Optimal fusion of genotype and drug embeddings in predicting cancer drug response

Abstract

Predicting cancer drug response using both genomics and drug features has shown some success compared to using genomics features alone. However, there has been limited research done on how best to combine or fuse the two types of features. Using a visible neural network with two deep learning branches for genes and drug features as the base architecture, we experimented with different fusion functions and fusion points. Our experiments show that injecting multiplicative relationships between gene and drug latent features into the original concatenation-based architecture DrugCell significantly improved the overall predictive performance and outperformed other baseline models. We also show that different fusion methods respond differently to different fusion points, indicating that the relationship between drug features and different hierarchical biological level of gene features is optimally captured using different methods. Considering both predictive performance and runtime speed, tensor product partial is the best-performing fusion function to combine late-stage representations of drug and gene features to predict cancer drug response.