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A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations
Genomic copy number variations (CNVs) are among the most important structural variations. They are linked to several diseases and cancer types. Cancer is a leading cause of death worldwide. Several studies were conducted to investigate the causes of cancer and its association with genomic changes to...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6806227/ https://www.ncbi.nlm.nih.gov/pubmed/31569801 http://dx.doi.org/10.3390/s19194207 |
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author | AlShibli, Ahmad Mathkour, Hassan |
author_facet | AlShibli, Ahmad Mathkour, Hassan |
author_sort | AlShibli, Ahmad |
collection | PubMed |
description | Genomic copy number variations (CNVs) are among the most important structural variations. They are linked to several diseases and cancer types. Cancer is a leading cause of death worldwide. Several studies were conducted to investigate the causes of cancer and its association with genomic changes to enhance its management and improve the treatment opportunities. Classification of cancer types based on the CNVs falls in this category of research. We reviewed the recent, most successful methods that used machine learning algorithms to solve this problem and obtained a dataset that was tested by some of these methods for evaluation and comparison purposes. We propose three deep learning techniques to classify cancer types based on CNVs: a six-layer convolutional net (CNN6), residual six-layer convolutional net (ResCNN6), and transfer learning of pretrained VGG16 net. The results of the experiments performed on the data of six cancer types demonstrated a high accuracy of 86% for ResCNN6 followed by 85% for CNN6 and 77% for VGG16. The results revealed a lower prediction accuracy for one of the classes (uterine corpus endometrial carcinoma (UCEC)). Repeating the experiments after excluding this class reveals improvements in the accuracies: 91% for CNN6 and 92% for Res CNN6. We observed that UCEC and ovarian serous carcinoma (OV) share a considerable subset of their features, which causes a struggle for learning in the classifiers. We repeated the experiment again by balancing the six classes through oversampling of the training dataset and the result was an enhancement in both overall and UCEC classification accuracies. |
format | Online Article Text |
id | pubmed-6806227 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-68062272019-11-07 A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations AlShibli, Ahmad Mathkour, Hassan Sensors (Basel) Article Genomic copy number variations (CNVs) are among the most important structural variations. They are linked to several diseases and cancer types. Cancer is a leading cause of death worldwide. Several studies were conducted to investigate the causes of cancer and its association with genomic changes to enhance its management and improve the treatment opportunities. Classification of cancer types based on the CNVs falls in this category of research. We reviewed the recent, most successful methods that used machine learning algorithms to solve this problem and obtained a dataset that was tested by some of these methods for evaluation and comparison purposes. We propose three deep learning techniques to classify cancer types based on CNVs: a six-layer convolutional net (CNN6), residual six-layer convolutional net (ResCNN6), and transfer learning of pretrained VGG16 net. The results of the experiments performed on the data of six cancer types demonstrated a high accuracy of 86% for ResCNN6 followed by 85% for CNN6 and 77% for VGG16. The results revealed a lower prediction accuracy for one of the classes (uterine corpus endometrial carcinoma (UCEC)). Repeating the experiments after excluding this class reveals improvements in the accuracies: 91% for CNN6 and 92% for Res CNN6. We observed that UCEC and ovarian serous carcinoma (OV) share a considerable subset of their features, which causes a struggle for learning in the classifiers. We repeated the experiment again by balancing the six classes through oversampling of the training dataset and the result was an enhancement in both overall and UCEC classification accuracies. MDPI 2019-09-27 /pmc/articles/PMC6806227/ /pubmed/31569801 http://dx.doi.org/10.3390/s19194207 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article AlShibli, Ahmad Mathkour, Hassan A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations |
title | A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations |
title_full | A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations |
title_fullStr | A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations |
title_full_unstemmed | A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations |
title_short | A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations |
title_sort | shallow convolutional learning network for classification of cancers based on copy number variations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6806227/ https://www.ncbi.nlm.nih.gov/pubmed/31569801 http://dx.doi.org/10.3390/s19194207 |
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