Oral Presentations

Predicting Polypharmacy Side-effects Using Knowledge Graph Embeddings

11:44 AM–12:06 PM Mar 26, 2020 (America - Chicago)



Programmatic Theme: Translational Bioinformatics

Abstract: Polypharmacy is the use of drug combinations, which is commonly used for treating complex and terminal diseases. Despite its effectiveness in many cases, it poses high risks of adverse side effects. Polypharmacy side-effects occur due to unwanted interactions of combined drugs, and they can cause severe complications to patients, increasing the risks of morbidity and leading to new mortalities. The use of drug polypharmacy is currently in its early stages, thus, the knowledge of their probable side-effects is limited. This encouraged multiple works to investigate machine learning techniques to efficiently and reliably predict adverse effects of drug combinations. In this context, the Decagon model is known to provide state-of-the-art results. It models polypharmacy side-effect data as a knowledge graph and formulates finding possible adverse effects as a link prediction task over the knowledge graph. The link prediction is solved using an embedding model based on graph convolutions. Despite its effectiveness, the Decagon approach still suffers from a high rate of false positives. In this work, we propose a new knowledge graph embedding technique that uses multi-part embedding vectors to predict polypharmacy side-effects. Like in the Decagon model, we model polypharmacy side effects as a knowledge graph. However, we perform the link prediction task using an approach based on tensor decomposition. Our experimental evaluation shows that our approach outperforms the Decagon model with 12% and 16% margins in terms of the area under the ROC and precision-recall curves, respectively.

Learning Objective: Predicting Polypharmacy Side-effects Using Knowledge Graph Embeddings


Vit Novacek, National University of Ireland Galway
Sameh Mohamed (Presenter)
National University of Ireland Galway

Keywords, Themes & Types