An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification

BACKGROUND:Bacterial 16S Ribosomal RNAs profiling have been widely used in the classification of microbiota associated diseases. Dimensionality reduction is among the keys in mining high-dimensional 16S rRNAs' expression data. High levels of sparsity and redundancy are common in 16S rRNA gene microbial surveys. Traditional feature selection methods are generally restricted to measuring correlated abundances, and are limited in discrimination when so few microbes are actually shared across communities.RESULTS:Here we present a Feature Merging and Selection algorithm (FMS) to deal with 16S rRNAs' expression data. By integrating Linear Discriminant Analysis method, FMS can reduce the feature dimension with higher accuracy and preserve the relationship between different features as well. Two 16S rRNAs' expression datasets of pneumonia and dental decay patients were used to test the validity of the algorithm. Combined with SVM, FMS discriminated different classes of both pneumonia and dental caries better than other popular feature selection methods.CONCLUSIONS:FMS projects data into lower dimension with preservation of enough features, and thus improve the intelligibility of the result. The results showed that FMS is a more valid and reliable methods in feature reduction.