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A pathway-based approach for analyzing microarray data using random forests

ICIC Express Letters 2012年第5期6卷 1253-1257页

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

Although machine learning methods, such as random forests, have been developed to correlate survival outcomes with a set of genes, less study has assessed the abilities of these methods in incorporating pathway information for analyzing microarray data. In general, genes that are identified without incorporating biological knowledge are more difficult to interpret. Thus, the pathway-based survival analysis using machine learning methods represents a promising approach for generating new biological hypothesis from microarray studies. The two popular variants of random forests used in this research for survival data are random survival forests and bivariate node-splitting random survival forests. There are three types of datasets used for this research and each dataset with a three-level outcome. This research which compared the four splitting rules available in random survival forests to identify log-rank test is the most accurate in terms of prediction error. To evaluate the accuracy of pathway based survival approach, this research considered employing area under the receiver operating characteristic curve for censored data. The use of random survival forests for survival outcomes in analyzing microarray data allows researchers to obtain results that are more closely tied with the biological mechanism of diseases.

关键词： Genes

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Stabilization of linear systems with distributed input delay and input saturation

Stabilization of linear systems with distributed input delay...

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作者： Zhou, Bin Gao, Huijun Lin, Zongli Duan, Guang-Ren Center for Control Theory and Guidance Technology Harbin Institute of Technology Harbin 150001 China Research Institute of Intelligent Control and Systems Harbin Institute of Technology Harbin 150001 China Charles L. Brown Department of Electrical and Computer Engineering University of Virginia Charlottesville VA 22904-4743 United States

This paper is concerned with stabilization of a linear system with distributed input delay and input saturation. Both constant and time-varying delays are considered. In the case that the input delay is constant, under the stabilizability assumption on an auxiliary system, it is shown that the system can be stabilized by state feedback for an arbitrarily large delay as long as the open-loop system is not exponentially unstable. In the case that the input delay is time-varying, but bounded, it is shown that the system can be stabilized by state feedback if the non-asymptotically stable poles of the open-loop system are all located at the origin. In both cases, stabilizing controllers are explicitly constructed by utilizing the parametric Lyapunov equation based low gain design approach we recently developed. It is also shown that in the presence of actuator saturation and under the same assumptions on the system, these controllers achieve semi-global stabilization. Some discussions on the assumptions we impose on the system are given. A numerical example illustrates the effectiveness of the proposed stabilization approach. © 2012 Elsevier Ltd. All rights reserved.

关键词： Stabilization

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

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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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Fractional-order circuit elements with memory

Fractional-order circuit elements with memory

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2012 13th International Carpathian Control Conference, ICCC 2012

作者： Petráš, Ivo Chen, YangQuan Institute of Control and Informatization of Production Processes BERG Faculty Technical University of Košice B. Němcovej 3 04200 Košice Slovakia Department of Electrical and Computer Engineering Center for Self-Organizing and Intelligent Systems Utah State University 4120 Old Main Hill Logan UT 84322-4120 United States

ISBN: (纸本)9781457718687

This paper deals with the fractional-order memristive, memcapacitative, and meminductive systems and their utilization in design of the new circuits with memory. We provide a mathematical description of such systems by using a technique of the fractional calculus. Some possible applications of "mem" systems are mentioned in article as well. © 2012 IEEE.

关键词： Calculations

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Recent advances on the energy management of a Hybrid Electric Vehicle

Recent advances on the energy management of a Hybrid Electri...

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Mediterranean Conference on Control & Automation

作者： D. S. Efstathiou A. K. Petrou P. Spanoudakis N. C. Tsourveloudis K. P. Valavanis Intelligent Systems and Robotics Lab Technical University of Crete Chania Greece Machine Tools Laboratory Technical University of Crete Chania Greece Department of Electrical and Computer Engineering University of Denver Denver CO 80208 USA

ISBN: (纸本)9781467325301

This paper presents new innovative subsystems of the ER11 prototype urban vehicle which is powered by hydrogen fuel cells and ultra-capacitors. The subsystems described here are: 1) the energy management system, which is responsible for the optimization of the fuel efficiency and the increased mileage of the vehicle, 2) the driver's monitoring and control panel and 3) the power transmission system, which offers the possibility of continuous change of gear. The powertrain of the test-bed vehicle consists of an electric motor, a fuel (Η2) cell system, an ultra-capacitor bank and a DC/DC converter. Testing verified that the proposed energy management system is benefitted by the variable transmission of power leading to less fuel consumption.

关键词： Recent advances energy management Hybrid Electric Vehicle

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The CAM software for nonnegative blind source separation in R-Java

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The Journal of Machine Learning Research 2013年第1期14卷

作者： Kevin Murphy Bernhard Schölkopf Niya Wang Fan Meng Li Chen Subha Madhavan Robert Clarke Eric P. Hoffman Jianhua Xuan Yue Wang Google MPI for Intelligent Systems Department of Electrical and Computer Engineering Virginia Polytechnic Institute and State University Arlington VA National Cancer Institute National Institutes of Health Gaithersburg MD Innovation Center for Biomedical Informatics Georgetown University Washington DC Lombardi Comprehensive Cancer Center Georgetown University Washington DC Research Center for Genetic Medicine Children's National Medical Center Washington DC

We describe a R-Java CAM (convex analysis of mixtures) package that provides comprehensive analytic functions and a graphic user interface (GUI) for blindly separating mixed nonnegative sources. This open-source multiplatform software implements recent and classic algorithms in the literature including Chan et al. (2008), Wang et al. (2010), Chen et al. (2011a) and Chen et al. (2011b). The CAM package offers several attractive features: (1) instead of using proprietary MATLAB, its analytic functions are written in R, which makes the codes more portable and easier to modify; (2) besides producing and plotting results in R, it also provides a Java GUI for automatic progress update and convenient visual monitoring; (3) multi-thread interactions between the R and Java modules are driven and integrated by a Java GUI, assuring that the whole CAM software runs responsively; (4) the package offers a simple mechanism to allow others to plug-in additional R-functions.

关键词： affinity propagation clustering blind source separation compartment modeling convex analysis of mixtures information-based model selection

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Robust Fractional Order Differentiator

Robust Fractional Order Differentiator

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The 24th Chinese Control and Decision Conference (第24届中国控制与决策学术年会 2012 CCDC)

作者： Dali Chen Dingyu Xue YangQuan Chen College of Information Science and Engineering. Northeastern University. Shenyang. 110004. China Center for Self-Organizing and Intelligent Systems (CSOIS). Department of Electrical and Computer En

A robust fractional order differentiator is proposed to estimate the fractional order derivative of the given contaminated signal. Least square polynomial fitting technique is used to minimize the noise and Griinwald-Letnikov definition is used to calculate the fractional order derivative. A concise method is proposed to speed up the computation time and a parameter setting strategy is present for user. The frequency domain analysis demonstrates that the proposed differentiator essentially is a fractional order low-pass filter. The accuracy and robustness are evaluated by the experiments.

关键词： Fractional Order Differentiator Robust Least Squares.

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Fractional Analysis And Synthesis Of The Variability Of Irradiance And PV Power Time Series

Fractional Analysis And Synthesis Of The Variability Of Irra...

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第五届国际自动控制联合会分数阶导数及其应用会议

作者： Xianming Ye Xiaohua Xia Jiangfeng Zhang YangQuan Chen Department of Electrical Electronic and Computer EngineeringUniversity of Pretoria Pretoria 0002 South Africa Center for Self-Organizing & Intelligent Systems (CSOIS) Electrical & Computer Engineering Dept. Utah State University 4120 Old Main Hill Logan UT84322 USA

＜正＞The prediction of the power output of the photovoltaic（PV）system offers useful information for planning the operation and management strategy,which also helps to maintain or even to improve the power-supply re... 详细信息

关键词： ARMA ARFIMA PV load prediction sampling rate. Power output Time series irradiance Mean square error sampling rate synthesis

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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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Remarks on fractional order control systems

Remarks on fractional order control systems

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American Control Conference (ACC)

作者： Xuefeng Zhang Yangquan Chen Faculty of School of Sciences Northeastern University Shenyang Liaoning China Center for Self-Organizing and Intelligent Systems (CSOIS) Electrical and Computer Engineering Department Utah State University Logan UT USA

ISBN: (纸本)9781457710957

Fractional order systems(FOS) have attracted much attention since it plays an important role in many fields of science and engineering. Fractional order systems have many relationship with integer order systems(IOS). Can a fractional order system be replaced with an integer order system in the sense of solution equivalence? This paper deals with the relationship between FOS and IOS. It is concluded that the research of fractional order systems is necessary and its properties can not be replaced by any other system. The stability and composite derivative of FOS are discussed. Some mistake criteria of fractional order systems are pointed out by counterexamples.

关键词： Stability criteria Control systems Equations Mathematical model Laplace equations Time domain analysis

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