DEEP is a hierarchical phenotype-driven deep learning framework for drug clinical efficacy prediction.This accession contains a stable, frozen release DEEP's source code, along with data and model checkpoints to reproduce the major results in the paper 'Hierarchical phenotype-driven deep learning for end-to-end drug discovery'. The most up-to-date version can be accessed on github at: https://github.com/yangkaiyuan1027/DEEP .