This repository is the official implementation of "DrugRepBench: a multi-scenario benchmark for knowledge graph-based drug repurposing".
To install requirements:
pip install -r requirements.txt
We will use two KG examples to demonstrate the process of creating our benchmark. First, navigate to the directory data_process and run the 1merge.py file to merge the two KG files.
cd data_process
python 1merge.py
Then, run file 2kg_build.py to build a new KG based on the merged information.
python 2kg_build.py
The test samples for Fine-grained Cold-Start Scenarios can be obtained by running file 3kg_divide.py.
python 3kg_divide.py
Running 4hard_negative.py can obtain data information for the Hard Negative Sampling Scenario, but you need to first construct the embedding of the KG node and the mechanistic difference set of the candidate drugs.
The content of benchmark DrugRepBench is located under the directory benchmark and includes graph.txt, train.txt, valid.txt, and three test Scenarios.