Our models were evaluated through 5-fold cross-validation for models trained under random and kinase-based splits, and 3-fold crossvalidation for those under the family-based split. In each cross-validation cycle, performance metrics were computed on the holdout fold, and results were aggregated across cycles using the mean and the standard deviation to compare model performance. To determine the statistical significance of the results, the statsmodels package was used to run ANOVA for multiple variables and Tukey's HSD tests for post-hoc pairwise comparisons with adjusted pvalues. A result was considered statistically significant if the p-value was less than 0.05. In all other cases, all variables (data split, embedding, trimming, SNA, permutations and permutation phase) were taken into account as stated.