Robust Selection of Predictive Genes via a Simple Classifier.
Identifying genes that direct the mechanism of a disease from expression data is extremely useful in understanding how that mechanism works. This in turn may lead to better diagnoses and potentially could lead to a cure for that disease. This task becomes extremely challenging when the data are characterised by only a small number of samples and a high number of dimensions, as is often the case with gene expression data. Motivated by this challenge, we present a general framework that focuses on simplicity and data perturbation. These are the keys for robust identification of the most predictive features in such data. Within this framework, we propose a simple selective naive Bayes classifier discovered using a global search technique, and combine it with data perturbation to increase its robustness for small sample sizes. An extensive validation of the method was carried out using two applied datasets from the field of microarrays and a simulated dataset, all confounded by small sample sizes and high dimensionality. The method has been shown to be capable of selecting genes known to be associated with prostate cancer and viral infections.
Vinciotti
Veronica
V
School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, UK. veronica.vinciotti@brunel.ac.uk
Tucker
Allan
A
Kellam
Paul
P
Liu
Xiaohui
X
D001185:Artificial Intelligence; D014408:Biomarkers, Tumor / Q000032:analysis*; D003936:Diagnosis, Computer-Assisted / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis*; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D014408:Biomarkers, Tumor; D005819:Genetic Markers; D009363:Neoplasm Proteins