# MolGraph: a Python package for the implementation of molecular graphs and graph neural networks with TensorFlow and Keras

arXiv: https://arxiv.org/abs/2208.09944 · HTML: https://mlsanity.com/paper/2208.09944/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 42 references that are in the map.
- First posted on arXiv 21 Aug 2022.

## Builds on (most cited first, 19 of 19)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [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)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [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)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems](https://mlsanity.com/paper/1603.04467/) (2016)
- [Geometric deep learning on graphs and manifolds using mixture model CNNs](https://mlsanity.com/paper/1611.08402/) (2016)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [Graph Neural Networks in TensorFlow and Keras with Spektral](https://mlsanity.com/paper/2006.12138/) (2020)

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

- [Multi-Objective Reinforcement Learning for Generating Covalent Inhibitor Candidates](https://mlsanity.com/paper/2604.20019/) (2026)

## Abstract (arXiv)

Molecular machine learning (ML) has proven important for tackling various molecular problems, such as predicting molecular properties based on molecular descriptors or fingerprints. Since relatively recently, graph neural network (GNN) algorithms have been implemented for molecular ML, showing comparable or superior performance to descriptor or fingerprint-based approaches. Although various tools and packages exist to apply GNNs in molecular ML, a new GNN package, named MolGraph, was developed in this work with the motivation to create GNN model pipelines highly compatible with the TensorFlow and Keras application programming interface (API). MolGraph also implements a chemistry module to accommodate the generation of small molecular graphs, which can be passed to a GNN algorithm to solve a molecular ML problem. To validate the GNNs, they were benchmarked against the datasets of MoleculeNet, as well as three chromatographic retention time datasets. The results on these benchmarks illustrate that the GNNs performed as expected. Additionally, the GNNs proved useful for molecular identification and improved interpretability of chromatographic retention time data. MolGraph is available at https://github.com/akensert/molgraph. Installation, tutorials and implementation details can be found at https://molgraph.readthedocs.io/en/latest/.