TY - GEN
T1 - A hybrid of SVM and SCAD with group-specific tuning parameters in identification of informative genes and biological pathways
AU - Misman, Muhammad Faiz
AU - Chan, Weng Howe
AU - Mohamad, Mohd Saberi
AU - Deris, Safaai
PY - 2013
Y1 - 2013
N2 - 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.
AB - 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.
KW - Gene selection
KW - Pathway analysis
KW - Smoothly clipped absolute deviation
KW - Support vector machines
UR - https://www.scopus.com/pages/publications/84892874095
UR - https://www.scopus.com/inward/citedby.url?scp=84892874095&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-40319-4_23
DO - 10.1007/978-3-642-40319-4_23
M3 - Conference contribution
AN - SCOPUS:84892874095
SN - 9783642403187
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 258
EP - 269
BT - Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops
T2 - 17th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2013
Y2 - 14 April 2013 through 17 April 2013
ER -
