Halimah A. Agbaje

Protein-novelty, sequence-similarity, and negative-sampling controls reveal benchmark-specific discrimination in protein–protein interaction prediction

Protein–protein interaction (PPI) predictors are often evaluated with random pair splits that permit proteins to recur across training and test sets, while constructed negative pairs can introduce a separate source of benchmark-specific signal. We reassessed the Guo yeast benchmark using a matched protein-novelty curve...