AI models are increasingly developed to predict the effect of perturbations on gene expression, but current benchmarks fail to reliably measure model performance. Here, we argue that new benchmarks that directly measure the value of model predictions for specific scientific discovery outcomes are needed to address this gap. We present PerturbHD, an evaluation framework for AI-enabled hit discovery, to demonstrate the benefits our proposed approach.
Coordinated Temporal Dynamics of Glucocorticoid Receptor Binding and Chromatin Landscape Drive Transcriptional Regulation
Glucocorticoid receptor (GR) signaling elicits diverse transcriptional responses through dynamic and context-dependent interactions with chromatin. Here, we define a temporally resolved and mechanistically integrated framework