Motivation Deep neural network (DNN) algorithms were utilized in predicting various biomedical phenotypes recently, and demonstrated very good prediction performances without selecting features. This study proposed a hypothesis that the DNN models may be further improved by feature selection algorithms. Results A comprehensive comparative study was carried out by evaluating 11 feature selection algorithms on three conventional DNN algorithms, i.e. convolution neural network (CNN), deep belief network (DBN) and recurrent neural network (RNN), and three recent DNNs, i.e. MobilenetV2, ShufflenetV2 and Squeezenet. Five binary classification methylomic datasets were chosen to calculate the prediction performances of CNN/DBN/RNN models using feature selected by the 11 feature selection algorithms. Seventeen binary classification transcriptome and two multi-class transcriptome datasets were also utilized to evaluate how the hypothesis may generalize to different data types. The experimental data supported our hypothesis that feature selection algorithms may improve DNN models, and the DBN models using features selected by SVM-RFE usually achieved the best prediction accuracies on the five methylomic datasets. Availability and implementation All the algorithms were implemented and tested under the programming environment Python version 3.6.6. Supplementary information Supplementary data are available at Bioinformatics online.

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Different kernels cause various class discriminations owing to their different geometrical structures of the data in the feature space. In this paper, a method of kernel optimization by maximizing a measure of class separability in the empirical feature space with sparse representation-based classifier (SRC) is proposed to solve the problem of automatically choosing kernel functions and their parameters in kernel learning. The proposed method first adopts a so-called data-dependent kernel to generate an efficient kernel optimization algorithm. Then, a constrained optimization function using general gradient descent method is created to find combination coefficients varied with the input data. After that, optimized kernel PCA (KOPCA) is obtained via combination coefficients to extract features. Finally, the sparse representation-based classifier is used to perform pattern classification task. Experimental results on MSTAR SAR images show the effectiveness of the proposed method.