Evaluating Knowledge Graph Embeddings for Protein Function

A group project in the context of the CDT in Biomedical AI, at the University of Edinburgh.
Authors: Aryo Pradipta Gema, Dominik Grabarzcyk, Wolf De Wulf
Supervisors: Dr. Javier Alfaro, Dr. Pasquale Minervini, Dr. Antonio Vergari, Dr. Ajitha Rajan

1. Installation

Recompile AnyBURL using scripts/recompile_anyburl.sh

2. Data

Data used is taken from biokge to obtain the same splits. The train.csv, valid.csv and test.csv can be used directly.

3. Running scripts

Configuration files can be found ing the config/ folder. An example using default settings for learning and inferrence can be found in config/base

To train one can update the scripts/train.sh file. Inference should loop over the provided time intervals.

Evaulation can be done using the scripts/evaluate.sh file, where paths should be updated to reflect local paths.

4. Questions

Feel free to contact any of the authors via email if you have questions.