ppxscal/embedding_network huggingface dataset:
The beta-binomial distribution for estimating the number of false rejections in microarray gene expression studies
Authors: Daniel L. Hunt, Cheng Cheng, Stanley Pounds
Venue: Computational Statistics Data Analysis (2009)

In differential expression analysis of microarray data, it is common to assume independence among null hypotheses (and thus gene expression levels). The independence assumption implies that the number of false rejections V follows a binomial distribution and leads to an estimator of the empirical false discovery rate (eFDR). The number of false rejections V is modeled with the beta-binomial distribution. An estimator of the beta-binomial false discovery rate (bbFDR) is then derived. This approach accounts for how the correlation among non-differentially expressed genes influences the distribution of V. Permutations are used to generate the observed values for V under the null hypotheses and a beta-binomial distribution is fit to the values of V. The bbFDR estimator is compared to the eFDR estimator in simulation studies of correlated non-differentially expressed genes and is found to outperform the eFDR for certain scenarios. As an example, this method is also used to perform an analysis that compares the gene expression of soft-tissue sarcoma samples to normal-tissue samples.
NURBS Interpolation Method with Feedrate Correction in 3-axis CNC System
Authors: Liangji Chen, Huiying Li
Venue: Proceedings of the 2009 International Conference on Computer Engineering and Technology - Volume 01 (2009)

A real-time Non-Uniform Rational B-Spline (NURBS) curve directly interpolation method is presented for computer numerical control (CNC) machines to achieve the goal of high-speed and highly accurate machining. To the feedrate fluctuation of the interpolation method, the feedrate correction method is also proposed. To implement the proposed methods, Taylor expansion and numerical calculation methods are used. The given example shows that the feasibility of the methods applied to achieve high-speed and high-effect machining.
A Simulating Algorithm for Protein Folding Process
Authors: Jing Zhang, Song Li
Venue: Proceedings of the 2009 WRI International Conference on Communications and Mobile Computing - Volume 03 (2009)

It is a difficult problem of studying the protein folding process in the protein research field. In this paper, a new simulation algorithm-snake simulation algorithm is put forward to solve the problem. In order to prove the key function in snake simulation algorithm is correct and feasible, theory of molecule oscillation and molecule kinetics are used. In addition, bring forward a model that describes the process of protein folding, concludes that all the protein structure can be constructed by two type functions. Compared with other five protein folding algorithms, the snake simulation algorithm has a great advantage in the energy and similar of protein structure.
Mathematical Mathematical User Interfaces
Authors: Harold Thimbleby, Will Thimbleby
Venue: Engineering Interactive Systems: EIS 2007 Joint Working Conferences, EHCI 2007, DSV-IS 2007, HCSE 2007, Salamanca, Spain, March 22-24, 2007. Selected Papers (2008)

Taking Mathematica and xThink as representatives of the state of the art in interactive mathematics, we argue conventional mathematical user interfaces leave much to be desired, because they separate the mathematics from the context of the user interface, which remains as unmathematical as ever. We put the usability of such systems into mathematical perspective, and compare the conventional approach with a novel declarative, gesture-based approach, exemplified by TruCalc, a novel calculator we have developed.
Classification of Quaternary [21s+1,3] Optimal Self-orthogonal Codes
Authors: Xuejun Zhao, Ruihu Li, Yingjie Lei
Venue: Proceedings of the 2009 International Conference on Computer Engineering and Technology - Volume 01 (2009)

The classification of quaternary [21s+t,3,d] codes with d≥16s and without zero coordinates is reduced to the classification of quaternary [21c(3,s,t)+t,k,d] code for s≥1 and 0≤t≤20, where c(3,s,t)≤ min{s, 3t} is a function of 3, s, and t. Quaternary optimal Hermitian self-orthogonal codes are characterized by systems of linear equations. Based on these two results, the complete classification of [21s+1,3] optimal self-orthogonal codes for s≥1 is obtained, and the generator matrices and weight polynomials of these 3-dimensional optimal self-orthogonal codes are also given.
Mixed-mode multicore reliability
Authors: Philip M. Wells, Koushik Chakraborty, Gurindar S. Sohi
Venue: Proceeding of the 14th international conference on Architectural support for programming languages and operating systems (2009)

Future processors are expected to observe increasing rates of hardware faults. Using Dual-Modular Redundancy (DMR), two cores of a multicore can be loosely coupled to redundantly execute a single software thread, providing very high coverage from many difference sources of faults. This reliability, however, comes at a high price in terms of per-thread IPC and overall system throughput. We make the observation that a user may want to run both applications requiring high reliability, such as financial software, and more fault tolerant applications requiring high performance, such as media or web software, on the same machine at the same time. Yet a traditional DMR system must fully operate in redundant mode whenever any application requires high reliability. This paper proposes a Mixed-Mode Multicore (MMM), which enables most applications, including the system software, to run with high reliability in DMR mode, while applications that need high performance can avoid the penalty of DMR. Though conceptually simple, two key challenges arise: 1) care must be taken to protect reliable applications from any faults occurring to applications running in high performance mode, and 2) the desire to execute additional independent software threads for a performance application complicates the scheduling of computation to cores. After solving these issues, an MMM is shown to improve overall system performance, compared to a traditional DMR system, by approximately 2X when one reliable and one performance application are concurrently executing.
Investigation of ZnO nanopillars fabrication in a new Thomas Swan close coupled showerhead MOCVD reactor
Authors: A. Behrends, A. Bakin, A. Waag
Venue: Microelectronics Journal (2009)

Self-organized ZnO nanopillars were grown on a-plane Al"2O"3 in a vertical MOCVD reactor using diethylzinc and N"2O as precursors. This is the very first Thomas Swan reactor that is specially designed for the growth of ZnO and GaN. The influence of different growth parameters including growth time, VI/II-ratio, substrate temperature and reactor pressure on the shape of the nanostructures is investigated by field emission scanning electron microscopy. An explanation for the formation of nanopillars is given resulting in high substrate temperatures and low VI/II-ratios for the best results. It is shown that the density, length and diameter can be controlled choosing appropriate growth parameters.
Solving models with inequalities using standard econometric software
Authors: Arie ten Cate
Venue: Computational Statistics Data Analysis (2009)

Simultaneous econometric models may contain pairs of complementary inequalities. It is discussed how to reformulate such models and solve them with econometric software which can handle only equalities. Two approaches are applied: the normal map representation and the Fischer-Burmeister NCP function. The latter seems to work best. The software programs TSP, SAS/ETS and EViews are tested. The test model describes two markets for electricity, each with fluctuating demand and an endogenous production capacity; the capacity of the trade link between the regions is also endogenous.
Collaboration in Distributed Software Development
Authors: Filippo Lanubile
Venue: Software Engineering: International Summer Schools, ISSSE 2006-2008, Salerno, Italy, Revised Tutorial Lectures (2009)

Software development is an intense collaborative process where success depends on the ability to create, share and integrate information. Given the trend towards globalization in the software development industry, distance creates an additional challenge to development processes, as fewer opportunities for rich interaction and lower frequencies of direct communication. The chapter introduces a taxonomy of software engineering tools for distributed projects and presents collaborative development environments, ranging from classic platforms for dispersed developers in open source software projects to modern environments for flexible and distributed processes. Moreover, it introduces computer-mediated communication theories which reveal some patterns of tool usage to overcome the challenges of distance. Building upon the theoretical background of media selection, the chapter summarizes research activities aimed to build an evidence-based model of task-technology fit for communication-intensive activities such as distributed requirements workshops.
A Framework for Proactive Self-adaptation of Service-Based Applications Based on Online Testing
Authors: Julia Hielscher, Raman Kazhamiakin, Andreas Metzger, Marco Pistore
Venue: Proceedings of the 1st European Conference on Towards a Service-Based Internet (2008)

Service-based applications have to continuously and dynamically self-adapt in order to timely react to changes in their context, as well as to efficiently accommodate for deviations from their expected functionality or quality of service. Currently, self-adaptation is triggered by monitoring events. Yet, monitoring only observes changes or deviations after they have occurred. Therefore, self-adaptation based on monitoring is reactive and thus often comes too late, e.g., when changes or deviations already have led to undesired consequences. In this paper we present the PROSA framework, which aims to enable proactive self-adaptation. To this end, PROSA exploits online testing techniques to detect changes and deviations before they can lead to undesired consequences. This paper introduces and illustrates the key online testing activities needed to trigger proactive adaptation, and it discusses how those activities can be implemented by utilizing and extending existing testing and adaptation techniques.
A note on atomicity: Boosting Test&Set to solve consensus
Authors: Damien Imbs, Michel Raynal
Venue: Information Processing Letters (2009)

This short note shows how a simple extension of object types with consensus number 2 boosts them to an infinite consensus number. This extension is a simple embedding of a shared memory write within the base operation defining the corresponding type with consensus number 2. The style of this note is voluntarily informal.
Educating the Educators Online
Authors: Ursula Donnelly, Philip Turbitt
Venue: Proceedings of the 2009 International Conference on Mobile, Hybrid, and On-line Learning (2009)

Advances in Internet and mobile technology along with global access to broadband connectivity has led to a huge increase in the numbers of people studying and learning through distance education. E-learning because of its flexibility provides non-traditional students with an opportunity to incorporate study into their existing lifestyle, irrespective of geographic location or personal time constraints. At the University of Ulster a Virtual Learning Environment (VLE), WebCT, was put in place in 2001 to meet the changing learning needs of students and, provide access to a dedicated area for each module of study. Wide scale implementation of e-learning brings with it a requirement for significant staff development in order to equip the tutors with the requisite skills and expertise to facilitate online tuition. This paper describes a unique e-tutor training program aimed at equipping online tutors with the skills necessary to mentor, facilitate and deliver a high standard of learning online. Analysis and evaluation of feedback from the e-tutor training program provides evidence of the need to implement such a program as a solid foundation for advancing the e-learning agenda.
Abstraction of transaction demarcation in component-oriented platforms
Authors: Romain Rouvoy, Philippe Merle
Venue: Proceedings of the ACM/IFIP/USENIX 2003 International Conference on Middleware (2003)

Component-oriented middleware becomes the privileged substrate for distributed computing in heterogeneous and open environments. Technically they promote the notion of container as structure to host application components. They transparently take charge of a large set of technical or non-functional services like security or transactions. The transaction service is integrated using a set of transaction demarcation (TD) policies. Nevertheless, they are strongly linked to a specific transactional monitor and they are not often isolated. The main contribution of this paper is to propose a component-based framework to deal with TD policies. Thus, this framework allows one to instantiate several configurations of TD policies with different platforms like EJB, CCM, OSGi, WebServices and several transactional monitors like JTS, OTS, WS-T, BTP, etc. It proposes an extensible abstraction of TD policies. This framework shows that no performance degradation is introduced by the refactoring process.
Cousins Virtual Jane and Virtual Joe, extraordinary virtual helpers
Authors: Seugnet Blignaut, Lynette Nagel
Venue: Computers Education (2009)

Higher education institutions deliver web-based learning with varied success. The success rate of distributed online courses remains low. Factors such as ineffective course facilitation and insufficient communication contribute to the unfulfilled promises of web-based learning. Students consequently feel unmotivated. Instructor control and in the courseroom further isolates students, whereas success rate increases when students unite in virtual communities. King (2002) increased student participation in his online classes by creating a virtual student, Joe, as a participating student and supplementary facilitator. This investigation responds to King's call for further directions on how a virtual helper enhances online facilitation. This inspired our investigation of how Virtual Jane might augment online facilitation. King's prediction, ''It seems that Joe Bags may have a family in the future,'' (p. 164) became a reality in a South African masters' web-based class on web-based learning.
STRANGERS
Authors: Derek Besant
Venue: ACM SIGGRAPH ASIA 2008 artgallery: emerging technologies (2008)

Out-of-focus elements read as individual faces, familiar yet unfamiliar. The works speak about recognition of what we think we know ... but they are elusive.
Multiresolution Animated Models Generation Based on Deformation Distance Analysis
Authors: Shixue Zhang, Enhua Wu
Venue: Proceedings of the 2009 International Conference on Computer Modeling and Simulation (2009)

In computer graphics, animated models have been widely used to represent time-varying data. Reducing the models complexly is a common way to overcome the rendering limitations. In this paper, we propose an efficient method for generating multiresolution animated models based on deformation distance analysis. Our method obtains different LOD models by performing iterative edge contraction operations. We use deformation distance to analysis the deformation degree of the triangle planes during the whole animation, and define a deformation weight to be added to the aggregated edge contraction cost. Thus features in areas with large deformation can be preserved well. Besides, we propose a mesh optimization method for dynamic model sequence, which can efficiently improve the temporal coherence and reduce visual artifacts between adjacent frames. The results show our approach is efficient, easy to implement, and good quality animated approximations with well-preserved fine details can be generated at any given frame.
Interfacing people with their machines
Authors: Nancy B. Finn
Venue: Proceedings of the May 16-19, 1983, national computer conference (1983)

As computer technology proliferates, the techniques applied to the interface of people with their machines will assume great importance if the large dollar investments in equipment are to be recouped in the form of increased productivity. This paper propounds the theory that change in any form is difficult for people to accept, especially in the office environment, and that it is essential to involve the work force in the change to automated information processing if new technology is to succeed. The paper outlines several ways to accomplish this, including polls and individual interviews with all employees before the system is purchased and the design of a public relations effort to help employees understand the applications of automation to their personal roles. The paper also covers various ergonomic questions related to computer systems, such as noise, heat, illumination, static, terminal design, and general environmental questions. The issue of accommodating people in an office to office automation is a complex one, requiring a concerted effort on the part of all managers involved with the implementation.
A Spectrum Sensing Scheme for Cognitive Radios
Authors: Jianli Xie, Cuiran Li, Chengshu Li
Venue: Proceedings of the 2009 WRI International Conference on Communications and Mobile Computing - Volume 01 (2009)

Cognitive radio (CR) is viewed as a possible solution to the problem of radio spectrum congestion. CR is the promising radio technology which aims to detect and utilize the temporally unused spectrum bands by sensing its radio environment in order to improve spectrum utilization. To enhance the sensing performance, cooperative spectrum sensing has been proposed. However, when the number of cognitive user tends to be very large, the bandwidth for reporting sensing results to the common receiver will be very huge. In the paper, we therefore introduce a new credibility factor sensing (CFS) algorithm with quantization to decrease the average number of sensing bits to the common receiver. According to the energy detection, if the energy is located in the "Decision" region, then the cognitive user sends 1 bit or 2 bits quantization for reporting its sensing result based on credibility factor and likelihood decision. Otherwise, the cognitive user sends nothing. Performance evaluations clearly reveal that the average number of sensing bits decreases greatly without noticeable loss in sensing performance.
Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns
Authors: Matteo Ré, Giulio Pavesi
Venue: Artificial Intelligence in Medicine (2009)

Objective: In the last few years several complete genome sequences have been made available to the research community. The annotation of their complete inventory of protein coding genes, however, has been so far an elusive goal. Classical ab initio gene prediction methods have been of great support for this task, but show notable weakness in the prediction of genes with unusual structural features. On the other hand, annotation on the basis of similarity to already known genes in other species does not permit the detection of genuinely novel genes and also introduces a potential source of classification error when based on similarity to sequences erroneously annotated as protein coding. Finally, several methods for the functional classification and assessment of evolutionarily conserved regions have been proposed, but, to our knowledge, signal processing techniques have not been applied yet to this problem, despite their proven usefulness at the single genome level. Results: In this article we introduce the use of signal processing in comparative genomics and we propose a simple test able to evaluate the coding potential of a pairwise genomic sequence alignment according to the pattern and periodicity with which substitutions and gaps appear in the alignment. We assess the feasibility of our approach on an annotated set of human-mouse genomic alignments. Conclusion: Results show that the application of signal processing techniques to sequence alignments can be a useful tool for the identification of evolutionarily conserved protein-coding regions.
Issues and methods for practical distributed data processing applications: I
Authors: Maurice Blackman, Hugh Ryan
Venue: Proceedings of the June 7-10, 1982, national computer conference (1982)

This paper presents methods for one of two key activities in the creation of practical distributed data processing (DDP) systems for business computing. The first activity, discussed in this paper, is to select a configuration of hardware and software to support the implementation of a multiapplication plan. The second, discussed in a companion paper, is to select data distribution and manipulation approaches for one application within the limits set by the results of the first activity. To establish a justification for the methods, the paper selects a definition of DDP, discusses the alternatives to DDP for reaching the objectives of the enterprise, and identifies the design issues to be solved or avoided in a practical system for a commercial establishment.
A Rigorous Proof of MIMO Channel Capacity's Increase with Antenna Number
Authors: Jianmin Gong, M. R. Soleymani, J. F. Hayes
Venue: Wireless Personal Communications: An International Journal (2009)

It is well known that adding more antennas at the transmitter or at the receiver offers larger channel capacity in the multiple-input multiple-output communication systems. In this letter, a simple proof is presented for the fact that the channel capacity increases with an increase in the number of receive antennas. The proof is based on the famous capacity formula of Foschini and Gans and uses matrix theory.
Facial emotion and gesture reproduction method for substitute robot of remote person
Authors: Kenzo Kurihara, Daisuke Sugiyama, Shigeru Matsumoto, Nobuyuki Nishiuchi, Kazuaki Masuda
Venue: Computers and Industrial Engineering (2009)

CEOs of big companies may travel frequently to give their philosophies and policies to the employees who are working at world wide branches. Video technology makes it possible to give their lectures anywhere and anytime in the world very easily. However, 2-dimentional video systems lack the reality. If we can give natural realistic lectures through humanoid robots, CEOs do not need to meet the employees in person. They can save their time and money for traveling. We propose a substitute robot of remote person. The substitute robot is a humanoid robot that can reproduce the lecturers' facial expressions and body movements, and that can send the lecturers to everywhere in the world instantaneously with the feeling of being at a live performance. There are two major tasks for the development; they are the facial expression recognition/reproduction and the body language reproduction. For the former task, we proposed a facial expression recognition method based on a neural network model. We recognized five emotions, or surprise, anger, sadness, happiness and no emotion, in real time. We also developed a facial robot to reproduce the recognized emotion on the robot face. Through experiments, we showed that the robot could reproduce the speakers' emotions with its face. For the latter task, we proposed a degradation control method to reproduce the natural movement of the lecturer even when a robot rotary joint fails. For the fundamental stage of our research for this sub-system, we proposed a control method for the front view movement model, or 2-dimentional model.