Quick Start

Follow these steps to get started with OpenDDI:

Step 1: Clone the Repository

git clone <REPO-URL>
cd OpenDDI

Step 2: Install Dependencies

General Dependencies

You can install the general dependencies:

conda env create -f openddi.yml
pip install torch-scatter==2.0.7 torch-sparse==0.6.9 -f https://data.pyg.org/whl/torch-1.7.0+cu110.html

Step 3: Run the Main Script

After installing the dependencies, you can run the main script using the following command:

python openddi/main.py --model <model_name> --matrix <matrix_name> --modality <modality_name> --epochs <epochs> --batch <batch>

Optional arguments:

  • --model <model_name>: Model choice, e.g., MRCGNN, GOGNN, ZeroDDI, TIGER, MVA, MUFFIN, CASTER, MMDGDTI, MKGFENN, etc.

  • --matrix <matrix_name>: Interaction matrix, e.g., binary, ChCh-Miner, Ryus, Dengs, zeroddi, multilabel, twosides, etc.

  • --modality<modality_name>: Modality types, e.g., smiles, sequence, 3d, mechanism, text, drkg, etc. (can specify multiple)

  • --epochs <epochs>: Number of epochs to run.

  • --batch <batch>: The batch size to use.

Note that the above list includes only a subset of the available parameters. For a complete list of parameters and their descriptions, see the Parameters section.

Example Command:

To run the MRCGNN model on the Ryus DDI dataset with smiles sequence 3d mechanism text modalities, you can run the following command:

python openddi/main.py --model MRCGNN --matrix Ryus --modality smiles sequence 3d mechanism text --epochs 100 --batch 4096

This command will:

  • Use the MRCGNN model

  • Use the Ryus dataset

  • Use the smiles sequence 3d mechanism text modalities

  • Train for 100 epochs with a batch size of 4096