A benchmark study comparing deep learning and path analysis approaches for multi-class link prediction on a disease-specific literature knowledge graph.

Abstract

Identifying and understanding multi-type drug-drug interactions and their associated toxicities is crucial for preventing adverse outcomes, especially in vulnerable populations, such as cancer patients, who may already have compromised health statuses. This paper provides a benchmark study that compares various commonly-used Machine Learning-based approaches, such as graph embeddings and path analysis, aiming at predicting different types of drug-drug interaction links in a disease-specific knowledge graph, constructed from biomedical literature. These approaches are evaluated based on an external interaction dataset collected from Drugbank. We first introduce a simplified taxonomy of multi-type interactions and then compare the models' performance over the different drug-drug interaction types. Overall, the graph embeddings approach outperforms the competition, while the path-based analysis allows for an interpretation of predictions, using the most important features of each path.