# CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations

arXiv: https://arxiv.org/abs/2307.13275 · HTML: https://mlsanity.com/paper/2307.13275/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 23 of its 50 references that are in the map.
- First posted on arXiv 25 Jul 2023.

## Builds on (most cited first, 23 of 23)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [Understanding over-squashing and bottlenecks on graphs via curvature](https://mlsanity.com/paper/2111.14522/) (2021)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [DeeperGCN: All You Need to Train Deeper GCNs](https://mlsanity.com/paper/2006.07739/) (2020)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [Graph-Bert: Only Attention is Needed for Learning Graph Representations](https://mlsanity.com/paper/2001.05140/) (2020)
- [ChemBERTa-2: Towards Chemical Foundation Models](https://mlsanity.com/paper/2209.01712/) (2022)
- [N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules](https://mlsanity.com/paper/1806.09206/) (2018)
- [Molecule Attention Transformer](https://mlsanity.com/paper/2002.08264/) (2020)
- [SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery](https://mlsanity.com/paper/1911.04738/) (2019)
- [Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs](https://mlsanity.com/paper/2110.01191/) (2021)
- [DGL-LifeSci: An Open-Source Toolkit for Deep Learning on Graphs in Life Science](https://mlsanity.com/paper/2106.14232/) (2021)
- [Ricci Curvature of the Internet Topology](https://mlsanity.com/paper/1501.04138/) (2015)

## Abstract (arXiv)

AI-driven drug design relies significantly on predicting molecular properties, which is a complex task. In current approaches, the most commonly used feature representations for training deep neural network models are based on SMILES and molecular graphs. While these methods are concise and efficient, they have limitations in capturing complex spatial information. Recently, researchers have recognized the importance of incorporating three-dimensional information of molecular structures into models. However, capturing spatial information requires the introduction of additional units in the generator, bringing additional design and computational costs. Therefore, it is necessary to develop a method for predicting molecular properties that effectively combines spatial structural information while maintaining the simplicity and efficiency of graph neural networks. In this work, we propose an embedding approach CTAGE, utilizing k-hop discrete Ricci curvature to extract structural insights from molecular graph data. This effectively integrates spatial structural information while preserving the training complexity of the network. Experimental results indicate that introducing node curvature significantly improves the performance of current graph neural network frameworks, validating that the information from k-hop node curvature effectively reflects the relationship between molecular structure and function.