Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction

Abstract Summary Drug response is conventionally measured at the cell level, often quantified by metrics like IC50. However, to gain a deeper understanding of drug response, cellular outcomes need to be understood in terms of pathway perturbation. This perspective leads us to recognize a challenge posed by the gap between two widely used large-scale databases, LINCS L1000 and GDSC, measuring drug response at different levels—L1000 captures information at the gene expression level, while GDSC operates at the cell line level. Our study aims to bridge this gap by integrating the two databases through transfer learning, focusing on condition-specific perturbations in gene interactions from L1000 to interpret drug response integrating both gene and cell levels in GDSC. This transfer learning strategy involves pretraining on the transcriptomic-level L1000 dataset, with parameter-frozen fine-tuning to cell line-level drug response. Our novel condition-specific gene–gene attention (CSG2A) mechanism dynamically learns gene interactions specific to input conditions, guided by both data and biological network priors. The CSG2A network, equipped with transfer learning strategy, achieves state-of-the-art performance in cell line-level drug response prediction. In two case studies, well-known mechanisms of drugs are well represented in both the learned gene–gene attention and the predicted transcriptomic profiles. This alignment supports the modeling power in terms of interpretability and biological relevance. Furthermore, our model’s unique capacity to capture drug response in terms of both pathway perturbation and cell viability extends predictions to the patient level using TCGA data, demonstrating its expressive power obtained from both gene and cell levels. Availability and implementation The source code for the CSG2A network is available at https://github.com/eugenebang/CSG2A.