Modified binary inertial particle swarm optimization for gene selection in DNA microarray data

Carlos Garibay; Gildardo Sanchez-Ante; Luis E. Falcon-Morales; Humberto Sossa

doi:10.1007/978-3-319-19264-2_26

Modified binary inertial particle swarm optimization for gene selection in DNA microarray data

Carlos Garibay, Gildardo Sanchez-Ante, Luis E. Falcon-Morales, Humberto Sossa

Centro de Investigación en Computación (CIC)

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

DNA microarrays are being used to characterize the genetic expression of several illnesses, such as cancer. There has been interest in developing automated methods to classify the data generated by those microarrays. The problem is complex due to the availability of just a few samples to train the classifiers, and the fact that each sample may contain several thousands of features. One possibility is to select a reduced set of features (genes). In this work we propose a wrapper method that is a modified version of the Inertial Geometric Particle Swarm Optimization. We name it MIGPSO.We compare MIGPSO with other approaches. The results are promising. MIGPSO obtained an increase in accuracy of about 4%. The number of genes selected is also competitive.

Original language	English
Title of host publication	Pattern Recognition-7th Mexican Conference, MCPR 2015, Proceedings
Editors	José Arturo Olvera López, Jesús Ariel Carrasco-Ochoa, José Francisco Martínez-Trinidad, Fazel Famili, Juan Humberto Sossa-Azuela
Publisher	Springer Verlag
Pages	271-281
Number of pages	11
ISBN (Electronic)	9783319192635
DOIs	https://doi.org/10.1007/978-3-319-19264-2_26
State	Published - 2015
Event	7th Mexican Conference on Pattern Recognition, MCPR 2015 - Mexico City, Mexico Duration: 24 Jun 2015 → 27 Jun 2015

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9116
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	7th Mexican Conference on Pattern Recognition, MCPR 2015
Country/Territory	Mexico
City	Mexico City
Period	24/06/15 → 27/06/15

Keywords

DNA microarray
Feature selection
PSO
Wrappermethod

Access to Document

10.1007/978-3-319-19264-2_26

Cite this

Garibay, C., Sanchez-Ante, G., Falcon-Morales, L. E., & Sossa, H. (2015). Modified binary inertial particle swarm optimization for gene selection in DNA microarray data. In J. A. Olvera López, J. A. Carrasco-Ochoa, J. F. Martínez-Trinidad, F. Famili, & J. H. Sossa-Azuela (Eds.), Pattern Recognition-7th Mexican Conference, MCPR 2015, Proceedings (pp. 271-281). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9116). Springer Verlag. https://doi.org/10.1007/978-3-319-19264-2_26

Garibay, Carlos ; Sanchez-Ante, Gildardo ; Falcon-Morales, Luis E. et al. / Modified binary inertial particle swarm optimization for gene selection in DNA microarray data. Pattern Recognition-7th Mexican Conference, MCPR 2015, Proceedings. editor / José Arturo Olvera López ; Jesús Ariel Carrasco-Ochoa ; José Francisco Martínez-Trinidad ; Fazel Famili ; Juan Humberto Sossa-Azuela. Springer Verlag, 2015. pp. 271-281 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "DNA microarrays are being used to characterize the genetic expression of several illnesses, such as cancer. There has been interest in developing automated methods to classify the data generated by those microarrays. The problem is complex due to the availability of just a few samples to train the classifiers, and the fact that each sample may contain several thousands of features. One possibility is to select a reduced set of features (genes). In this work we propose a wrapper method that is a modified version of the Inertial Geometric Particle Swarm Optimization. We name it MIGPSO.We compare MIGPSO with other approaches. The results are promising. MIGPSO obtained an increase in accuracy of about 4%. The number of genes selected is also competitive.",

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author = "Carlos Garibay and Gildardo Sanchez-Ante and Falcon-Morales, {Luis E.} and Humberto Sossa",

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Garibay, C, Sanchez-Ante, G, Falcon-Morales, LE & Sossa, H 2015, Modified binary inertial particle swarm optimization for gene selection in DNA microarray data. in JA Olvera López, JA Carrasco-Ochoa, JF Martínez-Trinidad, F Famili & JH Sossa-Azuela (eds), Pattern Recognition-7th Mexican Conference, MCPR 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9116, Springer Verlag, pp. 271-281, 7th Mexican Conference on Pattern Recognition, MCPR 2015, Mexico City, Mexico, 24/06/15. https://doi.org/10.1007/978-3-319-19264-2_26

Modified binary inertial particle swarm optimization for gene selection in DNA microarray data. / Garibay, Carlos; Sanchez-Ante, Gildardo; Falcon-Morales, Luis E. et al.
Pattern Recognition-7th Mexican Conference, MCPR 2015, Proceedings. ed. / José Arturo Olvera López; Jesús Ariel Carrasco-Ochoa; José Francisco Martínez-Trinidad; Fazel Famili; Juan Humberto Sossa-Azuela. Springer Verlag, 2015. p. 271-281 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9116).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Modified binary inertial particle swarm optimization for gene selection in DNA microarray data

AU - Garibay, Carlos

AU - Sanchez-Ante, Gildardo

AU - Falcon-Morales, Luis E.

AU - Sossa, Humberto

N1 - Publisher Copyright: © Springer International Publishing Switzerland 2015.

PY - 2015

Y1 - 2015

N2 - DNA microarrays are being used to characterize the genetic expression of several illnesses, such as cancer. There has been interest in developing automated methods to classify the data generated by those microarrays. The problem is complex due to the availability of just a few samples to train the classifiers, and the fact that each sample may contain several thousands of features. One possibility is to select a reduced set of features (genes). In this work we propose a wrapper method that is a modified version of the Inertial Geometric Particle Swarm Optimization. We name it MIGPSO.We compare MIGPSO with other approaches. The results are promising. MIGPSO obtained an increase in accuracy of about 4%. The number of genes selected is also competitive.

AB - DNA microarrays are being used to characterize the genetic expression of several illnesses, such as cancer. There has been interest in developing automated methods to classify the data generated by those microarrays. The problem is complex due to the availability of just a few samples to train the classifiers, and the fact that each sample may contain several thousands of features. One possibility is to select a reduced set of features (genes). In this work we propose a wrapper method that is a modified version of the Inertial Geometric Particle Swarm Optimization. We name it MIGPSO.We compare MIGPSO with other approaches. The results are promising. MIGPSO obtained an increase in accuracy of about 4%. The number of genes selected is also competitive.

KW - DNA microarray

KW - Feature selection

KW - PSO

KW - Wrappermethod

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DO - 10.1007/978-3-319-19264-2_26

M3 - Contribución a la conferencia

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 271

EP - 281

BT - Pattern Recognition-7th Mexican Conference, MCPR 2015, Proceedings

A2 - Olvera López, José Arturo

A2 - Carrasco-Ochoa, Jesús Ariel

A2 - Martínez-Trinidad, José Francisco

A2 - Famili, Fazel

A2 - Sossa-Azuela, Juan Humberto

PB - Springer Verlag

T2 - 7th Mexican Conference on Pattern Recognition, MCPR 2015

Y2 - 24 June 2015 through 27 June 2015

ER -

Garibay C, Sanchez-Ante G, Falcon-Morales LE, Sossa H. Modified binary inertial particle swarm optimization for gene selection in DNA microarray data. In Olvera López JA, Carrasco-Ochoa JA, Martínez-Trinidad JF, Famili F, Sossa-Azuela JH, editors, Pattern Recognition-7th Mexican Conference, MCPR 2015, Proceedings. Springer Verlag. 2015. p. 271-281. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-19264-2_26

Modified binary inertial particle swarm optimization for gene selection in DNA microarray data

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