📣 AttentionDDI 💊

This repository contains the code for the AttentionDDI model implementation with PyTorch.

AttentionDDI is a Siamese multi-head self-Attention multi-modal neural network model used for drug-drug interaction (DDI) predictions.

Publication

Schwarz, Kyriakos, et al. “AttentionDDI: Siamese Attention-Based Deep Learning Method for Drug–Drug Interaction Predictions.” BMC Bioinformatics, vol. 22, no. 1, Dec. 2021, pp. 1–19. bmcbioinformatics.biomedcentral.com, https://doi.org/10.1186/s12859-021-04325-y.

Installation

• git clone the repo and cd into it.
• Run pip install -e . to install the repo's python package.

Running 🏃

1. use notebooks/jupyter/AttnWSiamese_data_generation.ipynb to generate DataTensors from the drug similarity matrices.
2. use notebooks/jupyter/AttnWSiamese_hyperparam.ipynb to find the best performing model hyperparameters.
3. use notebooks/jupyter/AttnWSiamese_train_eval.ipynb to train / test on the best hyperparameters.