Authors: Behrooz Azarkhalili, Ali Saberi, Hamidreza Chitsaz, Ali Sharifi-Zarchi
All codes for obtaining and pre-processing data are provided in PreProcess folder. These are custom R scripts for downloading mRNA and miRNA expression profiles from The Cancer Genome Atlas (TCGA) from Genomic Data Commons (http://gdc.cancer.gov).
All codes for hyper-parameter optimization and training different deep neural network architectures (Variational AutoEncoder, Contractive AutoEncoder, Dropout Variational AutoEncoder and Variational Contractive AutoEncoder) are provided in DeepLearning folder.
Deep neural networks are developed using Keras python package and TensorFlow backend.