distance pastoral care
Authors: Stella Mills
Venue: Interacting with Computers (2006)

Computer-based information and communication technologies (ICT) have become a part of many people's working lives. Such technology is used in the form of e-mails and video-conferencing across many sectors of society and these are sometimes claimed to have replaced the need for face-to-face meetings. However, certain areas of work still seem to need face-to-face meetings; this paper focuses on one such area of work, that of Christian pastoral care. The article discusses the needs of clients and carers involved in crisis care within a Christian ethos and assesses why ICT tools seem to be mainly superfluous in situations where crisis caring has to take place at a distance. Caplan's model of crisis is used to indicate typical characteristics of people in crisis. Evidence from the Foot and Mouth epidemic of 2001 in the UK is used to investigate the usage of ICT in a real situation where distance pastoral care was essential. The findings show that the telephone was by far the best ICT tool although e-mail and the Internet were used in more formal business situations
Clover: Connecting technology and character education using personally-constructed animated vignettes
Authors: Brian P. Bailey, Sharon Y. Tettegah, Terry J. Bradley
Venue: Interacting with Computers (2006)

Schools are increasingly integrating character education to facilitate improved moral thinking and pro social behavior among students. An effective method for delivering character education is problem solving moral and social situations represented visually as animated vignettes. However, schools are rarely able to use animated vignettes since existing tools do not allow them to be easily created and having them created externally is overly expensive. In this paper, we describe the design, use, and evaluation of a computational tool that enables students to construct their own animated vignettes. By building, sharing, and responding to vignettes, students become engaged in problem solving moral and social situations. Evaluations showed that users are able to build meaningful vignettes, our tool is easy to learn and fun to use, and our tool's multimedia features are often used and well-liked. Educators can download and use our tool while researchers can draw upon our design rationale and lessons learned when building similar tools.
Bayesian analysis of finite mixture models of distributions from exponential families
Authors: M. J. Rufo, J. Martín, C. J. Pérez
Venue: Computational Statistics (2006)

This paper deals with the Bayesian analysis of finite mixture models with a fixed number of component distributions from natural exponential families with quadratic variance function (NEF-QVF). A unified Bayesian framework addressing the two main difficulties in this context is presented, i.e., the prior distribution choice and the parameter unidentifiability problem. In order to deal with the first issue, conjugate prior distributions are used. An algorithm to calculate the parameters in the prior distribution to obtain the least informative one into the class of conjugate distributions is developed. Regarding the second issue, a general algorithm to solve the label-switching problem is presented. These techniques are easily applied in practice as it is shown with an illustrative example.
Tracking hand and finger movements for behaviour analysis
Authors: Enrica Dente, Anil Anthony Bharath, Jeffrey Ng, Aldert Vrij, Samantha Mann, Anthony Bull
Venue: Pattern Recognition Letters (2006)

In this paper, we describe ongoing work into methods for the automated tracking of hand and finger movements in interview situations. The aim of this work is to aid visual behaviour analysis in studies of deception detection. Existing techniques for tracking hand and finger movements are reviewed to place current and future work into context. Posterior probability maps of skin tone, based on Parzen colour space probability density estimates, are used for initial hand segmentation. Blob features are then used to produce a markup of hand-states. A complex wavelet decomposition, coupled to weightings provided by the posterior probability map, is applied to detect small hand and finger movements. We discuss our hand tracking algorithm based on blob feature extraction and the results obtained from motion and orientation parameters in a ''high-stakes experiment'', designed around a real-life situation. We suggest the role of kinematic models of upper body, limb and finger motion for future work.
SMP-SoC is the answer if you ask the right questions
Authors: Philip Machanick
Venue: Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing countries (2006)

With growing interest in multiprocessor system-on-chip (SoC) designs and the increasing number of multicore designs at the high to medium end of the desktop and server markets, the question arises as to whether there should be convergence of the two concepts. This paper explores design principles for SoC multiprocessors and relates them to more general system requirements. It makes a case for focusing design efforts on symmetric multiprocessor (SMP) SoC designs, which have the best chance of making an impact in a wide range of markets, rather than designs for very specific niches, such as the IBM-Sony-Toshiba Cell processor. If SMP-SoC designs are successful, they could represent the next change in packaging in the general computer market: the next step after the microprocessor. A case is made not only for designing a SMP-SoC alternative to the Cell, but for using such a design as an alternative to an aggressively-pipelined uniprocessor.