A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways

Muhammad Faiz Misman; Weng Howe Chan; Mohd Saberi Mohamad; Safaai Deris

doi:10.1007/978-3-642-40319-4_23

A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways

Muhammad Faiz Misman
, Weng Howe Chan
, Mohd Saberi Mohamad
, Safaai Deris

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

1 Citation (Scopus)

Abstract

Advancements in pathway-based microarray classification approach leads to a new era of genomic research. However, it is limited by issues regarding the quality of the pathway data as these data are usually curated from biological literatures and in specific biological experiment (e.g. lung cancer experiment), context free pathway information collection process lead to the presence of uninformative genes in the pathways. Many methods in this approach neglect these limitations by treating all genes in a pathway as significant. In this paper, we propose a hybrid of support vector machine and smoothly clipped absolute deviation with group-specific tuning parameters (gSVM-SCAD) to select informative genes within pathways before the pathway evaluation process. Experiments conducted on gender and lung cancer datasets shows that gSVM-SCAD obtains significant results in identifying significant genes and pathways, and in classification accuracy.

Original language	English
Title of host publication	Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops
Subtitle of host publication	DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers
Pages	258-269
Number of pages	12
DOIs	https://doi.org/10.1007/978-3-642-40319-4_23
Publication status	Published - 2013
Externally published	Yes
Event	17th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2013 - Gold Coast, QLD, Australia Duration: Apr 14 2013 → Apr 17 2013

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	7867 LNAI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	17th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2013
Country/Territory	Australia
City	Gold Coast, QLD
Period	4/14/13 → 4/17/13

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Gene selection
Pathway analysis
Smoothly clipped absolute deviation
Support vector machines

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-40319-4_23

Cite this

Misman, M. F., Chan, W. H., Mohamad, M. S., & Deris, S. (2013). A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways. In Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers (pp. 258-269). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7867 LNAI). https://doi.org/10.1007/978-3-642-40319-4_23

A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways. / Misman, Muhammad Faiz; Chan, Weng Howe; Mohamad, Mohd Saberi et al.
Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. 2013. p. 258-269 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7867 LNAI).

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

Misman, MF, Chan, WH, Mohamad, MS & Deris, S 2013, A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways. in Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7867 LNAI, pp. 258-269, 17th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2013, Gold Coast, QLD, Australia, 4/14/13. https://doi.org/10.1007/978-3-642-40319-4_23

Misman MF, Chan WH, Mohamad MS, Deris S. A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways. In Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. 2013. p. 258-269. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-40319-4_23

Misman, Muhammad Faiz ; Chan, Weng Howe ; Mohamad, Mohd Saberi et al. / A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways. Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. 2013. pp. 258-269 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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ER -

A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways

Abstract

Publication series

Conference

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this