# A Deep Learning Approach to the Prediction of Drug Side-Effects on Molecular Graphs

arXiv: https://arxiv.org/abs/2211.16871 · HTML: https://mlsanity.com/paper/2211.16871/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 61 references that are in the map.
- First posted on arXiv 30 Nov 2022.

## Builds on (most cited first, 21 of 21)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (2018)
- [Spectral Networks and Locally Connected Networks on Graphs](https://mlsanity.com/paper/1312.6203/) (2013)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [Self-Normalizing Neural Networks](https://mlsanity.com/paper/1706.02515/) (2017)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Modeling polypharmacy side effects with graph convolutional networks](https://mlsanity.com/paper/1802.00543/) (2018)
- [Molecular graph generation with Graph Neural Networks](https://mlsanity.com/paper/2012.07397/) (2020)
- [Drug-Drug Adverse Effect Prediction with Graph Co-Attention](https://mlsanity.com/paper/1905.00534/) (2019)
- [Conditional Constrained Graph Variational Autoencoders for Molecule Design](https://mlsanity.com/paper/2009.00725/) (2020)
- [Modular multi-source prediction of drug side-effects with DruGNN](https://mlsanity.com/paper/2202.08147/) (2022)

## Abstract (arXiv)

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the structure of the drug, resulting in a loss of information. Graph neural networks have seen great success in recent years, thanks to their ability of exploiting the information conveyed by the graph structure and labels. These models have been used in a wide variety of biological applications, among which the prediction of drug side-effects on a large knowledge graph. Exploiting the molecular graph encoding the structure of the drug represents a novel approach, in which the problem is formulated as a multi-class multi-label graph-focused classification. We developed a methodology to carry out this task, using recurrent Graph Neural Networks, and building a dataset from freely accessible and well established data sources. The results show that our method has an improved classification capability, under many parameters and metrics, with respect to previously available predictors.