  In the last decades, people have been consuming and combining more drugs than
before, increasing the number of Drug-Drug Interactions (DDIs). To predict
unknown DDIs, recently, studies started incorporating Knowledge Graphs (KGs)
since they are able to capture the relationships among entities providing
better drug representations than using a single drug property. In this paper,
we propose the medicX end-to-end framework that integrates several drug
features from public drug repositories into a KG and embeds the nodes in the
graph using various translation, factorisation and Neural Network (NN) based KG
Embedding (KGE) methods. Ultimately, we use a Machine Learning (ML) algorithm
that predicts unknown DDIs. Among the different translation and
factorisation-based KGE models, we found that the best performing combination
was the ComplEx embedding method with a Long Short-Term Memory (LSTM) network,
which obtained an F1-score of 95.19% on a dataset based on the DDIs found in
DrugBank version 5.1.8. This score is 5.61% better than the state-of-the-art
model DeepDDI. Additionally, we also developed a graph auto-encoder model that
uses a Graph Neural Network (GNN), which achieved an F1-score of 91.94%.
Consequently, GNNs have demonstrated a stronger ability to mine the underlying
semantics of the KG than the ComplEx model, and thus using higher dimension
embeddings within the GNN can lead to state-of-the-art performance.
