# Semi-Supervised Junction Tree Variational Autoencoder for Molecular Property Prediction

arXiv: https://arxiv.org/abs/2208.05119 · HTML: https://mlsanity.com/paper/2208.05119/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 25 references that are in the map.
- First posted on arXiv 10 Aug 2022.

## Builds on (most cited first, 22 of 22)

- [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)
- [An Introduction to Variational Autoencoders](https://mlsanity.com/paper/1906.02691/) (2019)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [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)
- [Semi-Supervised Learning with Deep Generative Models](https://mlsanity.com/paper/1406.5298/) (2014)
- [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization](https://mlsanity.com/paper/1908.01000/) (2019)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation](https://mlsanity.com/paper/1806.02473/) (2018)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [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)
- [Deep Reinforcement Learning for De-Novo Drug Design](https://mlsanity.com/paper/1711.10907/) (2017)
- [Syntax-Directed Variational Autoencoder for Structured Data](https://mlsanity.com/paper/1802.08786/) (2018)
- [Constrained Generation of Semantically Valid Graphs via Regularizing Variational Autoencoders](https://mlsanity.com/paper/1809.02630/) (2018)
- [Auxiliary Deep Generative Models](https://mlsanity.com/paper/1602.05473/) (2016)
- [Learning Disentangled Representations with Semi-Supervised Deep Generative Models](https://mlsanity.com/paper/1706.00400/) (2017)
- [ASGN: An Active Semi-supervised Graph Neural Network for Molecular Property Prediction](https://mlsanity.com/paper/2007.03196/) (2020)
- [Conditional molecular design with deep generative models](https://mlsanity.com/paper/1805.00108/) (2018)
- [Semi-Supervised Generative Modeling for Controllable Speech Synthesis](https://mlsanity.com/paper/1910.01709/) (2019)

## Abstract (arXiv)

Molecular Representation Learning is essential to solving many drug discovery and computational chemistry problems. It is a challenging problem due to the complex structure of molecules and the vast chemical space. Graph representations of molecules are more expressive than traditional representations, such as molecular fingerprints. Therefore, they can improve the performance of machine learning models. We propose SeMole, a method that augments the Junction Tree Variational Autoencoders, a state-of-the-art generative model for molecular graphs, with semi-supervised learning. SeMole aims to improve the accuracy of molecular property prediction when having limited labeled data by exploiting unlabeled data. We enforce that the model generates molecular graphs conditioned on target properties by incorporating the property into the latent representation. We propose an additional pre-training phase to improve the training process for our semi-supervised generative model. We perform an experimental evaluation on the ZINC dataset using three different molecular properties and demonstrate the benefits of semi-supervision.