# Scaffold Embeddings: Learning the Structure Spanned by Chemical Fragments, Scaffolds and Compounds

arXiv: https://arxiv.org/abs/2103.06867 · HTML: https://mlsanity.com/paper/2103.06867/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 62 references that are in the map.
- First posted on arXiv 11 Mar 2021.

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [Semi-Supervised Learning with Deep Generative Models](https://mlsanity.com/paper/1406.5298/) (2014)
- [Grammar Variational Autoencoder](https://mlsanity.com/paper/1703.01925/) (2017)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)
- [OpenNMT: Open-source Toolkit for Neural Machine Translation](https://mlsanity.com/paper/1709.03815/) (2017)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [Application of generative autoencoder in de novo molecular design](https://mlsanity.com/paper/1711.07839/) (2017)

## Abstract (arXiv)

Molecules have seemed like a natural fit to deep learning's tendency to handle a complex structure through representation learning, given enough data. However, this often continuous representation is not natural for understanding chemical space as a domain and is particular to samples and their differences. We focus on exploring a natural structure for representing chemical space as a structured domain: embedding drug-like chemical space into an enumerable hypergraph based on scaffold classes linked through an inclusion operator. This paper shows how molecules form classes of scaffolds, how scaffolds relate to each in a hypergraph, and how this structure of scaffolds is natural for drug discovery workflows such as predicting properties and optimizing molecular structures. We compare the assumptions and utility of various embeddings of molecules, such as their respective induced distance metrics, their extendibility to represent chemical space as a structured domain, and the consequences of utilizing the structure for learning tasks.