An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways

Incorporation of pathway knowledge into microarray analysis has been favoured by researchers owing to the improved biological interpretation of the analysis outcome. However, most of the pathway data are manually curated without specific biological context. Inclusion of non-informative genes in the...

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Main Authors:	Chan, Weng Howe, Mohd Saberi , Mohamad, Safaai , Deris, Corchado, Juan Manuel, Omatu, Sigeru, Zuwairie, Ibrahim, Shahreen, Kasim
Format:	Article
Language:	English
Published:	Inderscience Enterprises Ltd. 2016
Subjects:	TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://umpir.ump.edu.my/id/eprint/13631/ http://umpir.ump.edu.my/id/eprint/13631/ http://umpir.ump.edu.my/id/eprint/13631/ http://umpir.ump.edu.my/id/eprint/13631/1/An%20Improved%20gSVM-SCADL2%20with%20Firefly%20Algorithm%20for%20Identification%20of%20Informative%20Genes%20and%20Pathways.pdf

id	ump-13631
recordtype	eprints
spelling	ump-136312017-08-22T07:12:02Z http://umpir.ump.edu.my/id/eprint/13631/ An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways Chan, Weng Howe Mohd Saberi , Mohamad Safaai , Deris Corchado, Juan Manuel Omatu, Sigeru Zuwairie, Ibrahim Shahreen, Kasim TK Electrical engineering. Electronics Nuclear engineering Incorporation of pathway knowledge into microarray analysis has been favoured by researchers owing to the improved biological interpretation of the analysis outcome. However, most of the pathway data are manually curated without specific biological context. Inclusion of non-informative genes in the analysis of context specific microarray data could lead to classifier with poor discriminative power. Thus, one of the main challenges is how to effectively identify informative genes from the pathway data. This paper proposes a firefly optimised penalised support vector machine with SCADL2 penalty function (SVM-SCADL2-FFA) in optimising tuning parameters for each pathway for efficient identification of informative genes and pathways. Experiments are done on lung cancer and gender data sets. Tenfold CV is used to evaluate the performance in terms of accuracy, specificity, sensitivity and F-score. The identified informative genes are validated through online databases. Our proposed method shows consistent improvements compared to previous works. Inderscience Enterprises Ltd. 2016 Article PeerReviewed application/pdf en http://umpir.ump.edu.my/id/eprint/13631/1/An%20Improved%20gSVM-SCADL2%20with%20Firefly%20Algorithm%20for%20Identification%20of%20Informative%20Genes%20and%20Pathways.pdf Chan, Weng Howe and Mohd Saberi , Mohamad and Safaai , Deris and Corchado, Juan Manuel and Omatu, Sigeru and Zuwairie, Ibrahim and Shahreen, Kasim (2016) An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways. International Journal of Bioinformatics Research and Applications, 12 (1). http://www.inderscienceonline.com/doi/pdf/10.1504/IJBRA.2016.075404#d1429e145 DOI: 10.1504/IJBRA.2016.075404
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Malaysia Pahang
building	UMP Institutional Repository
collection	Online Access
language	English
topic	TK Electrical engineering. Electronics Nuclear engineering
spellingShingle	TK Electrical engineering. Electronics Nuclear engineering Chan, Weng Howe Mohd Saberi , Mohamad Safaai , Deris Corchado, Juan Manuel Omatu, Sigeru Zuwairie, Ibrahim Shahreen, Kasim An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways
description	Incorporation of pathway knowledge into microarray analysis has been favoured by researchers owing to the improved biological interpretation of the analysis outcome. However, most of the pathway data are manually curated without specific biological context. Inclusion of non-informative genes in the analysis of context specific microarray data could lead to classifier with poor discriminative power. Thus, one of the main challenges is how to effectively identify informative genes from the pathway data. This paper proposes a firefly optimised penalised support vector machine with SCADL2 penalty function (SVM-SCADL2-FFA) in optimising tuning parameters for each pathway for efficient identification of informative genes and pathways. Experiments are done on lung cancer and gender data sets. Tenfold CV is used to evaluate the performance in terms of accuracy, specificity, sensitivity and F-score. The identified informative genes are validated through online databases. Our proposed method shows consistent improvements compared to previous works.
format	Article
author	Chan, Weng Howe Mohd Saberi , Mohamad Safaai , Deris Corchado, Juan Manuel Omatu, Sigeru Zuwairie, Ibrahim Shahreen, Kasim
author_facet	Chan, Weng Howe Mohd Saberi , Mohamad Safaai , Deris Corchado, Juan Manuel Omatu, Sigeru Zuwairie, Ibrahim Shahreen, Kasim
author_sort	Chan, Weng Howe
title	An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways
title_short	An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways
title_full	An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways
title_fullStr	An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways
title_full_unstemmed	An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways
title_sort	improved gsvm-scadl2 with firefly algorithm for identification of informative genes and pathways
publisher	Inderscience Enterprises Ltd.
publishDate	2016
url	http://umpir.ump.edu.my/id/eprint/13631/ http://umpir.ump.edu.my/id/eprint/13631/ http://umpir.ump.edu.my/id/eprint/13631/ http://umpir.ump.edu.my/id/eprint/13631/1/An%20Improved%20gSVM-SCADL2%20with%20Firefly%20Algorithm%20for%20Identification%20of%20Informative%20Genes%20and%20Pathways.pdf
first_indexed	2023-09-18T22:16:28Z
last_indexed	2023-09-18T22:16:28Z
_version_	1777415370606379008

An Improved gSVM-SCADL2 with Firefly Algorithm for Identification of Informative Genes and Pathways

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