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Australian Control Conference (AUCC)

作者： Ian Petersen PPGI/IM - Graduate Program in Informatics Rio de Janeiro - RJ Brazil

I would like to welcome all of the participants to the 2nd Australian Control Conference (AUCC) and the city of Sydney on behalf of the AUCC 2012 Organising and Technical program Committees, as well as our main sponsor Engineers, Australia. AUCC is a conference series that is organised by Engineers Australia through its National Committee for Automation, Control and Instrumentation (NCACI). The conference is technically co-sponsored by the IEEE Control Systems Society and is held annually in various locations in Australia. The first AUCC was held in Melbourne in 2011 and the next AUCC will be held in Perth in 2013.

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Knowledge acquisition in the construction of ontologies: A case study in the domain of hematology

Knowledge acquisition in the construction of ontologies: A c...

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3rd International Conference on Biomedical Ontology 2012, ICBO 2012

作者： Mendonça, Fabrício M. Coelho, Kátia C. Andrade, André Q. Almeida, Mauricio B. Graduate Program in Information Science Federal University of Minas Gerais Brazil Institute for Medical Informatics Medical University of Graz Austria Department of Information Theory and Management Federal University of Minas Gerais Brazil

The activities of organizing knowledge recorded in texts and obtaining knowledge from human experts-the knowledge acquisition process-are essential for scientific development. In this article, we propose methodological steps for knowledge acquisition, which have been applied to the construction of biomedical ontologies. The methodological steps are tested in a real case of knowledge acquisition in the domain of the human blood. We hope to contribute to the improvement of knowledge acquisition for the representation of scientific knowledge in ontologies.

关键词： Knowledge acquisition

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Modeling of solitary pulmonary nodules in PET/CT images using Monte Carlo methods

Modeling of solitary pulmonary nodules in PET/CT images usin...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： George Tzanoukos Anastasios Gaitanis Alexandros Georgakopoulos Achilleas Chatziioannou Sofia Chatziioannou George Spyrou post-graduate Program: “Information Technologies in Medicine and Biology” (ITMB) National Center for Scientific Research (NCSR) “Demokritos” Athens CO Greece Department of Biomedical Technology Biomedical Research Foundation of the Academy of Athens (BRFAA) Athens Greece Nuclear Medicine Department Biomedical Research Foundation of the Academy of Athens (BRFAA) Athens Greece First Radiology Department University of Athens Athens Greece Biomedical Informatics Unit Biomedical Research Foundation of the Academy of Athens (BRFAA) Athens Greece

The assessment of solitary pulmonary nodules (SPN) is a very difficult task in PET imaging due to adjacent normal structures. Physicians and computational systems as well, would gain benefit if trained to a large number of SPN cases with controlled topological and morphological characteristics. Our objective was to develop a method for the modeling of the solitary pulmonary nodules in CT and PET images. The modeling of SPN was implemented by Monte Carlo methods taking into consideration morphological characteristics, internal features and Standardized Uptake Value (SUV) activity distribution. For the validation of the model, an observer study from three independent medical experts was performed. The reviewers characterized the lesions as simulated or real and finally they classified them as benign or malignant. According to the results of the human observer study a significant percentage of simulated images could not be differentiated from real ones and the simulated class (benign or malignant) was consistent with the observers' classification.

关键词： Positron emission tomography Lesions Computed tomography Cancer Observers Computational modeling Monte Carlo methods

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Metabolomics and Network Biology for sensitive monitoring of how growth environment changes affect the physiology of industrial-scale perfusion cultures

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IFAC Proceedings Volumes 2013年第31期46卷 227-232页

作者： S.I. Vernardis C.T. Goudar M.I. Klapa Metabolic Engineering and Systems Biology Laboratory Institute of Chemical Engineering Foundation for Research and Technology-Hellas Patras GR- 265 04 Greece Cell Culture Development Global Biological Development Bayer HealthCare 800 Dwight Way Berkeley CA 94710 Interdepartmental Graduate Program in “Informatics in Life Sciences” Medical School University of Patras Greece & Current Address: Cell Science and Technology AMGEN Inc. Thousand Oaks CA 91320 USA Secondary Affiliation: Depts of Chemical & Biomolecular Eng and Bioengineering University of Maryland College Park MD 20742 USA

Metabolomic analysis can indeed enhance the prime variable dataset for the monitoring of perfusion cultures by providing a higher resolution view of the metabolic state. Metabolic profiles can capture physiological state shifts over the course of the perfusion cultures and indicate a metabolic “signature” of the phase transitions, which is not observable from prime variable data. Notably, metabolomics provides orthogonal (to prime variables) evidence that all cultures follow this same metabolic state shift with cell age, independently of bioreactor scale. Additionally, this analysis can increase the information content of process development experiments by helping better understand the impact of changes in bioreactor operating conditions on cell physiology. In this context, metabolic profiling could be integrated into the monitoring of cell physiology in perfusion cultures.

关键词： industrial cell culture engineering GC-MS metabolomics perfusion cultures multivariate statistical analysis metabolic network reconstruction growth environmental variations

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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

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Scientific data 2017年第1期4卷 170179页

作者： Jason Flannick Christian Fuchsberger Anubha Mahajan Tanya M Teslovich Vineeta Agarwala Kyle J Gaulton Lizz Caulkins Ryan Koesterer Clement Ma Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Dennis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmu Department of Molecular Biology Massachusetts General Hospital Boston Massachusetts USA. Program in Medical and Population Genetics Broad Institute Cambridge Massachusetts USA. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor Michigan USA. Wellcome Trust Centre for Human Genetics Nuffield Department of Medicine University of Oxford Oxford UK. Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge Massachusetts USA. Department of Statistics University of Oxford Oxford UK. Genetics of Complex Traits University of Exeter Medical School University of Exeter Exeter UK. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Department of Twin Research and Genetic Epidemiology King's College London London UK. Oxford Centre for Diabetes Endocrinology and Metabolism Radcliffe Department of Medicine University of Oxford Oxford UK. Department of Human Genetics Wellcome Trust Sanger Institute Hinxton Cambridgeshire UK. School of Computer Science McGill University Montreal Quebec Canada. McGill University and Génome Québec Innovation Centre Montreal Quebec Canada. Human Genetics Center The University of Texas Graduate School of Biomedical Sciences at Houston The University of Texas Health Science Center at Houston Houston Texas USA. Department of Biostatistics Boston University School of Public Health Boston Massachusetts USA. National Heart Lung and Blood Institute's Framingham Heart Study Framingham Massachusetts USA. Medical Genomics and Metabolic Genetics Branch National Human Genome Research Institute National Institutes of Health Bethesda Maryland USA. Department of Biostatistics Harvard School of Public Health Boston Massachusetts USA. Chronic Disease Epidemiology Swiss Tropical and Public Health Institute University of Basel Basel Switzerland. Institute of Genetic Epidemiology Helmholtz Zentrum München German R

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

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A soft IP core generating SoCs for the efficient stochastic simulation of large Biomolecular Networks using FPGAs

A soft IP core generating SoCs for the efficient stochastic ...

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IEEE International Conference on Electronics, Circuits and Systems (ICECS)

作者： Orsalia Georgia Hazapis Evangelos Logaras Elias S. Manolakos Graduate Program Information Technologies in Medicine and Biology Department of Informatics and Telecommunications University of Athens Greece

A soft IP core, expressed in parametric VHDL, has been developed and used to synthesize different multiprocessor Systems on Chip (SoCs) for the stochastic simulation of large-size biochemical reaction networks based on Gillespie's First Reaction Method (FRM). The SoCs can be configured to have up to N=8 Processing Elements and simulate efficiently in hardware biomolecular networks with up to m=16K reactions. The FPGA implementations of the SoCs are communicating with a host PC via the serial and Ethernet ports for control and data transmission respectively. When mapped to a Virtex-5 Xilinx FPGA the FRM SoCs can deliver simulation performance (in Mega-Reactions/sec) that may exceed by up to two orders of magnitude the performance of well known software simulators running on fast PCs.

关键词： Biological system modeling System-on-a-chip Field programmable gate arrays IP networks Computer architecture Stochastic processes Hardware

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Music genre classification using dynamic selection of ensemble of classifiers

Music genre classification using dynamic selection of ensemb...

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IEEE International Conference on Systems, Man and Cybernetics

作者： Paulo Ricardo Lisboa de Almeida Eunelson José da Silva Júnior Tatiana Montes Celinski Alceu de Souza Britto Luis Eduardo Soares de Oliveira Alessandro Lameiras Koerich Department of Informatics (DeInfo) State University of Ponta Grossa Ponta Grossa Parana Brazil Post-graduate Program in Informatics (PPGIa) Pontifical Catholic University of Paraná Curitiba Parana Brazil Post-graduate Program in Informatics (PPGInf) Federal University of Parana Curitiba Parana Brazil

This paper presents a dynamic ensemble selection method for music genre classification which employs two pools of diverse classifiers. The pools of classifiers are created by using different features types extracted from three distinct segments of each music piece. From these initial pools of weak classifiers, ensembles of classifiers are dynamically selected for each test pattern using the k-nearest oracles method. The experiments compare the performance of different selection strategies on the Latin Music Database to those related to the use of best single classifier, and to the combination of all classifiers in the pool. It was possible to observe that the most promising selection strategy evaluated allows improving the classification accuracy from 63.71% to 70.31%.

关键词： Feature extraction Accuracy Multiple signal classification Databases informatics Educational institutions Music

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Evaluation of process variability on current for nanotechnologies devices

Evaluation of process variability on current for nanotechnol...

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2012 IEEE 3rd Latin American Symposium on Circuits and Systems, LASCAS 2012

作者： Meinhardt, Cristina Reis, Ricardo Computer Science Center - C3 Federal University of Rio Grande - FURG Rio Grande Brazil Graduate Program in Computing Institute of Informatics Federal University of Rio Grande Do Sul - UFRGS Porto Alegre Brazil

ISBN: (纸本)9781467312080

The continuous shrinking of devices has introduced new challenges to integrated circuit design, mainly to deal with the parametric variations in process parameters. This paper presents an evaluation of the process variability on the current Ids of nanotechnologies devices, individually and simultaneously, taking into account the correlation among them. The results show that the deviation from mean value is quite significant ≈ 16% for high performance models. The variation of L has the dominant effect on the overall variation of the device in high performance models while the dominant effect on the overall variation of the device in low power models still being due to Vth variations. Lastly, the effect of process parameter variations deteriorates with technology scaling, with a considerable increase in the deviation from the 22nm to 16nm technology. © 2012 IEEE.

关键词： Nanotechnology

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Scenario-based collaboration: An approach to refinement of plans through Public Engagement

Scenario-based collaboration: An approach to refinement of p...

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International Conference on Computer Supported Cooperative Work in Design

作者： Samuel de Oliveira Apolonio Adriana S. Vivacqua Marcos R. S. Borges PPGI/IM - Graduate Program in Informatics Institute of Mathematics Federal University of Rio de Janeiro (UFRJ) Brazil PPGI/IM — Graduate Program in Informatics Institute of Mathematics Federal University of Rio de Janeiro (UFRJ) Rio de Janeiro Brazil

Design is a knowledge intensive activity, which depends on information to be undertaken. Previous designs, recent innovations, new techniques and materials must be taken into account when working on a new project, whatever its nature. Designing a plan is no different from designing a physical artifact, in that several constraints and requirements must be taken into account. Therefore, a collaborative approach that enables the refinement of plans through Public Engagement is of paramount importance to the design process. Many studies have been undertaken regarding the promotion of public participation in the planning process. In this situation, the population can be seen as an important source of information, because they experience the environments addressed by the proposed plan on a daily basis. However, the interaction between government and population presents cultural, political and technological challenges. In this paper, we present the Scenario-Based Collaboration Process (SBCP), which aims to Refine Plans through Public Engagement.

关键词： Planning informatics Lead Collaboration Irrigation

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A novel application of crossover operator to a hybrid optimization framework: Investigation into cutting problems

A novel application of crossover operator to a hybrid optimi...

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Congress on Evolutionary Computation

作者： Rommel Dias Saraiva Plácido Rogério Pinheiro State University of Ceará Fortaleza Brazil Graduate Program in Applied Informatics University of Fortaleza-UNIFOR Fortaleza Brazil

ISBN: (纸本)9781467315104

The Generate and Solve (GS) is a hybrid optimization framework that combines a metaheuristic engine (genetic algorithm), which works as a generator of reduced instances of the original optimization problem, and an integer programming solver. GS has been recently introduced in the literature and achieved promising results in cutting and packing problem instances. In this paper, we present a novel application of crossover operator, the Uniform Order-Based Crossover, to the GS framework. As a means to assess the potentialities behind the novel application, we provide as instantiation of the framework for dealing specifically with the constrained two-dimensional non-guillotine cutting problem. Computational experiments performed over standard benchmark problems are reported and discussed here, evidencing the effectiveness of the novel operator.

关键词： Genetic algorithms Optimization Biological cells Heuristic algorithms Integer linear programming Search problems Hybrid power systems

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