# Accurate Prediction of Free Solvation Energy of Organic Molecules via Graph Attention Network and Message Passing Neural Network from Pairwise Atomistic Interactions

arXiv: https://arxiv.org/abs/2105.02048 · HTML: https://mlsanity.com/paper/2105.02048/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 67 references that are in the map.
- First posted on arXiv 15 Apr 2021.

## Builds on (most cited first, 13 of 13)

- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [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)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [Order Matters: Sequence to sequence for sets](https://mlsanity.com/paper/1511.06391/) (2015)
- [Machine learning for electronically excited states of molecules](https://mlsanity.com/paper/2007.05320/) (2020)
- [Combining SchNet and SHARC: The SchNarc machine learning approach for excited-state dynamics](https://mlsanity.com/paper/2002.07264/) (2020)
- [Wavelet Scattering Regression of Quantum Chemical Energies](https://mlsanity.com/paper/1605.04654/) (2016)
- [MLSolv-A: A Novel Machine Learning-Based Prediction of Solvation Free Energies from Pairwise Atomistic Interactions](https://mlsanity.com/paper/2005.06182/) (2020)

## Abstract (arXiv)

Deep learning based methods have been widely applied to predict various kinds of molecular properties in the pharmaceutical industry with increasingly more success. Solvation free energy is an important index in the field of organic synthesis, medicinal chemistry, drug delivery, and biological processes. However, accurate solvation free energy determination is a time-consuming experimental process. Furthermore, it could be useful to assess solvation free energy in the absence of a physical sample. In this study, we propose two novel models for the problem of free solvation energy predictions, based on the Graph Neural Network (GNN) architectures: Message Passing Neural Network (MPNN) and Graph Attention Network (GAT). GNNs are capable of summarizing the predictive information of a molecule as low-dimensional features directly from its graph structure without relying on an extensive amount of intra-molecular descriptors. As a result, these models are capable of making accurate predictions of the molecular properties without the time consuming process of running an experiment on each molecule. We show that our proposed models outperform all quantum mechanical and molecular dynamics methods in addition to existing alternative machine learning based approaches in the task of solvation free energy prediction. We believe such promising predictive models will be applicable to enhancing the efficiency of the screening of drug molecules and be a useful tool to promote the development of molecular pharmaceutics.