Regularized logistic regression with adjusted adaptive elastic net for gene selection in high dimensional cancer classification

2015 ◽  
Vol 67 ◽  
pp. 136-145 ◽  
Author(s):  
Zakariya Yahya Algamal ◽  
Muhammad Hisyam Lee
Keyword(s):  
Logistic Regression ◽  
Gene Selection ◽  
Elastic Net ◽  
Cancer Classification ◽  
High Dimensional ◽  
Adaptive Elastic Net

scholarly journals Cancer classification and biomarker selection via a penalized logsum network-based logistic regression model

2021 ◽  
Vol 29 ◽  
pp. 287-295
Author(s):  
Zhiming Zhou ◽  
Haihui Huang ◽  
Yong Liang
Keyword(s):  
Logistic Regression ◽  
Regression Model ◽  
Logistic Regression Model ◽  
Gene Selection ◽  
Simulated Data ◽  
Biological Data ◽  
Cancer Classification ◽  
High Dimensional ◽  
Data Set ◽  
Biomarker Selection

BACKGROUND: In genome research, it is particularly important to identify molecular biomarkers or signaling pathways related to phenotypes. Logistic regression model is a powerful discrimination method that can offer a clear statistical explanation and obtain the classification probability of classification label information. However, it is unable to fulfill biomarker selection. OBJECTIVE: The aim of this paper is to give the model efficient gene selection capability. METHODS: In this paper, we propose a new penalized logsum network-based regularization logistic regression model for gene selection and cancer classification. RESULTS: Experimental results on simulated data sets show that our method is effective in the analysis of high-dimensional data. For a large data set, the proposed method has achieved 89.66% (training) and 90.02% (testing) AUC performances, which are, on average, 5.17% (training) and 4.49% (testing) better than mainstream methods. CONCLUSIONS: The proposed method can be considered a promising tool for gene selection and cancer classification of high-dimensional biological data.

scholarly journals The Higher-Order of Adaptive Lasso and Elastic Net Methods for Classification on High Dimensional Data

Mathematics ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1091
Author(s):  
Autcha Araveeporn
Keyword(s):  
Logistic Regression ◽  
Categorical Data ◽  
High Dimensional Data ◽  
Higher Order ◽  
Elastic Net ◽  
Adaptive Lasso ◽  
High Dimensional ◽  
Independent Variables ◽  
Dependent Variables ◽  
Adaptive Elastic Net

The lasso and elastic net methods are the popular technique for parameter estimation and variable selection. Moreover, the adaptive lasso and elastic net methods use the adaptive weights on the penalty function based on the lasso and elastic net estimates. The adaptive weight is related to the power order of the estimator. Normally, these methods focus to estimate parameters in terms of linear regression models that are based on the dependent variable and independent variable as a continuous scale. In this paper, we compare the lasso and elastic net methods and the higher-order of the adaptive lasso and adaptive elastic net methods for classification on high dimensional data. The classification is used to classify the categorical data for dependent variable dependent on the independent variables, which is called the logistic regression model. The categorical data are considered a binary variable, and the independent variables are used as the continuous variable. The high dimensional data are represented when the number of independent variables is higher than the sample sizes. For this research, the simulation of the logistic regression is considered as the binary dependent variable and 20, 30, 40, and 50 as the independent variables when the sample sizes are less than the number of the independent variables. The independent variables are generated from normal distribution on several variances, and the dependent variables are obtained from the probability of logit function and transforming it to predict the binary data. For application in real data, we express the classification of the type of leukemia as the dependent variables and the subset of gene expression as the independent variables. The criterion of these methods is to compare by the average percentage of predicted accuracy value. The results are found that the higher-order of adaptive lasso method is satisfied with large dispersion, but the higher-order of adaptive elastic net method outperforms on small dispersion.

GENE SELECTION USING LOGISTIC REGRESSIONS BASED ON AIC, BIC AND MDL CRITERIA

2005 ◽  
Vol 01 (01) ◽  
pp. 129-145 ◽  
Author(s):  
XIAOBO ZHOU ◽  
XIAODONG WANG ◽  
EDWARD R. DOUGHERTY
Keyword(s):  
Logistic Regression ◽  
Regression Model ◽  
Logistic Regression Model ◽  
Gene Selection ◽  
Information Criterion ◽  
Cancer Classification ◽  
Data Sets ◽  
Classification Methods ◽  
Gene Expressions ◽  
Experimental Conditions

In microarray-based cancer classification, gene selection is an important issue owing to the large number of variables (gene expressions) and the small number of experimental conditions. Many gene-selection and classification methods have been proposed; however most of these treat gene selection and classification separately, and not under the same model. We propose a Bayesian approach to gene selection using the logistic regression model. The Akaike information criterion (AIC), the Bayesian information criterion (BIC) and the minimum description length (MDL) principle are used in constructing the posterior distribution of the chosen genes. The same logistic regression model is then used for cancer classification. Fast implementation issues for these methods are discussed. The proposed methods are tested on several data sets including those arising from hereditary breast cancer, small round blue-cell tumors, lymphoma, and acute leukemia. The experimental results indicate that the proposed methods show high classification accuracies on these data sets. Some robustness and sensitivity properties of the proposed methods are also discussed. Finally, mixing logistic-regression based gene selection with other classification methods and mixing logistic-regression-based classification with other gene-selection methods are considered.

scholarly journals Gene Selection in Cancer Classification Using Sparse Logistic Regression with L1/2 Regularization

2018 ◽  
Vol 8 (9) ◽  
pp. 1569 ◽  
Author(s):  
Shengbing Wu ◽  
Hongkun Jiang ◽  
Haiwei Shen ◽  
Ziyi Yang
Keyword(s):  
Logistic Regression ◽  
Gene Selection ◽  
Classification Performance ◽  
Cancer Classification ◽  
Sparse Logistic Regression ◽  
The Subject ◽  
Selection For ◽  
Microarray Datasets ◽  
Sparse Methods

In recent years, gene selection for cancer classification based on the expression of a small number of gene biomarkers has been the subject of much research in genetics and molecular biology. The successful identification of gene biomarkers will help in the classification of different types of cancer and improve the prediction accuracy. Recently, regularized logistic regression using the L 1 regularization has been successfully applied in high-dimensional cancer classification to tackle both the estimation of gene coefficients and the simultaneous performance of gene selection. However, the L 1 has a biased gene selection and dose not have the oracle property. To address these problems, we investigate L 1 / 2 regularized logistic regression for gene selection in cancer classification. Experimental results on three DNA microarray datasets demonstrate that our proposed method outperforms other commonly used sparse methods ( L 1 and L E N ) in terms of classification performance.

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 On the Performance of Variable Selection and Classification via Rank-Based Classifier

Mathematics ◽  
2019 ◽  
Vol 7 (5) ◽  
pp. 457 ◽  
Author(s):  
Md Sarker ◽  
Michael Pokojovy ◽  
Sangjin Kim
Keyword(s):  
Gene Expression ◽  
Logistic Regression ◽  
Gene Expression Data ◽  
Gene Selection ◽  
Laplacian Matrix ◽  
Adaptive Lasso ◽  
High Dimensional ◽  
Expression Data ◽  
Correlation Pattern ◽  
Future Outcomes

In high-dimensional gene expression data analysis, the accuracy and reliability of cancer classification and selection of important genes play a very crucial role. To identify these important genes and predict future outcomes (tumor vs. non-tumor), various methods have been proposed in the literature. But only few of them take into account correlation patterns and grouping effects among the genes. In this article, we propose a rank-based modification of the popular penalized logistic regression procedure based on a combination of ℓ 1 and ℓ 2 penalties capable of handling possible correlation among genes in different groups. While the ℓ 1 penalty maintains sparsity, the ℓ 2 penalty induces smoothness based on the information from the Laplacian matrix, which represents the correlation pattern among genes. We combined logistic regression with the BH-FDR (Benjamini and Hochberg false discovery rate) screening procedure and a newly developed rank-based selection method to come up with an optimal model retaining the important genes. Through simulation studies and real-world application to high-dimensional colon cancer gene expression data, we demonstrated that the proposed rank-based method outperforms such currently popular methods as lasso, adaptive lasso and elastic net when applied both to gene selection and classification.

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