title: Multiclass molecular cancer classification by kernel subspace methods with effective kernel parameter selection.
abstract: Microarray techniques provide new insights into molecular classification of cancer types, which is critical for cancer treatments and diagnosis. Recently, an increasing number of supervised machine learning methods have been applied to cancer classification problems using gene expression data. Support vector machines (SVMs), in particular, have become one of the most effective and leading methods. However, there exist few studies on the application of other kernel methods in the literature. We apply a kernel subspace (KS) method to multiclass cancer classification problems, and assess its validity by comparing it with multiclass SVMs. Our comparative study using seven multiclass cancer datasets demonstrates that the KS method has high performance that is comparable to multiclass SVMs. Furthermore, we propose an effective criterion for kernel parameter selection, which is shown to be useful for the computation of the KS method.
authors.affiliation: Department of Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan. niijima@grt.kyushu-u.ac.jp
authors.forename: Satoshi
authors.initials: S
authors.lastname: Niijima
authors.forename: Satoru
authors.initials: S
authors.lastname: Kuhara
mesh_terms: D001185:Artificial Intelligence; D014408:Biomarkers, Tumor / Q000032:analysis*; D016000:Cluster Analysis; D003936:Diagnosis, Computer-Assisted / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis*; D009369:Neoplasms / Q000145:classification* / Q000175:diagnosis / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins