ppxscal/embedding_network huggingface dataset:
Formulating and testing hypotheses in functional genomics
Authors: Joaquin Dopazo
Venue: Artificial Intelligence in Medicine (2009)

Objective: The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the results, relating the available genomic information to the hypotheses that originated the experiment. Methods and results: Initially, this interpretation has been made on a pre-selection of relevant genes, based on the experimental values, followed by the study of the enrichment in some functional properties. Nevertheless, functional enrichment methods, demonstrated to have a flaw: the first step of gene selection was too stringent given that the cooperation among genes was ignored. The assumption that modules of genes related by relevant biological properties (functionality, co-regulation, chromosomal location, etc.) are the real actors of the cell biology lead to the development of new procedures, inspired in systems biology criteria, generically known as gene-set methods. These methods have been successfully used to analyze transcriptomic and large-scale genotyping experiments as well as to test other different genome-scale hypothesis in other fields such as phylogenomics.
Analytical Inductive Functional Programming
Authors: Emanuel Kitzelmann
Venue: Logic-Based Program Synthesis and Transformation: 18th International Symposium, LOPSTR 2008, Valencia, Spain, July 17-18, 2008, Revised Selected Papers (2009)

We describe a new method to induce functional programs from small sets of non-recursive equations representing a subset of their input-output behaviour. Classical attempts to construct functional Lisp programs from input/output-examples are analytical, i.e., a Lisp program belonging to a strongly restricted program class is algorithmically derived from examples. More recent approaches enumerate candidate programs and only test them against the examples until a program which correctly computes the examples is found. Theoretically, large program classes can be induced generate-and-test based, yet this approach suffers from combinatorial explosion. We propose a combination of search and analytical techniques. The method described in this paper is search based in order to avoid strong a-priori restrictions as imposed by the classical analytical approach. Yet candidate programs are computed based on analytical techniques from the examples instead of being generated independently from the examples. A prototypical implementation shows first that programs are inducible which are not in scope of classical purely analytical techniques and second that the induction times are shorter than in recent generate-and-test based methods.
Fuzzy ensemble clustering based on random projections for DNA microarray data analysis
Authors: Roberto Avogadri, Giorgio Valentini
Venue: Artificial Intelligence in Medicine (2009)

Objective: Two major problems related the unsupervised analysis of gene expression data are represented by the accuracy and reliability of the discovered clusters, and by the biological fact that the boundaries between classes of patients or classes of functionally related genes are sometimes not clearly defined. The main goal of this work consists in the exploration of new strategies and in the development of new clustering methods to improve the accuracy and robustness of clustering results, taking into account the uncertainty underlying the assignment of examples to clusters in the context of gene expression data analysis. Methodology: We propose a fuzzy ensemble clustering approach both to improve the accuracy of clustering results and to take into account the inherent fuzziness of biological and bio-medical gene expression data. We applied random projections that obey the Johnson-Lindenstrauss lemma to obtain several instances of lower dimensional gene expression data from the original high-dimensional ones, approximately preserving the information and the metric structure of the original data. Then we adopt a double fuzzy approach to obtain a consensus ensemble clustering, by first applying a fuzzy k-means algorithm to the different instances of the projected low-dimensional data and then by using a fuzzy t-norm to combine the multiple clusterings. Several variants of the fuzzy ensemble clustering algorithms are proposed, according to different techniques to combine the base clusterings and to obtain the final consensus clustering. Results and conclusion: We applied our proposed fuzzy ensemble methods to the gene expression analysis of leukemia, lymphoma, adenocarcinoma and melanoma patients, and we compared the results with other state of the art ensemble methods. Results show that in some cases, taking into account the natural fuzziness of the data, we can improve the discovery of classes of patients defined at bio-molecular level. The reduction of the dimension of the data, achieved through random projections techniques, is well-suited to the characteristics of high-dimensional gene expression data, thus resulting in improved performance with respect to single fuzzy k-means and with respect to ensemble methods based on resampling techniques. Moreover, we show that the analysis of the accuracy and diversity of the base fuzzy clusterings can be useful to explain the advantages and the limitations of the proposed fuzzy ensemble approach.
Membrane and bipolar plates materials for regenerative fuel cells
Authors: Salwan S. Dihrab, K. Sopian, A. Zaharim
Venue: Proceedings of the 8th conference on Simulation, modelling and optimization (2008)

Unitized regenerative fuel cell is a unique fuel cell can work in both electrolyser and fuel cell in one cell at different mode, its useful in some application in which the weight is an important issue. This article reviews current literature with the objective of identifying the latest development in membrane and bipolar plates materials for the Unitized Regenerative Fuel Cell (URFC). The result shows that the choice of both the bipolar plates and the catalyst for URFC electrodes is a delicate task because a very good candidate for fuel cell mode will not function well in the electrolyser mode and therefore it is suggested that a compromise should be considered. It is recommended that aluminum or titanium with a gold-coated layer is a very suitable candidate as the bipolar plate and IrOX , Ru or both with Pt is suitable for oxygen side catalyst in the URFC.
Sampling methods for shortest vectors, closest vectors and successive minima
Authors: Johannes Blömer, Stefanie Naewe
Venue: Theoretical Computer Science (2009)

We study four problems from the geometry of numbers, the shortest vector problem(Svp), the closest vector problem(Cvp), the successive minima problem(Smp), and the shortest independent vectors problem (Sivp). Extending and generalizing results of Ajtai, Kumar, and Sivakumar we present probabilistic single exponential time algorithms for all four problems for all @?"p norms. The results on Smp and Sivp are new for all norms. The results on Svp and Cvp generalize previous results of Ajtai et al. for the Euclidean @?"2 norm to arbitrary @?"p norms. We achieve our results by introducing a new lattice problem, the generalized shortest vector problem (GSvp). We describe a single exponential time algorithm for GSvp. We also describe polynomial time reductions from Svp,Cvp,Smp, and Sivp to GSvp, establishing single exponential time algorithms for the four classical lattice problems. This approach leads to a unified algorithmic treatment of the lattice problems Svp,Cvp,Smp, and Sivp.
Empathy in virtual learning environments
Authors: Judith Molka-Danielsen, Bryan W. Carter, Alastair Creelman
Venue: International Journal of Networking and Virtual Organisations (2009)

How do we engage teachers and learners in the learning process and what are the benefits of this? How do we get students to learn? Many academic institutions of all levels are asking these questions. Throughout the years new teaching methodologies and strategies have been explored and applied (Blumenfeld et al., 1991; Dewey, 1997). In assessments of these, some have been associated with improving the targeted students' levels of knowledge, understanding, functionality and motivations (Gulbahar and Tinmaz, 2006; Kjellin and Stenfors, 2003). In this study we review a variety of teaching methodologies and introduce a research hypothesis that these methodologies have an unlike potential for supporting empathic aspects of the teacher and learner relationship and that, further, Virtual Learning Environments (VLEs) will have strong potential for empathic support. We set up an evaluation framework using a qualitative approach to examine the empathic factor in VLEs. Finally, we identify design factors for VLEs that could impact learning and suggest these as the focus for future study.
Tank allocation problems in maritime bulk shipping
Authors: Lars Magnus Hvattum, Kjetil Fagerholt, Vinícius Amaral Armentano
Venue: Computers and Operations Research (2009)

In real world maritime routing problems, many restrictions and regulations influence the daily operations. The effects of several of these restrictions have not yet been studied in depth from an operations research perspective. This paper introduces the problem of allocating bulk cargoes to tanks in maritime shipping. A model and several variations are presented, and it is shown that the main problem consists of a number of complicating constraints. The problem studied is crucial when determining whether a given route is feasible for a given ship, and computational experiments are performed to assess the difficulty of solving realistically sized instances. The proposed formulation is hoped to provide a suitable starting point for research on stowage problems in maritime bulk shipping.
Generic middleware substrate through modelware
Authors: Charles Zhang, Dapeng Gao, Hans-Arno Jacobsen
Venue: Proceedings of the ACM/IFIP/USENIX 2005 International Conference on Middleware (2005)

Conventional middleware architectures suffer from insufficient module-level reusability and the ability to adapt in face of functionality evolution and diversification. To overcome these deficiencies, we propose the Modelware methodology adopting the Model Driven Architecture (MDA) approach and aspect oriented programming (AOP). We advocate the use of models and views to separate intrinsic functionalities of middleware from extrinsic ones. This separation effectively lowers the concern density per component and fosters the coherence and the reuse of the components of middleware architectures. Comparing to the conventionally designed version, Modelware improves the standard benchmark performance by as much as 40% through architectural optimizations. Our evaluation also shows that Modelware considerably reduces coding efforts in supporting the funcitonal evolution of middleware and dramatically different application domains.
Temporal-Awareness in SLAs: Why Should We Be Concerned?
Authors: C. Müller, A. Ruiz-Cortés, P. Fernández
Venue: Service-Oriented Computing - ICSOC 2007 Workshops: ICSOC 2007, International Workshops, Vienna, Austria, September 17, 2007, Revised Selected Papers (2009)

Traditionally, Service Level Agreements have been decomposed in two sets of properties: functionals (what) and non-functionals (how). However, in our opinion, there has been a third key element that has had a minor attention from academy: temporal awareness (when). We believe temporality is a main concern that should be addressed in realistic scenarios. In doing so, this position paper discuss our experience in extending the specification WS-Agreement with a temporal Domain Specific Language; importantly, main aim of the paper is to provoke a debate about the importance of temporality in SLAs.
Key-Dependent S-Box Generation in AES Block Cipher System
Authors: Kazys Kazlauskas Jaunius Kazlauskas
Venue: Informatica (2009)

Advanced Encryption Standard (AES) block cipher system is widely used in cryptographic applications. A nonlinear substitution operation is the main factor of the AES cipher system strength. The purpose of the proposed approach is to generate the random S-boxes changing for every change of the secret key. The fact that the S-boxes are randomly key-dependent and unknown is the main strength of the new approach, since both linear and differential cryptanalysis require known S-boxes. In the paper, we briefly analyze the AES algorithm, substitution S-boxes, linear and differential cryptanalysis, and describe a randomly key-dependent S-box and inverse S-box generation algorithm. After that, we introduce the independency measure of the S-box elements, and experimentally investigate the quality of the generated S-boxes.
Process Improvement with CMMI v1.2 and ISO Standards, 1 edition
Authors: Boris Mutafelija, Harvey Stromberg
Venue:  (2008)

In this age of globalization, process improvement practitioners must be able to comprehend and work with the different standards and frameworks used around the world. While many systems and software engineering organizations rely on a single standard as the primary driver of process improvement efforts (CMMI-based process improvement in the U.S. and ISO 9001 around the world), the most successful incorporate multiple frameworks. Process Improvement with CMMI v1.2 and ISO Standards helps users become more versatile in using multiple process standards when creating organizational and project processes. Compares and Contrasts Different StandardsThe book begins by discussing the motivations for process improvement, the factors that make improvement difficult, and the conditions and activities that enable improvement. It examines the structure and content of Capability Maturity Model IntegrationSM, version 1.2, provides summaries of several ISO standards, and discusses the detailed relationships between four specific ISO standards (ISO 9001, ISO 15288, ISO 12207, and ISO 20000) and CMMI. The book concludes by addressing the synergy and use of multiple frameworks, discussing the process of conducting appraisals against multiple frameworks, and examining the collection of objective evidence required by each standard and appraisal method. The authors also discuss similarities and differences among the appraisal and certification approaches. Free DownloadsThis volume is highly supplemented with numerous appendices to clarify material and a website is provided where readers can download detailed maps and corresponding correlation matrices. This bonus material allows users to further experiment with the framework relationships and be more equipped to deal with the myriad of standards and frameworks they may encounter.
Preventing identity theft with electronic identity cards and the trusted platform module
Authors: Andreas Klenk, Holger Kinkelin, Christoph Eunicke, Georg Carle
Venue: Proceedings of the Second European Workshop on System Security (2009)

Together with the rapidly growing number of services in the Internet, authentication becomes an issue of increasing importance. A very common situation is that for each service, users must remember the associated name and password they are registered under. This method is prone to identity theft and its usability leaves much to be desired. The Trusted Platform Module (TPM) is a microcontroller with cryptographic functions that is integrated into many computers. It is capable to protect against software attacks. TPM can generate and store non-migratable keying material for authentication and is an effective safeguard against the acquisition and use of an identity by an adversary. Even though TPM prohibits identity theft, Internet services still have few options to verify the true identity of a user. Electronic identity cards (eID) assert for the identity of their owner. Their large-scale deployment can be expected in the near future. The use of eIDs is impaired, though. They must be present for each authentication, and all devices must be equipped with a compatible card reader. We mitigate the problems of both approaches by using eIDs for establishing trust in user specific TPM authentication credentials. The eID and a compatible reader must be present only at one time for establishing the initial trust. We integrated our identity theft resistant authentication method with the OpenID identity system to allow a large number of services to profit from verified and trustworthy identity assertions.
Do web sites change customers' beliefs? A study of prior-posterior beliefs in e-commerce
Authors: Fatemeh "Mariam" Zahedi, Jaeki Song
Venue: Information and Management (2009)

Web sites are the main interface between online merchants and their customers. Despite the consequent importance of web-site design, there is little theoretical foundation that can be used to assess how web-design factors lead e-customers to revise their earlier beliefs. Our study examined web customers' salient beliefs and the role of web-design elements in altering customers' existing beliefs after their exposure to an e-commerce web site. Using salient beliefs and categories of web-design elements identified previously, we developed a conceptual model of belief revisions due to exposure to web-design elements and internal cues. The empirical analysis of the model indicated that web customers were influenced by the external cues from the design factors as well as the internal ones from their prior beliefs. Our findings have implications in designing web sites for e-commerce.
Lifetime-maximized cluster association in two-tiered wireless sensor networks
Authors: Wen-Zhan Song, WeiZhao Wang, Kousha Moaveni-Nejad, Xiang-Yang Li
Venue: Wireless Communications Mobile Computing (2009)

In this paper, we study the two-tiered wireless sensor network (WSN) architecture and propose the optimal cluster association algorithm for it to maximize the overall network lifetime. A two-tiered WSN is formed by number of small sensor nodes (SNs), powerful application nodes (ANs), and base-stations (BSs, or gateways). SNs capture, encode, and transmit relevant information to ANs, which then send the combined information to BSs. Assuming the locations of the SNs, ANs, and BSs are fixed, we consider how to associate the SNs to ANs such that the network lifetime is maximized while every node meets its bandwidth requirement. When the SNs are homogeneous (e.g., same bandwidth requirement), we give optimal algorithms to maximize the lifetime of the WSNs; when the SNs are heterogeneous, we give a 2-approximation algorithm that produces a network whose lifetime is within 1-2 of the optimum. We also present algorithms to dynamically update the cluster association when the network topology changes. Numerical results are given to demonstrate the efficiency and optimality of the proposed approaches. In simulation study, comparing network lifetime, our algorithm outperforms other heuristics almost twice. Copyright &copy; 2007 John Wiley & Sons, Ltd.
Optical wireless communications method for location-based information support using a corner-reflecting terminal and a distance image camera
Authors: Xin Lin, Kazutaka Kosugi, Hideo Itoh
Venue: Proceedings of the 5th conference on Applied electromagnetics, wireless and optical communications (2007)

Optical wireless communications system with a corner-reflecting terminal (CRT) and a distance image camera (DIC) is proposed for location-based information support. By using the CRT and the DIC, the user location can be tracked and detected, and the distance from the camera to the user who is tracked can be obtained real-timely. Therefore, the information support of users can be implemented based only on their physical locations and without the private data such as an address or ID number. We also performed two experiments based on the proposed system and method, and their effectiveness is demonstrated in multi-terminal location detection and indoor data communications.
From interaction to trajectories: designing coherent journeys through user experiences
Authors: Steve Benford, Gabriella Giannachi, Boriana Koleva, Tom Rodden
Venue: Proceedings of the 27th international conference on Human factors in computing systems (2009)

The idea of interactional trajectories through interfaces has emerged as a sensitizing concept from recent studies of tangible interfaces and interaction in museums and galleries. We put this concept to work as a lens to reflect on published studies of complex user experiences that extend over space and time and involve multiple roles and interfaces. We develop a conceptual framework in which trajectories explain these user experiences as journeys through hybrid structures, punctuated by transitions, and in which interactivity and collaboration are orchestrated. Our framework is intended to sensitize future studies, help distill craft knowledge into design guidelines and patterns, identify technology requirements, and provide a boundary object to connect HCI with Performance Studies.
An Overview of the MABS and RPG Techniques in Natural Resources Management
Authors: Diana F. Adamatti
Venue: Proceedings of the 2009 International Conference on Computer Engineering and Technology - Volume 02 (2009)

The Natural Resources Management area is substantial to the development of the all countries, because the resources are more scarce and the number of people bigger. For these reasons, they are more difficult to manage. In this way, find good techniques to learn how to treat with these resources in a sustainable way is an important activity of sciences. Specifically in computer science, several works have been used MABS (Multi-Agent-Based Simulation) and RPG (Role-Playing Games) techniques to test and better understand this area. In this paper, we present an overview of this area and some works related, focusing in our researches.
Design and implementation of a cipher system (LAM) on a FPGA based on PCI architecture
Authors: Panagiotis Margaronis, Lambrinoudakis Kostantinos, Gritzalis Stefanos, Antonidakis Emmanouil, Chrysocheris Ilias
Venue: Proceedings of the 6th conference on Microelectronics, nanoelectronics, optoelectronics (2007)

This paper presents the design and implementation of a digital integrated encryption/decryption circuitry called LAM which is based on Peripheral Component Interconnect (PCI) Architecture for the use on a Personal Computer (PC) communication card. The implementation of a hardware PC cryptography card has been designed using a Field Programmable Gate Array (FPGA) chip in combination with the digital part of the PCI Bus. The main objective of this paper is to provide the reader with a deep insight of the design of a digital cryptographic circuit, which was designed for a FPGA chip with the use of Very (High-Speed Integrated Circuit) Hardware Description Language (VHDL) for a PCI card. A demonstration of the LAM circuitry and PCI Interface will be presented. To see the effect of the LAM cryptography in the operation of the card, it was also simulated and analyzed. The Simulations were run under various conditions, which are applicable to most PCI applications.
Deriving IT Configurations from Business Processes
Authors: Sven Graupner, Jerry Rolia, Nigel Edwards
Venue: Proceedings of the 2008 10th IEEE Conference on E-Commerce Technology and the Fifth IEEE Conference on Enterprise Computing, E-Commerce and E-Services (2008)

Identifying proper business processes, formalizing and documenting them has always been a challenge. Maintaining them in synchronization with changing business needs makes the problem harder. It becomes even harder when business processes are fully or partially implemented in IT systems where changes to the business cause changes in IT configurations. This paper presents an approach how IT configurations can be derived from business process definitions. Additional information needs to be supplemented to enable the desired function. This information is made available in form of models about application components and their performance characteristics. A series of transformations has been defined between models that constitute the Model Information Flow. The work is part of joint research between HP Labs and SAP Research.