DrugFormer: Graph‐Enhanced Language Model to Predict Drug Sensitivity

Abstract Drug resistance poses a crucial challenge in healthcare, with response rates to chemotherapy and targeted therapy remaining low. Individual patient's resistance is exacerbated by the intricate heterogeneity of tumor cells, presenting significant obstacles to effective treatment. To address this challenge, DrugFormer, a novel graph‐augmented large language model designed to predict drug resistance at single‐cell level is proposed. DrugFormer integrates both serialized gene tokens and gene‐based knowledge graphs for the accurate predictions of drug response. After training on comprehensive single‐cell data with drug response information, DrugFormer model presents outperformance, with higher F1, precision, and recall in predicting drug response. Based on the scRNA‐seq data from refractory multiple myeloma (MM) and acute myeloid leukemia (AML) patients, DrugFormer demonstrates high efficacy in identifying resistant cells and uncovering underlying molecular mechanisms. Through pseudotime trajectory analysisunique drug‐resistant cellular states associated with poor patient outcomes are revealed. Furthermore, DrugFormer identifies potential therapeutic targets, such as COX8A, for overcoming drug resistance across different cancer types. In conclusion, DrugFormer represents a significant advancement in the field of drug resistance prediction, offering a powerful tool for unraveling the heterogeneity of cellular response to drugs and guiding personalized treatment strategies.