ppxscal/embedding_network huggingface dataset:
Proteomic Feature Maps: A new visualization approach in proteomics analysis
Authors: Eugenia G. Giannopoulou, Spiros D. Garbis, Antonia Vlahou, Sofia Kossida, George Lepouras, Elias S. Manolakos
Venue: Journal of Biomedical Informatics (2009)

The different steps of a proteomics analysis workflow generate a plethora of features for each extracted proteomic object (a protein spot in 2D gel electrophoresis (2-DE), or a peptide peak in liquid chromatography-mass spectrometry (LC-MS) analysis). Yet, the joint visualization of multiple object features on 2D gel-like maps is rather limited in currently available proteomics software packages. We introduce a new, simple, and intuitive visualization method that utilizes spheres to represent proteomic objects on proteomic feature maps, and exploits the spheres size and color to provide simultaneous visualization of user-selected feature pairs. Our contribution, a unified and flexible visualization mechanism that can be easily applied at any stage of a 2-DE or a LC-MS based differential proteomics study, is demonstrated and discussed using five representative scenarios. The joint visualization of proteomic object features and their spatial distribution is a powerful tool for inspecting and comparing the proteomics analysis results, attracting the users attention to useful information, such as differential expression trends and patterns, and even assisting in the evaluation and refinement of a proteomics experiment.
Deluxe Facilitator's Set, 2nd edition
Authors: James M. Kouzes, Barry Z. Posner
Venue: Wiley Application Development (2007)

Learn how to apply robust application design to your J2EE projects There are a number of best practices you need to consider to build highly effective J2EE components and integrate them into applications. These practices include evaluating and selecting the right set of software components and services to handle the job. In this book, Darren Broemmer supplies you with a set of best practices for J2EE development and then teaches you how to use them to construct an application architecture referred to as the reference architecture. The design and implementation of the reference architecture is based on a set of guiding principles that are used to optimize and automate J2EE development. In addition to the author's thorough discussions of the latest technologies for J2EE implementation-including EJB 2, Jakarta Struts, Servlets, Java Server Pages, UML, design patterns, Common Business Logic Foundation components, and XML-Broemmer addresses such topics as: * Understanding J2EE application architecture * Building business applications with J2EE, a business object architecture, and extensible components created with design patterns * Designing and implementing a sample banking Web application * Integrating proven performance-engineering and optimization practices in the development process * Using metadata-driven, configurable foundation components to automate much of the development and processing of Web-based business applications The companion Web site contains the source code for a Common Business Logic Foundation and sample applications from the book, including a Jakarta Struts project and a banking application. Links to the Jakarta Struts frameworks and J2EE application servers such as BEA WebLogic and IBM WebSphere are also provided.
Design and development of a novel paddle test structure for the mechanical behavior measurement of thin films application for MEMS
Authors: Chi-Jia Tong, Ming-Tzer Lin
Venue: Microsystem Technologies (2009)

A new technique was developed for studying the mechanical behavior of thin films on substrate applications for micro-electro-mechanical system (MEMS). The test structure was designed on novel &#x201c;paddle&#x201d; cantilever beam coated thin film specimens with dimensions of a few hundred to 50&#x00a0;nm. This beam has a triangle shape that provides a uniform plane strain distribution. Standard clean room processing was used to prepare the paddle sample. The experiment can be operated using the electrostatic force to deflect the &#x201c;paddle&#x201d; cantilever beam and measure the mechanical response of the sample with surface deposited thin film. A capacitance measurement is used to observe the deflection of the cantilever plate on the other side of the sample with respect to the electrostatic force on the one side. The measured strain was then converted through this capacitance measurement to conduct mechanical behavior studies on the coated thin film. Both system performance experiments and calculations were studied to verify the design concepts. The residual thin film stress measurements were performed and compared with the calculated results from three different forces exerted on the &#x201c;paddle&#x201d; cantilever beam, including the force due to the film, compliance force, and electrostatic force.
Experimental Formats & Packaging
Authors: Roger Fawcett-Tang, Daniel Mason
Venue:  (2007)

New Mini Format!Experimental Formats & Packaging examines exciting design problems, such as how to make a book that does not look like a book, and how to create packaging that can be taken into new design dimensions while still fulfilling its essential, functional role.While both formats and packaging are notoriously difficult areas in which to be innovative and revolutionary, the authors have brought together examples that combine awareness of process and materials and creativity without compromising other methods of communication. Over 100 illustrated case studies reveal the ideas and philosophies behind each project, while an extensive directory of materials and processes, plus a range of basic box templates, provides an invaluable grounding to encourage a more experimental approach to design.Experimental Formats and Packaging combines the content of two highly successful titles in one great value book.**North American Rights Only**
A generalization and a quasi-fractal scheme of the Fibonacci integer sequence
Authors: J-B. Cazier, C. Mandakas, V. Gekas
Venue: Proceedings of the 10th WSEAS international conference on Mathematical methods, computational techniques and intelligent systems (2008)

Sequences of integers can produce irrational or asymmetric numbers. For example the golden section number, φ, can be obtained using the ratios of subsequent terms of the Fibonacci integer sequence. In the Academy of Plato there was research on the square roots of integer numbers. As Theon o Smyrnaios tells us another famous irrational number, the square root of two, was produced as the common limit of convergence of two series of fractionals. We have shown that the numerators and denominators of those fractionals belong to the terms of certain integer sequence similar to the Fibonacci sequence, i.e. there are terms of a new, being a modified Fibonacci, integer sequence. We have also reported two new integer sequences in which the two ratios given by Archimedes as approximatios of the square root of three. In this paper we furthermore generalize the method to give approximations of the square root of all the terms of the Fibbonacci integer sequence i.e the square roots of 5, 8, 13, 21 etc. Thus a quasi fractal (self-similar sceme) appears. The practical interest of these numbers is that they appear in many systems of Physics, in general such as it is the golden tree and the bronchic tree of the respiratory system.
Measuring the Similarity of Geometric Graphs
Authors: Otfried Cheong, Joachim Gudmundsson, Hyo-Sil Kim, Daria Schymura, Fabian Stehn
Venue: Proceedings of the 8th International Symposium on Experimental Algorithms (2009)

What does it mean for two geometric graphs to be similar? We propose a distance for geometric graphs that we show to be a metric, and that can be computed by solving an integer linear program. We also present experiments using a heuristic distance function.
Reflectance measures of grassland biophysical structure
Authors: Yuhong He, Xulin Guo, J. F. Wilmshurst
Venue: International Journal of Remote Sensing (2009)

The goal of this study is to develop an efficient method to retrieve vegetation biophysical properties based on ground LAI measurements and satellite data, and thus avoid the labour-intensive and time-consuming process for collecting biomass and canopy height in the future. The field data was conducted in Grasslands National Park (GNP), Saskatchewan, Canada. The two vegetation indices, ATSAVI and RDVI, were derived from SPOT 4 HRV images to estimate LAI and to prepare LAI and biophysical maps for the GNP. The results demonstrated strong relationships between LAI and selected vegetation indices. However, a detailed accuracy assessment indicated that ATSAVI was likely to be better in estimating and mapping LAI than the RDVI. The accuracy of the LAI map was calculated to be 66.7%. The significant relationship between measured LAI and the biophysical data solves the difficulty for mapping biophysical information due to insufficient sampling coverage for GNP.
Parallel solution of large-scale algebraic Bernoulli equations with the matrix sign function method
Authors: Sergio Barrachina, Peter Benner, Enrique S. Quintana-Orti
Venue: International Journal of Computational Science and Engineering (2009)

We investigate the numerical solution of algebraic Bernoulli equations (ABE) via the Newton iteration for the matrix sign function. Bernoulli equations are nonlinear matrix equations arising in control and systems theory in the context of stabilisation of linear systems, coprime factorisation of rational matrix-valued functions, as well as model reduction. The algorithm proposed here is easily parallelisable and thus provides an efficient tool to solve large-scale problems. We report the parallel performance and scalability of our parallel implementations on a cluster of Intel Xeon processors.
Novel semantic features for verb sense disambiguation
Authors: Dmitriy Dligach, Martha Palmer
Venue: Proceedings of the 46th Annual Meeting of the Association for Computational Linguistics on Human Language Technologies: Short Papers (2008)

We propose a novel method for extracting semantic information about a verb's arguments and apply it to Verb Sense Disambiguation (VSD). We contrast this method with two popular approaches to retrieving this information and show that it improves the performance of our VSD system and outperforms the other two approaches
Weakly Supervised Approaches for Ontology Population
Authors: Hristo Tanev, Bernardo Magnini
Venue: Proceeding of the 2008 conference on Ontology Learning and Population: Bridging the Gap between Text and Knowledge (2008)

We present a weakly supervised approach to automatic ontology population from text and compare it with two other unsupervised approaches. In our experiments we populate a part of our ontology of Named Entities. We considered two high level categories-geographical locations and person names and ten sub-classes for each category. For each sub-class we automatically learn a syntactic model from a list of training examples and a parsed corpus. A novel syntactic indexing method allowed us to use large quantities of syntactically annotated data. The syntactic model for each named entity sub-class is a set of weighted syntactic features, i.e. words which typically co-occur with the members of the class in the corpus. The method is weakly supervised, since no manually annotated corpus is used in the learning process. The syntactic models are used to classify the unknown Named Entities in the test set. The method achieved promising results, i.e. 65% accuracy, and outperforms significantly the other two approaches.
A Default Logic Based Framework for Argumentation
Authors: Emanuel Santos, João Pavão Martins
Venue: Proceeding of the 2008 conference on ECAI 2008: 18th European Conference on Artificial Intelligence (2008)

We extend the logic-based framework of Besnard and Hunter for Default Logic. We present structural sound results that provide a natural extension and introduce new concepts that enable us to characterize an argument based on its use of incomplete information.
Artificial Brains. An Inexpensive Method for Accelerating the Evolution of Neural Network Modules for Building Artificial Brains
Authors: Hugo de Garis, Liu Rui, Huang Di, Hu Jing
Venue: Proceeding of the 2007 conference on Advances in Artificial General Intelligence: Concepts, Architectures and Algorithms: Proceedings of the AGI Workshop 2006 (2007)

This chapter shows how a “Celoxica” electronic board (containing a Xilinx Virtex II FPGA chip) can be used to accelerate the evolution of neural network modules that are to be evolved quickly enough, so that building artificial brains that consist of 10,000s of interconnected modules, can be made practical. We hope that this work will prove to be an important stepping stone towards making the new field of brain building both practical and cheap enough for many research groups to start building their own artificial brains.
Using pedagogical dialogue as a vehicle to encourage faculty technology use
Authors: Terri Friel, Jody Britten, Beverly Compton, Amy Peak, Kurt Schoch, W. Kent VanTyle
Venue: Computers Education (2009)

The pace of technology adoption by university faculty is often slow. Slow faculty technology adoption may result from fear of failure, disinterest, or aversion to change. However, in 2007 we experienced a different faculty response while training faculty for technology-enhanced teaching at Butler University. During a technology upgrade of classrooms on our campus, we installed SMART^(TM) interactive whiteboards and Sympodiums^(TM) (SMART Technologies), visual presenters and CopyCams^(TM) (Polyvision/Steelcase). The technology trainers and information technology (IT) department anticipated a lack of faculty interest in training on these technologies. It was posited that faculty would not be interested in learning about these interactive and presentation technologies unless this learning could be connected in some way to their individual teaching interests and responsibilities. A novel, collaborative training model was developed to achieve this goal of placing technology training into a pedagogical context. A multidisciplinary group of faculty, working closely with representatives from IR, served as trainers for this highly successful faculty development effort in which 27% of the university faculty were trained over a three month period. This article details the methods and outcomes of this collaborative training team approach.
Concurrent Conceptual Design of Movable-Counterweights Method
Authors: Ying Zhang, Yan-An Yao, Jian-Zhong Cha
Venue: Proceeding of the 2006 conference on Leading the Web in Concurrent Engineering: Next Generation Concurrent Engineering (2006)

The movable counterweights method is presented for improving the dynamic balancing of mechanisms balanced by counterweight method. Differing from general ones, the movable counterweights are not fixed to the links on which they are placed but free to slip along them or rotate around the attached pivot centers. The process to generate schemes for the movable counterweight is described and hundreds of moving solutions are obtained. In the conceptual design stage of the movable counterweights, a design procedure based on the philosophy of concurrent engineering is developed. Both optimization of the structural parameters and dynamic simulation of various moving solutions are carried on simultaneously under an integrate circumstance of MATLAB and ADAMS. Results obtained can help designers to evaluate the alternative schemes numerically at the conceptual design stage and select a promising one for further design. Examples are given to illustrate the design procedure.
Effort, Revenue, and Cost Sharing Mechanisms for Collaborative New Product Development
Authors: Sreekumar R. Bhaskaran, V. Krishnan
Venue: Management Science (2009)

The growing sophistication of component technologies and the rising costs and uncertainties of developing and launching new products require firms to collaborate in the development of new products. However, the management of new product development that occurs jointly between firms presents a new set of challenges in sharing the costs and benefits of innovation. Although collaboration enables each firm to focus on what it does best, it also introduces new issues associated with the alignment of decisions and incentives that have to be managed alongside conventional performance and timing uncertainties of new product development. In this paper, we conceptualize and formulate the joint development of products involving two firms with differing development capabilities and examine the implications of arrangements that go beyond sharing of revenues to include sharing of development cost and work. We term these approaches that involve sharing of the development cost and sharing of the development work investment sharing and innovation sharing, respectively. These cost and effort sharing mechanisms have subtle interactions with the degree to which revenues are shared between firms and the type of development project under consideration. Our analysis shows that investment and innovation sharing are particularly relevant for products with no preexisting revenues, and their benefits also depend on the degree to which revenues are shared between the firms. Whereas investment sharing is more attractive for new-to-the-world product projects with significant timing uncertainty, innovation sharing plays an important role in environments where projects experience product quality uncertainty, firms are similar in their capabilities, and the costs of integration of work across firms can be controlled. Our key contribution involves the modeling of joint work and decision making between collaborating firms and unearthing the complementary role of revenue, cost, and innovative effort sharing mechanisms for new product development. We translate our analytical findings into a managerial framework and illustrate the results with examples from the life-sciences and electronics industries.
Near-optimum detection with low complexity for uplink virtual MIMO systems
Authors: Sanhae Kim, Oh-Soon Shin, Yoan Shin
Venue: EURASIP Journal on Wireless Communications and Networking (2009)

In mobile worldwide interoperability for microwave access (WiMAX) or 3rd Generation partnership project long-term evolution (3GPP-LTE), uplink virtual multiple input multiple output (MIMO) technology is adopted to perform spatial multiple access with two portable subscriber stations (PSSs), where each PSS has an antenna. As two PSSs transmit simultaneously on the same orthogonal frequency division multiple access (OFDMA) resource blocks, the overall uplink capacity will be doubled. To employ this interesting technique with high performance, most system venders demand the optimal maximum-likelihood detection (MLD) scheme in the radio access station (RAS). However, the optimal MLD is difficult to implement due to its explosive computational complexity. In this paper, we propose two efficient MIMO decoding schemes that achieve near-optimum performance with low complexity for uplink virtual MIMO systems that have an iterative channel decoder using bit log-likelihood ratio (LLR) information. The simulation results show that the proposed schemes have almost the same block error rate (BLER) performance as that of the optimal MLD with only about 15.75% and 28% computational complexity in terms of real multiplication, when both PSSs transmit 16 quadrature amplitude modulation (QAM) signals, and only about 3.77% and 7.22% for 64 QAM signals.
Traffic congestion identification by combining PCA with higher-order Boltzmann machine
Authors: Zhanquan Sun, Yinglong Wang
Venue: Neural Computing and Applications (2009)

Traffic congestion identification is a popular research topic of intelligent transport systems. Identification rate of existing methods usually cannot meet the practical requirements. To improve the identification rate and reduce the computation cost, a novel intelligent identification method is proposed. The proposed method combines principal component analysis (PCA) method with higher-order Boltzmann machine (BM). PCA is used to reduce the dimension of input feature space. It can not only reduce the computation cost but also filter noise of the source data. BM is a kind of stochastic network that can obtain the global optimum solution. Higher-order BM without hidden units can save lots of computation cost without decreasing modeling power. The trained higher-order BM is used to identify traffic state. The efficiency of the proposed method is illustrated through analyzing Jinan urban transportation data.
Modified vacation policy for M/G/1 retrial queue with balking and feedback
Authors: Jau-Chuan Ke, Fu-Min Chang
Venue: Computers and Industrial Engineering (2009)

This paper studies a general retrial queue with balking and Bernoulli feedback, where the server operates a modified vacation policy. If the server is busy or on vacation, an arriving customer either enters an orbit with probability b, or balks (does not enter) with probability 1-b. Otherwise the service of the arriving customer commences immediately. At any service completion epoch, the test customer may either enter the orbit for another service with probability p or leave the system with probability 1-p. If the orbit is empty, the server takes at most J vacations until at least one customer is recorded in the orbit when the server returns from a vacation. This retrial system has potential applications in e-mail system and WWW server. By applying the supplementary variable technique, some important performance measures are derived. The effect of various retrial/vacation time distributions and different values of J on the system performance measures is also investigated. The analyses and results presented in this paper may be useful for network system designers and software system engineers.
Ldiff: An enhanced line differencing tool
Authors: Gerardo Canfora, Luigi Cerulo, Massimiliano Di Penta
Venue: Proceedings of the 2009 IEEE 31st International Conference on Software Engineering (2009)

Differencing tools are highly relevant for a series of software engineering tasks, including analyzing developers' activities, assessing the changeability of software artifacts, and monitoring the maintenance of critical assets such as source clones and vulnerable instructions. This tool demonstration shows the features of ldiff, an enhanced, language-independent line differencing tool. L-diff builds upon the Unix diff and overcomes its limitations in determining whether an artifact line has been changed or is the result of additions and removals, and in tracking artifact fragments that have been moved upward or downward within the file. The paper describes the tool and shows its capability of analyzing changes on different kinds of software artifacts, including use cases, code developed with different programming languages, and test cases.