DeepDR: a deep learning library for drug response prediction

SUMMARY: Accurate drug response prediction is critical to advancing precision medicine and drug discovery. Recent advances in deep learning (DL) have shown promise in predicting drug response; however, the lack of convenient tools to support such modeling limits their widespread application. To address this, we introduce DeepDR, the first DL library specifically developed for drug response prediction. DeepDR simplifies the process by automating drug and cell featurization, model construction, training, and inference, all achievable with brief programming. The library incorporates three types of drug features along with nine drug encoders, four types of cell features along with nine cell encoders, and two fusion modules, enabling the implementation of up to 135 DL models for drug response prediction. We also explored benchmarking performance with DeepDR, and the optimal models are available on a user-friendly visual interface. AVAILABILITY AND IMPLEMENTATION: DeepDR can be installed from PyPI (https://pypi.org/project/deepdr). The source code and experimental data are available on GitHub (https://github.com/user15632/DeepDR).