A New Approach for Feature Selection from Microarray Data Based on Mutual Information

With the development of microarray technology, massive microarray data is produced by gene expression experiments, and it provides a new approach for the study of human disease. Due to the characteristics of high dimensionality, much noise and data redundancy for microarray data, it is difficult to my knowledge from microarray data profoundly and accurately,and it also brings enormous difficulty for information genes selection. Therefore, a new feature selection algorithm for high dimensional microarray data is proposed in this paper, which mainly involves two steps. In the first step, mutual information method is used to calculate all genes, and according to the mutual information value, information genes is selected as candidate genes subset and irrelevant genes are filtered. In the second step, an improved method based on Lasso is used to select information genes from candidate genes subset, which aims to remove the redundant genes. Experimental results show that the proposed algorithm can select fewer genes, and it has better classification ability, stable performance and strong generalization ability. It is an effective genes feature selection algorithm.

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Robust Feature Selection from Microarray Data Based on Cooperative Game Theory and Qualitative Mutual Information

Advances in Bioinformatics ◽

10.1155/2016/1058305 ◽

2016 ◽

Vol 2016 ◽

pp. 1-16 ◽

Cited By ~ 9

Author(s):

Atiyeh Mortazavi ◽

Mohammad Hossein Moattar

Keyword(s):

Feature Selection ◽

Mutual Information ◽

Cooperative Game ◽

Microarray Data ◽

Second Phase ◽

Data Sets ◽

Forward Selection ◽

Selection Scheme ◽

Fisher Ratio ◽

Low Efficiency

High dimensionality of microarray data sets may lead to low efficiency and overfitting. In this paper, a multiphase cooperative game theoretic feature selection approach is proposed for microarray data classification. In the first phase, due to high dimension of microarray data sets, the features are reduced using one of the two filter-based feature selection methods, namely, mutual information and Fisher ratio. In the second phase, Shapley index is used to evaluate the power of each feature. The main innovation of the proposed approach is to employ Qualitative Mutual Information (QMI) for this purpose. The idea of Qualitative Mutual Information causes the selected features to have more stability and this stability helps to deal with the problem of data imbalance and scarcity. In the third phase, a forward selection scheme is applied which uses a scoring function to weight each feature. The performance of the proposed method is compared with other popular feature selection algorithms such as Fisher ratio, minimum redundancy maximum relevance, and previous works on cooperative game based feature selection. The average classification accuracy on eleven microarray data sets shows that the proposed method improves both average accuracy and average stability compared to other approaches.

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Feature selection based on mutual information for gear imbalanced problem faulty diagnosis

2012 International Conference on System Simulation (ICUSS 2012) ◽

10.1049/cp.2012.0506 ◽

2012 ◽

Cited By ~ 1

Author(s):

T.Y. Liu

Keyword(s):

Feature Selection ◽

Mutual Information

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A fuzzy gaussian rank aggregation ensemble feature selection method for microarray data

International Journal of Knowledge-based and Intelligent Engineering Systems ◽

10.3233/kes-190134 ◽

2021 ◽

Vol 24 (4) ◽

pp. 289-301

Author(s):

B. Venkatesh ◽

J. Anuradha

Keyword(s):

Feature Selection ◽

Microarray Data ◽

Classification Accuracy ◽

Performance Metrics ◽

Feature Selection Method ◽

Selection Method ◽

Support Vector ◽

Svm Classifier ◽

Binary Particle Swarm Optimization ◽

Selection Methods

In Microarray Data, it is complicated to achieve more classification accuracy due to the presence of high dimensions, irrelevant and noisy data. And also It had more gene expression data and fewer samples. To increase the classification accuracy and the processing speed of the model, an optimal number of features need to extract, this can be achieved by applying the feature selection method. In this paper, we propose a hybrid ensemble feature selection method. The proposed method has two phases, filter and wrapper phase in filter phase ensemble technique is used for aggregating the feature ranks of the Relief, minimum redundancy Maximum Relevance (mRMR), and Feature Correlation (FC) filter feature selection methods. This paper uses the Fuzzy Gaussian membership function ordering for aggregating the ranks. In wrapper phase, Improved Binary Particle Swarm Optimization (IBPSO) is used for selecting the optimal features, and the RBF Kernel-based Support Vector Machine (SVM) classifier is used as an evaluator. The performance of the proposed model are compared with state of art feature selection methods using five benchmark datasets. For evaluation various performance metrics such as Accuracy, Recall, Precision, and F1-Score are used. Furthermore, the experimental results show that the performance of the proposed method outperforms the other feature selection methods.

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Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction

Scientific Reports ◽

10.1038/s41598-021-92864-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Li-Hsin Cheng ◽

Te-Cheng Hsu ◽

Che Lin

Keyword(s):

Breast Cancer ◽

Neural Network ◽

Feature Selection ◽

Systems Biology ◽

Ensemble Learning ◽

Microarray Data ◽

Deep Neural Network ◽

Prediction Models ◽

Biological Knowledge ◽

Prognosis Prediction

AbstractBreast cancer is a heterogeneous disease. To guide proper treatment decisions for each patient, robust prognostic biomarkers, which allow reliable prognosis prediction, are necessary. Gene feature selection based on microarray data is an approach to discover potential biomarkers systematically. However, standard pure-statistical feature selection approaches often fail to incorporate prior biological knowledge and select genes that lack biological insights. Besides, due to the high dimensionality and low sample size properties of microarray data, selecting robust gene features is an intrinsically challenging problem. We hence combined systems biology feature selection with ensemble learning in this study, aiming to select genes with biological insights and robust prognostic predictive power. Moreover, to capture breast cancer's complex molecular processes, we adopted a multi-gene approach to predict the prognosis status using deep learning classifiers. We found that all ensemble approaches could improve feature selection robustness, wherein the hybrid ensemble approach led to the most robust result. Among all prognosis prediction models, the bimodal deep neural network (DNN) achieved the highest test performance, further verified by survival analysis. In summary, this study demonstrated the potential of combining ensemble learning and bimodal DNN in guiding precision medicine.

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