Classification of cancer cells and gene selection based on microarray data using MOPSO algorithm
Purpose Microarray information is crucial for the identification and categorisation of malignant tissues. The very limited sample size in the microarray has always been a challenge for classification design in cancer research. As a result, by pre-processing gene selection approaches and genes lackin...
Gespeichert in:
Veröffentlicht in: | Journal of cancer research and clinical oncology 2023-11, Vol.149 (16), p.15171-15184 |
---|---|
Hauptverfasser: | , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 15184 |
---|---|
container_issue | 16 |
container_start_page | 15171 |
container_title | Journal of cancer research and clinical oncology |
container_volume | 149 |
creator | Rahimi, Mohammad Reza Makarem, Dorna Sarspy, Sliva Mahdavi, Sobhan Akhavan Albaghdadi, Mustafa Fahem Armaghan, Seyed Mostafa |
description | Purpose
Microarray information is crucial for the identification and categorisation of malignant tissues. The very limited sample size in the microarray has always been a challenge for classification design in cancer research. As a result, by pre-processing gene selection approaches and genes lacking their information, the microarray data are deleted prior to categorisation. In essence, an appropriate gene selection technique can significantly increase the accuracy of illness (cancer) classification.
Methods
For the classification of high-dimensional microarray data, a novel approach based on the hybrid model of multi-objective particle swarm optimisation (MOPSO) is proposed in this research. First, a binary vector representing each particle’s position is presented at random. A gene is represented by each bit. Bit 0 denotes the absence of selection of the characteristic (gene) corresponding to it, while bit 1 denotes the selection of the gene. Therefore, the position of each particle represents a set of genes, and the linear Bayesian discriminant analysis classification algorithm calculates each particle’s degree of fitness to assess the quality of the gene set that particle has chosen. The suggested methodology is applied to four different cancer database sets, and the results are contrasted with those of other approaches currently in use.
Results
The proposed algorithm has been applied on four sets of cancer database and its results have been compared with other existing methods. The results of the implementation show that the improvement of classification accuracy in the proposed algorithm compared to other methods for four sets of databases is 25.84% on average. So that it has improved by 18.63% in the blood cancer database, 24.25% in the lung cancer database, 27.73% in the breast cancer database, and 32.80% in the prostate cancer database. Therefore, the proposed algorithm is able to identify a small set of genes containing information in a way choose to increase the classification accuracy.
Conclusion
Our proposed solution is used for data classification, which also improves classification accuracy. This is possible because the MOPSO model removes redundancy and reduces the number of redundant and redundant genes by considering how genes are correlated with each other. |
doi_str_mv | 10.1007/s00432-023-05308-7 |
format | Article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2858405166</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2858405166</sourcerecordid><originalsourceid>FETCH-LOGICAL-c352t-df7b46700da6c4d3102f8debb6fb91998695f9464edf24f8a40e1b9d07d17dfa3</originalsourceid><addsrcrecordid>eNp9kEtLxDAUhYMoOI7-AVcBN26qN6-mXcrgC5QR1HVM86gd-hiTzmL-vZmpILhwdR9853LPQeicwBUBkNcRgDOaAWUZCAZFJg_QjOxWhDFxiGZAJMkEJfkxOolxBWkWks7Qx6LVMTa-MXpshh4PHhvdGxewcW0bse4trl3vcHStM3uk0tFZnJquMWHQIegttnrUeBObvsbPy5fXJdZtPYRm_OxO0ZHXbXRnP3WO3u9u3xYP2dPy_nFx85QZJuiYWS8rnksAq3PDLSNAfWFdVeW-KklZFnkpfMlz7qyn3BeagyNVaUFaIq3XbI4up7vrMHxtXBxV18SdB927YRMVLUTBQZA8T-jFH3Q1bEKfvktUQQnhhEKi6EQlkzEG59U6NJ0OW0VA7UJXU-gqha72oSuZRGwSxQT3tQu_p_9RfQMkvYSN</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2882114120</pqid></control><display><type>article</type><title>Classification of cancer cells and gene selection based on microarray data using MOPSO algorithm</title><source>SpringerLink Journals - AutoHoldings</source><creator>Rahimi, Mohammad Reza ; Makarem, Dorna ; Sarspy, Sliva ; Mahdavi, Sobhan Akhavan ; Albaghdadi, Mustafa Fahem ; Armaghan, Seyed Mostafa</creator><creatorcontrib>Rahimi, Mohammad Reza ; Makarem, Dorna ; Sarspy, Sliva ; Mahdavi, Sobhan Akhavan ; Albaghdadi, Mustafa Fahem ; Armaghan, Seyed Mostafa</creatorcontrib><description>Purpose
Microarray information is crucial for the identification and categorisation of malignant tissues. The very limited sample size in the microarray has always been a challenge for classification design in cancer research. As a result, by pre-processing gene selection approaches and genes lacking their information, the microarray data are deleted prior to categorisation. In essence, an appropriate gene selection technique can significantly increase the accuracy of illness (cancer) classification.
Methods
For the classification of high-dimensional microarray data, a novel approach based on the hybrid model of multi-objective particle swarm optimisation (MOPSO) is proposed in this research. First, a binary vector representing each particle’s position is presented at random. A gene is represented by each bit. Bit 0 denotes the absence of selection of the characteristic (gene) corresponding to it, while bit 1 denotes the selection of the gene. Therefore, the position of each particle represents a set of genes, and the linear Bayesian discriminant analysis classification algorithm calculates each particle’s degree of fitness to assess the quality of the gene set that particle has chosen. The suggested methodology is applied to four different cancer database sets, and the results are contrasted with those of other approaches currently in use.
Results
The proposed algorithm has been applied on four sets of cancer database and its results have been compared with other existing methods. The results of the implementation show that the improvement of classification accuracy in the proposed algorithm compared to other methods for four sets of databases is 25.84% on average. So that it has improved by 18.63% in the blood cancer database, 24.25% in the lung cancer database, 27.73% in the breast cancer database, and 32.80% in the prostate cancer database. Therefore, the proposed algorithm is able to identify a small set of genes containing information in a way choose to increase the classification accuracy.
Conclusion
Our proposed solution is used for data classification, which also improves classification accuracy. This is possible because the MOPSO model removes redundancy and reduces the number of redundant and redundant genes by considering how genes are correlated with each other.</description><identifier>ISSN: 0171-5216</identifier><identifier>EISSN: 1432-1335</identifier><identifier>DOI: 10.1007/s00432-023-05308-7</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Accuracy ; Algorithms ; Bayesian analysis ; Cancer ; Cancer Research ; Classification ; Discriminant analysis ; DNA microarrays ; Genes ; Hematology ; Internal Medicine ; Lung cancer ; Medical research ; Medicine ; Medicine & Public Health ; Oncology ; Prostate cancer</subject><ispartof>Journal of cancer research and clinical oncology, 2023-11, Vol.149 (16), p.15171-15184</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c352t-df7b46700da6c4d3102f8debb6fb91998695f9464edf24f8a40e1b9d07d17dfa3</citedby><cites>FETCH-LOGICAL-c352t-df7b46700da6c4d3102f8debb6fb91998695f9464edf24f8a40e1b9d07d17dfa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00432-023-05308-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00432-023-05308-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids></links><search><creatorcontrib>Rahimi, Mohammad Reza</creatorcontrib><creatorcontrib>Makarem, Dorna</creatorcontrib><creatorcontrib>Sarspy, Sliva</creatorcontrib><creatorcontrib>Mahdavi, Sobhan Akhavan</creatorcontrib><creatorcontrib>Albaghdadi, Mustafa Fahem</creatorcontrib><creatorcontrib>Armaghan, Seyed Mostafa</creatorcontrib><title>Classification of cancer cells and gene selection based on microarray data using MOPSO algorithm</title><title>Journal of cancer research and clinical oncology</title><addtitle>J Cancer Res Clin Oncol</addtitle><description>Purpose
Microarray information is crucial for the identification and categorisation of malignant tissues. The very limited sample size in the microarray has always been a challenge for classification design in cancer research. As a result, by pre-processing gene selection approaches and genes lacking their information, the microarray data are deleted prior to categorisation. In essence, an appropriate gene selection technique can significantly increase the accuracy of illness (cancer) classification.
Methods
For the classification of high-dimensional microarray data, a novel approach based on the hybrid model of multi-objective particle swarm optimisation (MOPSO) is proposed in this research. First, a binary vector representing each particle’s position is presented at random. A gene is represented by each bit. Bit 0 denotes the absence of selection of the characteristic (gene) corresponding to it, while bit 1 denotes the selection of the gene. Therefore, the position of each particle represents a set of genes, and the linear Bayesian discriminant analysis classification algorithm calculates each particle’s degree of fitness to assess the quality of the gene set that particle has chosen. The suggested methodology is applied to four different cancer database sets, and the results are contrasted with those of other approaches currently in use.
Results
The proposed algorithm has been applied on four sets of cancer database and its results have been compared with other existing methods. The results of the implementation show that the improvement of classification accuracy in the proposed algorithm compared to other methods for four sets of databases is 25.84% on average. So that it has improved by 18.63% in the blood cancer database, 24.25% in the lung cancer database, 27.73% in the breast cancer database, and 32.80% in the prostate cancer database. Therefore, the proposed algorithm is able to identify a small set of genes containing information in a way choose to increase the classification accuracy.
Conclusion
Our proposed solution is used for data classification, which also improves classification accuracy. This is possible because the MOPSO model removes redundancy and reduces the number of redundant and redundant genes by considering how genes are correlated with each other.</description><subject>Accuracy</subject><subject>Algorithms</subject><subject>Bayesian analysis</subject><subject>Cancer</subject><subject>Cancer Research</subject><subject>Classification</subject><subject>Discriminant analysis</subject><subject>DNA microarrays</subject><subject>Genes</subject><subject>Hematology</subject><subject>Internal Medicine</subject><subject>Lung cancer</subject><subject>Medical research</subject><subject>Medicine</subject><subject>Medicine & Public Health</subject><subject>Oncology</subject><subject>Prostate cancer</subject><issn>0171-5216</issn><issn>1432-1335</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp9kEtLxDAUhYMoOI7-AVcBN26qN6-mXcrgC5QR1HVM86gd-hiTzmL-vZmpILhwdR9853LPQeicwBUBkNcRgDOaAWUZCAZFJg_QjOxWhDFxiGZAJMkEJfkxOolxBWkWks7Qx6LVMTa-MXpshh4PHhvdGxewcW0bse4trl3vcHStM3uk0tFZnJquMWHQIegttnrUeBObvsbPy5fXJdZtPYRm_OxO0ZHXbXRnP3WO3u9u3xYP2dPy_nFx85QZJuiYWS8rnksAq3PDLSNAfWFdVeW-KklZFnkpfMlz7qyn3BeagyNVaUFaIq3XbI4up7vrMHxtXBxV18SdB927YRMVLUTBQZA8T-jFH3Q1bEKfvktUQQnhhEKi6EQlkzEG59U6NJ0OW0VA7UJXU-gqha72oSuZRGwSxQT3tQu_p_9RfQMkvYSN</recordid><startdate>20231101</startdate><enddate>20231101</enddate><creator>Rahimi, Mohammad Reza</creator><creator>Makarem, Dorna</creator><creator>Sarspy, Sliva</creator><creator>Mahdavi, Sobhan Akhavan</creator><creator>Albaghdadi, Mustafa Fahem</creator><creator>Armaghan, Seyed Mostafa</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TO</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope></search><sort><creationdate>20231101</creationdate><title>Classification of cancer cells and gene selection based on microarray data using MOPSO algorithm</title><author>Rahimi, Mohammad Reza ; Makarem, Dorna ; Sarspy, Sliva ; Mahdavi, Sobhan Akhavan ; Albaghdadi, Mustafa Fahem ; Armaghan, Seyed Mostafa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c352t-df7b46700da6c4d3102f8debb6fb91998695f9464edf24f8a40e1b9d07d17dfa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Accuracy</topic><topic>Algorithms</topic><topic>Bayesian analysis</topic><topic>Cancer</topic><topic>Cancer Research</topic><topic>Classification</topic><topic>Discriminant analysis</topic><topic>DNA microarrays</topic><topic>Genes</topic><topic>Hematology</topic><topic>Internal Medicine</topic><topic>Lung cancer</topic><topic>Medical research</topic><topic>Medicine</topic><topic>Medicine & Public Health</topic><topic>Oncology</topic><topic>Prostate cancer</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rahimi, Mohammad Reza</creatorcontrib><creatorcontrib>Makarem, Dorna</creatorcontrib><creatorcontrib>Sarspy, Sliva</creatorcontrib><creatorcontrib>Mahdavi, Sobhan Akhavan</creatorcontrib><creatorcontrib>Albaghdadi, Mustafa Fahem</creatorcontrib><creatorcontrib>Armaghan, Seyed Mostafa</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Research Library (Corporate)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of cancer research and clinical oncology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rahimi, Mohammad Reza</au><au>Makarem, Dorna</au><au>Sarspy, Sliva</au><au>Mahdavi, Sobhan Akhavan</au><au>Albaghdadi, Mustafa Fahem</au><au>Armaghan, Seyed Mostafa</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Classification of cancer cells and gene selection based on microarray data using MOPSO algorithm</atitle><jtitle>Journal of cancer research and clinical oncology</jtitle><stitle>J Cancer Res Clin Oncol</stitle><date>2023-11-01</date><risdate>2023</risdate><volume>149</volume><issue>16</issue><spage>15171</spage><epage>15184</epage><pages>15171-15184</pages><issn>0171-5216</issn><eissn>1432-1335</eissn><abstract>Purpose
Microarray information is crucial for the identification and categorisation of malignant tissues. The very limited sample size in the microarray has always been a challenge for classification design in cancer research. As a result, by pre-processing gene selection approaches and genes lacking their information, the microarray data are deleted prior to categorisation. In essence, an appropriate gene selection technique can significantly increase the accuracy of illness (cancer) classification.
Methods
For the classification of high-dimensional microarray data, a novel approach based on the hybrid model of multi-objective particle swarm optimisation (MOPSO) is proposed in this research. First, a binary vector representing each particle’s position is presented at random. A gene is represented by each bit. Bit 0 denotes the absence of selection of the characteristic (gene) corresponding to it, while bit 1 denotes the selection of the gene. Therefore, the position of each particle represents a set of genes, and the linear Bayesian discriminant analysis classification algorithm calculates each particle’s degree of fitness to assess the quality of the gene set that particle has chosen. The suggested methodology is applied to four different cancer database sets, and the results are contrasted with those of other approaches currently in use.
Results
The proposed algorithm has been applied on four sets of cancer database and its results have been compared with other existing methods. The results of the implementation show that the improvement of classification accuracy in the proposed algorithm compared to other methods for four sets of databases is 25.84% on average. So that it has improved by 18.63% in the blood cancer database, 24.25% in the lung cancer database, 27.73% in the breast cancer database, and 32.80% in the prostate cancer database. Therefore, the proposed algorithm is able to identify a small set of genes containing information in a way choose to increase the classification accuracy.
Conclusion
Our proposed solution is used for data classification, which also improves classification accuracy. This is possible because the MOPSO model removes redundancy and reduces the number of redundant and redundant genes by considering how genes are correlated with each other.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s00432-023-05308-7</doi><tpages>14</tpages></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0171-5216 |
ispartof | Journal of cancer research and clinical oncology, 2023-11, Vol.149 (16), p.15171-15184 |
issn | 0171-5216 1432-1335 |
language | eng |
recordid | cdi_proquest_miscellaneous_2858405166 |
source | SpringerLink Journals - AutoHoldings |
subjects | Accuracy Algorithms Bayesian analysis Cancer Cancer Research Classification Discriminant analysis DNA microarrays Genes Hematology Internal Medicine Lung cancer Medical research Medicine Medicine & Public Health Oncology Prostate cancer |
title | Classification of cancer cells and gene selection based on microarray data using MOPSO algorithm |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-18T12%3A15%3A01IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Classification%20of%20cancer%20cells%20and%20gene%20selection%20based%20on%20microarray%20data%20using%20MOPSO%20algorithm&rft.jtitle=Journal%20of%20cancer%20research%20and%20clinical%20oncology&rft.au=Rahimi,%20Mohammad%20Reza&rft.date=2023-11-01&rft.volume=149&rft.issue=16&rft.spage=15171&rft.epage=15184&rft.pages=15171-15184&rft.issn=0171-5216&rft.eissn=1432-1335&rft_id=info:doi/10.1007/s00432-023-05308-7&rft_dat=%3Cproquest_cross%3E2858405166%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2882114120&rft_id=info:pmid/&rfr_iscdi=true |