# Delta Gap

On 509 unseen perturbations from the Replogle K562 screen, GEARS reaches a global Pearson correlation of 0.977 between predicted and observed transcriptomes, but only 0.076 once the control baseline is subtracted and the perturbation-induced delta is scored; a trivial baseline that predicts the same mean training delta for every perturbation reaches 0.267. The gap arises because global correlation is dominated by thousands of non-responsive genes, so delta-space evaluation is proposed as the primary benchmark, together with two post-hoc corrections that need no retraining and a retrieval upper bound that localizes the residual.

On 509 unseen perturbations from the Replogle K562 screen, GEARS reaches a global Pearson correlation of 0.977 between predicted and observed transcriptomes, but only 0.076 once the control baseline is subtracted and the perturbation-induced delta is scored; a trivial baseline that predicts the same mean training delta for every perturbation reaches 0.267. The gap arises because global correlation is dominated by thousands of non-responsive genes, so delta-space evaluation is proposed as the primary benchmark, together with two post-hoc corrections that need no retraining and a retrieval upper bound that localizes the residual.