scholarly journals PLS Dimension Reduction for Classification with Microarray Data

2004 ◽  
Vol 3 (1) ◽  
pp. 1-30 ◽  
Author(s):  
Anne-Laure Boulesteix
Keyword(s):  
Dimension Reduction ◽  
Microarray Data ◽  
Gene Selection ◽  
Simple Procedure ◽  
Binary Classification ◽  
Real Data ◽  
Good Prediction ◽  
Linear Discriminant ◽  
Cancer Data ◽  
Good Prediction Accuracy

Partial Least Squares (PLS) dimension reduction is known to give good prediction accuracy in the context of classification with high-dimensional microarray data. In this paper, the classification procedure consisting of PLS dimension reduction and linear discriminant analysis on the new components is compared with some of the best state-of-the-art classification methods. Moreover, a boosting algorithm is applied to this classification method. In addition, a simple procedure to choose the number of PLS components is suggested. The connection between PLS dimension reduction and gene selection is examined and a property of the first PLS component for binary classification is proved. In addition, we show how PLS can be used for data visualization using real data. The whole study is based on 9 real microarray cancer data sets.

scholarly journals Principal Component Analysis Sebagai Ekstraksi Fitur Data Microarray Untuk Deteksi Kanker Berbasis Linear Discriminant Analysis

2019 ◽  
Vol 3 (2) ◽  
pp. 72
Author(s):  
Widi Astuti ◽  
Adiwijaya Adiwijaya
Keyword(s):  
Principal Component Analysis ◽  
Discriminant Analysis ◽  
Linear Discriminant Analysis ◽  
Microarray Data ◽  
Principal Component ◽  
Component Analysis ◽  
High Dimensions ◽  
Linear Discriminant ◽  
Cancer Data ◽  
Colon Cancer Data

Cancer is one of the leading causes of death globally. Early detection of cancer allows better treatment for patients. One method to detect cancer is using microarray data classification. However, microarray data has high dimensions which complicates the classification process. Linear Discriminant Analysis is a classification technique which is easy to implement and has good accuracy. However, Linear Discriminant Analysis has difficulty in handling high dimensional data. Therefore, Principal Component Analysis, a feature extraction technique is used to optimize Linear Discriminant Analysis performance. Based on the results of the study, it was found that usage of Principal Component Analysis increases the accuracy of up to 29.04% and f-1 score by 64.28% for colon cancer data.

scholarly journals Improved Lasso (ILASSO) for Gene Selection and Classification in High Dimensional DNA Microarray Data

2021 ◽  
Vol 17 (08) ◽  
pp. 91
Author(s):  
Isah Aliyu Kargi ◽  
Norazlina Bint Ismail ◽  
Ismail Bin Mohamad
Keyword(s):  
Microarray Data ◽  
Gene Selection ◽  
Poor Performance ◽  
Real Data ◽  
Ordinary Least Squares ◽  
Elastic Net ◽  
Likelihood Method ◽  
High Dimensional ◽  
Initial Weight ◽  
Highly Correlated

<p class="0abstract">Classification and selection of gene in high dimensional microarray data has become a challenging problem in molecular biology and genetics. Penalized Adaptive likelihood method has been employed recently for classification of cancer to address both gene selection consistency and estimation of gene coefficients in high dimensional data simultaneously. Many studies from the literature have proposed the use of ordinary least squares (OLS), maximum likelihood estimation (MLE) and Elastic net as the initial weight in the Adaptive elastic net, but in high dimensional microarray data the MLE and OLS are not suitable. Likewise, considering the Elastic net as the initial weight in Adaptive elastic yields a poor performance, because the ridge penalty in the Elastic net grouped coefficient of highly correlated genes closer to each other.  As a result, the estimator fails to differentiate coefficients of highly correlated genes that have different sign being grouped together. To tackle this issue, the present study proposed Improved LASSO (ILASSO) estimator which add the ridge penalty to the original LASSO with an Adaptive weight to both    and  simultaneously. Results from the real data indicated that ILASSO has a better performance compared to other methods in terms of the number of gene selected, classification precision, Sensitivity and Specificity.</p>

scholarly journals Recursive Feature Selection with Significant Variables of Support Vectors

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Chen-An Tsai ◽  
Chien-Hsun Huang ◽  
Ching-Wei Chang ◽  
Chun-Houh Chen
Keyword(s):  
Support Vector Machine ◽  
Gene Selection ◽  
Classification Performance ◽  
Recursive Feature Elimination ◽  
Support Vector ◽  
Good Prediction ◽  
Simulation Experiments ◽  
Ranking Criteria ◽  
Good Prediction Accuracy ◽  
Microarray Datasets

The development of DNA microarray makes researchers screen thousands of genes simultaneously and it also helps determine high- and low-expression level genes in normal and disease tissues. Selecting relevant genes for cancer classification is an important issue. Most of the gene selection methods use univariate ranking criteria and arbitrarily choose a threshold to choose genes. However, the parameter setting may not be compatible to the selected classification algorithms. In this paper, we propose a new gene selection method (SVM-t) based on the use oft-statistics embedded in support vector machine. We compared the performance to two similar SVM-based methods: SVM recursive feature elimination (SVMRFE) and recursive support vector machine (RSVM). The three methods were compared based on extensive simulation experiments and analyses of two published microarray datasets. In the simulation experiments, we found that the proposed method is more robust in selecting informative genes than SVMRFE and RSVM and capable to attain good classification performance when the variations of informative and noninformative genes are different. In the analysis of two microarray datasets, the proposed method yields better performance in identifying fewer genes with good prediction accuracy, compared to SVMRFE and RSVM.

scholarly journals Deteksi Kanker Berdasarkan Klasifikasi Microarray Data

2018 ◽  
Vol 2 (4) ◽  
pp. 181
Author(s):  
Adiwijaya Adiwijaya
Keyword(s):  
Gene Expression ◽  
Dimension Reduction ◽  
Dna Microarray ◽  
Microarray Data ◽  
Expression Patterns ◽  
Back Propagation ◽  
Good Method ◽  
Accurate Analysis ◽  
Training Time ◽  
Cancer Data

Cancer is one of the diseases that can cause human death in the world and become the biggest cause of death after heart disease. Therefore we need a DNA microarray technology which is used to examine how gene expression patterns change under different conditions, so that the technology is able to detect a person with cancer or not with accurate analysis. The size of the dimension in the microarray data can affect the gene expression analysis that is used to find informative genes, for that we need a good method of dimension reduction and classification so that it can get the best results and accuracy. Many techniques can be applied in DNA microarray, one of them is BPNN Back Propagation Neural Network as a classification and PCA as dimension reduction, where both have been tested in several previous studies. By applying BPNN and PCA on several types of cancer data, it was found that BPNN and PCA get more than 80% accuracy results with training time 0-4 seconds.

scholarly journals Gene Correlation Guided Gene Selection for Microarray Data Classification

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Dong Yang ◽  
Xuchang Zhu
Keyword(s):  
Microarray Data ◽  
Gene Selection ◽  
Effective Means ◽  
Cluster Structure ◽  
Coefficient Matrix ◽  
Cancer Data ◽  
Redundant Genes ◽  
Gene Correlation ◽  
High Gene ◽  
Microarray Datasets

The microarray cancer data obtained by DNA microarray technology play an important role for cancer prevention, diagnosis, and treatment. However, predicting the different types of tumors is a challenging task since the sample size in microarray data is often small but the dimensionality is very high. Gene selection, which is an effective means, is aimed at mitigating the curse of dimensionality problem and can boost the classification accuracy of microarray data. However, many of previous gene selection methods focus on model design, but neglect the correlation between different genes. In this paper, we introduce a novel unsupervised gene selection method by taking the gene correlation into consideration, named gene correlation guided gene selection (G3CS). Specifically, we calculate the covariance of different gene dimension pairs and embed it into our unsupervised gene selection model to regularize the gene selection coefficient matrix. In such a manner, redundant genes can be effectively excluded. In addition, we utilize a matrix factorization term to exploit the cluster structure of original microarray data to assist the learning process. We design an iterative updating algorithm with convergence guarantee to solve the resultant optimization problem. Experimental results on six publicly available microarray datasets are conducted to validate the efficacy of our proposed method.

scholarly journals Impact of class-imbalance on multi-class high-dimensional class prediction

2012 ◽  
Vol 9 (1) ◽  
Author(s):  
Rok Blagus ◽  
Lara Lusa
Keyword(s):  
Sample Size ◽  
Binary Classification ◽  
Class Imbalance ◽  
Imbalanced Data ◽  
Real Data ◽  
High Dimensional ◽  
Class Imbalance Problem ◽  
Class Prediction ◽  
Linear Discriminant ◽  
Imbalance Problem

The goal of multi-class supervised classification is to develop a rule that accurately predicts the class membership of new samples when the number of classes is larger than two. In this paper we consider high-dimensional class-imbalanced data: the number of variables greatly exceeds the number of samples and the number of samples in each class is not equal. We focus on Friedman's one-versus-one approach for three-class problems and show how its class probabilities depend on the class probabilities from the binary classification sub-problems. We further explore its performance using diagonal linear discriminant analysis (DLDA) as a base classifier and compare its performance with multi-class DLDA, using simulated and real data. Our results show that the class-imbalance has a significant effect on the classification results: the classification is biased towards the majority class as in the two-class problems and the problem is magnified when the number of variables is large. The amount of the bias depends also, jointly, on the magnitude of the differences between the classes and on the sample size: the bias diminishes when the difference between the classes is larger or the sample size is increased. Also variable selection plays an important role in the class-imbalance problem and the most effective strategy depends on the type of differences that exist between classes. DLDA seems to be among the least sensible classifiers to class-imbalance and its use is recommended also for multi-class problems. Whenever possible the experiments should be planned using balanced data in order to avoid the class-imbalance problem.

scholarly journals Gene selection ensembles and classifier ensembles for medical diagnosis

2019 ◽  
Vol 56 (2) ◽  
pp. 117-138
Author(s):  
Małgorzata Ćwiklińska-Jurkowska
Keyword(s):  
Microarray Data ◽  
Gene Selection ◽  
Data Sets ◽  
Selection Methods ◽  
Classifier Ensembles ◽  
K Nearest Neighbors ◽  
Data Set ◽  
Cancer Data ◽  
Misclassification Rates ◽  
Selection Of

SummaryThe usefulness of combining methods is examined using the example of microarray cancer data sets, where expression levels of huge numbers of genes are reported. Problems of discrimination into two groups are examined on three data sets relating to the expression of huge numbers of genes. For the three examined microarray data sets, the cross-validation errors evaluated on the remaining half of the whole data set, not used earlier for the selection of genes, were used as measures of classifier performance. Common single procedures for the selection of genes—Prediction Analysis of Microarrays (PAM) and Significance Analysis of Microarrays (SAM)—were compared with the fusion of eight selection procedures, or of a smaller subset of five of them, excluding SAM or PAM. Merging five or eight selection methods gave similar results. Based on the misclassification rates for the three examined microarray data sets, for any examined ensemble of classifiers, the combining of gene selection methods was not superior to single PAM or SAM selection for two of the examined data sets. Additionally, the procedure of heterogeneous combining of five base classifiers—k-nearest neighbors, SVM linear and SVM radial with parameter c=1, shrunken centroids regularized classifier (SCRDA) and nearest mean classifier—proved to significantly outperform resampling classifiers such as bagging decision trees. Heterogeneously combined classifiers also outperformed double bagging for some ranges of gene numbers and data sets, but merging is generally not superior to random forests. The preliminary step of combining gene rankings was generally not essential for the performance for either heterogeneously or homogeneously combined classifiers.

scholarly journals Statistical Redundancy Testing for Improved Gene Selection in Cancer Classification Using Microarray Data

2007 ◽  
Vol 3 ◽  
pp. 117693510700300 ◽  
Author(s):  
Simin Hu ◽  
J. Sunil Rao
Keyword(s):  
Microarray Data ◽  
Gene Selection ◽  
Real Data ◽  
Cancer Classification ◽  
Simulation Studies ◽  
Selection Methods ◽  
Gene Subset ◽  
High Quality ◽  
Eigenvalue Ratio ◽  
Selection For

In gene selection for cancer classification using microarray data, we define an eigenvalue-ratio statistic to measure a gene's contribution to the joint discriminability when this gene is included into a set of genes. Based on this eigenvalue-ratio statistic, we define a novel hypothesis testing for gene statistical redundancy and propose two gene selection methods. Simulation studies illustrate the agreement between statistical redundancy testing and gene selection methods. Real data examples show the proposed gene selection methods can select a compact gene subset which can not only be used to build high quality cancer classifiers but also show biological relevance.

Method of determination of the text direction on the image with the use of convolutional neural network

2020 ◽  
pp. 96-99
Author(s):  
P.L. Nikolaev
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Deep Neural Network ◽  
Binary Classification ◽  
Synthetic Data ◽  
Real Data ◽  
Method Of Determination ◽  
Classification Of Images

This article deals with method of binary classification of images with small text on them Classification is based on the fact that the text can have 2 directions – it can be positioned horizontally and read from left to right or it can be turned 180 degrees so the image must be rotated to read the sign. This type of text can be found on the covers of a variety of books, so in case of recognizing the covers, it is necessary first to determine the direction of the text before we will directly recognize it. The article suggests the development of a deep neural network for determination of the text position in the context of book covers recognizing. The results of training and testing of a convolutional neural network on synthetic data as well as the examples of the network functioning on the real data are presented.

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