# Predicting Drug-Drug Interactions Using Knowledge Graphs

arXiv: https://arxiv.org/abs/2308.04172 · HTML: https://mlsanity.com/paper/2308.04172/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 11 of its 49 references that are in the map.
- First posted on arXiv 8 Aug 2023.

## Builds on (most cited first, 11 of 11)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Embedding Entities and Relations for Learning and Inference in Knowledge Bases](https://mlsanity.com/paper/1412.6575/) (2014)
- [Complex Embeddings for Simple Link Prediction](https://mlsanity.com/paper/1606.06357/) (2016)
- [A Survey on Knowledge Graphs: Representation, Acquisition and Applications](https://mlsanity.com/paper/2002.00388/) (2020)
- [Modeling polypharmacy side effects with graph convolutional networks](https://mlsanity.com/paper/1802.00543/) (2018)
- [Holographic Embeddings of Knowledge Graphs](https://mlsanity.com/paper/1510.04935/) (2015)
- [PyTorch-BigGraph: A Large-scale Graph Embedding System](https://mlsanity.com/paper/1903.12287/) (2019)
- [DGL-KE: Training Knowledge Graph Embeddings at Scale](https://mlsanity.com/paper/2004.08532/) (2020)
- [Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network](https://mlsanity.com/paper/1908.01288/) (2019)
- [Optimizing Memory Efficiency of Graph Neural Networks on Edge Computing Platforms](https://mlsanity.com/paper/2104.03058/) (2021)

## Built on by (most cited first, 1 of 1)

- [medicX-KG: A Knowledge Graph for Pharmacists' Drug Information Needs](https://mlsanity.com/paper/2506.17959/) (2025)

## Abstract (arXiv)

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.