Fig. 1: Schematic overview of the mAP framework.

A A typical output of a profiling experiment contains multiple replicate profiles for each perturbation and controls. B To measure average precision (AP) per perturbation replicate, we selected one replicate profile as a query and measured distances to its other replicates and controls. C Profiles were then ranked by decreasing similarity (increasing distance) to the query; the rank list was converted to binary form and used to calculate precision P_k and recall R_k at each rank k. D Average precision was calculated by averaging precision values over those ranks k containing perturbation replicates, which corresponds to a non-interpolated approximation of the area under the precision-recall curve. E By applying this procedure to each perturbation replicate, we calculated a set of AP scores that were then averaged to obtain a mAP score for a perturbation’s phenotypic activity. F One can also apply the same framework to retrieving groups of perturbations with the same biological annotations (rather than groups of replicates of the same perturbation)—for example, compounds that share the same mechanism of action (MoA)—by calculating the mAP score per each group of perturbations (MoA). Source data are provided as a Source Data file.