ppxscal/embedding_network huggingface dataset:
The study of bioinformatics based on codon usage in DNA sequence
Authors: Kun-Lin Hsieh, Cheng-Chang Jeng, I-Ching Yang, Yan-Kwang Chen, Chun-Nan Lin
Venue: Proceedings of the 6th WSEAS International Conference on Systems Theory & Scientific Computation (2006)

To recognize the DNA sequence and mine the hidden information to achieve the classification of organisms are viewed as a difficult work to biologists. As we known, the amino acids are the basic elements to construct DNA. Hence, if the codon usage of amino acids can be analyzed well, the useful information about classification of organisms may be obtained. Hence, in this study, we will use the clustering technique into designing a novel approach based on Fuzzy C-means (FCM), and it will provide the useful information about organisms classification based on the codon usage. Finally, we also apply a case including eighteen bacteria to demonstrate the rationality and feasibility of our proposed approach.
The funnel that grew our cis major in the cs desert
Authors: Janice Pearce, Mario Nakazawa
Venue: Proceedings of the 39th SIGCSE technical symposium on Computer science education (2008)

Across the US, plummeting CS enrollments and disappointing student retention have caused serious concern in recent years. Yet, in the Spring of 2007, the Berea College faculty unanimously adopted a CIS major in response to the rise in enrollment in CS0 and retention into CS1. This paper details how using a funnel approach to attract students into the discipline via multiple CS0-level courses resulted in the exception to the trend.
Proceedings of the twentieth annual symposium on Parallelism in algorithms and architectures
Venue: ACM Symposium on Parallel Algorithms and Architectures (2008)

This volume consists of papers that were presented at the 20th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA'07), held on June 14-16, 2008, in Munich, Germany. It was sponsored by the ACM Special Interest Groups on Algorithms and Computation Theory (SIGACT) and Computer Architecture (SIGARCH) and organized in cooperation with the European Association for Theoretical Computer Science (EATCS). Financial support was provided by the German Research Foundation (DFG), Akamai, Intel, and Sun Microsystems. The 36 regular presentations that appeared at the conference were selected by the program committee after an electronic discussion and a meeting of two days that took place at Sun Labs, Burlington, Massachusetts, on March 20-21. Of these papers, the paper "Utilizing Shared Data in Chip Multiprocessors with the Nahalal Architecture" by Zvika Guz, Idit Keidar, Avinoam Kolodny, and Uri Weiser was selected to receive the best paper award. Fourteen papers were selected by Jim Larus for the special track on "Hardware and Software Techniques for Multicore Programming". The regular presentations were selected out of 128 submitted abstracts. The mix of selected papers reflects the unique nature of SPAA in bringing together the theory and practice of parallel computing. SPAA defines parallelism very broadly to encompass any computational device or scheme that can perform multiple operations or tasks simultaneously or concurrently. This year, the selection of papers was closer to SPAA's roots, in that technical papers included a large number of papers on parallel and multicore algorithms and architectures. The technical papers in this volume are to be considered preliminary versions, and authors are generally expected to publish polished and complete versions in archival scientific journals. In addition to the regular presentations, this volume includes 13 brief announcements and the abstracts of 4 posters that were presented at the SPAA review sessions. The committee's decisions in accepting brief announcements and posters were based on the perceived interest of these contributions, with the goal that they serve as bases for further significant advances in parallelism in computing. Extended versions of the SPAA brief announcements and posters may be published later in other conferences or journals. Finally, this year, there were 6 invited talks by Kunle Olukotun, Arnold Rosenberg, Leslie Valiant, Hagit Attiya, Charles Leiserson, and Burton Smith, to celebrate SPAA's 20 th anniversary.
Ray shooting and intersection searching amidst fat convex polyhedra in 3-space
Authors: Boris Aronov, Mark de Berg, Chris Gray
Venue: Computational Geometry: Theory and Applications (2008)

We present a data structure for ray-shooting queries in a set of convex fat polyhedra of total complexity n in R^3. The data structure uses O(n^2^+^@e) storage and preprocessing time, and queries can be answered in O(log^2n) time. A trade-off between storage and query time is also possible: for any m with n
Multicarrier demodulation for frequency selective channels subject to narrow band interferences
Authors: Guido H. Jajamovich, Cecilia G. Galarza
Venue: Digital Signal Processing (2008)

Nowadays, multicarrier modulation (MCM) systems based on the discrete Fourier transform are commonly used to transmit over frequency selective channels subject to aggressive noise disturbances. However, these transceivers suffer from poor subchannel spectral containment, that is, the level of inter-channel interference is not negligible. It can be shown that the system performance decreases when it is subject to a disturbance with most of its energy concentrated on a narrow frequency band. To improve the quality of service under these conditions, we present general MCM systems based on filter bank transformations. Lately, we add an equalizer at the channel output to implement these techniques over frequency selective channels, and we introduce a set of design strategies for the equalizer. Finally, we evaluate the performance of the overall system by simulating a frequency selective channel subject to narrow band interference.
An Algorithm for Approximating the Satisfiability Problem of High-level Conditions
Authors: Karl-Heinz Pennemann
Venue: Electronic Notes in Theoretical Computer Science (ENTCS) (2008)

The satisfiability problem is the fundamental problem in proving the conflict-freeness of specifications, or in finding a counterexample for an invalid statement. In this paper, we present a non-deterministic, monotone algorithm for this undecidable problem on graphical conditions that is both correct and complete, but in general not guaranteed to terminate. For a fragment of high-level conditions, the algorithm terminates, hence it is able to decide. Instead of enumerating all possible objects of a category to approach the problem, the algorithm uses the input condition in a constructive way to progress towards a solution. To this aim, programs over transformation rules with external interfaces are considered. We use the framework of weak adhesive HLR categories. Consequently, the algorithm is applicable to a number of replacement capable structures, such as Petri-Nets, graphs or hypergraphs.
Role of abrasives in high selectivity STI CMP slurries
Authors: R. Manivannan, S. Ramanathan
Venue: Microelectronic Engineering (2008)

In this study chemical mechanical planarization slurries for shallow trench isolation exhibiting high oxide to nitride polish rate selectivity were investigated and it was found that the abrasives play a major role in suppressing the nitride polish rate and enhancing selectivity. When glutamic acid is used as a selectivity enhancing additive, only ceria based slurries exhibit high selectivity while silica based slurries show low selectivity under identical conditions. A mechanism involving active sites on the ceria abrasive and interaction of glutamic acid with the active sites is proposed to explain the role of abrasive in enhancing selectivity.
Modelling inter-process dependencies with high-level business process modelling languages
Authors: Georg Grossmann, Michael Schrefl, Markus Stumptner
Venue: Proceedings of the fifth on Asia-Pacific conference on conceptual modelling - Volume 79 (2008)

The work presented in this paper targets the software integration on the level of business process models. The goal is to create the behavioural description of an integrated system that is consistent with the behavioural descriptions of the original local systems intended to be integrated. We build the behavioural description from existing models of the local systems by inserting dependencies between them. By this means, simulation and verification of interactions between them is possible and incompatibilities can be identified at an early stage before a new system is introduced. So far, business process modelling languages have mainly focused on a single application system although B2B and enterprise application integration demand on models to express cross organisational communication and inter-process dependencies. In this paper, we investigate commonly used business process languages on their suitability to model inter-process dependencies. The result shows that there is no language which supports all identified dependencies directly and that all languages demand from the modeller to consider their low-level semantics which prevent him from focusing on the design. We propose a set of extensions of UML 2.0 Activity Diagrams to overcome these limits.
Proceedings of the ACM workshop on Programmable routers for extensible services of tomorrow
Venue: Applications, Technologies, Architectures, and Protocols for Computer Communication (2008)

It is our great pleasure to welcome you to PRESTO'08 -- the workshop on Programmable Routers for Extensible Services of Tomorrow. Recently, there has been renewed interest in the networking research community in re-architecting the distribution of functions in an IP network. Also, researchers and practitioners in industry have been exploring the notion of open routers, which allows new functionality to be easily added into routers, as well as exploring router virtualization as a way to support a diverse set of applications and users. These efforts span the range from building open-source routing software, to making routers third-party-developer friendly by exposing router APIs, as recent industry announcements indicate. Programmable network elements hold the promise of accelerating innovation and service deployment. At the same time programmability could exacerbate already challenging network management tasks. The mission of this workshop is to foster the exchange of ideas between researchers and industry practitioners with a goal of driving service innovation in IP networks using novel extensible router architectures. The call for papers attracted 26 submissions from Europe, Japan, China, and the United States. The program committee accepted 12 papers that cover a variety of topics including programmable packet processing, virtualization, next generation data-center architectures, software routers and new network services. In addition, the program includes a mini-panel accompanying each session aimed at stimulating discussion and at providing an industry perspective. We hope that these proceedings will serve as a valuable reference for researchers and developers interested in programmable router architectures.
The new institutional portal of UA methodology of development
Authors: Diogo Casanova, Joaquim Sousa Pinto, Cláudio Teixeira, André Monteiro
Venue: Proceedings of the 2007 Euro American conference on Telematics and information systems (2007)

A university institutional portal is a step forward in managing information for the vision of a university directed to its public. Knowing the importance of this tool, the University of Aveiro (UA) developed in the last years its institutional portal. In this paper, we look for describing the diverse steps in the implementation of this application, since the necessary survey of requirements, followed by i) the necessity of development and integration of information subsystems; ii) the development of an institutional image and identity, and iii) the involvement of the university community at the final stage of the process. We also aim to describe the diverse phases of the Portal implementation until its launching.
The delay-friendliness of TCP
Authors: Eli Brosh, Salman Abdul Baset, Dan Rubenstein, Henning Schulzrinne
Venue: Proceedings of the 2008 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2008)

TCP has traditionally been considered unfriendly for real-time applications. Nonetheless, popular applications such as Skype use TCP since UDP packets cannot pass through many NATs and firewalls. Motivated by this observation, we study the delay performance of TCP for real-time media flows. We develop an analytical performance model for the delay of TCP. We use extensive experiments to validate the model and to evaluate the impact of various TCP mechanisms on its delay performance. Based on our results, we derive the working region for VoIP and live video streaming applications and provide guidelines for delay-friendly TCP settings. Our research indicates that simple application-level schemes, such as packet splitting and parallel connections, can reduce the delay of real-time TCP flows by as much as 30% and 90%, respectively.
Building an Open Toolkit of Digital Certificate Validation for Mobile Web Services
Authors: Florina Almenarez, Andres Marin, Daniel Diaz, Alberto Cortes, Celeste Campo, Carlos Garcia-Rubio
Venue: Proceedings of the 2008 Sixth Annual IEEE International Conference on Pervasive Computing and Communications (2008)

Mobile devices can both consume and provide services. They act indeed as a peer, according to the OMA Mobile Web Services Specification. It is a move from simple data sharing to full deliver of application services down to mobile devices. The use of digital certificates to ensure the provision of services is suitable because devices can belong to different trust domains without having previously an established relationship. Besides, by interoperability issues, the use of PKI continues to grow and move into diverse environments. However, applications making use of such certificates are burdened with theoverhead of constructing and validating the certification paths. These processes can become more complex and costly than fixed-infrastructure networks due to the wireless communications and restricted processing and power capabilities. The IETF PKIX WG has specified differentmechanisms for delegating the certificate validation and making lighter the status information obtaining. However, these are not supported currently by mobile devices. For these reasons, we propose to develop an open toolkit for X.509 public key certificate validating based on OpenSSL. This toolkit is being developed and tested successfully onPDAs.
Local oxidation of titanium films by non-contact atomic force microscopy
Authors: Te-Hua Fang, Tong Hong Wang, Kuan-Te Wu
Venue: Microelectronic Engineering (2008)

Characteristics of local nanolithography on oxidative titanium dots and wires were studied using an amplitude modulation atomic force microscopy in the non-contact mode. Nanolithographic experiments were conducted to investigate the influence that different experimental parameters had on the height, the width, the growth rate, the morphology, and the composition of the nanostructures using Auger electron spectroscopy. The results indicate that anodization time, applied voltage, and tip-sample distance are proportional to the heights and widths of the dots. When the tip-sample distance was too close during continued anodization, concave dots appeared because the oxide that enclosed the tip. Carbon nanotube probe fabricated dots are also presented and compared.
Model for a gradual objects recognition
Authors: M. Sadgal, A. El Fazziki, A. Ait Ouahman
Venue: Proceedings of the 2nd WSEAS International Conference on Electronics, Control and Signal Processing (2003)

The objects appearance in the images is modified because of several external factors (i.e.: illumination, rotate, pose) and the application of the standard comparison algorithms does not answer suitably. For landing this problem, we present here an architecture based on a gradual recognition: The object is represented on a scale of categories, and the task of the algorithms of recognition is to concentrate on the determination of the category the most detailed according to information extracted from the image. It is not necessary any more to pass by several intermediate phases before starting the process of recognition. On this principle, we propose a model for the internal representation of a system of vision which tries to generalize the recognition of objects by taking into account the categorization.
Cost-sensitive multi-class classification from probability estimates
Authors: Deirdre B. O'Brien, Maya R. Gupta, Robert M. Gray
Venue: Proceedings of the 25th international conference on Machine learning (2008)

For two-class classification, it is common to classify by setting a threshold on class probability estimates, where the threshold is determined by ROC curve analysis. An analog for multi-class classification is learning a new class partitioning of the multiclass probability simplex to minimize empirical misclassification costs. We analyze the interplay between systematic errors in the class probability estimates and cost matrices for multiclass classification. We explore the effect on the class partitioning of five different transformations of the cost matrix. Experiments on benchmark datasets with naive Bayes and quadratic discriminant analysis show the effectiveness of learning a new partition matrix compared to previously proposed methods.
Cyclic Extensions of Order Varieties
Authors: Pierre Ille, Paul Ruet
Venue: Electronic Notes in Theoretical Computer Science (ENTCS) (2008)

We study complexity problems involving three sorts of combinational structures: cyclic orders, order varieties and cycles. It is known that the problem of telling whether a cyclic order is included in some cycle is NP-complete. We show that the same question for order varieties, a special class of cyclic orders, is in L. For this, we relate the entropy relation between partial orders to the forcing relation of graph theory.
Screening of Apoptotic Genes by Morphological Analysis of High Throughput Fluorescence Microscopy Images
Authors: Yongsu Chae, Soo Jung Kim, Desok Kim
Venue: Proceedings of the 2007 Frontiers in the Convergence of Bioscience and Information Technologies (2007)

Apoptosis is a programmed cell death required for development and maintenance of normal tissue. However, cancer cells often evade apoptosis by inactivating apoptotic genes. Thus, the discovery of apoptotic genes has become important in cancer research. We developed a morphological analysis to quantify apoptosis automatically. Cellular images were acquired by high throughput fluorescence microscopy and normalized. Nuclear and chromatin images were segmented by top hat operations and touching nuclei were further separated by erosion, labeling, and conditional dilation. Shape and intensity features were extracted from nuclear and chromatin images to produce discriminant functions by logistic regression. Nuclear objects were classified as isolated and touching with 91.7% accuracy. Apoptotic and mitotic nuclei were identified with 88.8% accuracy. Automatic apoptotic rates were highly correlated with manual rates {\text{(}}\rho {\text{ =0}}{\text{.91, p
Opinion mining from noisy text data
Authors: Lipika Dey, S K Mirajul Haque
Venue: Proceedings of the second workshop on Analytics for noisy unstructured text data (2008)

The proliferation of Internet has not only generated huge volumes of unstructured information in the form of web documents, but a large amount of text is also generated in the form of emails, blogs, and feedbacks etc. The data generated from online communication acts as potential gold mines for discovering knowledge. Text analytics has matured and is being successfully employed to mine important information from unstructured text documents. Most of these techniques use Natural Language Processing techniques which assume that the underlying text is clean and correct. Statistical techniques, though not as accurate as linguistic mechanisms, are also employed for the purpose to overcome the dependence on clean text. The chief bottleneck for designing statistical mechanisms is however its dependence on appropriately annotated training data. None of these methodologies are suitable for mining information from online communication text data due to the fact that they are often noisy. These texts are informally written. They suffer from spelling mistakes, grammatical errors, improper punctuation and irrational capitalization. This paper focuses on opinion extraction from noisy text data. It is aimed at extracting and consolidating opinions of customers from blogs and feedbacks, at multiple levels of granularity. Ours is a hybrid approach, in which we initially employ a semi-supervised method to learn domain knowledge from a training repository which contains both noisy and clean text. Thereafter we employ localized linguistic techniques to extract opinion expressions from noisy text. We have developed a system based on this approach, which provides the user with a platform to analyze opinion expressions extracted from a repository.
Integrating The Concept Of Synthesis In The Software Architecture Design Process
Authors: Bedir Tekinerdogan, Mehmet Aksit
Venue: Journal of Integrated Design Process Science (2006)

Synthesis is a widely applied problem-solving approach of mature engineering disciplines including the sub-processes of technical problem analysis, identification and composition of solution domain concepts, and alternative-space analysis. Current software development processes do not adopt an explicit synthesis process and as such may fall short in identifying, composing and evaluating the relevant concerns. In order to advance ad hoc software development process to a mature engineering discipline it is necessary to integrate the concept of synthesis in current software engineering processes. In software engineering, software architecture design forms a key artifact including the early design decisions, which embodies the overall structure that impacts the quality of the overall system. For ensuring the quality of software architecture, it is necessary to identify and compose the relevant concerns. For this, we integrate the concept of synthesis in the software architecture design process and present the synthesis-based software architecture design process. This approach differs from existing software architecture design approaches since it explicitly includes the synthesis sub-processes of technical problem analysis, solution domain analysis and alternative space analysis, integrating these in a common process.
On a cubically convergent derivative-free root finding method
Authors: Miodrag S. Petkovic, Ljiljana D. Petkovic
Venue: International Journal of Computer Mathematics (2007)

Using a method for accelerating convergence and Weierstrass' correction, a cubically convergent method without derivatives for the simultaneous determination of polynomial zeros is derived. The proposed method possesses approximately the structure of Halley's method. Using the Gauss-Seidel approach, the single-step method is outlined. Convergence analysis and computational aspects are reported.
XOP: Sharing XML Data Objects through Peer-to-Peer Networks
Authors: Itamar de Rezende, Frank Siqueira
Venue: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications (2008)

This paper describes an architecture for sharing data in XML format through a peer-to-peer (P2P) network, which interconnects devices ranging from high-end servers to mobile devices. The XOP architecture allows devices with low storage capacity and subject to disconnection to use other peers of the P2P network for storing data. Users are able to locate and access data in a friendly and flexible way. Shared data is described using an extensible ontology, built using the OWL language, in order to provide more precise search results. This paper also describes a prototype of this architecture and analyzes the obtained performance.