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5th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 IEEE.

关键词： Yeast

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Simultaneous Identification for Synergistic Transcription Factors and their Transcription Factor Binding Sites

Simultaneous Identification for Synergistic Transcription Fa...

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International Conference on Complex, Intelligent and Software Intensive Systems, CISIS

作者： Zing Tsung-Yeh Tsai Grace Tzu-Wei Huang Huai-Kuang Tsai Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh USA Computer Science and Engineering National Taiwan Ocean University Keelung Taiwan

关键词： Bioinformatics Analysis of variance DNA Databases Gene expression Proteins Stress

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Bioanalysis Young Investigator: Halil Tekin

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Bioanalysis 2011年第16期3卷 1815-1816页

作者： Halil Tekin Ali Khademhosseini Robert S Langer a Position PhD CandidatePhD Electrical Engineering and Computer Science – Bio-Electrical Engineering AreaResearch area Tissue engineering stimuli-responsive platforms and high-throughput screening systemsDepartment of Electrical Engineering & Computer Science of MIT 65 Landsdowne Street Rm. 252 Cambridge MA02139 USA. halil@mit.edu b Harvard-MIT Health Sciences & Technology Department of Medicine Harvard Medical School Brigham & Women’s Hospital Wyss Institute for Biologically Inspired Engineering 65 Landsdowne Street Rm 252 Cambridge MA02139 USA. alik@rics.bwh.harvard.edu c David H Koch Institute of Integrative Cancer Research at MIT Departments of Chemical Engineering & Biological Engineering of MIT Harvard-MIT Health Sciences & Technology 77 Massachusetts Avenue Rm 76-661 MA USA. rlanger@mit.edu

Supervisor’s supporting commentsI am very pleased to nominate Halil Tekin for theBioanalysisYoung Investigator award. Halil has proven himself to be an excellent researcher, a very bright laboratory member and a strong leader since joining my laboratory. He has excelled at all of the skills required of a phd candidate at MIT with his research focusing primarily on future advances in drug development, drug discovery and medicine with high-throughput drug toxicity screening. His efforts have focused on developing novel biomimetic tissue constructs by microengineering methods to further advance the applications of implantable tissues and drug toxicity screening devices. Halil has demonstrated an unprecedented ability not only to learn new material quickly, but more importantly to synthesize new information and ask the important questions needed to move science forward. I am constantly impressed with Halil’s ability, drive and determination in learning, and contributing to the research conducted in my laboratory. Halil’s unique combination of a strong electrical engineering background and his current knowledge and experience in tissue engineering has enabled him to look at fundamental challanges in a novel and insightful way, which resulted in very interesting *** is an exceptional phd student conducting outstanding research in tissue engineering which can bring novel applications in human health care. Halil published a paper in a top journal in the field of microtechnology,Lab on a Chip, describing a new way of making cell aggregates and then retrieving them from the microwells in a controllable manner for further experimentation and analysis. He also published a paper inLangmuir, introducing a novel method to fabricate conformally coated thermo-responsive microgrooves to form stripe tissues and harvest them in a temperature-dependent manner. These responsive microstructures can be scalable into high-throughput systems and potentially be useful in tissue

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Investigation of transient cavitating flow in viscoelastic pipes

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IOP Conference Series: Earth and Environmental science 2010年第1期12卷

作者： A Keramat A S Tijsseling A Ahmadi PhD student Department of Civil Engineering Shahrood University of Technology Iran Department of Mathematics and Computer Science Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands Department of Civil Engineering Shahrood University of Technology Iran Post Code: *** University Boulevard Shahrood Iran presently Department of Mathematics and Computer Science Eindhoven University of Technology The Netherlands

A study on water hammer in viscoelastic pipes when the fluid pressure drops to liquid vapour pressure is performed. Two important concepts including column separation and the effects of retarded strains in the pipe wall on the fluid response have been investigated separately in recent works, but there is some curiosity as to how the results for pressure and discharge are when column separation occurs in a viscoelastic pipe. For pipes made of plastic such as polyethylene (PE) and polyvinyl chloride (PVC), viscoelasticity is a crucial mechanical property which changes the hydraulic and structural transient responses. Based on previous developments in the analysis of water hammer, a model which is capable of analysing column separation in viscoelastic pipes is presented and used for solving the selected case studies. For the column-separation modelling the Discrete Vapour Cavity Model (DVCM) is utilised and the viscoelasticity property of the pipe wall is modelled by Kelvin-Voigt elements. The effects of viscoelasticity play an important role in the column separation phenomenon because it changes the water hammer fundamental frequency and so affects the time of opening or collapse of the cavities. Verification of the implemented computer code is performed for the effects of viscoelasticity and column separation – separately and simultaneously – using experimental results from the literature. In the provided examples the focus is placed on the simultaneous effect of viscoelasticity and column separation on the hydraulic transient response. The final conclusions drawn are that if rectangular grids are utilised the DVCM gives acceptable predictions of the phenomenon and that the pipe wall material's retarded behaviour strongly dampens the pressure spikes caused by column separation.

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Numerical simulation of continuous casting process of bloom by fifite point method

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TMS 2009 Annual Meeting and Exhibition

作者： Jenabali-Jahromi, Seyed Ahmad Alizadeh, Mostafa Nasihatkon, Sayyed Behrouz Professor Department of materials science and engineering Shiraz University Shiraz Iran PhD student Department of materials science and engineering Shiraz University Shiraz Iran M.S. student Department of computer engineering Shiraz University Shiraz Iran

ISBN: (纸本)9780873397353

In this paper a meshless method called Finite Point Method (FPM) is developed to simulate the solidification process of continuously cast bloom steel in both primary and secondary cooling region. The method is based on the use of a weighted least-square interpolation procedure. A transverse slice of bloom as it moves with casting speed is considered as computational domain. The two dimensional heat transfer equation together with temperature dependent thermophysical properties is solved in the computational domain. The present work is verified in the mold region by the comparison of the surface temperature simulated by FPM and finite volume method (FVM) and also comparison of solidified shell thickness simulated by FPM and measured on a breakout bloom. For secondary cooling region the validation is done by comparison of the surface temperature simulated by FPM, FVM and thermovision measurements.

关键词： Continuous casting

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An incremental approach for niching and building block detection via clustering

An incremental approach for niching and building block detec...

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7th International Conference on Intelligent Systems Design and Applications, ISDA'07

作者： Emmendorfer, Leonardo Ramos Pozo, Aurora Trinidad Ramirez Numerical Methods in Engineering PhD Program Federal University of Paraná Brazil Department of Computer Science Federal University of Paraná Brazil

ISBN: (纸本)0769529763

Diversity preservation has already been established as an important concern for evolutionary computation. Clustering techniques were, among others, successfully applied to this purpose. Another important aspect of the research on evolutionary computation is related to linkage learning - the detection of the problem structure avoiding disruption of building blocks when new individuals are generated. This paper presents a novel approach which is a new estimation of distribution algorithm (EDA) where clustering plays two roles: diversity preservation and linkage learning. Initial empirical investigations illustrate the behavior of the algorithm when solving two benchmark optimization problems. © 2007 IEEE.

关键词： Evolutionary algorithms

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A weighted k-nearest neighbor method for gene ontology based protein function prediction

A weighted k-nearest neighbor method for gene ontology based...

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2nd International Multi-Symposiums on computer and Computational sciences 2007, IMSCCS'07

作者： Kharsikar, Saket Mugler, Dale Sheffer, Daniel Moore, Francisco Duan, Zhong-Hui Department of Biomedical Engineering University of Akron Akron OH 44236 United States Department of Theoretical and Applied Mathematics University of Akron Akron OH 44236 United States Integrated Bioscience PhD Program University of Akron Akron OH 44236 United States Department of Biology University of Akron Akron OH 44236 United States Department of Computer Science University of Akron Akron OH 44236 United States

ISBN: (纸本)0769530397

Numerous genome projects have produced a large and ever increasing amount of genomic sequence data. However, the biological functions of many proteins encoded by the sequences remain unknown. Protein function annotation and prediction become an essential and challenging task of post-genomic research. In this paper, we present an automated protein function prediction system based on a set of proteins of known biological functions. The functions of the proteins are characterized with gene ontology (GO) annotations. The prediction system uses a novel measure to calculate the pair-wise overall similarity between protein sequences. The protein function prediction is performed based on the GO annotations of similar sequences using a weighted k-nearest neighbor method. We show the prediction accuracies obtained using the model organism yeast (Sacchyromyces cerevisiae). The results indicate that the weighted k-nearest neighbor method significantly outperforms the regular k-nearest neighbor method for protein molecular function prediction. © 2007 IEEE.

关键词： Proteins

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Design of Sequential Experiment for Creating of Interval Model for Ecological Monitoring Systems

Design of Sequential Experiment for Creating of Interval Mod...

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IEEE International Workshop on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications

作者： Mykola Dyvak Petro Stakhiv Andriy Pukas Ternopil National Economic University Ternopil Ukraine Department of Theoretical and General Electrical Engineering Lviv Polytechnic National University Lviv Ukraine PhD Student Department of Computer Science Ternopil National Economic University 11 Lvivska Str. Ternopil Ukraine 46004. apu@tanet.edu.te.ua

The process of construction of interval model of the field of nitric oxide concentrations based on results of sequential experiment is presented in paper. This model is used in the task of the ecological monitoring fo... 详细信息

关键词： Biological system modeling Monitoring Atmospheric measurements Pollution measurement Air pollution Time measurement Contamination Humidity measurement Pressure measurement Laboratories

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Using Correlation to Improve Boosting Technique: An Application for Time Series Forecasting

Using Correlation to Improve Boosting Technique: An Applicat...

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International Conference on Tools for Artificial Intelligence (ICTAI)

作者： Luzia Vidal De Souza Aurora T Ramirez Pozo Anselmo Chaves Neto Departament of Design PhD student Numerical Methods In Engineering Federal University of Parana Curitiba Parana Brazil Computer Science Department Federal University of Parana (UFPR) Curitiba Parana Brazil Statistical Department Federal University of Parana (UFPR) Curitiba Parana Brazil

Time series forecasting has been widely used to support decision making, in this context a highly accurate prediction is essential to ensure the quality of the decisions. Ensembles of machines currently receive a lot of attention; they combine predictions from different forecasting methods as a procedure to improve the accuracy. This paper explores genetic programming and boosting technique to obtain an ensemble of regressors and proposes a new formula for the final hypothesis. This new formula is based on the correlation coefficient instead of the geometric median used by the boosting algorithm. To validate this method, experiments were performed, the mean squared error (MSE) has been used to compare the accuracy of the proposed method against the results obtained by GP, GP using a boosting technique and the traditional statistical methodology (ARMA). The results show advantages in the use of the proposed approach

关键词： Boosting Genetic programming Machine learning Artificial neural networks Evolutionary computation Economic forecasting Stock markets Predictive models Machine learning algorithms Classification algorithms

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AFOPT algorithm for multilevel databases

AFOPT algorithm for multilevel databases

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International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC)

作者： R. Gyorodi C. Gyorodi M. Pater O. Boc Z. David Assistant professor Phd. Engineering Department of Computer Science Faculty of Electrotehnics and Informatics University of Oradea Oradea Romania Lecturer Engineering Phd. Student Department of Computer Science Faculty of Electrotehnics and Informatics University of Oradea Oradea Romania MSc student Department of Computer Science Faculty of Electrotehnics and Informatics University of Oradea Oradea Romania

With the widespread computerization in business, government, and science, the efficient and effective discovery of interesting information from large databases becomes essential. Previous studies on data mining have been focused on the discovery of knowledge at single conceptual level, either at the primitive level or at a rather high conceptual level. This paper presents an algorithm based on the AFOPT algorithm for multilevel databases that uses the benefits of multileveled databases, by using the information gained by studying items from one concept level for the study of the items from the following concept levels.

关键词： Itemsets Data mining Transaction databases computer science Informatics Government Machine learning Association rules Performance gain Pattern matching

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