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International Joint Conference on Neural Networks (IJCNN)

作者： Francesco Iorio Loredana Murino Diego di Bernardo Giancarlo Raiconi Roberto Tagliaferri Telethon Institute for Genetics and Medicine Napoli Italy Department of Mathematics and Computer Science (DMI) University of Salerno Fisciano Italy Department of Systems and Computer Science Federico II University of Naples Napoli Italy Italy

We investigated the possibility of gaining information on the mode of action of a set of compounds by means of Gene Ontology (GO) enrichment analysis. To this aim, we developed a new method, based on fuzzy-sets, which is able to compute sets of genes that are consistently differentially expressed when treating cells with the analyzed compounds. Then a Gene Ontology enrichment analysis is performed on these sets. The method has been tested on several different groups of drugs, whose similarity in mode of action has been predicted by a gene-expression based, unsupervised, approach and verified by searching literature. The obtained results show that GO terms that are overrepresented in these fuzzy sets provide a quick and "easy-tointerpret" view of the mode of action of the analyzed drugs.

关键词： Drugs Proteins Inhibitors Compounds Communities Clustering algorithms Biological processes

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Parallel computing algorithms for reverse-engineering and analysis of genome-wide gene regulatory networks from gene expression profiles

Parallel computing algorithms for reverse-engineering and an...

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9th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd International Workshop on High-Performance Computational Systems Biology, HiBi 2010

作者： Belcastro, Vincenzo Di Bernardo, Diego Gregoretti, Francesco Oliva, Gennaro Telethon Institute of Genetics and Medicine TIGEM Naples Italy Institute of High Performance Computing and Networking ICAR-CNR Naples Italy Open University PO Box 197 MK7 6BJ Milton Keynes United Kingdom Department of Systems and Computer Science Federico II University Naples Italy

ISBN: (纸本)9780769542652

A Gene Regulatory Network links pairs of genes through an edge if they physically or functionally interact. "Reverse engineering" a gene regulatory network means to infer the edges between genes from the available experimental data. Transcriptional responses (i.e. gene expression profiles obtained through microarray experiments) are often used to reverse-engineer a network of genes. Reverse-engineering consists in analyzing transcriptional responses to a set of treatments and adding an edge between genes if their expressions show a coordinated behavior on a subset of the treatments, according to some underlying model of gene regulation. Mammalian cells contain tens of thousands of genes, and it is necessary to analyze hundreds of transcriptional responses in order to have acceptable statistical evidence of interactions between genes. There currently exist several ready-to-use software packages able to infer gene networks, but few can be used to infer large-size networks from thousands of transcriptional responses as the dimension of the problem leads to high computational costs and memory requirements. We propose to exploit parallel computing techniques to overcome this problem. In this work, we designed and developed a parallel computing algorithm to reverse engineer large-scale gene regulatory networks from tens of thousands of gene expression profiles. The algorithm is based on computing pair-wise Mutual Information between each *** successfully tested it to infer the Mus Musculus (mouse) gene regulatory network in liver from 312 expression profiles collected from a public Internet repository. Each profile measures the expression of 45,101 genes (more specifically, transcripts). We analyzed all of the possible gene-pairs for a total amount of about 109 identifying about 6 · 107 edges. We used a hierarchical clustering algorithm to discover communities within the gene network, and found a modular structure that highlights genes involved in the same biolog

关键词： Reverse engineering

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Investigating epidemic diseases characterized by vertical transmission and contract: Cellular automata computational model

Investigating epidemic diseases characterized by vertical tr...

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IFAC International Workshop on "Supplemental Ways for Improving International Stability", SWiiS 2010 - Proceedings

作者： Chang, C.L. Jing, Y. Zhang, S. Stojanovski, G. Stankovski, M. Dimirovski, G. School of Information Science and Engineering Northeastern University 110004 Shenyang China Institute of ASE School FEIT SS Cyril and Methodius University Karpos II BB MK 1000 Skopje Macedonia Computer Eng. and Control Eng. Departments Dogus University TR-34722 Istanbul Turkey

ISBN: (纸本)9783902661920

A computationally and theoretically new model based on cellular automata is developed to generate descriptive emulation of epidemic disease processes, a particularly prevailing phenomenon in developing countries that may cause dramatic events. The feature phenomena of vertical transmission and contract of epidemic diseases are accounted for. Thus the proposed model captures the essence of the epidemic dynamics as demonstrated by the simulation experiments. The proposed model can serve as a background basis for developing more sophisticated models and algorithms to simulate scenario of real-world epidemics based on recorded data. © 2010 IFAC.

关键词： Cellular automata

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On 2-Site Voronoi Diagrams under Arithmetic Combinations of Point-to-Point Distances

On 2-Site Voronoi Diagrams under Arithmetic Combinations of ...

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International Symposium on Voronoi Diagrams in science and Engineering (ISVD)

作者： Kira Vyatkina Gill Barequet Department of Mathematics and Mechanics Saint Petersburg State University Saint Petersburg Russia Center of Graphics and Geometric Computing Department of Computer Science Technion-Israel Institute of Technology Haifa Israel

ISBN: (纸本)9781424476060;9780769541129

We consider a generalization of Voronoi diagrams, recently introduced by Barequet et al., in which the distance is measured from a pair of sites to a point. An easy way to define such distance was proposed together with the concept: it can be the sum-of, the product-of, or (the absolute value of) the difference-between Euclidean distances from either site to the respective point. We explore further the last definition, and analyze the complexity of the nearest- and the furthest-neighbor 2-site Voronoi diagrams for points in the plane with Manhattan or Chebyshev underlying metrics, providing extensions to general Minkowsky metrics and, for the nearest-neighbor case, to higher dimensions. In addition, we point out that the observation made earlier in the literature that 2-point site Voronoi diagrams under the sum-of and the product-of Euclidean distances are identical and almost identical to the second order Voronoi diagrams, respectively, holds in a much more general statement.

关键词： computer science Digital arithmetic Mathematics computer graphics Mechanical variables measurement Chebyshev approximation Application software History Information resources Books

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REAL-TIME BARE-HANDS-TRACKING FOR 3D GAMES 3

REAL-TIME BARE-HANDS-TRACKING FOR 3D GAMES

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2009 IADIS International Conference Interfaces and Human computer Interaction, IHCI 2009 and IADIS International Conference Game and Entertainment Technologies, GET 2009 - Part of the 3rd IADIS Multi Conference on computer science and Information Systems, MCCSIS 2009

作者： Schlattmann, Markus Broekelschen, Johannes Klein, Reinhard University of Bonn Institute of Computer Science II Computer Graphics Germany

ISBN: (纸本)9789728924850

Recently, stable markerless 6 DOF video-based hand-tracking devices became available. These devices simultaneously track the positions and orientations of both user hands in different postures with at least 40 frames per second. Such hand-tracking allows for using the human hands as natural input devices. To exploit these devices for interaction with an application, suitable interaction interfaces and techniques are required. Especially in the field of 3D gaming further developments and analyses of bare-handed interaction are needed. Therefore, we introduce a novel general interface for gaming purposes and analyzed various interaction modes/metaphors by coupling it to three popular 3D games (see Figure 1): a racing game, a flight simulator and a first-person shooter. Furthermore, we present an evaluation and discussion based on an informal user study. © 2009 IADIS Multi Conference on computer science and Information Systems

关键词： Flight simulators

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Estimating the quality of complexity measures in heuristics for reversible logic synthesis

Estimating the quality of complexity measures in heuristics ...

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Congress on Evolutionary Computation

作者： Marek Szyprowski Paweł Kerntopf Institute of Computer Science Department of Electronics and Information Technology Warsaw University of Technology Warsaw Poland Department of Theoretical Physics II University of Łódź Lodz Poland

Reversible circuits have been intensively studied in recent years due to their applications in many areas, including quantum computing, nanotechnology and low-power design. Synthesis of reversible circuits differs significantly from the traditional logic synthesis. No satisfactory synthesis algorithm has been proposed for such circuits so far. All existing heuristic approaches to reversible logic synthesis utilize complexity measures. In this paper such complexity measures are analyzed and quantitative comparison of these approaches is presented. Possibilities for improving heuristic algorithms for reversible circuit synthesis are also discussed.

关键词： Logic gates Complexity theory Boolean functions Length measurement Size measurement Libraries Cost function

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Extraction of Human Body Skeleton Based on Silhouette Images

Extraction of Human Body Skeleton Based on Silhouette Images

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International Workshop on Education Technology and computer science, ETCS

作者： Jianhao Ding Yigang Wang Lingyun Yu State Key Laboratory of CAD & CG University of Zhejiang Hangzhou China Institute of Computer graphics and Image Processing Hangzhou Dianzi University Hangzhou China Department of Mathematics and Computing Science University of Groningam Netherlands

ISBN: (纸本)9781424463886;9780769539874

Skeleton extraction is essential for general shape representation. A typical skeletonization algorithm should obtain the ability to preserve original object's topological and hierarchical properties. However, most of current methods are high memory cost, computationally intensive, and also require complex data structures. In this paper, we propose an efficient and accurate skeletonization method for the skeleton feature points extracted from human body based on silhouette images. First, the gradient of distance transform is used to detect critical points inside the foreground. Then, we converge and simplify critical points in order to generate the most important and elegant skeleton feature points. Finally, we present an algorithm which connects the skeleton feature points and estimates the position of skeleton joints.

关键词： Humans Skeleton Joints Iterative algorithms Euclidean distance Data mining Motion analysis Image converters Shape Feature extraction

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An interdisciplinary practical course on the application of grid computing

An interdisciplinary practical course on the application of ...

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2010 IEEE Education Engineering Conference, EDUCON 2010

作者： Rings, Thomas Grabowski, Jens Aschenbrenner, Andreas Kálmán, Tibor Lauer, Gerhard Meyer, Jörg Quadt, Arnulf Sax, Ulrich Viezens, Fred Institute of Computer Science University of Göttingen Göttingen Germany State and University Library Göttingen Germany Göttingen Germany Department of German Studies University of Göttingen Göttingen Germany II. Institute of Physics University of Göttingen Göttingen Germany Medical Informatics Information Technology University Medical Center Göttingen Germany Institute of Biometrics and Medical Informatics University of Magdeburg Magdeburg Germany

ISBN: (纸本)9781424465682

This article gives an overview of the organization and realization of an interdisciplinary practical course on grid computing. Both the lecturers and the attendees came from diverse backgrounds and disciplines including computer science, physics, medicine, and the humanities. We describe the management of the course, the assignments, the infrastructure developed and experienced in this interdisciplinary practical course at the University of Göttingen. The challenges and issues, the benefits, the expectations and their fulfillment are discussed. The experiences of the course show that diverse disciplines can be brought together to convey the benefits of grid technology by experiencing varied grid applications in production-like grid environments. © 2010 IEEE.

关键词： Grid computing

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Analysis and design of a versatile synthetic network for inducible gene expression in mammalian systems

Analysis and design of a versatile synthetic network for ind...

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IEEE Biomedical Circuits and Systems (BIOCAS)

作者： A. Polynikis G. Cuccato S. Criscuolo S. J. Hogan M. di Bernardo D. di Bernardo Department of Engineering Mathematics University of Bristol Bristol UK Telethon Institute for Genetics and Medicine Naples Italy Department of Systems and Computer Science University of Napoli Federico II Naples Italy

This paper presents a mathematical model for a novel synthetic gene regulatory network. The aim of this circuit is to behave as a bistable switch for in vivo delivery of short hairpin RNA (shRNA) which can induce RNA interference (RNAi) of a target mRNA. Through the mathematical analysis performed here, it will be shown how the circuit can be controlled to induce sustained expression of a shRNA, with a transient input of two different inducer molecules.

关键词： Proteins Mathematical model Bifurcation RNA Switching circuits Integrated circuit modeling Drugs

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Mortality Dependence of Cu Dual Damascene Interconnects on Adjacent Segment

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MRS Online Proceedings Library (OPL) 2011年第1期812卷 F7.2-F7.2页

作者： C.W. Chang C.L. Gan C.V. Thompson K.L. Pey W.K. Choi N. Hwang Advanced Materials for Micro- and Nano-Systems Singapore-MIT Alliance 4 Engineering Drive 3 Singapore 117576 School of Materials Engineering Nanyang Technological University Nanyang Avenue Singapore 639798 Department of Materials Science and Engineering Massachusetts Institute of Technology Cambridge Massachusetts 02139 School of Electrical & Electronics Engineering Nanyang Technological University Nanyang Avenue Singapore 639798 Department of Electrical and Computer Engineering National University of Singapore 4 Engineering Drive 3 Singapore 117576 Microsystems Modules & Components Laboratory Institute of Microelectronics Singapore 11 Science Park Road Singapore Science Park II Singapore 117685

Three terminal ‘dotted-I’ interconnect structures, with vias at both ends and an additional via in the middle, were tested under a variety of test conditions. Failures (mortalities) were observed even when segments were tested under conditions that would not have led to failure in two-terminal structures. Mortalities were found in right segments with jL values as low as 1250 A/cm, which is lower when compared to the immortality condition (jL)cr of 3700 A/cm reported for similar via-terminated structures. Moreover, we found that the mortality of a dotted-I segment is dependent on the direction and magnitude of the current in the adjacent segment. These results suggest that there is not a definite value of the jL product that defines true immortality in individual segments that are part of an interconnect tree. More importantly, the critical jL value for a single segment of Cu interconnects may be reduced or increased by an adjacent segment. Therefore independently determined (jL)cr values cannot be directly applied to interconnects with branched segments, but rather the magnitude as well as the direction of the current flow in the adjoining segments must be taken into consideration in evaluating the immortality of interconnect segments in an interconnect network.

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