Fig 9. Cross-validation schemes.

Three cross-validation schemes were tested. (A): standard k-fold stratified cross-validation that ignored the complex structure. (B): block k-fold cross-validation. Overlapping complexes were merged and the resulting complexes were shuffled. The folds were computed as evenly as possible without breaking any complex. (C): representative k-fold cross-validation. Overlapping complexes were merged and the resulting complexes from which unique representatives were chosen uniformly at random. Then a standard k-fold cross-validation was run on the representatives, but excluding the non-representatives from train and validation.