OpenDDI Documentation
=====================

Welcome to the **OpenDDI** documentation! OpenDDI is an open-source unified benchmarking framework designed for **Drug-Drug Interaction (DDI)** prediction. Published at ICML 2026, OpenDDI provides a comprehensive platform for evaluating and developing DDI prediction methodologies with standardized datasets, state-of-the-art models, and versatile evaluation tools.

Introduction
------------

**OpenDDI** is a unified benchmarking framework that integrates 20 state-of-the-art DDI prediction algorithms and supports 9 standardized datasets. The framework addresses the unique challenges of multimodal drug interaction data by providing comprehensive evaluation from five dimensions: data quality, effectiveness, generalization, efficiency, and robustness.

**Dataset Sources:**

OpenDDI integrates data from 12 authoritative biomedical data sources:

- DrugBank (Wishart et al., 2018)
- ChEMBL (Mendez et al., 2018)
- BindingDB (Liu et al., 2007)
- KEGG (Kanehisa et al., 2016)
- BIOSNAP DDI dataset
- Davis dataset
- DRKG (Drug Repurposing Knowledge Graph)
- MEDLINE
- OFFSIDES
- PharmGKB (Hewett et al., 2002)
- PubChem (Kim et al., 2016)
- TWOSIDES (Tatonetti et al., 2012)

Key Features
~~~~~~~~~~~~

- **Dataset Integration & Extension**: Unifies 6 existing datasets and introduces 3 new large-scale LLM-enhanced datasets, totaling 5.3 million DDIs across 34,000 drugs
- **Multimodal Drug Representation**: Integrates 5 biomedical modalities (SMILES, path/drug-mechanism network, 3D conformations, amino acid sequences, text descriptions)
- **Algorithm Benchmark**: Integrates 20 state-of-the-art algorithms supporting 3 downstream tasks (binary classification, multi-class classification, multi-label classification)
- **Standardized Evaluation**: Comprehensive evaluation from 5 dimensions (data quality, effectiveness, generalization, efficiency, robustness)

Installation
------------

Step 1: Clone the Repository
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

    git clone <REPO-URL>
    cd OpenDDI

Step 2: Install Dependencies
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

General Dependencies
^^^^^^^^^^^^^^^^^^^^

You can install the general dependencies:

.. code-block:: bash

    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:

.. code-block:: bash

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

.. toctree::
   :maxdepth: 1
   :caption: Tutorial

   Tutorial/quick_start
   Tutorial/example
   Tutorial/parameters

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   API/dataset
   API/models
   API/trainer
   API/utils
   API/evaluate
   API/pipeline
   API/main
   API/parms_setting

References
==========

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Index and Search
================

* :ref:`genindex`
* :ref:`search`