# Implementing graph neural networks with TensorFlow-Keras

arXiv: https://arxiv.org/abs/2103.04318 · HTML: https://mlsanity.com/paper/2103.04318/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 41 of its 76 references that are in the map.
- First posted on arXiv 7 Mar 2021.

## Builds on (most cited first, 30 of 41)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [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)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Spatio-Temporal Graph Convolutional Networks: A Deep Learning Framework for Traffic Forecasting](https://mlsanity.com/paper/1709.04875/) (2017)
- [Spectral Networks and Locally Connected Networks on Graphs](https://mlsanity.com/paper/1312.6203/) (2013)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [Dynamic Routing Between Capsules](https://mlsanity.com/paper/1710.09829/) (2017)
- [TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems](https://mlsanity.com/paper/1603.04467/) (2016)
- [Interaction Networks for Learning about Objects, Relations and Physics](https://mlsanity.com/paper/1612.00222/) (2016)
- [Graph U-Nets](https://mlsanity.com/paper/1905.05178/) (2019)
- [Representation Learning on Graphs: Methods and Applications](https://mlsanity.com/paper/1709.05584/) (2017)
- [Self-Attention Graph Pooling](https://mlsanity.com/paper/1904.08082/) (2019)
- [Learning Convolutional Neural Networks for Graphs](https://mlsanity.com/paper/1605.05273/) (2016)
- [Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs](https://mlsanity.com/paper/1704.02901/) (2017)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [Order Matters: Sequence to sequence for sets](https://mlsanity.com/paper/1511.06391/) (2015)
- [Learning Deep Generative Models of Graphs](https://mlsanity.com/paper/1803.03324/) (2018)
- [CayleyNets: Graph Convolutional Neural Networks with Complex Rational Spectral Filters](https://mlsanity.com/paper/1705.07664/) (2017)
- [Graph Convolutional Networks with EigenPooling](https://mlsanity.com/paper/1904.13107/) (2019)
- [Adversarially Regularized Graph Autoencoder for Graph Embedding](https://mlsanity.com/paper/1802.04407/) (2018)
- [Unifying machine learning and quantum chemistry -- a deep neural network for molecular wavefunctions](https://mlsanity.com/paper/1906.10033/) (2019)

## Built on by (most cited first, 3 of 3)

- [Graph neural networks for materials science and chemistry](https://mlsanity.com/paper/2208.09481/) (2022)
- [DenseGNN: universal and scalable deeper graph neural networks for high-performance property prediction in crystals and molecules](https://mlsanity.com/paper/2501.03278/) (2025)
- [A Crystal-Specific Pre-Training Framework for Crystal Material Property Prediction](https://mlsanity.com/paper/2306.05344/) (2023)

## Abstract (arXiv)

Graph neural networks are a versatile machine learning architecture that received a lot of attention recently. In this technical report, we present an implementation of convolution and pooling layers for TensorFlow-Keras models, which allows a seamless and flexible integration into standard Keras layers to set up graph models in a functional way. This implies the usage of mini-batches as the first tensor dimension, which can be realized via the new RaggedTensor class of TensorFlow best suited for graphs. We developed the Keras Graph Convolutional Neural Network Python package kgcnn based on TensorFlow-Keras that provides a set of Keras layers for graph networks which focus on a transparent tensor structure passed between layers and an ease-of-use mindset.