ppxscal/embedding_network huggingface dataset:
An object-oriented framework to organize genomic data
Authors: David Adelson, Michael Thon
Venue:  (2008)

Bioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already, or will soon be available for a number of livestock species. These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data. In term of exploring complex-intertwined genomic data, the way to organize them will be addressed in this study. Therefore, we investigated two issues in this study: one is an independent informatics framework including both back end and front end; another is how an informatics framework simplifies the user interface to explore data. We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data, and allow for query results to be presented via a user friendly web interface. A genome object-oriented framework (GOOF) was proposed with object-oriented Java technology and is independent of any database system. This framework seamlessly links the database system and web presentation components. The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data, meaning that users avoid constructing queries within the interface layer. Moreover, the module-based interface provided by GOOF could allow different users to access data in different interfaces and ways. In another words, GOOF not only gives a whole solution to informatics infrastructure, but also simplifies the organization of data modeling and presentation. In order to be a fast development solution, GOOF provides an automatic code engine by using meta-programming facilities in Java, which could allow users to generate a large amount of routine program codes. Moreover, the pre-built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema. In summary, we studied the way to model genomic data into an informatics framework, a one-stop approach, to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data.
Four measures for the dynamics of coalitions in social networks
Authors: Guido Boella, Leendert van der Torre, Serena Villata
Venue: Proceedings of the 20th ACM conference on Hypertext and hypermedia (2009)

We introduce four measures for the change of coalitions in social networks. The first one measures the change of the agents in the network over time, The second one measures the change of dependencies among the agents, due to addition or removal of powers and goals of the agents. The third one measures the change in normative dependencies like obligations and prohibitions introduced by norms. The fourth one measures changes in coalitions. If one of the first three measures is high, then the fourth measure is probably high too, if the change in agents and dependencies is a cause for a change in coalitions. If the first three measures are low, but the change in coalitions is high, it is due to internal processes like violations of the coalition agreements.
Aggregation Protocols for High Rate, Low Delay Data Collection in Sensor Networks
Authors: Jie Feng, Derek L. Eager, Dwight Makaroff
Venue: Proceedings of the 8th International IFIP-TC 6 Networking Conference (2009)

Sensor network applications commonly require sensor data to be periodically collected. Aggregation protocols can make this process considerably more efficient. This paper considers the problem of devising aggregation protocols for applications that must achieve as "real-time" a view of the monitored area as possible, entailing a high sampling rate and a low data collection delay, at the possible cost of some modest amount of data loss. We examine in particular broadcast-based protocols that minimize the number of packet transmissions, relying on multipath delivery rather than ARQ for reliability, and consider the question of whether such protocols can achieve lower collection delays and support higher sampling rates than conventional aggregation protocols. Our results suggest that broadcast-based protocols can yield significantly improved performance in some scenarios, when sensor data can be aggregated into packets of size that is independent (or largely independent) of the number of values being aggregated.
Plenary lecture 4: nanotechnology research efforts in Mexico
Authors: Armando Barranon
Venue: Proceedings of the 1st WSEAS international conference on Nanotechnology (2009)

In this plenary talk I will describe the research activities of about fifty Mexican nanotechnology research groups, comprising 300 researchers, and I will explain the need for governmental intervention in order to attain the objective of a Mexican Nanotechnology Initiative. In 2006 Mexican Council of Science of Technology funded several research groups to develop projects related to a Mexican National Initiative and in 2009 significant funds will be dedicated to technnological innovation in Mexican companies as well as technological invention derived from academic research. Proper screening of this funds may improve the production of Mexican patents and the development of large research networks all along Mexico where Nanotechnology research has been done mainly by public universities. Nanotechnology research groups in Mexico typically have five members and are devoted to a wide range of research subjects. Nanotechnology Laboratories have been founded in several Mexican States, using computational techniques, nanomicroscopy and chemical synthesis to develop new materials as well as new theoretical approaches to understand nanotechnology properties. Other Mexican nanotechnology research groups study the social and environmental impact of nanotechnology. The size frequency distribution of these research groups follows a power law in agreement with a model for social interaction although there are yet no signs of an institutional organization of these research groups which might lead to the creation of a Mexican Nanotechnology Initiative. Besides, it is also difficult to know which companies facing major economic hard times will have enough strength to complete the research and development tasks required to innovate. This will demand a proper selection of the companies funded and a careful screening of the funds devoted by CONACYT for innovation in Mexican companies.
Subcontracting Processes in Software Service Organisations - An Experience Report
Authors: Jakub Rudzki, Tarja Systä, Karri Mustonen
Venue: Proceedings of the International Conference on Software Process: Trustworthy Software Development Processes (2009)

Software systems and projects have become more and more distributed. This emphasises the need for ensured software quality, which impacts e.g. customer satisfaction, development costs, and delivery schedules. Concerns about the software quality become even more important in the case of subcontracted software projects, and in the case of multi-site projects in particular. In this paper we describe a practise-derived process to assess the potential subcontractors at their selection stage and later to evaluate the cooperation with them. For both purposes, particular criteria suites and frameworks are proposed. The criteria include software-specific and productivity metrics, but also more qualitative criteria. We report initial observations from usage of the process in industry. The assessment results are expected to help in making decisions about subcontractor selection, and later on assigning specific types of projects to specific subcontractors based on their suitability.
A Statistical Overlap Prior for Variational Image Segmentation
Authors: Ismail Ben Ayed, Shuo Li, Ian Ross
Venue: International Journal of Computer Vision (2009)

This study investigates variational image segmentation with an original data term, referred to as statistical overlap prior, which measures the conformity of overlap between the nonparametric distributions of image data within the segmentation regions to a learned statistical description. This leads to image segmentation and distribution tracking algorithms that relax the assumption of minimal overlap and, as such, are more widely applicable than existing algorithms. We propose to minimize active curve functionals containing the proposed overlap prior, compute the corresponding Euler-Lagrange curve evolution equations, and give an interpretation of how the overlap prior controls such evolution. We model the overlap, measured via the Bhattacharyya coefficient, with a Gaussian prior whose parameters are estimated from a set of relevant training images. Quantitative and comparative performance evaluations of the proposed algorithms over several experiments demonstrate the positive effects of the overlap prior in regard to segmentation accuracy and convergence speed.
Jorn barger, the newspage network and the emergence of the weblog community
Authors: Rudolf Ammann
Venue: Proceedings of the 20th ACM conference on Hypertext and hypermedia (2009)

Working from archival sources, this paper aims to reconstruct the emergence at Jorn Barger's initiative of the weblog community from a predecessor known as the NewsPage Network.
Self-optimizing interference management for the OFDMA downlink
Authors: Patrick Hosein
Venue: Proceedings of the 4th Annual International Conference on Wireless Internet (2008)

The next generations of wireless networks use OFDMA (Orthogonal Frequency Division Multiple Access) as the downlink radio transmission technology. With OFDMA, there is negligible interference between transmissions within a sector. However since transmissions in neighboring sectors may use the same frequency resources then such transmissions can cause interference. If this interference is too high then it negatively impacts the transmission rates achievable by users near the edge of the cell. Several approaches have been proposed to manage this cross-sector interference to achieve high sector throughput as well as acceptable performance for users near the cell edge. In this paper we summarize past approaches and then propose a simple distributed algorithm that requires no cross-sector coordination but achieves the desired performance characteristics. Since even the centralized version of this problem is intractable, our distributed algorithm is heuristic in nature but based on intuition gained from analytic results. Simplified simulation results are provided to support our claims.
Spectroscopic differentiation between O-atom vacancy and divacancy defects, respectively, in TiO2 and HfO2 by X-ray absorption spectroscopy
Authors: G. Lucovsky, K. -B. Chung, J. -W. Kim, D. Norlund
Venue: Microelectronic Engineering (2009)

Defect state features have been detected in second derivative O K edge spectra for thin films of nano-crystalline TiO"2 and HfO"2. Based on soft X-ray photoelectron band edge spectra, and the occurrence of occupied band edge 4f states in Gd(Sc,Ti)O"3, complementary spectroscopic features have been confirmed in the pre-edge (545eV) regimes of O K edge spectra. Qualitatively similar spectral features have been obtained for thin films of HfO"2 and TiO"2, and these have been assigned to defect states associated with vacancies. The two electrons/removed O-atom are not distributed uniformly over the TM atoms defining the vacancy geometry, but instead are localized in equivalent d-states: a d^2 state for a Ti monovacancy and a d^4 state for a Hf divacancy. This new model for electronic structure provides an unambiguous way to differentiate between monovacancy and divacancy arrangements, as well as immobile (or fixed) and mobile vacancies.
Training a real-world POMDP-based dialogue system
Authors: Blaise Thomson, Jost Schatzmann, Karl Weilhammer, Hui Ye, Steve Young
Venue: Proceedings of the Workshop on Bridging the Gap: Academic and Industrial Research in Dialog Technologies (2007)

Partially Observable Markov Decision Processes provide a principled way to model uncertainty in dialogues. However, traditional algorithms for optimising policies are intractable except for cases with very few states. This paper discusses a new approach to policy optimisation based on grid-based Q-learning with a summary of belief space. We also present a technique for bootstrapping the system using a novel agenda-based user model. An implementation of a policy trained using this system was tested with human subjects in an extensive trial. The policy gave highly competitive results, with a 90.6% task completion rate.
Comprehensive investigation of trap-assisted conduction in ultra-thin SrTiO3 layers
Authors: D. Manger, B. Kaczer, N. Menou, S. Clima, D. J. Wouters, V. V. Afanas'ev, J. A. Kittl
Venue: Microelectronic Engineering (2009)

The conduction in thin SrTiO"3 (STO) films has been investigated. Characterization of leakage current as a function of bias, temperature and film thickness indicates field enhanced hopping as the dominating conduction mechanism. The findings were confirmed by photo-conductivity measurements and agree well with simulation results.
The Impact of Structured Discussion on Students' Attitudes and Dispositions toward Argumentation
Authors: Khai Seng Hong, Ole C. Brudvik, Yam San Chee
Venue: Proceeding of the 2006 conference on Learning by Effective Utilization of Technologies: Facilitating Intercultural Understanding (2006)

Argumentation skills are highly valued in both education and business. As a process, participating in argumentation helps a person to develop their meta-cognitive and higher-order thinking abilities. This paper reports on empirical results on middle-school students' changes in attitudes towards argumentation as part of an ongoing design-based research study. Past attempts by researchers to foster students' argumentation skills have met with mixed results. General Web-based discussion boards often do not provide the structures and process scaffolds to help students acquire the target skill. In this study, a web-based structured argumentation board with sentence openers as scaffolds was designed to support students' engagement with argumentation over a four week long intervention. Two questionnaires, a pre-post and a post-then-pre, were designed to measure students' attitudes towards argumentation. The two questionnaires were used to identify any treatment dependent “response-shift bias”. Statistical results showed an improvement in students' attitudes toward argumentation. Qualitative analysis of student essays was also carried out and will be reported separately.
Characterization of a computational grid as a complex system
Authors: Lovro Ilijašić, Lorenza Saitta
Venue: Proceedings of the 6th international conference industry session on Grids meets autonomic computing (2009)

On the grid log data of more than 28 million jobs collected during 20 months, we use statistical and data mining methods to examine the relations primarily between users, computing elements and jobs in the network. The results of the large-scale analysis are used for building probabilistic models of the system behaviour. Bayesian Networks are constructed on historical data and are proven to be able to accurately predict abortion and lengths of newly arriving jobs.
Comparison of Neural Classification Algorithms Applied to Land Cover Mapping
Authors: Christian Thiel, Ferdinando Giacco, Friedhelm Schwenker, Günther Palm
Venue: Proceeding of the 2009 conference on New Directions in Neural Networks: 18th Italian Workshop on Neural Networks: WIRN 2008 (2009)

We compared the performance of several supervised classification algorithms on multi-source remotely sensed images. Apart from the Multi-Layer Perceptron, K-Nearest-Neighbour and Radial Basis Function network approaches, we looked more in detail at the Support Vector Machine classifier, which recently showed promising results in our setting. In particular, it is able to provide meaningful answers for the analysis of mixed pixels. They correspond to areas on the ground that comprise more than one distinct class, representing a major challenge for the interpretability of the final land-cover maps. To assess their impact, we performed a rejection-based analysis, allowing classifiers to refuse answers on pixels they can not associate mainly with one class. The experimental results lead to the conclusion that 1vs1 SVM approach with a linear kernel (using Bradley-Terry coupling) has to be preferred over all other classification algorithms examined, both in terms of accuracy as well as ease of visual interpretation.
Kinematic Geometry of Surface Machining, 1st edition
Authors: Stephen P. Radzevich
Venue:  (2007)

Despite decades of extensive research in this field, no solution to the problem of optimal part surface generation has been found. Kinematic Geometry Surface Machining fills the gap between the capabilities of modern multi-axis numerical controlled machines and the demands of the market. This book presents the latest research in the field of optimal surface generation. It provides an overview of modern CAD/CAM systems for high precision sculptured part surfaces. Including real-world examples and end-of-chapter references, the text also explains in detail how to develop the most cost-effective methods of machining for high quality sculptured surfaces on a multi-axis numerical controlled machine.
Semantic networks -based teachable agents in an educational game
Authors: Harri Ketamo
Venue: WSEAS Transactions on Computers (2009)

The aim of the study was to apply teachable agents into educational game meant for children less than 12 years of age and evaluate the outcome in context of cognitive psychology of learning. The study was done in two phases: design phase and evaluation phase (N=300). The design of the game was done in order to support relatively free use of teachable agents in an easy-to-use environment. The main findings of the study were a clear causality between quality of the taught semantic networks in game world and players' knowledge in real life and an evidence that learning away is an important feature when trying to enable conceptual change in educational games.
A singularity-avoiding moving least squares scheme for two-dimensional unstructured meshes
Authors: Samuel K. M. Chenoweth, Julio Soria, Andrew Ooi
Venue: Journal of Computational Physics (2009)

Moving least squares interpolation schemes are in widespread use as a tool for numerical analysis on scattered data. In particular, they are often employed when solving partial differential equations on unstructured meshes, which are typically needed when the geometry defining the domain is complex. It is known that such schemes can be singular if the data points in the stencil happen to be in certain special geometric arrangements, however little research has specifically addressed this issue. In this paper, a moving least squares scheme is presented which is an appropriate tool for use when solving partial differential equations in two dimensions, and the precise conditions under which singularities occur are identified. The theory is used to develop a stencil building algorithm which automatically detects singular stencils and corrects them in an efficient manner, while attempting to maintain stencil symmetry as closely as possible. Finally, the scheme is applied in a convection-diffusion equation solver and an incompressible Navier-Stokes solver, and the results are shown to compare favourably with known analytical solutions and previously published results.
Brief author index
Authors: Daniel Perovich, Maria Cecilia Bastarrica, Cristian Rojas
Venue: Proceedings of the 2009 ICSE Workshop on Sharing and Reusing Architectural Knowledge (2009)

Software Architecture (SA) allows for early assessment of and design for quality attributes of a software system, and it plays a critical role in current software development. However, there is no consensus on fundamental issues such as design methods and representation organization and languages, and current proposals lack specificity and preciseness. Thus, it is extremely difficult to build a complete and appropriate software architecture, even though it is recognized as a fundamental artifact. In this paper we define an architecture design method that enables the systematic and assisted construction of the SA of Enterprise Applications, taking into account major quality attributes involved in this family of systems. We apply Model-Driven Engineering techniques to achieve this goal. The architecture is treated as a mega-model (a model composed of related models) and the application of design decisions is encoded in terms of model transformations. The architectural rationale is explicitly registered as the set of transformations that yields the complete SA from scratch. We illustrate the application of the approach by designing the SA of a case study from the literature.
The lattice structure and refinement operators for the hypothesis space bounded by a bottom clause
Authors: Alireza Tamaddoni-Nezhad, Stephen Muggleton
Venue: Machine Learning (2009)

Searching the hypothesis space bounded below by a bottom clause is the basis of several state-of-the-art ILP systems (e.g. Progol, Aleph). These systems use refinement operators together with search heuristics to explore a bounded hypothesis space. It is known that the search space of these systems is limited to a sub-graph of the general subsumption lattice. However, the structure and properties of this sub-graph have not been properly characterised. In this paper firstly, we characterise the hypothesis space considered by the ILP systems which use a bottom clause to constrain the search. In particular, we discuss refinement in Progol as a representative of these ILP systems. Secondly, we study the lattice structure of this bounded hypothesis space. Thirdly, we give a new analysis of refinement operators, least generalisation and greatest specialisation in the subsumption order relative to a bottom clause. The results of this study are important for better understanding of the constrained refinement space of ILP systems such as Progol and Aleph, which proved to be successful for solving real-world problems (despite being incomplete with respect to the general subsumption order). Moreover, characterising this refinement sub-lattice can lead to more efficient ILP algorithms and operators for searching this particular sub-lattice. For example, it is shown that, unlike for the general subsumption order, efficient least generalisation operators can be designed for the subsumption order relative to a bottom clause.