An integrated feature selection and classification method to select minimum number of variables on the case study of gene expression data.
This paper introduces a novel generic approach for classification problems with the objective of achieving maximum classification accuracy with minimum number of features selected. The method is illustrated with several case studies of gene expression data. Our approach integrates filter and wrapper gene selection methods with an added objective of selecting a small set of non-redundant genes that are most relevant for classification with the provision of bins for genes to be swapped in the search for their biological relevance. It is capable of selecting relatively few marker genes while giving comparable or better leave-one-out cross-validation accuracy when compared with gene ranking selection approaches. Additionally, gene profiles can be extracted from the evolving connectionist system, which provides a set of rules that can be further developed into expert systems. The approach uses an integration of Pearson correlation coefficient and signal-to-noise ratio methods with an adaptive evolving classifier applied through the leave-one-out method for validation. Datasets of gene expression from four case studies are used to illustrate the method. The results show the proposed approach leads to an improved feature selection process in terms of reducing the number of variables required and an increased in classification accuracy.
Goh
Liang
L
Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, New Zealand. liang.goh@aut.ac.nz
Kasabov
Nikola
N
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; D018511:Systems Integration
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins