Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
Abstract
Genetic perturbation response prediction plays a critical role in virtual cell research, yet the performance of current deep learning models still leaves room for improvement. In this study, we present a prior-guided response inference model (PRIM) that leverages a valuable priori knowledge of gene expression in control cells to model the effects of perturbations at the cellular level. This allows PRIM to predict the amount of change in gene expression after perturbation to better approximate the real situation. Compared with existing deep learning approaches, PRIM achieves superior performance across multiple datasets and notable advantages in predicting combinatorial perturbation responses. Moreover, it is more lightweight than current deep learning models and enables faster forward inference. Importantly, PRIM effectively captures nonadditive genetic interactions and shows the potential to uncover associations between combinatorial perturbations and new biologically meaningful phenotypes. These findings provide new insights into the application of deep learning for predicting cellular responses to genetic perturbations.
- Received October 3, 2025.
- Accepted March 19, 2026.
- Published by Cold Spring Harbor Laboratory Press
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