README.md

DGEM-NN

Disease-drug transcriptomics-based matching with deep learning

For more information see our preprint: https://arxiv.org/abs/2303.11695

Running example

After cloning and pip installing requirements.txt:

• download the trained models and data from here
• unzip and place them in the data folder
• run the code as follows: PYTHONPATH=. python3 dgem_nn/scripts/predict.py --drugs-signatures-dir data/drugs_signatures --diseases-contrasts-dir data/sample_contrasts --model-path trained_models --predictions-dir ps --ensemble

Cite

      title={Transcriptomics-based matching of drugs to diseases with deep learning}, 
      author={Yannis Papanikolaou and Francesco Tuveri and Misa Ogura and Daniel O'Donovan},
      year={2023},
      eprint={2303.11695},
      archivePrefix={arXiv},
      primaryClass={q-bio.GN}
}