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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Kamath, Vidya P. Hall, Lawrence O. Yeatman, Timothy J. Eschrich, Steven A. Biomedical Engineering Program University of South Florida H. Lee Moffitt Cancer Center and Research Institute Tampa FL United States Dept. of Computer Science and Engineering University of South Florida Tampa FL United States Dept. Interdisciplinary Oncology H. Lee Moffitt Cancer Center and Research Institute Tampa FL United States

ISBN: (纸本)1424415098

Gene expression analysis techniques identify important genes that predict specified outcomes based on sample characteristics. Given the small sample sizes common to these studies and the large dimensionality of the data, feature selection methods are essential. In addition, cancer-related expression analysis often involves imbalanced datasets due to rare forms of disease. Popular methods of feature selection employ univariate techniques to identify the features most suitable for analysis. We propose a multivariate technique for selecting accurate subsets of features using an approach based on random subspaces. The random subspace method is used to explore random combinations of features and only subspaces that produce accurate classifiers are retained. The method is tested on two independent gene expression datasets and compared with a univariate approach. The multivariate feature selection method resulted in a 33% improvement in classification accuracy overall and 90% improvement in classification accuracy for the minority class. ©2007 IEEE.

关键词： Gene expression

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Delivering Context-aware Learning Guidance in the Mobile Learning Environment based on Information Theory

Delivering Context-aware Learning Guidance in the Mobile Lea...

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International Conference on Advanced Learning Technologies (ICALT)

作者： Rita Kuo Min-Chang Wu Alex Chang Maiga Chang Jia-Sheng Heh Department of Electronic Engineer Chung Yuan Christian University Taiwan Department of Information and Computer Engineering Chung Yuan Christian University Taiwan Program Office of National Science and Technology Program for Learning in Taiwan Taiwan

Mobile Learning makes students get the advantages of both traditional learning and e-learning. How to give students learning sequence suggestions in the mobile learning environment is a big issue and is also the goal of this paper. This research uses knowledge map to store the characteristics of each learning object and designs a situated map to represent spatial knowledge in the mobile learning environment. By using these two knowledge structures, knowledge map and situated map, the system created by this research can generate various navigation sentences and ask students to observe the characteristics of learning objects. This research also takes information theory into consideration in order to decide which navigation sentence should deliver to the student first. The system calculates the entropy for each generated sentence and finds the most appropriate one to deliver to the student. At the end of this paper, an experiment system is implemented for the 5th year biology course, Plant Observation.

关键词： Information theory Navigation Electronic learning Mobile computing Knowledge representation Humans Cognition Personal digital assistants US Department of Transportation Sequences

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Correcting base-assignment errors in repeat regions of shotgun assembly

Correcting base-assignment errors in repeat regions of shotg...

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作者： Zhi, Degui Keich, Uri Pevzner, Pavel Heber, Steffen Tang, Haixu Bioinformatics Program University of California San Diego San Diego CA 92093 Department of Computer Science 4130 Upson Hall Cornell University Ithaca NY 14853 Department of Computer Science and Engineering University of California San Diego San Diego CA 92093 North Carolina State University Raleigh NC 27695-7566 School of Informatics Center for Genomics and Bioinformatics Indiana University Bloomington IN 47408

Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the genome, current assemblers may place these reads arbitrarily. As a result, the base-assignment error rate in repeats is likely to be much higher than that in the rest of the genome. We developed an iterative algorithm, EULER-AIR, that is able to correct base-assignment errors in finished genome sequences in public databases. The Wolbachia genome is among the best finished genomes. Using this genome project as an example, we demonstrated that EULER-AIR can 1) discover and correct base-assignment errors, 2) provide accurate read assignments, 3) utilize finishing reads for accurate base-assignment and 4) provide guidance for designing finishing experiments. In the genome of Wolbachia, EULER-AIR found 16 positions with ambiguous base-assignment and two positions with erroneous bases. Besides Wolbachia, many other genome sequencing projects have significantly fewer finishing reads and, hence, are likely to contain more base-assignment errors in repeats. We demonstrate that EULER-AIR is a software tool that can be used to find and correct base-assignment errors in a genome assembly project. © 2007 IEEE.

关键词： Error analysis

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City traffic simulator using geographical information systems and agent-based simulation

City traffic simulator using geographical information system...

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2007 3rd IET International Conference on Intelligent Environments

作者： Haiyi Zhang Oscar L.M. De Farias Jodrey School of Computer Science Acadia University Wolfville NS Canada Post-Graduation Program in Computer Engineering Rio de Janeiro State University Rio de Janeiro Brazil

In this paper we explore the integration among geographical information systems (GIS) and agent based simulation tools. An agent-based geographical information system (ABGIS) could be characterized as a kind of system integrating features commonly found in geographical information system with the features of agent-based simulation tools. ABGIS would give to scientists and researches, not necessarily computer experts, access to powerful simulation tools and an environment that is an excellent metaphor to represent our spatio-temporal world. With ABGIS we could explore the dynamics of spatiotemporal systems, and particularly but not exclusively, complex systems.

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WS-Policy4MASC - A WS-Policy Extension Used in the MASC Middleware

WS-Policy4MASC - A WS-Policy Extension Used in the MASC Midd...

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IEEE International Conference on Services Computing (SCC)

作者： Vladimir Tosic Abdelkarim Erradi Piyush Maheshwari School of Computer Science and Engineering University of New South Wales Sydney Australia Department of Computer Science University of Western Ontario London Canada Empirical Software Engineering (ESE) Program NICTA Sydney Australia IBM India Research Laboratory New Delhi India

WS-Policy4MASC is a new XML language that we developed for specification of monitoring and control (particularly, adaptation) policies in the Manageable and Adaptable Services Compositions (MASC) middleware. It extends the Web Services Policy Framework (WS-Policy) by defining new types of policy assertions. Goal policy assertions specify requirements and guarantees to be met in desired normal operation. Action policy assertions specify actions to be taken if certain conditions are met or not met. Utility policy assertions specify monetary values assigned to particular situations. Meta-policy assertions are used to specify which action policy assertions are alternatives and which business value-driven conflict resolution strategy should be used. WS- Policy4MASC also enables detailed specification of additional information necessary for run-time policy-driven management. We evaluated feasibility of the WS- Policy4MASC solutions by implementing a policy repository and other modules in MASC. We examined their usefulness on a set of realistic scenarios.

关键词： Middleware Web services Monitoring XML Quality of service computer science Control systems Australia Council Software engineering Software development management

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New Insights in the Modification of the Work Function of Cathode Materials due to Thin Surface Coatings using Ab-initio Modelling

New Insights in the Modification of the Work Function of Cat...

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International Conference on Vacuum electronics

作者： Vasilios Vlahos Dane D. Morgan John H. Booske University of Wisconsin Madison Madison WI USA 1415 Engineering Dr. Madison WI Department of Materials Science and Engineering University of Wisconsin Madison Madison WI USA Department of Materials Science and Engineering Department of Electrical and Computer Engineering University of Wisconsin-Madison Madison USA Interdisciplinary Materials Science Program

The changes in the work function upon adsorption of coating layers on materials utilized in both field and thermionic emission applications have been investigated computationally within the framework of Density Functional Theory (DFT) [1] as implemented by the Vienna Ab-initio Simulation Package (VASP) [2]. This approach provides valuable information for understanding the origin of the improvement in the emitted current density by monitoring changes in the electronic structure of a material system upon adsorption of surface species. The presence of surface coatings induces changes in the charge density in the surface and sub-surface regions of the substrate, significantly influencing the value of the work function. The origin of the enhanced emission properties of Cesium-Iodide (Csl) coated Carbon-based field emission cathodes [3] as well as Barium-Oxide (Ba-O) Tungsten thermionic cathode systems has been investigated. The former is a promising cathode material system capable of operating under low global electric fields, demonstrating operation lifetimes in excess of one million pulses, and characterized by good shot-to-shot-reproducibility, low levels of outgassing, and no evident plasma formation upon appropriate conditioning.

关键词： Cathodes Coatings Thermionic emission Density functional theory Computational modeling Electronic packaging thermal management Current density Monitoring Tungsten Plasma applications

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Using pitch, amplitude modulation, and spatial cues for separation of harmonic instruments from stereo music recordings

Eurasip Journal on Advances in Signal Processing

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Eurasip Journal on Advances in Signal Processing 2007年 2007卷

作者： Woodruff, John Pardo, Bryan Music Technology Program School of Music Northwestern University Evanston IL 60208 United States Department of Electrical Engineering and Computer Science Northwestern University Evanston IL 60208 United States

Recent work in blind source separation applied to anechoic mixtures of speech allows for improved reconstruction of sources that rarely overlap in a time-frequency representation. While the assumption that speech mixtures do not overlap significantly in time-frequency is reasonable, music mixtures rarely meet this constraint, requiring new approaches. We introduce a method that uses spatial cues from anechoic, stereo music recordings and assumptions regarding the structure of musical source signals to effectively separate mixtures of tonal music. We discuss existing techniques to create partial source signal estimates from regions of the mixture where source signals do not overlap significantly. We use these partial signals within a new demixing framework, in which we estimate harmonic masks for each source, allowing the determination of the number of active sources in important time-frequency frames of the mixture. We then propose a method for distributing energy from time-frequency frames of the mixture to multiple source signals. This allows dealing with mixtures that contain time-frequency frames in which multiple harmonic sources are active without requiring knowledge of source characteristics. Copyright © 2007 Hindawi Publishing Corporation. All rights reserved.

关键词： Harmonic generation

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Creating geo-specific road databases from aerial photos for driving simulation

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WSEAS Transactions on computers 2007年第6期6卷 871-879页

作者： Guo, Dahai Weeks, Arthur Klee, Harold Computer Science Program Florida Gulf Coast University 10501 FGCU Boulevard South Fort Myers FL 33965 United States School of Electric Engineering and Computer Science University of Central Florida 4000 University Boulevard Orlando FL 32816 United States

Geo-specific road databases are sometimes necessary for driving simulation studies. However, manually creating them is very time consuming. One of the reasons is that a real road can have non-uniform cross sections due to irregular shaped road boundaries. Additionally, in the UCF (University of Central Florida) driving simulator system, the road database format requires identification of repeatable cross sections, also a labor intensive process. Even though some commercial software applications, such as the MultiGen Road Tool have road modeling functions, roads with non-uniform cross-sectional profiles are still hard to model.

关键词： Database systems

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Design and Evaluation of a Grid Computing Based Architecture for Integrating Heterogeneous IDSs

Design and Evaluation of a Grid Computing Based Architecture...

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IEEE GLOBECOM 2007 - IEEE Global Telecommunications Conference

作者： Paulo F. Silva Carlos B. Westphall Carla M. Westphall Marcos Dias de Assuncao Network and Management Laboratory Post-Graduate Program in Computer Science Federal University of Santa Catarina Florianopolis Brazil Grid Computing and Distributed Systems Laboratory Department of Computer Science and Software Engineering University of Melbourne VIC Australia

Intrusion detection systems (IDSs) have been substantially improved in recent past. However, network attacks have become more sophisticated and increasingly complex: many of current attacks are coordinated and originated in multiple networks. To detect these attacks, IDSs need to obtain information on network events from multiple networks or administrative domains. This work demonstrates that a Distributed IDS (DIDS) can be composed of existing IDSs, improving the detection of misuses in a multiple network environment. We use a grid middleware for creating a service-based intrusion detection grid. We demonstrate through experimental results that the proposed DIDS allows the integration of heterogeneous existing IDSs and improves the detection of attacks by exploring the synergy between existing IDSs.

关键词： Grid computing computer architecture Intrusion detection Resource management Laboratories computer science Electronic mail Middleware computer network management engineering management

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Evolving hypernetwork classifiers for microRNA expression profile analysis

Evolving hypernetwork classifiers for microRNA expression pr...

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Congress on Evolutionary Computation

作者： Sun Kim Soo-Jin Kim Byoung-Tak Zhang The Center for Bioinformatics Technology Graduate Program in Bioinformatics Seoul National University Seoul South Korea The School of Computer Science and Engineering Seoul National University Seoul South Korea

High-throughput microarrays inform us on different outlooks of the molecular mechanisms underlying the function of cells and organisms. While computational analysis for the microarrays show good performance, it is still difficult to infer modules of multiple co-regulated genes. Here, we present a novel classification method to identify the gene modules associated with cancers from microarray data. The proposed approach is based on 'hypernetworks', a hypergraph model consisting of vertices and weighted hyperedges. The hypernetwork model is inspired by biological networks and its learning process is suitable for identifying interacting gene modules. Applied to the analysis of microRNA (miRNA) expression profiles on multiple human cancers, the hypernetwork classifiers identified cancer-related miRNA modules. The results show that our method performs better than decision trees and naive Bayes. The biological meaning of the discovered miRNA modules has been examined by literature search.

关键词： Cancer Gene expression Biological system modeling Data analysis Support vector machines Support vector machine classification Evolutionary computation Humans Decision trees Diseases

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