ppxscal/embedding_network huggingface dataset:
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
Authors: Min Zhang, Lin Zhang, Jinfeng Zou, Chen Yao, Hui Xiao, Qing Liu, Jing Wang, Dong Wang, Chenguang Wang, Zheng Guo
Venue: Bioinformatics (2009)

Motivation: According to current consistency metrics such as percentage of overlapping genes (POG), lists of differentially expressed genes (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas such as proteomics and metabolism. A complex disease is often characterized with many coordinated molecular changes, which should be considered when evaluating the reproducibility of discovery lists from different studies. Results: We proposed metrics percentage of overlapping genes-related (POGR) and normalized POGR (nPOGR) to evaluate the consistency between two DEG lists for a complex disease, considering correlated molecular changes rather than only counting gene overlaps between the lists. Based on microarray datasets of three diseases, we showed that though the POG scores for DEG lists from different studies for each disease are extremely low, the POGR and nPOGR scores can be rather high, suggesting that the apparently inconsistent DEG lists may be highly reproducible in the sense that they are actually significantly correlated. Observing different discovery results for a disease by the POGR and nPOGR scores will obviously reduce the uncertainty of the microarray studies. The proposed metrics could also be applicable in many other high-throughput post-genomic areas. Contact: guoz@ems.hrbmu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
Autonomic Pervasive Grids: A Session Manager Service for Handling Mobile Users
Authors: A. Coronato, G. De Pietro
Venue: Proceeding of the 2005 conference on Self-Organization and Autonomic Informatics (I) (2005)

Grid computing environments are being extended in order to present some features that are typically found in pervasive computing environments. In particular, Grid environments have to allow mobile users to access to their services and resources, and self-adapt based on mobile user location and context. Moreover, mobile users have to have the possibility of changing their location without wondering about their pending computations. This requires that the environment be able to self-manage mobile users implicit disconnections, who may also reappear later and be willing of resuming their computations. In this paper, we present a session manager service for distributed federations of pervasive grids. The service makes mobile users able of leaving a pervasive grid and resuming later, and even in another grid of the federation, their computations. The service relies on the mobile agents technology. In particular, a personal agent is associated to every mobile user active in the environment. The personal agent offers the list of application services available at the location of the user and handles the list of activated services. If the user moves in another grid, the personal agent migrates in the new grid, handles the list of pending services, and updates the list of available services for the new location.
Protecting Your Children on the Internet: A Road Map for Parents and Teachers
Authors: Gregory S. Smith
Venue:  (2009)

The Internet and technologies that enable online interaction and access to a variety of content can be a perilous place for minors between 8 and 18. Parents and teachers are often ill-equipped to deal with the variety of devices and applications such as email, instant messaging, browsing, blogs, cell phones, and personal digital assistant devices (PDAs) that can facilitate the dangers lurking online. This book shares the risks of the Internet by detailing recent, real-world tragedies and revealing some of the secrets of online activities. It provides a pragmatic approach to help parents and teachers protect children against the threats of going online. Protecting Your Children on the Internet provides a road-map to enable parents and teachers to become more engaged in children's online activities, arming them with techniques and tips to help protect their children. Recommendations come by technology topic (search engines, social networking, cell phones, etc.) and by age category (elementary, middle, high school) to align with how parents and educators think when they're dealing with multiple children that span different risk profiles. Smith underscores his arguments through chilling, real-life stories, revealing approaches people use to deceive and conceal their activities online. Filled with practical advice and recommendations, this book is indispensable to anyone who uses the Internet and related technologies, especially to those charged with keeping children safe.
Charge retention improvement of charge-trapping type flash device by plasma immersion ion implantation
Authors: Li-Jung Liu, Kuei-Shu Chang-Liao, Tai-Yu Wu, Tien-Ko Wang, Wen-Fa Tsai, Chi-Fong Ai
Venue: Microelectronic Engineering (2009)

Electrical characteristics of charge trapping-type flash devices with HfAlO charge trapping layer nitrided by plasma immersion ion implantation (PIII) technique with different implantation energies and time are studied. Utilizing Fowler-Nordheim (FN) operation, the programming speed of flash memory with charge trapping layer nitrided at low implantation energy is faster than that of control sample. The erasing speed of PIII-treated sample is slightly slower than that of control one, which might be due to the formation of silicon nitride in the tunneling oxide. The retention characteristics of all PIII-treated samples are significantly improved. Different peak locations of implanted nitrogen concentrations are formed by different implantation energies, which cause various electrical characteristics of flash devices.
Introducing and Implementing Revit Architecture 2008, 1st edition
Authors: Lay Christopher Fox
Venue:  (2007)

This innovative book shows how building design strengths and methods can be used and applied with Autodesk Revit Architecture 2008. Coverage explores the ways in which Revit Architecture handles design and documentation tasks and the advantages it presents for creating fully integrated building information models. Tutorial exercises early in the book illustrate how Autodesk Revit Architecture can be combined effectively with AutoCAD and Architectural Desktop drawings to make the best use of existing files and work practices. Numerous other exercises illustrate how to use Revit Architecture's sophisticated and robust capabilities as a full-featured architectural design tool-- sketched massing objects that convert to building elements, configurable components, automatic coordination of all parts of the building model with views and annotations, simply controlled yet detailed graphic representation and output, strong data management via schedules, and color diagrams.
Application of Kohonen network for automatic point correspondence in 2D medical images
Authors: Vasiliki E. Markaki, Pantelis A. Asvestas, George K. Matsopoulos
Venue: Computers in Biology and Medicine (2009)

In this paper, a generalized application of Kohonen Network for automatic point correspondence of unimodal medical images is presented. Given a pair of two-dimensional medical images of the same anatomical region and a set of interest points in one of the images, the algorithm detects effectively the set of corresponding points in the second image, by exploiting the properties of the Kohonen self organizing maps (SOMs) and embedding them in a stochastic optimization framework. The correspondences are established by determining the parameters of local transformations that map the interest points of the first image to their corresponding points in the second image. The parameters of each transformation are computed in an iterative way, using a modification of the competitive learning, as implemented by SOMs. The proposed algorithm was tested on medical imaging data from three different modalities (CT, MR and red-free retinal images) subject to known and unknown transformations. The quantitative results in all cases exhibited sub-pixel accuracy. The algorithm also proved to work efficiently in the case of noise corrupted data. Finally, in comparison to a previously published algorithm that was also based on SOMs, as well as two widely used techniques for detection of point correspondences (template matching and iterative closest point), the proposed algorithm exhibits an improved performance in terms of accuracy and robustness.
Information architecture for intelligent decision support in intensive medicine
Authors: M. F. Santos, F. Portela, M. Vilas-Boas, J. Machado, A. Abelha, J. Neves, A. Silva, F. Rua
Venue: WSEAS Transactions on Computers (2009)

Daily, a great amount of data that is gathered in intensive care units, which makes intensive medicine a very attractive field for applying knowledge discovery in databases. Previously unknown knowledge can be extracted from that data in order to create prediction and decision models. The challenge is to perform those tasks in real-time, in order to assist the doctors in the decision making process. Furthermore, the models should be continuously assessed and optimized, if necessary, to maintain a certain accuracy. In this paper we propose an information architecture to support an adjustment to the INTCare system, an intelligent decision support system for intensive medicine. We focus on the automatization of data acquisition avoiding human intervention, describing its steps and some requirements.
Applications of Data Mining in E-Business Finance: Introduction
Authors: Carlos Soares, Yonghong Peng, Jun Meng, Takashi Washio, Zhi-Hua Zhou
Venue: Proceeding of the 2008 conference on Applications of Data Mining in E-Business and Finance (2008)

This chapter introduces the volume on Applications of Data Mining in E-Business and Finance. It discusses how application-specific issues can affect the development of a data mining project. An overview of the chapters in the book is then given to guide the reader.
ADEPT: a Tool for Developing Synthesis Skills
Authors: Elizabeth A. Kemp, Timothy Pick, Raymond H. Kemp
Venue: Proceeding of the 2005 conference on Towards Sustainable and Scalable Educational Innovations Informed by the Learning Sciences: Sharing Good Practices of Research, Experimentation and Innovation (2005)

A teaching system, ADEPT, has been developed to assist students to understand and apply the DECIDE framework for planning an interface evaluation. This planning activity is an example of a synthesis problem solving task. To assist students to develop the skills required to produce sophisticated plans, a scenario-based system which provides scaffolding was built. Related work was considered in order to ensure educational objectives were met. Technical issues and the role of authoring are also addressed.
A simple empirical topographic correction method for ETM+ imagery
Authors: Yongnian Gao, Wanchang Zhang
Venue: International Journal of Remote Sensing (2009)

A simple topographic correction approach, the Variable Empirical Coefficient Algorithm (VECA), was developed using theoretical and statistic analyses of the radiance values of remotely sensed data acquired for rugged terrain and the cosine of the solar illumination angle (cos i). Visual comparison and statistical analysis were used for evaluation of the proposed algorithm and the performance of the VECA approach was compared with 10 commonly used methods. The test site selected for this study is located on the south hill of the Qinling Mountain in Shanxi province, China, and the remotely sensed data used were from Landsat-7 Enhanced Thematic Mapper Plus (ETM+) images. The results indicate that the Cosine-T, Cosine-C, sun-canopy-senor (SCS) and Cosine-b correction have the problem of overcorrection, and the other corrections can be classed into three ranks: the VECA, b correction and C models performed the best, followed by the Teillet-regression correction model, and the SCS+C, Minnaert and Minnaert-SCS corrections performed the worst. The proposed VECA correction and the b correction are the most capable of removing the topographic effects of the ETM+ image. The VECA is not only simple in theory but also easy to operate, indicating that the VECA is an effective topographic correction tool in remote sensing techniques.
The relative utility of regression and artificial neural networks models for rapidly predicting the capacity of water supply reservoirs
Authors: Adebayo Adeloye
Venue: Environmental Modelling Software (2009)

Rapid prediction tools for reservoir over-year and within-year capacities that dispense with the sequential analysis of time-series runoff data are developed using multiple linear regression and multi-layer perceptron, artificial neural networks (MLP-ANNs). Linear regression was used to model the total (i.e. within-year+over-year) capacity using the over-year capacity as one of the inputs, while the ANNs were used to simultaneously model directly the over-year and total capacities. The inputs used for the ANNs were basic runoff and systems variables such as the coefficient of variation (Cv) of annual and monthly runoff, minimum monthly runoff, the demand ratio and reservoir reliability. The results showed that all the models performed well during their development and when they were tested with independent data sets. Both models offer faster prediction tools for reservoir capacity at gauged sites when compared with behaviour simulation. Additionally, when the predictor variables can be evaluated at un-gauged sites using e.g. catchment characteristics, they make capacity estimation at such un-gauged sites a feasible proposition.
Feature Based Affine Invariant Watermarking Robust to Geometric Distortions
Authors: Kuo Lung Hung, Shin-Wei He
Venue: Fundamenta Informaticae (2009)

This work, proposes a robust digital watermarking scheme based on feature points as a defense against illegal user attacks, such as, rotating, scaling and translation. First of all, a Gaussian filter is first adopted to discover the invariant feature points. The local maximum and the local minimum values are then calculated from those feature points. The Affine Invariant Region (AIR) is then divided by combination the values: local maximum, local minimum values and the center of mass. The AIR region is then transformed using affine transform to a block image, called the normalized image, in which the size of the block image is predefined. The watermarks are then embedded into the normalized image. Experimental results indicate that the proposed method can still extract the correct watermark, even after a geometric attack. The proposed method has a lower false positive rate and higher accuracy than Lu's [12] that making it a robust blind watermarking scheme.
Reachability in Timed Counter Systems
Authors: Florent Bouchy, Alain Finkel, Arnaud Sangnier
Venue: Electronic Notes in Theoretical Computer Science (ENTCS) (2009)

We introduce Timed Counter Systems, a new class of systems mixing clocks and counters. Such systems have an infinite state space, and their reachability problems are generally undecidable. By abstracting clock values with a Region Graph, we show the Counter Reachability Problem to be decidable for three subclasses: Timed VASS, Bounded Timed Counter Systems, and Reversal-Bounded Timed Counter Systems.
Modeling complexity of a complex gate oxide
Authors: Alexander A. Demkov, O. Sharia, X. Luo, G. Bersuker, J. Robertson
Venue: Microelectronic Engineering (2009)

Hafnium dioxide has been recently introduced as a gate dielectric in the field effect transistors. It belongs to a class of high dielectric constant or high-k dielectrics. We briefly discuss the structural and electronic properties of bulk hafnia, and show how oxygen vacancies believed to affect the band alignment across the metal oxide semiconductor (MOS) stack are stabilized in hafnia films next to high work function metals.
Active Concept Learning For Ontology Evolution
Authors: Murat Şensoy, Pınar Yolum
Venue: Proceeding of the 2008 conference on ECAI 2008: 18th European Conference on Artificial Intelligence (2008)

This paper proposes an approach that enables agents to teach each other concepts from their ontologies using examples. Unlike other concept learning approaches, our approach enables the learner to elicit the most informative examples interactively from the teacher. Hence, the learner participates to the learning process actively. We empirically compare the proposed approach with the previous concept learning approaches. Our experiments show that using the proposed approach, agents can learn new concepts successfully and with fewer examples.
Gaussian process approach for modelling of nonlinear systems
Authors: Gregor Gregorčič, Gordon Lightbody
Venue: Engineering Applications of Artificial Intelligence (2009)

Parametric modelling principals such as neural networks, fuzzy models and multiple model techniques have been proposed for modelling of nonlinear systems. Research effort has focused on issues such as the selection of the structure, constructive learning techniques, computational issues, the curse of dimensionality, off-equilibrium behaviour, etc. To reduce these problems, the use of non-parametrical modelling approaches have been proposed. This paper introduces the Gaussian process (GP) prior approach for the modelling of nonlinear dynamic systems. The relationship between the GP model and the radial basis function neural network is explained. Issues such as selection of the dimension of the input space and the computation load are also discussed. The GP modelling technique is demonstrated on an example of the nonlinear hydraulic positioning system.
Model-driven in reverse: the practical experience of the AQUA project
Authors: M. J. Escalona, J. J. Gutiérrez, L. Rodríguez-Catalán, A. Guevara
Venue: Proceedings of the 2009 Euro American Conference on Telematics and Information Systems: New Opportunities to increase Digital Citizenship (2009)

Model-Driven Web Engineering (MDWE) is a new paradigm which provides satisfactory results in software development. However, most experiments with MDWE towards the development of software from the requirements to the implementation stages. However, in practice, sometimes software development does not follow this classic path. In this paper, MDWE is presented as a suitable selection in software projects of technological evolution. The AQUA project is a very large and important project which is a fusion of three previous systems. Thus, this project starts with the original code of these three systems. The paper introduces the power of MDWE in this kind of systems.
Value Creating Strategies for IT Professionals
Authors: Riazul Hasan
Venue:  (2007)

Who should buy this book? - Target audience Value Creating Strategies for IT Professionals is a small useful synopsis written for Information Technology (IT) professionals (Systems Analysts, Network Administrators, Database Administrators, Programmers, Helpdesk Staff, Quality Assurance Analyst, IT Managers Etc). V C S contains some very practical scenarios aimed at generating value for your organization. Emphasis is placed throughout the book on knowing the operating environment of your employer's organization coupled with their culture, related U.S Government regulations & standards and their internal / external interfaces which exchange data / information with it on a regular basis. Mr. Riazul Hasan has worked as an IT professional for several U.S based organizations as consultant and employee; He holds a M.S in computer science from the Johns Hopkins University, Baltimore, Maryland, U.S.A. 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
Inferring activity time in news through event modeling
Authors: Vladimir Eidelman
Venue: Proceedings of the 46th Annual Meeting of the Association for Computational Linguistics on Human Language Technologies: Student Research Workshop (2008)

Many applications in NLP, such as question-answering and summarization, either require or would greatly benefit from the knowledge of when an event occurred. Creating an effective algorithm for identifying the activity time of an event in news is difficult in part because of the sparsity of explicit temporal expressions. This paper describes a domain-independent machine-learning based approach to assign activity times to events in news. We demonstrate that by applying topic models to text, we are able to cluster sentences that describe the same event, and utilize the temporal information within these event clusters to infer activity times for all sentences. Experimental evidence suggests that this is a promising approach, given evaluations performed on three distinct news article sets against the baseline of assigning the publication date. Our approach achieves 90%, 88.7%, and 68.7% accuracy, respectively, outperforming the baseline twice.
A bandwidth-efficient cooperative relaying scheme with space-time block coding and iterative decoding
Authors: Ho Van Khuong, Tho Le-Ngoc
Venue: Signal Processing (2009)

We propose a coded cooperative relaying scheme in which only newly generated parity bits of users are multiplexed, space-time block coded, and forwarded simultaneously by a multi-antenna relay to a common multi-antenna destination if the relay successfully decodes their information in order to improve bandwidth efficiency. Multiplexing introduces correlation between users' data, which offers effectively longer codes and facilitates high-performance iterative multi-user decoding at the destination. Additionally, space-time block coding makes bit-metrics calculation simple and increases spatial diversity of the received signal. Simulation results show that the proposed scheme significantly outperforms direct transmission under the same transmit power and bandwidth efficiency.
Financing as a Marketing Strategy
Authors: S. Hun Seog, Yong J. Hyun
Venue: Marketing Science (2009)

This paper investigates the issues concerning a film producer that finances production costs not only by the conventional funding from an institutional investor, but also by “Internet funding,” financing through the Internet from so-called netizen investors. In Internet funding, netizen investors engage in word-of-mouth activities. Assuming that information asymmetry exists between the producer and investors, we investigate how the Internet funding size varies with the word-of-mouth effect, the monitoring effect of the institutional investor, and the bargaining power of the producer over investors. When the producer has no bargaining power, the Internet funding size is determined by balancing the word-of-mouth effect with the monitoring effect by the institutional investment. If there is no word-of-mouth effect, there may be no Internet funding, because netizen investors interpret Internet funding as an indicator of a negative profit. When the producer has high bargaining power, full Internet funding is possible if the information asymmetry of the film quality is resolved. We discuss how information asymmetry can be resolved by the monitoring of the film quality, the producer's reputation, or the insurance on investment returns. Our model helps to capture several interesting aspects of Internet funding in the Korean film industry.