ppxscal/embedding_network huggingface dataset:
Speedups from extending embedded processors with a high-performance coarse-grained reconfigurable data-path
Authors: Michalis D. Galanis, Costas E. Goutis
Venue: Journal of Systems Architecture: the EUROMICRO Journal (2008)

In this paper, an embedded system that extends microprocessor cores with a high-performance coarse-grained reconfigurable data-path is introduced. The data-path have been previously introduced by the authors. It is composed by computational resources able to realize complex operations which aid in improving the performance of time critical application parts, called kernels. A compilation flow is defined for mapping high-level software descriptions to the microprocessor system. The kernel code is mapped using a properly developed mapping algorithm for the reconfigurable data-path, while the non-critical segments are executed on the microprocessor. Extensive exploration is performed by mapping four real-life applications on six different instances of the system. The results show that the speedup from executing kernels on the reconfigurable logic ranges from 6.3 to 154.3, relative to the software execution on the processor since the available processing elements of the data-path are efficiently utilized. Important overall application speedups, due to the kernels' acceleration, have been reported for the four applications. These overall performance improvements range from 1.70 to 3.70 relative to an all-processor execution. Furthermore, the experiments show that the proposed data-path achieves faster kernels' execution compared with other high-performance data-paths.
Animated database courseware (ADBC): database design, SQL, transactions and security
Authors: Meg Murray, Mario Guimaraes
Venue: Journal of Computing Sciences in Colleges (2008)

Many concepts are difficult to convey in traditional classroom lecture mediums. This is true with many database concepts. One way to supplement classroom teaching is through the use of software animations. This workshop will demonstrate how Animated Database Courseware (ADbC) might be incorporated into a database course. ADbC is an on going project funded by NSF-CCLI [grant # 0717707]. The project includes the development of several animations covering a wide variety of database concepts including database design, SQL, transactions processing and database security. Prototypes which have been developed are freely available at the website: http://adbc.kennesaw.edu.
A Common Concept Description of Natural Language Texts as the Foundation of Semantic Computing on the Web
Authors: Mitsuru Ishizuka
Venue: Proceedings of the 2008 IEEE International Conference on Sensor Networks, Ubiquitous, and Trustworthy Computing (sutc 2008) (2008)

In order to intelligently process vast information on the Web, we need to make computers understand the meaning of the Web contents and manipulate them taking account of their semantics. Since text is the major medium conveying information, it is thus natural and reasonable to set it as the immediate target that the computer understands the meaning, while there are other types of media such as picture, movie, etc. Toward this direction, the activity of the Semantic Web is going on. It aims to establish a standardized machine-readable description format of meta-data. However, the meta-data are only fragments of the Web contents. Unlike the Semantic Web, we aim to describe the concept meaning expressed in the whole natural language texts with a common format that the computer can understand. We have designed Concept Description Language (CDL) as a vehicle for this end, and started its standardization activity in W3C. There are several levels of the meaning of the texts, ranging from shallow level to deep one. While it is still difficult to make a consensus on how to describe the deep meaning, we think that a certain consensus can be attained on a way of describing the shallow meaning of the texts, based on the research results accumulated in the field of natural language processing such as machine translation over the last several decades. In CDL, besides lexicons, 45 relations are pre-defined as being necessary and sufficient for denoting every semantic relation between entities (lexicons in a simple case). These CDL relations can be used universally, while the ontologies in the Semantic Web are domain dependent and thus cause some problematic situations. Current issues of CDL are, among others, an easy semi-automatic way of converting natural language texts into the CDL description, and an effective mechanism of executing semantic retrieval on the CDL database. We believe that CDL contributes to build a framework of next-generation Web which provides the foundation for a variety of semantic computing. Also, CDL may contribute to overcome the language barrier among nations.
Fabrication of silicon dioxide nanochannel arrays without nanolithography for manipulation of DNA molecule
Authors: Y. H. Cho, S. W. Lee, T. Fujii, B. J. Kim
Venue: Microelectronic Engineering (2008)

In this paper, silicon dioxide (SiO"2) nanochannel arrays for DNA molecule stretching are presented. The fabrication of SiO"2 nanochannel is based on the combination of wet anisotropic etching, local oxidation of silicon (LOCOS) and plasma etching of silicon. This fabrication technique is suggested for generating SiO"2 layer, which is easily controllable by oxidation condition. Thus, this technique enables the generation of nanochannels with various nanoscale dimensions without using nanolithography. DNA stretching experiment using the fabricated nanochannels is shown. That is, single DNA molecules stained with a fluorescent dye can be effectively stretched in the nanochannels.
Global pairwise sequence alignment through mixed-integer linear programming: a template-free approach
Authors: S. R. McAllister, R. Rajgaria, C. A. Floudas
Venue: Optimization Methods Software (2007)

The problem of protein sequence alignment is the main starting point for biological analysis of genomic information. A new approach to global pairwise sequence alignment is proposed. This approach is formulated in a mathematically rigorous way, as a mixed integer linear optimization (MILP) problem. Not only does the proposed formulation guarantee the identification of the global optimal alignment, but it also allows for a complete rank-ordered list of any number of user specified top ranking pairwise alignments and for the incorporation of restraints based on restrictions necessary to maintain biological function. This approach has been applied to the alignment of transmembrane helices and serine proteases to demonstrate its utility and advantages over other algorithms.
A Framework for Interactive Parameter Sweep Applications
Authors: Adianto Wibisono, Zhiming Zhao, Adam Belloum, Marian Bubak
Venue: Proceedings of the 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (2008)

A typical parameter sweep application (PSA) is a parameterized application which has to be executed independently large number of times, to locate a particular point in the parameter space that satisfies certain criteria. Albeit simple in terms of computational model, parameter sweep studies occurs frequently in scientific computation across a broad range of scientific disciplines cite(Olabarriaga2007, ADDA, Stankovski2007, Sudholt2005). Including human knowledge in the runtime loop of parameter sweep application is essential to improve the efficiency of performing parameter sweep experiments. However, existing frameworks for performing parameter sweep such as Nimrod-G focuses mainly on the scheduling and the management of the computing resources required for the execution of PSAs. We argued that the batch based execution in existing frameworks hampers the inclusion of human expertise in runtime loop of parameter sweep, and we propose a new framework for interactive parameter sweep.
Adaptive lattice methods for multi-asset models
Authors: Kyoung-Sook Moon, Won-Jung Kim, Hongjoong Kim
Venue: Computers Mathematics with Applications (2008)

Adaptive lattice methods are developed to compute the price of multivariate contingent claims. A simple coordinate representation is used to extend one dimensional lattice methods to multivariate asset models. Two algorithms are proposed, one performing several levels of refinement for a time interval [T-@Dt,T] and the other performing one level of refinement for @l% of a given time domain [0,T], where T is the time to maturity, @Dt is the time step size and @l>0 is a constant. Numerical experiments are carried out for the European and American barrier-type options with one, two, or three underlying assets. In our numerical experiments, both adaptive algorithms improve efficiency over lattice methods with a uniform time step for the same level of accuracy.
Error estimates for abstract linear-quadratic optimal control problems using proper orthogonal decomposition
Authors: M. Hinze, S. Volkwein
Venue: Computational Optimization and Applications (2008)

In this paper we investigate POD discretizations of abstract linear-quadratic optimal control problems with control constraints. We apply the discrete technique developed by Hinze (Comput. Optim. Appl. 30:45-61, 2005) and prove error estimates for the corresponding discrete controls, where we combine error estimates for the state and the adjoint system from Kunisch and Volkwein (Numer. Math. 90:117-148, 2001; SIAM J. Numer. Anal. 40:492-515, 2002). Finally, we present numerical examples that illustrate the theoretical results.
Cooperative and human aspects of software engineering (CHASE 2008)
Authors: Li-te Cheng, Cleidson de Souza, Yvonne Dittrich, Orit Hazzan, Frank Maurer, Michael John, Helen Sharp, Jonathan Sillito, Susan Sim, Janice Singer, Margaret-Anne Storey, Bjørnar Tessem, Gina Venolia
Venue: Companion of the 30th international conference on Software engineering (2008)

The CHASE 2008 workshop is concerned with exploring the cooperative and human aspects of software engineering, and providing a forum for discussing high-quality resarch. Accepted papers reflect the diversity of the field of software engineering--ranging from requirements to testing, and from ethnographic research to experiments. Moreover, the background of attendees reflects the diversity of researchers in this domain, ranging from sociology to psychology, from informatics to software engineering. CHASE 2008 met its goals in presenting high-quality research and building community through a mixture of presentations, discussions, posters, and social activities.
Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes
Authors: Anindya Bhattacharya, Rajat K. De
Venue: Bioinformatics (2008)

Motivation: Cluster analysis (of gene-expression data) is a useful tool for identifying biologically relevant groups of genes that show similar expression patterns under multiple experimental conditions. Various methods have been proposed for clustering gene-expression data. However most of these algorithms have several shortcomings for gene-expression data clustering. In the present article, we focus on several shortcomings of conventional clustering algorithms and propose a new one that is able to produce better clustering solution than that produced by some others. Results: We present the Divisive Correlation Clustering Algorithm (DCCA) that is suitable for finding a group of genes having similar pattern of variation in their expression values. To detect clusters with high correlation and biological significance, we use the correlation clustering concept introduced by Bansal et al. Our proposed algorithm DCCA produces a clustering solution without taking number of clusters to be created as an input. DCCA uses the correlation matrix in such a way that all genes in a cluster have highest average correlation with genes in that cluster. To test the performance of the DCCA, we have applied DCCA and some well-known conventional methods to an artificial dataset, and nine gene-expression datasets, and compared the performance of the algorithms. The clustering results of the DCCA are found to be more significantly relevant to the biological annotations than those of the other methods. All these facts show the superiority of the DCCA over some others for the clustering of gene-expression data. Availability: The software has been developed using C and Visual Basic languages, and can be executed on the Microsoft Windows platforms. The software may be downloaded as a zip file from http://www.isical.ac.in/~rajat. Then it needs to be installed. Two word files (included in the zip file) need to be consulted before installation and execution of the software. Contact: rajat@isical.ac.in Supplementary information:Supplementary data are available at Bioinformatics online.
Integration of Host Position Prediction into Hierarchical Aggregation
Authors: Radim Burget, Dan Komosny, Vit Novoty
Venue: Proceedings of the Seventh International Conference on Networking (2008)

The current RTP/RTCP [1] standard is not optimal for deployment in large-scale sessions with a single source. As the IPTV market is expected to be growing in the coming years, many universities and research laboratories are involved in optimizing for this couple of protocols. One of the most promising technologies for such purposes seems to be the Hierarchical Aggregation (HA). It optimizes transmitting of RTCP back channel and this leads to lower bandwidth requirements. This paper describes hierarchical aggregation and proposes how host position prediction can be integrated. Furthermore, this paper proposes how the host prediction can be improved using additional feedback targets and how it can be used for statistical purposes.
Understanding the efficiency of social tagging systems using information theory
Authors: Ed H. Chi, Todd Mytkowicz
Venue: Proceedings of the nineteenth ACM conference on Hypertext and hypermedia (2008)

Given the rise in popularity of social tagging systems, it seems only natural to ask how efficient is the organically evolved tagging vocabulary in describing underlying document objects? Does this distributed process really provide a way to circumnavigate the traditional "vocabulary problem" with ontology? We analyze a social tagging site, namely del.icio.us, with information theory in order to evaluate the efficiency of this social tagging site for encoding navigation paths to information sources. We show that information theory provides a natural and interesting way to understand this efficiency - or the descriptive, encoding power of tags. Our results indicate the efficiency of tags appears to be waning. We discuss the implications of our findings and provide insight into how our methods can be used to design more usable social tagging software.
Evaluation of recommender systems: A new approach
Authors: Félix Hernández del Olmo, Elena Gaudioso
Venue: Expert Systems with Applications: An International Journal (2008)

It is difficult to deny that comparison between recommender systems requires a common way for evaluating them. Nevertheless, at present, they have been evaluated in many, often incompatible, ways. We affirm this problem is mainly due to the lack of a common framework for recommender systems, a framework general enough so that we may include the whole range of recommender systems to date, but specific enough so that we can obtain solid results. In this paper, we propose such a framework, attempting to extract the essential features of recommender systems. In this framework, the most essential feature is the objective of the recommender system. What is more, in this paper, recommender systems are viewed as applications with the following essential objective. Recommender systems must: (i) choose which (of the items) should be shown to the user, (ii) decide when and how the recommendations must be shown. Next, we will show that a new metric emerges naturally from this framework. Finally, we will conclude by comparing the properties of this new metric with the traditional ones. Among other things, we will show that we may evaluate the whole range of recommender systems with this single metric.
Comparison between New Quantum Approaches for Finding the Minimum or the Maximum of an Unsorted Set of Integers
Authors: Mir Shahriar Emami, Mohammad Reza Fattahi, Hossein Keshmiri
Venue: Proceedings of the Seventh IEEE/ACIS International Conference on Computer and Information Science (icis 2008) (2008)

The change has already begun. It is not a simple change but a revolution in the sense of speed and its impact. In this paper we are going to discuss on Quantum Computer as a Physical System and discuss on its main weakness and then based on our new approach we have solved a problem for finding the minimum or the maximum of a set of integers which has not been solved based on previous Quantum Computing Approach with Time Complexity about and then we Evaluate and Comprise it with another Quantum Algorithm with Time Complexity about which also is given by us and as a result we show that if the size of Quantum Resister is low then our first Quantum Approach which has lower Time Complexity is satisfactory and if the size of Quantum Register is high then as the Probability of Success of our first Approach decreases so our Second Approach is more convenient.
Microsystem research work at the university
Authors: Miroslav Husak
Venue: Proceedings of the 4th WSEAS International Conference on Telecommunications and Informatics (2005)

The paper describes methods of active involvement of students in research work and application of research work results in educational process at the same time. Several workplaces are described in detail where students work on defined tasks. Individual tasks represent partial solutions of large research projects. Student work methods and result presentations are presented. Stress is laid on individual work. This paper deals with questions concerning teaching microelectronic courses, more precisely courses connected with the area of microsystems, at a technical university. Educational methods based on individual students' projects are described. Attention is focused on arrangement of individual courses, output form of students' projects, ways of increasing education efficiency and time utilization, material, functional, technical and instrument support of individual projects and link-up to international cooperation. Most effort is devoted to individual students' projects, their natural motivation in selecting courses and realization of projects.
Embodied Evolution with a New Genetic Programming Variation Algorithm
Authors: Anderson Luiz Fernandes Perez, Guilherme Bittencourt, Mauro Roisenberg
Venue: Proceedings of the Fourth International Conference on Autonomic and Autonomous Systems (2008)

Embodied Evolution is a research area in Evolutionary Robotics in which the evolutionary algorithm is entirely decentralized among a population of robots. Evaluation, selection and reproduction are carried out by and between the robots, without any need for human intervention. This paper describes a new Evolutionary Control System (ECS) able to control a population of mobile robots. The ECS is based on a Genetic Programming algorithm and has two main modules. The first one, called EMSS (Execution, Management and Supervision System), is the system responsible for managing all the evolutionary process in each robot. The second module, called DGP (Distributed Genetic Programming), is an extension of classical Genetic Programming algorithm to support the robot control system evolution. To test the DGP's performance a simulation experiment, with the collision-free navigation task, was accomplished and its results are presented.
Patient registries in cognitive neuroscience research: Advantages, challenges, and practical advice
Authors: Lesley K. Fellows, Marianna Stark, Arlene Berg, Anjan Chatterjee
Venue: Journal of Cognitive Neuroscience (2008)

Neuropsychological work is the historical foundation of cognitive neuroscience and continues to be an important method in the study of the neural basis of human behavior, complementing newer techniques for investigating brain structure-function relationships in human subjects. Recent advances in neuroimaging, statistics and information management provide powerful tools to support neuropsychological research. At the same time, changing ethical requirements and privacy concerns impose increasingly high standards on the procedures used to recruit research participants, and on subsequent data management. Shared, centrally managed research registries provide a framework for facilitating access to this method for nonclinicians, addressing ethical concerns, streamlining recruitment and screening procedures, and coordinating subsequent research contacts and data storage. We report the experience of two such registries: the patient database of the Center for Cognitive Neuroscience at the University of Pennsylvania, and the Cognitive Neuroscience Research Registry at McGill University.
New algorithms and protocols for information authentication in automatic control systems
Authors: A. A. Moldovyan, N. A. Moldovyan
Venue: Automation and Remote Control (2008)

Consideration was given to new protocols for information authentication in the automatic control systems distinguished from the existing protocols for using the notion of collective public key calculated depending on the given subset of public keys. It was suggested to use special cases of rooting a simple modulo as a complicated computational problem underlying the cryptographic algorithms and protocols. New algorithms for digital signature, collective digital signature, and composition digital signature were founded on it. The proposed philosophy of collective digital signature was shown to be realizable on the basis of some existing digital signature algorithms. It enables one to develop protocols for simultaneous signing of contract or package of contracts by an arbitrary number of users.
Improving software concurrency with hardware-assisted memory snapshot
Authors: JaeWoong Chung, Jiwon Seo, Woongki Baek, Chi CaoMinh, Austen McDonald, Christos Kozyrakis, Kunle Olukotun
Venue: Proceedings of the twentieth annual symposium on Parallelism in algorithms and architectures (2008)

We propose a hardware-assisted memory snapshot to improve software concurrency. It is built on top of the hardware resources for transactional memory and allows for easy development of system software modules such as concurrent garbage collector and dynamic profiler.
The State Complexity of Two Combined Operations: Star of Catenation and Star of Reversal
Authors: Yuan Gao, Kai Salomaa, Sheng Yu
Venue: Fundamenta Informaticae (2008)

The state complexity of two combined operations, star of catenation and star of reversal, on regular languages is considered in this paper. Tight bounds are obtained for both combined operations. The results clearly show that the state complexity of a combined operation can be very different from the composition of the state complexities of its participating individual operations. A new approach for research in automata and formal language theory is also explained.
Stage: exploring erlang style concurrency in ruby
Authors: Jonathan Sillito
Venue: Proceedings of the 1st international workshop on Multicore software engineering (2008)

This paper introduces Stage, a Ruby implementation of Actors inspired by the concurrency support in the Erlang programming language. This implementation demonstrates how dynamic language features can be used to implement convenient and expressive concurrency support. Stage has several interesting features that contribute to this expressiveness, including: (1) pattern based support for receiving and handling messages using method calls and blocks, (2) a specialized form of predicate dispatch based on pattern matching for messages that supports overriding and the dynamic addition of alternatives, (3) support for a simple convention based dispatching of messages, and (4) techniques for extending the predicate dispatch to also consider an actor's state. This paper also provides several examples which illustrate how Stage can be used to effectively express concurrent problems.