Reliable single-cell perturbations explain and improve model performance

Abstract

Predicting single-cell transcriptional responses to perturbations is central to building the virtual cell, yet recent benchmarks show that simple baseline methods often outperform complex models, and model comparisons depend on the evaluation metric. Most studies assume that preprocessed RNA sequencing data are reliable ground truth for both training and evaluation. Here, we test this assumption by measuring the reliability of perturbations and their alignment with shared perturbation responses, classifying each perturbation as specific, shared, or unreliable. Among 7,170 perturbations from 29 datasets, 65% are unreliable, 11% shared, and 24% specific. Applying these quality labels to published benchmarks shows that model comparisons depend on perturbation quality. Training with reliable perturbations alone matches or outperforms full-data performance while using 55% of all training perturbations. Our framework also enables prospective experimental design: for most perturbations, a 28-cell pilot experiment accurately predicts how many cells a full screen needs to be reliable.