A feature selection method based on multiple kernel learning with expression profiles of different types

BACKGROUND: With the development of high-throughput technology, the researchers can acquire large number of expression data with different types from several public databases. Because most of these data have small number of samples and hundreds or thousands features, how to extract informative features from expression data effectively and robustly using feature selection technique is challenging and crucial. So far, a mass of many feature selection approaches have been proposed and applied to analyse expression data of different types. However, most of these methods only are limited to measure the performances on one single type of expression data by accuracy or error rate of classification. RESULTS: In this article, we propose a hybrid feature selection method based on Multiple Kernel Learning (MKL) and evaluate the performance on expression datasets of different types. Firstly, the relevance between features and classifying samples is measured by using the optimizing function of MKL. In this step, an iterative gradient descent process is used to perform the optimization both on the parameters of Support Vector Machine (SVM) and kernel confidence. Then, a set of relevant features is selected by sorting the optimizing function of each feature. Furthermore, we apply an embedded scheme of forward selection to detect the compact feature subsets from the relevant feature set. CONCLUSIONS: We not only compare the classification accuracy with other methods, but also compare the stability, similarity and consistency of different algorithms. The proposed method has a satisfactory capability of feature selection for analysing expression datasets of different types using different performance measurements. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13040-017-0124-x) contains supplementary material, which is available to authorized users.