Biomarkers identification for Schizophrenia via VAE and GSDAE-based data augmentation.

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Abstract

Deep learning has made great progress in analyzing MRI data, while the MRI data with high dimensional but small sample size (HDSSS) brings many limitations to biomarkers identification. Few-shot learning has been proposed to solve such problems and data augmentation is a typical method of it. The variational auto-encoder (VAE) is a generative method based on variational Bayesian inference that is used for data augmentation. Graph regularized sparse deep autoencoder (GSDAE) can reconstruct sparse samples and keep the manifold structure of data which will facilitate biomarkers selection greatly. To generate better HDSSS data for biomarkers identification, a data augmentation method based on VAE and GSDAE is proposed in this paper, termed GS-VDAE. Instead of utilizing the final products of GSDAE, our proposed model embeds the generation procedure into GSDAE for augmentation. In this way, the augmented samples will be rooted in the significant features extracted from the original samples, which can ensure the newly formed samples contain the most significant characteristics of the original samples. The classification accuracy of the samples generated directly from VAE is 0.74, while the classification accuracy of the samples generated from GS-VDAE is 0.84, which proves the validity of our model. Additionally, a regression feature selection method with truncated nuclear norm regularization is chosen for biomarkers selection. The biomarkers selection results of schizophrenia data reveal that the augmented samples obtained by our proposed method can get higher classification accuracy with less ranked features compared with original samples, which proves the validation of our model.Copyright © 2022 Elsevier Ltd. All rights reserved.