hfooladi / themap

Task Hardness Estimation for Molecular Activity Predcition

THEMAP

Task Hardness Estimation for Molecular Activity Predcition

Installation

THEMAP can be installed pip. First, create a new conda environemnt with the required packages. Then, clone this reposiroty, and finally, install the repository using pip.

conda env create -f environment.yml
conda activate themap
git clone https://github.com/HFooladi/THEMAP.git
cd THEMAP 
pip install -e .

Getting Started

For the FS-Mol dataset, moleuclar embedding for each assay (ChEMBL id) and also, chemical and protein distance have been calculated and deposited in the zenodo.

1. Download it from zenodo
2. Unzip the directory and place it into datasets such that you have the path datasets/fsmol_hardness

Then, you can go to the notebooks folder, and run the notebooks.

Citation

If you find the models useful in your research, we ask that you cite the following paper:

@article{fooladi2024qth,
  author = {Fooladi, Hosein and Hirte, Steffen and Kirchmair, Johannes},
  title={Quantifying the hardness of bioactivity prediction tasks for transfer learning},
  year={2024},
  doi={10.26434/chemrxiv-2024-871mt},
  url={https://chemrxiv.org/engage/chemrxiv/article-details/65b3cafd9138d23161cc5ea4},
  journal={ChemRxiv}
}