# Graph Context Encoder: Graph Feature Inpainting for Graph Generation and Self-supervised Pretraining

arXiv: https://arxiv.org/abs/2106.10124 · HTML: https://mlsanity.com/paper/2106.10124/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 25 of its 30 references that are in the map.
- First posted on arXiv 18 Jun 2021.

## Builds on (most cited first, 25 of 25)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Context Encoders: Feature Learning by Inpainting](https://mlsanity.com/paper/1604.07379/) (2016)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (2018)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [Graph U-Nets](https://mlsanity.com/paper/1905.05178/) (2019)
- [Geometric deep learning on graphs and manifolds using mixture model CNNs](https://mlsanity.com/paper/1611.08402/) (2016)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [GuacaMol: Benchmarking Models for De Novo Molecular Design](https://mlsanity.com/paper/1811.09621/) (2018)
- [Efficient Graph Generation with Graph Recurrent Attention Networks](https://mlsanity.com/paper/1910.00760/) (2019)
- [Learning Deep Generative Models of Graphs](https://mlsanity.com/paper/1803.03324/) (2018)
- [SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels](https://mlsanity.com/paper/1711.08920/) (2017)
- [Hierarchical Inter-Message Passing for Learning on Molecular Graphs](https://mlsanity.com/paper/2006.12179/) (2020)
- [A Two-Step Graph Convolutional Decoder for Molecule Generation](https://mlsanity.com/paper/1906.03412/) (2019)

## Built on by (most cited first, 1 of 1)

- [HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields](https://mlsanity.com/paper/2510.18122/) (2025)

## Abstract (arXiv)

We propose the Graph Context Encoder (GCE), a simple but efficient approach for graph representation learning based on graph feature masking and reconstruction. GCE models are trained to efficiently reconstruct input graphs similarly to a graph autoencoder where node and edge labels are masked. In particular, our model is also allowed to change graph structures by masking and reconstructing graphs augmented by random pseudo-edges. We show that GCE can be used for novel graph generation, with applications for molecule generation. Used as a pretraining method, we also show that GCE improves baseline performances in supervised classification tasks tested on multiple standard benchmark graph datasets.