Optimal Transport Based Graph Kernels for Drug Property Prediction (OTGK_DP)

This is the complete code for the OTGK_DP framework to predict ADMET durg properties. The work is pubished in the following papers:
(Paper)

@INPROCEEDINGS{10504311,
  author={Aburidi, Mohammed and Marcia, Roummel},
  booktitle={2024 IEEE First International Conference on Artificial Intelligence for Medicine, Health and Care (AIMHC)}, 
  title={Wasserstein Distance-Based Graph Kernel for Enhancing Drug Safety and Efficacy Prediction *}, 
  year={2024},
  volume={},
  number={},
  pages={113-119},
  keywords={Drugs;Proteins;Adaptation models;Toxicology;Pharmacodynamics;Predictive models;Safety;Optimal Transport;Wasserstein Distance;Graph Matching;Drug Discovery;ADMET Properties},
  doi={10.1109/AIMHC59811.2024.00029}}

Comments/Bugs/Problems: maburidi@ucmerced.edu maburidi@gmail.com

December, 2023. Initial release

Find the Colab tutorial in the tutorial folder to run this repository and to predict the drug properties.
The data used in this project is Therapeutics Data Commons - TDC)
To list all of the datasets in AMDE, run the following

from tdc import utils
utils.retrieve_dataset_names('ADME')

To list all of the datasets in TOX, run the following

from tdc import utils
utils.retrieve_dataset_names('TOX')

Make sure to install the following dependincies:

PyTDC
rdkit
torch_geometric
POT
py3Dmol

Main Results:

Cite as:

@inproceedings{aburidi2024_1,
   author = {M. Aburidi and R. Marica},
   journal = {Scientific Reports},
   title = {Optimal Transport-Based Graph Kernels for Drug Property Prediction},
   url = {},
   year = {2024},
}

@INPROCEEDINGS{10504311,
  author={Aburidi, Mohammed and Marcia, Roummel},
  booktitle={2024 IEEE First International Conference on Artificial Intelligence for Medicine, Health and Care (AIMHC)}, 
  title={Wasserstein Distance-Based Graph Kernel for Enhancing Drug Safety and Efficacy Prediction}, 
  year={2024},
  volume={},
  number={},
  pages={113-119},
  keywords={Drugs;Proteins;Adaptation models;Toxicology;Pharmacodynamics;Predictive models;Safety;Optimal Transport;Wasserstein Distance;Graph Matching;Drug Discovery;ADMET Properties},
  doi={10.1109/AIMHC59811.2024.00029}}