# Molecular distance matrix prediction based on graph convolutional networks

arXiv: https://arxiv.org/abs/2107.01035 · HTML: https://mlsanity.com/paper/2107.01035/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 27 references that are in the map.
- First posted on arXiv 1 Jul 2021.

## Builds on (most cited first, 9 of 9)

- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [Molecular geometry prediction using a deep generative graph neural network](https://mlsanity.com/paper/1904.00314/) (2019)
- [Learning Neural Generative Dynamics for Molecular Conformation Generation](https://mlsanity.com/paper/2102.10240/) (2021)
- [A Generative Model for Molecular Distance Geometry](https://mlsanity.com/paper/1909.11459/) (2019)
- [An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming](https://mlsanity.com/paper/2105.07246/) (2021)
- [Machine Learning based prediction of noncentrosymmetric crystal materials](https://mlsanity.com/paper/2002.11295/) (2020)

## Abstract (arXiv)

Molecular structure has important applications in many fields. For example, some studies show that molecular spatial information can be used to achieve better prediction results when predicting molecular properties. However, traditional molecular geometry calculations, such as density functional theory (DFT), are time-consuming. In view of this, we propose a model based on graph convolutional networks to predict the pairwise distance between atoms, also called distance matrix prediction of the molecule(DMGCN). In order to indicate the effect of DMGCN model, the model is compared with the model DeeperGCN-DAGNN and the method of calculating molecular conformation in RDKit. Results show that the MAE of DMGCN is smaller than DeeperGCN-DAGNN and RDKit. In addition, the distances predicted by the DMGCN model and the distances calculated by the QM9 dataset are used to predict the molecular properties, thus showing the effectiveness of the distance predicted by the DMGCN model.