Fig. 2. Deep autoencoder (deepAE) outperformed shallow autoencoder (shallowAE) up to 512 hidden nodes in terms of accuracy.

1 − coefficient of determination (R²), in training and validation set using the full data set variance (a) and the gene-wise variances (b, c). The left panel shows the mean behavior of R² values on the full data set. The distribution of R² values across each gene is shown for both models, shallowAE (b), and three-layer deepAE (c), with increase in the number of hidden nodes in each layer from 64 to 1024.