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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| Format: | Article |
| Language: | English |
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Inderscience Enterprises Ltd.
2016
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| Online Access: | http://umpir.ump.edu.my/id/eprint/13631/1/An%20Improved%20gSVM-SCADL2%20with%20Firefly%20Algorithm%20for%20Identification%20of%20Informative%20Genes%20and%20Pathways.pdf |
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| 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 |
| collection | UMP |
| 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. |
| first_indexed | 2024-03-06T12:05:09Z |
| format | Article |
| id | UMPir13631 |
| institution | Universiti Malaysia Pahang |
| language | English |
| last_indexed | 2024-03-06T12:05:09Z |
| publishDate | 2016 |
| publisher | Inderscience Enterprises Ltd. |
| record_format | dspace |
| spelling | UMPir136312017-08-22T07:12:02Z 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). (Published) http://www.inderscienceonline.com/doi/pdf/10.1504/IJBRA.2016.075404#d1429e145 DOI: 10.1504/IJBRA.2016.075404 |
| 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 |
| title | 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_short | 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 |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | http://umpir.ump.edu.my/id/eprint/13631/1/An%20Improved%20gSVM-SCADL2%20with%20Firefly%20Algorithm%20for%20Identification%20of%20Informative%20Genes%20and%20Pathways.pdf |
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