Literature DB >> 33362861

Machine Learning Based Computational Gene Selection Models: A Survey, Performance Evaluation, Open Issues, and Future Research Directions.

Nivedhitha Mahendran1, P M Durai Raj Vincent1, Kathiravan Srinivasan1, Chuan-Yu Chang2.   

Abstract

Gene Expression is the process of determining the physical characteristics of living beings by generating the necessary proteins. Gene Expression takes place in two steps, translation and transcription. It is the flow of information from DNA to RNA with enzymes' help, and the end product is proteins and other biochemical molecules. Many technologies can capture Gene Expression from the DNA or RNA. One such technique is Microarray DNA. Other than being expensive, the main issue with Microarray DNA is that it generates high-dimensional data with minimal sample size. The issue in handling such a heavyweight dataset is that the learning model will be over-fitted. This problem should be addressed by reducing the dimension of the data source to a considerable amount. In recent years, Machine Learning has gained popularity in the field of genomic studies. In the literature, many Machine Learning-based Gene Selection approaches have been discussed, which were proposed to improve dimensionality reduction precision. This paper does an extensive review of the various works done on Machine Learning-based gene selection in recent years, along with its performance analysis. The study categorizes various feature selection algorithms under Supervised, Unsupervised, and Semi-supervised learning. The works done in recent years to reduce the features for diagnosing tumors are discussed in detail. Furthermore, the performance of several discussed methods in the literature is analyzed. This study also lists out and briefly discusses the open issues in handling the high-dimension and less sample size data.
Copyright © 2020 Mahendran, Durai Raj Vincent, Srinivasan and Chang.

Entities:  

Keywords:  gene selection; machine learning; microarray gene expression; supervised gene selection; unsupervised gene selection

Year:  2020        PMID: 33362861      PMCID: PMC7758324          DOI: 10.3389/fgene.2020.603808

Source DB:  PubMed          Journal:  Front Genet        ISSN: 1664-8021            Impact factor:   4.599


  53 in total

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Journal:  Comput Biol Med       Date:  2016-12-05       Impact factor: 4.589

2.  A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-Class Sensitivity Information.

Authors:  Fei Han; Chun Yang; Ya-Qi Wu; Jian-Sheng Zhu; Qing-Hua Ling; Yu-Qing Song; De-Shuang Huang
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2017 Jan-Feb       Impact factor: 3.710

3.  Gene selection for tumor classification using neighborhood rough sets and entropy measures.

Authors:  Yumin Chen; Zunjun Zhang; Jianzhong Zheng; Ying Ma; Yu Xue
Journal:  J Biomed Inform       Date:  2017-02-13       Impact factor: 6.317

4.  Gene selection from microarray data for cancer classification--a machine learning approach.

Authors:  Yu Wang; Igor V Tetko; Mark A Hall; Eibe Frank; Axel Facius; Klaus F X Mayer; Hans W Mewes
Journal:  Comput Biol Chem       Date:  2005-02       Impact factor: 2.877

5.  Application of high-dimensional feature selection: evaluation for genomic prediction in man.

Authors:  M L Bermingham; R Pong-Wong; A Spiliopoulou; C Hayward; I Rudan; H Campbell; A F Wright; J F Wilson; F Agakov; P Navarro; C S Haley
Journal:  Sci Rep       Date:  2015-05-19       Impact factor: 4.379

6.  Iterative ensemble feature selection for multiclass classification of imbalanced microarray data.

Authors:  Junshan Yang; Jiarui Zhou; Zexuan Zhu; Xiaoliang Ma; Zhen Ji
Journal:  J Biol Res (Thessalon)       Date:  2016-07-04       Impact factor: 1.889

7.  Cancer Characteristic Gene Selection via Sample Learning Based on Deep Sparse Filtering.

Authors:  Jian Liu; Yuhu Cheng; Xuesong Wang; Lin Zhang; Z Jane Wang
Journal:  Sci Rep       Date:  2018-05-29       Impact factor: 4.379

8.  Hybrid Method Based on Information Gain and Support Vector Machine for Gene Selection in Cancer Classification.

Authors:  Lingyun Gao; Mingquan Ye; Xiaojie Lu; Daobin Huang
Journal:  Genomics Proteomics Bioinformatics       Date:  2017-12-12       Impact factor: 7.691

9.  An Efficient Feature Selection Strategy Based on Multiple Support Vector Machine Technology with Gene Expression Data.

Authors:  Ying Zhang; Qingchun Deng; Wenbin Liang; Xianchun Zou
Journal:  Biomed Res Int       Date:  2018-08-30       Impact factor: 3.411

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  4 in total

1.  Feasibility of predicting allele specific expression from DNA sequencing using machine learning.

Authors:  Zhenhua Zhang; Freerk van Dijk; Niek de Klein; Mariëlle E van Gijn; Lude H Franke; Richard J Sinke; Morris A Swertz; K Joeri van der Velde
Journal:  Sci Rep       Date:  2021-05-19       Impact factor: 4.379

2.  Mutational Slime Mould Algorithm for Gene Selection.

Authors:  Feng Qiu; Pan Zheng; Ali Asghar Heidari; Guoxi Liang; Huiling Chen; Faten Khalid Karim; Hela Elmannai; Haiping Lin
Journal:  Biomedicines       Date:  2022-08-22

3.  A novel biomarker selection method combining graph neural network and gene relationships applied to microarray data.

Authors:  Weidong Xie; Wei Li; Shoujia Zhang; Linjie Wang; Jinzhu Yang; Dazhe Zhao
Journal:  BMC Bioinformatics       Date:  2022-07-26       Impact factor: 3.307

4.  Stable Iterative Variable Selection.

Authors:  Mehrad Mahmoudian; Mikko S Venäläinen; Riku Klén; Laura L Elo
Journal:  Bioinformatics       Date:  2021-07-16       Impact factor: 6.937

  4 in total

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