Gene encoder: a feature selection technique through unsupervised deep learning-based clustering for large gene expression data

2020 ◽  
Author(s):  
Uzma ◽  
Feras Al-Obeidat ◽  
Abdallah Tubaishat ◽  
Babar Shah ◽  
Zahid Halim
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Deep Learning ◽  
Gene Expression Data ◽  
Expression Data ◽  
Feature Selection Technique ◽  
Selection Technique ◽  
Large Gene ◽  
Unsupervised Deep Learning

A new distributed feature selection technique for classifying gene expression data

2019 ◽  
Vol 12 (04) ◽  
pp. 1950039 ◽  
Author(s):  
Sarah M. Ayyad ◽  
Ahmed I. Saleh ◽  
Labib M. Labib
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Fuzzy Inference ◽  
Research Area ◽  
Selection Method ◽  
Expression Data ◽  
Feature Selection Technique ◽  
Inference System ◽  
Selection Technique

Classification of gene expression data is a pivotal research area that plays a substantial role in diagnosis and prediction of diseases. Generally, feature selection is one of the extensively used techniques in data mining approaches, especially in classification. Gene expression data are usually composed of dozens of samples characterized by thousands of genes. This increases the dimensionality coupled with the existence of irrelevant and redundant features. Accordingly, the selection of informative genes (features) becomes difficult, which badly affects the gene classification accuracy. In this paper, we consider the feature selection for classifying gene expression microarray datasets. The goal is to detect the most possibly cancer-related genes in a distributed manner, which helps in effectively classifying the samples. Initially, the available huge amount of considered features are subdivided and distributed among several processors. Then, a new filter selection method based on a fuzzy inference system is applied to each subset of the dataset. Finally, all the resulted features are ranked, then a wrapper-based selection method is applied. Experimental results showed that our proposed feature selection technique performs better than other techniques since it produces lower time latency and improves classification performance.

scholarly journals Classification of Gene Expression Data using Efficient Feature Selection Technique and Resampling Method

2019 ◽  
Vol 8 (6) ◽  
pp. 406-414
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Classification Model ◽  
Support Vector ◽  
Expression Data ◽  
Feature Selection Technique ◽  
Selection Technique ◽  
Resampling Method

Microarray technology has been developed as one of the powerful tools that have attracted many researchers to analyze gene expression level for a given organism. It has been observed that gene expression data have very large (in terms of thousands) of features and less number of samples (in terms of hundreds). This characteristic makes difficult to do an analysis of gene expression data. Hence efficient feature selection technique must be applied before we go for any kind of analysis. Feature selection plays a vital role in the classification of gene expression data. There are several feature selection techniques have been induced in this field. But Support Vector Machine with Recursive Feature Elimination (SVM-RFE) has been proven as the promising feature selection methods among others. SVM-RFE ranks the genes (features) by training the SVM classification model and with the combination of RFE method key genes are selected. Huge time consumption is the main issue of SVM-RFE. We introduced an efficient implementation of linier SVM to overcome this problem and improved the RFE with variable step size. Then, combined method was used for selecting informative genes. Effective resampling method is proposed to preprocess the datasets. This is used to make the distribution of samples balanced, which gives more reliable classification results. In this paper, we have also studied the applicability of common classifiers. Detailed experiments are conducted on four commonly used microarray gene expression datasets. The results show that the proposed method comparable classification performance

scholarly journals Deep-Learning-Based Cancer Profiles Classification Using Gene Expression Data Profile

2022 ◽  
Vol 2022 ◽  
pp. 1-13
Author(s):  
Hatim Z Almarzouki
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Deep Learning ◽  
Gene Expression Data ◽  
Microarray Data ◽  
Detection Accuracy ◽  
Expression Data ◽  
Gene Expressions ◽  
Feature Selection Technique ◽  
Single Experiment

The quantity of data required to give a valid analysis grows exponentially as machine learning dimensionality increases. In a single experiment, microarrays or gene expression profiling assesses and determines gene expression levels and patterns in various cell types or tissues. The advent of DNA microarray technology has enabled simultaneous intensive care of hundreds of gene expressions on a single chip, advancing cancer categorization. The most challenging aspect of categorization is working out many information points from many sources. The proposed approach uses microarray data to train deep learning algorithms on extracted features and then uses the Latent Feature Selection Technique to reduce classification time and increase accuracy. The feature-selection-based techniques will pick the important genes before classifying microarray data for cancer prediction and diagnosis. These methods improve classification accuracy by removing duplicate and superfluous information. The Artificial Bee Colony (ABC) technique of feature selection was proposed in this research using bone marrow PC gene expression data. The ABC algorithm, based on swarm intelligence, has been proposed for gene identification. The ABC has been used here for feature selection that generates a subset of features and every feature produced by the spectators, making this a wrapper-based feature selection system. This method’s main goal is to choose the fewest genes that are critical to PC performance while also increasing prediction accuracy. Convolutional Neural Networks were used to classify tumors without labelling them. Lung, kidney, and brain cancer datasets were used in the procedure’s training and testing stages. Using the cross-validation technique of k-fold methodology, the Convolutional Neural Network has an accuracy rate of 96.43%. The suggested research includes techniques for preprocessing and modifying gene expression data to enhance future cancer detection accuracy.

Efficient Feature Selection Model for Gene Expression Data

2011 ◽  
Vol 110-116 ◽  
pp. 1948-1952
Author(s):  
Patharawut Saengsiri ◽  
Sageemas Na Wichian ◽  
Phayung Meesad
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Selection Model ◽  
Support Vector ◽  
Expression Data ◽  
Accuracy Rate ◽  
Feature Selection Technique ◽  
Wrapper Approach ◽  
Filter Approach

Finding subset of informative gene is very crucial for biology process because several genes increase sharply and most of them are not related with others. In general, feature selection technique consists of two steps 1) all genes is ranked by a filter approach 2) rank list is sent to a wrapper approach. Nevertheless, the accuracy rate for recognition gene is not enough. Therefore, this paper proposes efficient feature selection model for gene expression data. First, two filter approaches are used to define many subset of attribute such as Correlation based Feature Selection (Cfs) and Gain Ratio (GR). Second, wrapper approach is used to evaluate each length of attribute that based on Support Vector Machine (SVM) and Random Forest (RF). The result of experiment depicts CfsSVM, CfsRF, GRSVM, and GRRF based on proposed model produce higher accuracy rate such as 87.10%, 90.32%, 87.10, and 88.71%, respectively.

An Integrated Feature Selection Algorithm for Cancer Classification using Gene Expression Data

2019 ◽  
Vol 21 (9) ◽  
pp. 631-645 ◽  
Author(s):  
Saeed Ahmed ◽  
Muhammad Kabir ◽  
Zakir Ali ◽  
Muhammad Arif ◽  
Farman Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Classification Accuracy ◽  
Early Stage ◽  
Small Sample Size ◽  
Feature Selection Method ◽  
Small Sample ◽  
Expression Data ◽  
Base Function

Aim and Objective: Cancer is a dangerous disease worldwide, caused by somatic mutations in the genome. Diagnosis of this deadly disease at an early stage is exceptionally new clinical application of microarray data. In DNA microarray technology, gene expression data have a high dimension with small sample size. Therefore, the development of efficient and robust feature selection methods is indispensable that identify a small set of genes to achieve better classification performance. Materials and Methods: In this study, we developed a hybrid feature selection method that integrates correlation-based feature selection (CFS) and Multi-Objective Evolutionary Algorithm (MOEA) approaches which select the highly informative genes. The hybrid model with Redial base function neural network (RBFNN) classifier has been evaluated on 11 benchmark gene expression datasets by employing a 10-fold cross-validation test. Results: The experimental results are compared with seven conventional-based feature selection and other methods in the literature, which shows that our approach owned the obvious merits in the aspect of classification accuracy ratio and some genes selected by extensive comparing with other methods. Conclusion: Our proposed CFS-MOEA algorithm attained up to 100% classification accuracy for six out of eleven datasets with a minimal sized predictive gene subset.

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