Reconstruction of metabolic pathways by the MPI-VGAE framework and applications of MPI-VGAE to KEGG metabolic reactions. Panel A shows the box plot of AUC and AP scores of metabolic pathway reconstruction by the VGAE model. To evaluate the metabolic pathway reconstruction performance of the VGAE model, 402 metabolic pathways from KEGG database were included. Panels B and C show the scatter plot of AUC and AP scores versus the number of MPIs in the metabolic pathway. Panel D shows the confusion matrix on the metabolic reaction network. Panels E and F show ROC and PR curve of metabolic reaction prediction by different machine learning models.