Parallel protein secondary structure prediction schemes using Pthread and OpenMP over hyper-threading technology

Protein secondary structure prediction has a fundamental influence on today’s bioinformatics research. In this work, tertiary classifiers for the protein secondary structure prediction are implemented on Denoeux Belief Neural Network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 matrix and PSSM matrix are experimented separately as the encoding schemes for DBNN. Hydrophobicity matrix, BLOSUM62 matrix and PSSM matrix are applied to DBNN architecture for the first time. The experimental results contribute to the design of new encoding schemes. Our accuracy of the tertiary classifier with PSSM encoding scheme reaches 72.01%, which is almost 10% better than the previous results obtained in 2003. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the Hyper-Threading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that Hyper-Threading technology for Intel architecture is efficient for parallel biological algorithms.

MedSMan: a live multimedia stream querying system

Querying live media streams is a challenging problem that is becoming an essential requirement in a growing number of applications. Research in multimedia information systems has addressed and made good progress in dealing with archived data. Meanwhile, research in stream databases has received significant attention for querying alphanumeric symbolic streams. The lack of a data model capable of representing different multimedia data in a declarative way, hiding the media heterogeneity and providing reasonable abstractions for querying live multimedia streams poses the challenge of how to make the best use of data in video, audio and other media sources for various applications. In this paper we propose a system that enables directly capturing media streams from sensors and automatically generating more meaningful feature streams that can be queried by a data stream processor. The system provides an effective combination between extendible digital processing techniques and general data stream management research. Together with other query techniques developed in related data stream management streams, our system can be used in those application areas where multifarious live media senors are deployed for surveillance, disaster response, live conferencing, telepresence, etc.

Matrix-based streamization approach for improving locality and parallelism on FT64 stream processor

FT64 is the first 64-bit stream processor designed for scientific computing. It is critical to exploit optimizing streamization approaches for scientific applications on FT64 due to the inefficiency of direct streamization approach. In this paper, we propose a novel matrix-based streamization approach for improving locality and parallelism of scientific applications on FT64. First, a Data&Computation Matrix is built to abstract the relationship between loops and arrays of the original programs, and it is helpful for formulating the streamization problem. Second, three key techniques for optimizing streamization approach are proposed based on the transformations of the matrix, i.e., coarse-grained program transformations, fine-grained program transformations, and stream organization optimizations. Finally, we apply our approach to ten typical scientific application kernels on FT64. The experimental results show that the matrix-based streamization approach achieves an average speedup of 2.76 over the direct streamization approach, and performs equally to or better than the corresponding Fortran programs on Itanium 2 except CG. It is certain that the matrix-based streamization approach is a promising and practical solution to efficiently exploit the tremendous potential of FT64.

CTL* model checking on a shared-memory architecture

In this article we present the parallelisation of an explicit-state CTL^* model checking algorithm for a virtual shared-memory high-performance parallel machine architecture. The algorithm uses a combination of private and shared data structures for implicit and dynamic load balancing with minimal synchronisation overhead. The performance of the algorithm and the impact that different design decisions have on the performance are analysed using both mathematical cost models and experimental results. The analysis shows not only the practicality and effective speedup of the algorithm, but also the main pitfalls of parallelising model checking for shared-memory architectures.

The 2007 IEEE CEC simulated car racing competition

This paper describes the simulated car racing competition that was arranged as part of the 2007 IEEE Congress on Evolutionary Computation. Both the game that was used as the domain for the competition, the controllers submitted as entries to the competition and its results are presented. With this paper, we hope to provide some insight into the efficacy of various computational intelligence methods on a well-defined game task, as well as an example of one way of running a competition. In the process, we provide a set of reference results for those who wish to use the simplerace game to benchmark their own algorithms. The paper is co-authored by the organizers and participants of the competition.

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Multimodal support to group dynamics

The complexity of group dynamics occurring in small group interactions often hinders the performance of teams. The availability of rich multimodal information about what is going on during the meeting makes it possible to explore the possibility of providing support to dysfunctional teams from facilitation to training sessions addressing both the individuals and the group as a whole. A necessary step in this direction is that of capturing and understanding group dynamics. In this paper, we discuss a particular scenario, in which meeting participants receive multimedia feedback on their relational behaviour, as a first step towards increasing self-awareness. We describe the background and the motivation for a coding scheme for annotating meeting recordings partially inspired by the Bales’ Interaction Process Analysis. This coding scheme was aimed at identifying suitable observable behavioural sequences. The study is complemented with an experimental investigation on the acceptability of such a service.

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Methods for quantitative usability requirements: a case study on the development of the user interface of a mobile phone

Quantitative usability requirements are a critical but challenging, and hence an often neglected aspect of a usability engineering process. A case study is described where quantitative usability requirements played a key role in the development of a new user interface of a mobile phone. Within the practical constraints of the project, existing methods for determining usability requirements and evaluating the extent to which these are met, could not be applied as such, therefore tailored methods had to be developed. These methods and their applications are discussed.

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ONTRACK: Dynamically adapting music playback to support navigation

Listening to music on personal, digital devices whilst mobile is an enjoyable, everyday activity. We explore a scheme for exploiting this practice to immerse listeners in navigation cues. Our prototype, ONTRACK, continuously adapts audio, modifying the spatial balance and volume to lead listeners to their target destination. First we report on an initial lab-based evaluation that demonstrated the approach’s efficacy: users were able to complete tasks within a reasonable time and their subjective feedback was positive. Encouraged by these results we constructed a handheld prototype. Here, we discuss this implementation and the results of field-trials. These indicate that even with a low-fidelity realisation of the concept, users can quite effectively navigate complicated routes.

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Connecting the family with awareness systems

Awareness systems have attracted significant research interest for their potential to support interpersonal relationships. Investigations of awareness systems for the domestic environment have suggested that such systems can help individuals stay in touch with dear friends or family and provide affective benefits to their users. Our research provides empirical evidence to refine and substantiate such suggestions. We report our experience with designing and evaluating the ASTRA awareness system, for connecting households and mobile family members. We introduce the concept of connectedness and its measurement through the Affective Benefits and Costs of communication questionnaire (ABC-Q). We inform results that testify the benefits of sharing experiences at the moment they happen without interrupting potential receivers. Finally, we document the role that lightweight, picture-based communication can play in the range of communication media available.

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Interacting with mobile services: an evaluation of camera-phones and visual tags

We present a study of using camera-phones and visual-tags to access mobile services. Firstly, a user-experience study is described in which participants were both observed learning to interact with a prototype mobile service and interviewed about their experiences. Secondly, a pointing-device task is presented in which quantitative data was gathered regarding the speed and accuracy with which participants aimed and clicked on visual-tags using camera-phones. We found that participants’ attitudes to visual-tag-based applications were broadly positive, although they had several important reservations about camera-phone technology more generally. Data from our pointing-device task demonstrated that novice users were able to aim and click on visual-tags quickly (well under 3 s per pointing-device trial on average) and accurately (almost all meeting our defined speed/accuracy tradeoff of 6% error-rate). Based on our findings, design lessons for camera-phone and visual-tag applications are presented.

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Segmentation and recognition of motion capture data stream by classification

Three dimensional human motions recorded by motion capture and hand gestures recorded by using data gloves generate variable-length data streams. These data streams usually have dozens of attributes, and have different variations for similar motions. To segment and recognize motion streams, a classification-based approach is proposed in this paper. Classification feature vectors are extracted by utilizing singular value decompositions (SVD) of motion data. The extracted feature vectors capture the dominating geometric structures of motion data as revealed by SVD. Multi-class support vector machine (SVM) classifiers with class probability estimates are explored for classifying the feature vectors in order to segment and recognize motion streams. Experiments show that the proposed approach can find patterns in motion data streams with high accuracy.

Hypermatrix oriented supernode amalgamation

In this paper, we introduce a supernode amalgamation algorithm which takes into account the characteristics of a hypermatrix data structure. The resulting frontal tree is then used to create a variable-sized partitioning of the hypermatrix. The sparse hypermatrix Cholesky factorization obtained runs slightly faster than the one which uses a fixed-sized partitioning. The algorithm also reduces data dependencies which limit exploitation of parallelism.

E-redesigning of society: towards experiential connectivity of generations in Lithuania

The paper reflects on the unique experience of social and technological development in Lithuania since the regaining of independence as a newly reshaped society constructing a distinctive competitive IST-based model at global level. This has presented Lithuanian pattern of how to integrate different experiences and relations between generations in implementing complex information society approaches. The resulting programme in general is linked to the Lisbon objectives of the European Union. The experience of transitional countries in Europe, each different but facing some common problems, may be useful to developing countries in Africa.

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Reconfigurable hardware solution to parallel prefix computation

This paper presents the design and implementation of an efficient reconfigurable parallel prefix computation hardware on field-programmable gate arrays (FPGAs). The design is based on a pipelined dataflow algorithm, and control logic is added to reconfigure the system for arbitrary parallelism degree. The system receives multiple input streams of elements in parallel and produces output streams in parallel. It has an advantage of controlling the degree of parallelism explicitly at run time. The time complexity of the design is O(d+(N−d)/d), where d and N are parallelism degree and stream size, respectively. When the stream size is sufficiently larger than the initial trigger time of the pipeline (d), the time complexity becomes O(N/d). Unlike the prefix computation circuits found in the literature, the design is scalable for different problem sizes including unknown sized data. The design is modular based on a finite state machine, and implemented and tested for target FPGA devices Xilinx Spartan2S XC2S300EFT256-6Q and XC2S600EFG676-6.

Was kann die Wirtschaftsinformatik dazu beitragen,E-Health voran zu bringen?

Ohne Zusammenfassung

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Ethical regulations on robotics in Europe

There are only a few ethical regulations that deal explicitly with robots, in contrast to a vast number of regulations, which may be applied. We will focus on ethical issues with regard to “responsibility and autonomous robots”, “machines as a replacement for humans”, and “tele-presence”. Furthermore we will examine examples from special fields of application (medicine and healthcare, armed forces, and entertainment). We do not claim to present a complete list of ethical issue nor of regulations in the field of robotics, but we will demonstrate that there are legal challenges with regard to these issues.

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Scientific models and ethical issues in hybrid bionic systems research

Research on hybrid bionic systems (HBSs) is still in its infancy but promising results have already been achieved in laboratories. Experiments on humans and animals show that artificial devices can be controlled by neural signals. These results suggest that HBS technologies can be employed to restore sensorimotor functionalities in disabled and elderly people. At the same time, HBS research raises ethical concerns related to possible exogenous and endogenous limitations to human autonomy and freedom. The analysis of these concerns requires reflecting on the availability of scientific models accounting for key aspects of sensorimotor coordination and plastic adaptation mechanisms in the brain.

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Inverse multi-objective robust evolutionary design

In this paper, we present an Inverse Multi-Objective Robust Evolutionary (IMORE) design methodology that handles the presence of uncertainty without making assumptions about the uncertainty structure. We model the clustering of uncertain events in families of nested sets using a multi-level optimization search. To reduce the high computational costs of the proposed methodology we proposed schemes for (1) adapting the step-size in estimating the uncertainty, and (2) trimming down the number of calls to the objective function in the nested search. Both offline and online adaptation strategies are considered in conjunction with the IMORE design algorithm. Design of Experiments (DOE) approaches further reduce the number of objective function calls in the online adaptive IMORE algorithm. Empirical studies conducted on a series of test functions having diverse complexities show that the proposed algorithms converge to a set of Pareto-optimal design solutions with non-dominated nominal and robustness performances efficiently.

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Supporting ordering and consistency in a distributed Event Heap for Ubiquitous Computing

The Stanford Event Heap has been shown to provide appropriate support for constructing interactive workspace applications. Given this success it is natural to consider the Event Heap as a platform to support other classes of Ubiquitous Computing applications. In this paper we argue that the distributed, spontaneous nature of these applications places additional demands on the Event Heap that require extensions to both the engineering and API. Suitable extensions are described and their use to support a typical Ubicomp application is discussed.

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Legal safeguards for privacy and data protection in ambient intelligence

To get the maximum benefit from ambient intelligence (AmI), we need to anticipate and react to possible drawbacks and threats emerging from the new technologies in order to devise appropriate safeguards. The SWAMI project took a precautionary approach in its exploration of the privacy risks in AmI and sought ways to reduce them. It constructed four “dark scenarios” showing possible negative implications of AmI, notably for privacy protection. Legal analysis of the depicted futures showed the shortcomings of the current legal framework in being able to provide adequate privacy protection in the AmI environment. In this paper, the authors, building upon their involvement in SWAMI research as well as the further advancement of EU privacy analysis, identify various outstanding issues regarding the legal framework that still need to be resolved in order to deal with AmI in an equitable and efficacious way. This article points out some of the lacunae in the legal framework and postulates several privacy-specific safeguards aimed at overcoming them.

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