Fig 1.
Detailed illustration of neighbour connection.
This figure illustrates the Neighbour Connection of node i in a more detailed way. The node i has only one neighbour j. And the figure draws the linear scaling factor from the hidden feature 1 in layer l to the hidden feature 1 in layer l + 1 with respect to the node i and its neighbouring node j.
Fig 2.
The structure of the NCNN model is composed of the neighbour connection layer with a flattening operation and the full connection layer.
Table 1.
MAE comparison between D-GEX and NCNN model in the prediction of GEO data when varying the number of hidden layers and hidden size.
Fig 3.
Density plot of different models with the best structure.
Fig 4.
The comparison of mean average error of predictions on each gene in GEO dataset.
The y value is the mean average error from NCNN model on each target gene; the x value is the mean average error from MLP model on each target gene. Each dot below the diagonal means that NCNN has lower prediction error on this gene than the comparing method.
Fig 5.
The comparison of mean average error of predictions on each gene in GEO dataset.
The y value is the mean average error from NCNN model on each target gene; the x value is the mean average error from GCN model on each target gene. Each dot below the diagonal means that NCNN has lower prediction error on this gene than the comparing method.
Table 2.
The parameter complexity of different models and the number of parameters they actually use.
Table 3.
MAE comparison between D-GEX and NCNN model in the prediction of GTEx data when varying the number of hidden layers and hidden size.
Fig 6.
Density plot of different models with the best structure.
Fig 7.
The comparison of mean average error of predictions on each gene in GTEx dataset.
The y value is the mean average error from NCNN model on each target gene; the x value is the mean average error from MLP model on each target gene. Each dot below the diagonal means that NCNN has lower prediction error on this gene than the comparing method.
Fig 8.
The comparison of mean average error of predictions on each gene in GTEx dataset.
The y value is the mean average error from NCNN model on each target gene; the x value is the mean average error from GCN model on each target gene. Each dot below the diagonal means that NCNN has lower prediction error on this gene than the comparing method.