Fast-Adapting Graph Neural Network with Prior Knowledge for Drug Response Prediction Across Preclinical and Clinical Data

Efficient drug response prediction is crucial for reducing drug development costs and time, but current computational models struggle with limited experimental data and out-of-distribution issues between in vitro and in vivo settings. To address this, we introduced drug response prediction meta-learner (metaDRP), a novel few-shot learning model designed to enhance predictive accuracy with limited sample sizes across diverse drug-tissue tasks. metaDRP achieves performance comparable to state-of-the-art models in both genomics of drug sensitivity in cancer (GDSC) drug screening and in vivo datasets, while effectively mitigating out-of-distribution problems, making it reliable for translating findings from controlled environments to clinical applications. Additionally, metaDRP’s inherent interpretability offers reliable insights into drug mechanisms of action, such as elucidating the pathways and molecular targets of drugs like epothilone B and pemetrexed. This work provides a promising approach to overcoming data scarcity and out-of-distribution challenges in drug response prediction, while promoting the integration of few-shot learning in this field.