146277

Machine Learning Model for Cancer Diagnosis based on RNAseq Microarray

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Last updated: 04 Jan 2025

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Abstract

Microarray technology is one of the most important recent breakthroughs in experimental molecular biology. This novel technology for thousands of genes concurrently allows the supervising of expression levels in cells and has been increasingly used in cancer research to understand more of the molecular variations among tumors so that a more reliable classification becomes attainable. Machine learning techniques are loosely used to create substantial and precise classification models. In this paper, a function called Feature Reduction Classification Optimization (FeRCO) is proposed. FeRCO function uses machine learning techniques applied upon RNAseq microarray data for predicting whether the patient is diseased or not. The main purpose of FeRCO function is to define the minimum number of features using the most fitting reduction technique along with classification technique that give the highest classification accuracy. These techniques include Support Vector Machine (SVM) both linear and kernel, Decision Trees (DT), Random Forest (RF), K-Nearest Neighbours (KNN) and Naïve Bayes (NB). Principle Component Analysis (PCA) both linear and kernel, Linear Discriminant Analysis (LDA) and Factor Analysis (FA) along with different machine learning techniques were used to find a lower-dimensional subspace with better discriminatory features for better classification. The major outcomes of this research can be considered as a roadmap for interesting researchers in this field to be able to choose the most suitable machine learning algorithm whatever classification or reduction. The results show that FA and LPCA are the best reduction techniques to be used with the three datasets providing an accuracy up to 100% with TCGA and simulation datasets and accuracy up to 97.86% with WDBC datasets. LSVM is the best classification technique to be used with Linear PCA (LPCA), FA and LDA. RF is the best classification technique to be used with Kernel PCA (KPCA).

DOI

10.21608/mjeer.2021.146277

Keywords

Cancer Classification, Diagnosis, Gene expression, Gene Reduction, Machine Learning

Authors

First Name

Hanaa

Last Name

Torkey

MiddleName

-

Affiliation

dept. computer science and engineeing Faculty of Eleronic Engineering, Menoufia University Menoufia, Menouf

Email

htorkey@el-eng.menoufia.edu.eg

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-

Orcid

-

First Name

Mostafa

Last Name

Atlam

MiddleName

-

Affiliation

dept. computer science and engineeing Faculty of Eleronic Engineering, Menoufia University Menoufia, Menouf

Email

mostafasami768@el-eng.menofia.edu.eg

City

-

Orcid

-

First Name

Nawal

Last Name

El-Fishawy

MiddleName

-

Affiliation

dept. computer science and engineeing Faculty of Eleronic Engineering, Menoufia University Menoufia, Menouf

Email

nelfishawy@hotmail.com

City

-

Orcid

-

First Name

Hanaa

Last Name

Salem

MiddleName

-

Affiliation

Communications and Computers Engineering Department, Faculty of Engineering, Delta University for Science and Tecnology, Gamasa, Egypt.

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Volume

30

Article Issue

1

Related Issue

21538

Issue Date

2021-01-01

Receive Date

2021-02-04

Publish Date

2021-01-01

Page Start

65

Page End

75

Print ISSN

1687-1189

Online ISSN

2682-3535

Link

https://mjeer.journals.ekb.eg/article_146277.html

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https://mjeer.journals.ekb.eg/service?article_code=146277

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9

Type

Original Article

Type Code

1,088

Publication Type

Journal

Publication Title

Menoufia Journal of Electronic Engineering Research

Publication Link

https://mjeer.journals.ekb.eg/

MainTitle

Machine Learning Model for Cancer Diagnosis based on RNAseq Microarray

Details

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Article

Created At

22 Jan 2023