Outputs

The tool creates several files and folders in the specified output directory. Below is the list and description of each output generated by the tool.

Training

  • model_final.pt:

    The trained model.

  • std.txt:

    Standard deviation values for a given training data based on the specified z-score method (‘zscore’ and ‘robustz’).

    GDSC1   0.0     1.0
GDSC2   0.0     1.0
  • training_process.tsv:

    Progress of training in each epoch.

    epoch   train_corr      train_loss      true_auc        pred_auc        val_corr        val_loss        grad_norm       elapsed_time
0       0.0300  40.2999 0.7485  0.0637  nan     5.0000  0.0036  3.5948
1       -0.0034 40.3000 0.7476  0.0652  0.0921  5.0000  0.0253  3.3162
2       0.0722  40.2994 0.7477  0.0750  0.1169  5.0000  0.2334  3.2454
3       0.1603  40.2977 0.7497  0.0976  0.1607  5.0000  0.4573  3.3437

Prediction

  • predict.txt:

    File containing prediction results.

    8.3823e-01
7.6122e-01
7.3318e-01
  • predict_feature_grad_0.txt (predict_feature_grad_1.txt, predict_feature_grad_2.txt):

    Files containing the gradients for each feature.

    -3.5083e-04     -1.5043e-03     1.4109e-02      4.2064e-04      -2.6275e-02 ..
7.7715e-03      -2.1520e-02     -5.5406e-03     -1.3177e-03     -4.9724e-05 ..
9.3111e-03      -2.0868e-02     3.6902e-05      6.6282e-03      -3.1622e-03 ..
  • hidden directory:

    Directory with files containing the gradients of the hidden layer outputs.

  • rlipp.out:

    Output file with interpretation of predictions made by VNN.

    Warning

    The P_rho score is correlation coefficient. Generally 1 (positive values) mean positive correlation, 0 no correlation, and -1 (negative values) negative correlation. However, uf training was not sufficient, the system’s important scores like P_rho can be negative, which not necessarily mean negative correlation, but just the fact that the model has not learned meaningful patters from the data, and the hidden values are mostly random, which can result in arbitrary correlation. Recommended: increase number of epochs for training

    Term    P_rho   P_pval  C_rho   C_pval  RLIPP
0       1.000e+00       0.000e+00       9.951e-01       0.000e+00       1.005e+00
1       7.716e-01       5.312e-67       3.923e-01       1.064e-13       1.967e+00
2       5.519e-01       6.151e-28       4.664e-01       2.182e-19       1.183e+00
3       7.867e-01       2.638e-71       7.438e-01       7.026e-60       1.058e+00
  • gene_rho.out:

    Output file with Spearman correlation between gene embeddings and predicted AUC.

    Gene    Rho     P_val
ABCB1   -1.215e-01      2.667e-02
ABCC3   -9.125e-03      8.682e-01
ABL1    5.741e-02       2.962e-01
ABL2    -5.068e-02      3.565e-01

Annotation

  • hierarchy.cx2:

    File with hierarchy in HCX format annotated with interpretation results that will help determine importance of the subsystems in the hierarchical network.

  • rlipp.out:

    Aggregated interpretation scores of each provided RO-crates with prediction and interpretation results.

    Term    P_rho   P_pval  C_rho   C_pval  RLIPP   Disease
0       1.00000e+00     0.00000e+00     9.95100e-01     0.00000e+00     1.00500e+00     unspecified
1       7.71600e-01     5.31200e-67     3.92300e-01     1.06400e-13     1.96700e+00     unspecified
2       5.51900e-01     6.15100e-28     4.66400e-01     2.18200e-19     1.18300e+00     unspecified

Logs and Metadata

  • output.log:

    A standard log file recording events, errors, and other messages during the execution of the tool.

  • error.log:

    A specialized log file recording only error messages encountered during the execution of the tool.