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Multivariate analysis of gene expression data and missing value imputation based on llsimpute algorithm

ICIC Express Letters 2012年第5期6卷 1335-1339页

作者： Moorthy, Kohbalan Mohamad, Mohd Saberi Deris, Safaai Ibrahim, Zuwairie Artificial Intelligence and Bioinformatics Research Group Faculty of Computer Science and Information Systems 81310 UTM Skudai Johor Malaysia Department of Mechatronics and Robotics Center of Artificial Intelligence and Robotics Faculty of Electrical Engineering Universiti Teknologi Malaysia 81310 UTM Skudai Johor Malaysia

Microarray ade4 or known as MADE4 is a multivariate software analysis package for microarray gene expression data. This software package is capable of accepting wide variety of gene expression data formats such as Bioconductor Affy Batch and exprSet. This MADE4 R package extends the advantages of ade4 package in multivariate statistical and graphical functions for the use in the microarray data application. Moreover, MADE4 provides new graphical and visualization tools that assist in the interpretation of multivariate analysis of microarray data. Besides that, LLSimpute algorithm has been incorporated to assist in handling of datasets with missing values and this has eased the application for the users to analysis on gene expression data that contain missing values.

关键词： Autocorrelation

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Fault tolerant adaptive estimation of nonlinear processes using redundant measurements

Fault tolerant adaptive estimation of nonlinear processes us...

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Mediterranean Conference on Control and Automation (MED)

作者： M. Miranda A. Edelmayer Laboratory of Unit Operations Department of Chemical Engineering Faculty of Engineering University of Los Andes Merida Venezuela Systems and Control Laboratory Computer and Automation Research Institute Hungarian Academy of Sciences (ATOMKI) Budapest Hungary

This paper presents a dual layer approach for robust fault tolerant estimation of nonlinear processes using a combined adaptive extended Kalman filter and fault detection and filter reconfiguration. From the one hand, the filter is made robust in face of environment uncertainty using adaptive filtering. To this end, the filter identifies the measurement covariance by means of recursive estimation, upon which the adaptation relies, to suppress the effect of sporadic variations in the quality of measurements as well as compensates for incipient sensor faults. From the other hand, fault monitoring is continuously applied to the filter's innovation in an attempt to initiate filter reconfiguration when the adaptation mechanism alone is not able to overcome the failure situation. The discussion of the results is embedded in the application framework of state estimation of a batch distillation process.

关键词： Temperature measurement Mathematical model Estimation Technological innovation Noise Fault tolerance Fault tolerant systems

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A tuning parameter selector method for the gsvm-scad in determining significant genes and biological pathway

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ICIC Express Letters 2012年第4期6卷 851-856页

作者： Misman, Muhammad Faiz Mohamad, Mohd Saberi Deris, Safaai Hashim, Siti Zaiton Mohd Leham, Nurdyana Ibrahim, Zuwairie Artificial Intelligence and Bioinformatics Research Group Faculty of Computer Science and Information Systems 81310 UTM Skudai Johor Darul Takzim Malaysia Department of Mechatronics and Robotics Center for Artificial Intelligence and Robotics Faculty of Electrical Engineering Universiti Teknologi Malaysia 81310 UTM Skudai Johor Darul Takzim Malaysia

A hybrid of support vector machines and a smoothly clipped absolute deviation with group-specific penalty terms (gSVM-SCAD) is a penalized classifier that has been used to identify and select significant pathways in pathway-based microarray analysis. Despite its advantages in identifying significant pathways, the gSVM-SCAD has some limitations, as it depends on the proper choice of tuning parameter. If the tuning parameter is too small, it can bring little sparsity and overfit to the classifier model, while if it is too large, it can make much sparsity to the classifier model and produce poor discriminating power. Therefore, it is important to choose an appropriate tuning parameter selector method for the gSVM-SCAD. The generalized cross validation (GACV) has been widely used as a tuning parameter selector method. Unfortunately, GACV has some limitations where it poorly performs when dealing with the low number of variables (in this paper referred as genes) and large sample sizes. This is because some pathways contain not more than 100 genes and even some pathways contain less than 10 genes. This scenario can lead to the poor performance of SCAD in selecting the informative genes and simultaneously identifying significant ones. In order to surmount the limitations of the gSVM-SCAD, we proposed to use the B-type generalized approximate cross validation (BGACV) as a tuning parameter selector method for gSVM-SCAD. ICIC International © 2012.

关键词： Genes

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Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

Genome-scale identification of cell-wall related genes in Ar...

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2012全国植物生物学大会

作者： Shan Wang Yanbin Yin Qin Ma Xiaojia Tang Dongyun Hao Ying Xu Key Lab for Molecular Enzymology and Engineering of the Ministry of Education Jilin UniversityChangchun China College of Computer Science and Technology Jilin University Changchun China Biotechnology Research Centre Jilin Academy of Agricultural Sciences (JAAS) Changchun China Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology and Institute of Bioinformatics BESC BioEerngy Science Center University of Georgia Athens GA USA BESC BioEerngy Science Center University of Georgia Athens GA USA Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology and Institute of Bioinformatics Key Lab for Molecular Enzymology and Engineering of the Ministry of Education Jilin UniversityChangchun China Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology and Institute of Bioinformatics

Identification of the novel genes relevant to plant cell-wall (PCW) synthesis represents a highly important and challenging *** substantial efforts have been invested into studying this problem, the vast majority of t... 详细信息

关键词： Plant cell wall Arabidopsis Co-expression network analyses Bi-clustering Cis regulatory motifs

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Virtual worlds in Australian and New Zealand higher education: Remembering the past, Understanding the present and imagining the future 30

Virtual worlds in Australian and New Zealand higher educatio...

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30th Annual conference on Australian Society for computers in Learning in Tertiary Education, ASCILITE 2013

作者： Gregory, Sue Gregory, Brent Reiners, Torsten Fardinpour, Ali Hillier, Mathew Lee, Mark J.W. Jacka, Lisa Butler, Des Holloway, David Grant, Scott Hearns, Merle Flintoff, Kim Jegathesan, Jay Jay Ellis, David McDonald, Marcus Stokes-Thompson, Frederick Gaukrodger, Belma Zagami, Jason Campbell, Chris Wang, Xiangyu Salinas, Jamie Garcia Loke, Swee-Kin Scutter, Sheila Newman, Christine Gu, Ning Schutt, Stefan Farley, Helen Bogdanovych, Anton Trescak, Tomas Simoff, Simeon Steel, Caroline Neuendorf, Penny Bower, Matt Orwin, Lindy McKeown Kerr, Tom Warren, Ian Wood, Denise Miller, Charlynn Mathews, Shane Linegar, Dale Knox, Vicki Masters, Yvonne Brown, Ross Meredith, Grant Atkins, Clare Giovanangeli, Angela Le Rossignol, Karen Cram, Andrew Muir-Cochrane, Eimear Basu, Arin Jacobson, Michael Larson, Ian School of Education University of New England Australia UNE Business School University of New England Australia Curtin Business School Curtin University Australia Curtin Business School Curtin University Australia Teaching and Educational Development Institute The University of Queensland Australia School of Education Charles Sturt University Australia School of Education Southern Cross University Australia Queensland University of Technology Australia School of Information Systems and Technology University of Wollongong Australia School of Cultures Languages and Linguistics Monash University Australia School of Foundation Studies Manukau Institute of Technology Australia Curtin Teaching and Learning Curtin University Australia School of Physics The University of Western Australia Australia School of Education Southern Cross University Australia School of Health Sciences RMIT University Australia Learning and Teaching Unit University of South Australia Australia Flexible Learning Nelson Marlborough Institute of Technology Australia School of Education and Professional Studies Griffith University Australia School of Education The University of Queensland Australia School of Built Environment Curtin University Australia School of Social and Behavioural Sciences The University of Queensland Australia Higher Education Development Centre University of Otago Australia School of Medicine and Dentistry James Cook University Australia eLearning Services Queensland University of Technology Australia School of Architecture and Built Environment University of Newcastle Australia Centre for Cultural Diversity and Wellbeing Victoria University Australia Australian Digital Futures Institute University of Southern Queensland Australia Computing and ICT University of Western Sydney Australia Deans Unit School of Computing Engineering and Math University of Western Sydney Australia School of Computing Engineering and Math University of Western Sydney Australia School of

ISBN: (纸本)9781741384031

3D virtual reality, including the current generation of multi-user virtual worlds, has had a long history of use in education and training, and it experienced a surge of renewed interest with the advent of Second Life in 2003. What followed shortly after were several years marked by considerable hype around the use of virtual worlds for teaching, learning and research in higher education. For the moment, uptake of the technology seems to have plateaued, with academics either maintaining the status quo and continuing to use virtual worlds as they have previously done or choosing to opt out altogether. This paper presents a brief review of the use of virtual worlds in the Australian and New Zealand higher education sector in the past and reports on its use in the sector at the present time, based on input from members of the Australian and New Zealand Virtual Worlds Working Group. It then adopts a forward-looking perspective amid the current climate of uncertainty, musing on future directions and offering suggestions for potential new applications in light of recent technological developments and innovations in the area. © 2013 Sue Gregory.

关键词： Augmented reality

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Energy-efficient differentiated coverage of dynamic objects using an improved evolutionary multi-objective optimization algorithm with fuzzy-dominance

Energy-efficient differentiated coverage of dynamic objects ...

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Congress on Evolutionary Computation

作者： Soumyadip Sengupta Swagatam Das Md. Nasir Athanasios V. Vasilakos Witold Pedrycz Department of Electronics and Telecommunication Eng Jadavpur University Kolkata India Electronics and Communication Sciences Unit Indian Statistical Institute Kolkata India Middle East Technical University Mersin Turkey Systems Research Institute Polish Academy of Sciences Warsaw Poland Electrical and Computer Engineering Department University of Alberta Edmonton Canada

ISBN: (纸本)9781467315104

We present an energy efficient sensor manager for differentiated coverage of dynamic object group changing their positions with time. The information about the location of the object group is provided to the sensor manager. The manager invokes optimization algorithm whenever the obtained coverage falls below a threshold to sleep schedule the sensor network. Multi-objective Optimization (MO) algorithms help in finding a better trade-off among energy consumption, lifetime, and coverage. Here the motion of the particle is modeled to follow a polynomial variation and with a constant acceleration. We formulate the scheduling problem as a combinatorial, constrained and multi-objective optimization problem with energy and non-coverage as the two objectives to be minimized. The proposed scheme uses a recent variant of a powerful MO algorithm known as Decomposition based Multi-Objective Evolutionary Algorithm (MOEA/D). Systematic comparison with the original MOEA/D and another well-known MO algorithm, NSGA-II (Non-dominated Sorting Genetic Algorithm) quantifies the superiority of the proposed approach.

关键词： Optimization Wireless sensor networks Mathematical model Energy efficiency Energy consumption Monitoring Tracking

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Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012

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BMC bioinformatics 2012年第SUPPL 18期13卷 A1-A1页

作者： Alexander Goncearenco Priscila Grynberg Olga B Botvinnik Geoff Macintyre Thomas Abeel Computational Biology Unit Department of Informatics University of Bergen Bergen Norway Departamento de Bioquímica e Imunologia Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte MG Brazil Department of Biomolecular Engineering and Bioinformatics University of California - Santa Cruz USA NICTA Victoria Research Lab The University of Melbourne Victoria 3010 Australia VIB Department of Plant Systems Biology Ghent University Gent Belgium Broad Institute of MIT and Harvard Cambridge MA USA

The report summarizes the scientific content of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB) held in conjunction with the Intelligent systems for ...

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EQTL AND MUTATIONAL ANALYSIS OF NB-LRR MEDIATED IMMunitY TO POWDERY MILDEW

EQTL AND MUTATIONAL ANALYSIS OF NB-LRR MEDIATED IMMUNITY TO ...

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The 13th International Cereal Rusts and Powdery Mildews Conference(第13届国际禾谷类锈病与白粉病大会)

作者： Roger WISE Priyanka SURANA Greg FUERST Ruo XU Divya MISTRY Julie DICKERSON Dan NETTLETON Department of Statistics Iowa State UniversityAmesIowa 50011 Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011 Department of StatisticsIowa State UniversityAmesIowa 50011 Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011 Department of Electrical and Computer Engineering Iowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011 Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011 Department of Plant Pathology and MicrobiologyCenter for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011 Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011 Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011 Crop and Insect GeneticsGenomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011 Crop and Insect Genetics Genomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011

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systems BIOLOGY IN BARLEY POWDERY MILDEW INTERACTIONS

SYSTEMS BIOLOGY IN BARLEY POWDERY MILDEW INTERACTIONS

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The 13th International Cereal Rusts and Powdery Mildews Conference(第13届国际禾谷类锈病与白粉病大会)

作者： Roger WISE Priyanka SURANA Greg FUERST Ruo XU Dan NETTLETON Divya MISTRY Julie DICKERSON Lin WANG Tom BRUTNELL Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011USA Department of Statistics Iowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011USA Department of Plant Pathology and MicrobiologyCenter for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011USA Crop and Insect Genetics Genomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011USA Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011USA Department of StatisticsIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011USA Crop and Insect GeneticsGenomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011USA Department of Electrical and Computer Engineering Iowa State UniversityAmesIowa 50011USA Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNY

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Green flexible opportunistic computing with virtualization

Green flexible opportunistic computing with virtualization

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11th IEEE International Conference on computer and Information Technology, CIT 2011 and 11th IEEE International Conference on Scalable Computing and Communications, SCALCOM 2011

作者： Castro, Harold Sotelo, German Diaz, Cesar O. Bouvry, Pascal Department of Systems and Computer Engineering Universidad de Los Andes Bogota Colombia Computer Science and Communications Research Unit University of Luxembourg L-1359 Luxembourg-Kirchberg Luxembourg

ISBN: (纸本)9780769543888

Energy efficiency and High computing power are basic design considerations across modern-day computing solutions due to different concerns such as system performance, operational cost, and environmental issues. Opportunistic grid infrastructures offer computational power at low cost focused on harvesting idle computing cycles of existing commodity computing resources. Other than allowing to customize the end user offer, virtualization is considered as one key techniques to reduce energy consumption in large-scale systems and contributes to the scalability of the system. This paper presents an energy efficient approach for opportunistic grids based on virtualization. The experimental results show that virtualization significantly improves the energy efficiency of opportunistic grids compared with dedicated computing systems without disturbing the end-user. © 2011 IEEE.

关键词： Virtualization

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