# Open-Source Molecular Processing Pipeline for Generating Molecules

arXiv: https://arxiv.org/abs/2408.06261 · HTML: https://mlsanity.com/paper/2408.06261/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 35 references that are in the map.
- First posted on arXiv 12 Aug 2024.

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

- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [Density estimation using Real NVP](https://mlsanity.com/paper/1605.08803/) (2016)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Glow: Generative Flow with Invertible 1x1 Convolutions](https://mlsanity.com/paper/1807.03039/) (2018)
- [Normalizing Flows for Probabilistic Modeling and Inference](https://mlsanity.com/paper/1912.02762/) (2019)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Gated Graph Sequence Neural Networks](https://mlsanity.com/paper/1511.05493/) (2015)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [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)
- [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)
- [Syntax-Directed Variational Autoencoder for Structured Data](https://mlsanity.com/paper/1802.08786/) (2018)
- [Rao-Blackwellizing the Straight-Through Gumbel-Softmax Gradient Estimator](https://mlsanity.com/paper/2010.04838/) (2020)
- [Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity](https://mlsanity.com/paper/1703.10603/) (2017)
- [MolGrow: A Graph Normalizing Flow for Hierarchical Molecular Generation](https://mlsanity.com/paper/2106.05856/) (2021)
- [FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning](https://mlsanity.com/paper/2209.15315/) (2022)
- [FastFlows: Flow-Based Models for Molecular Graph Generation](https://mlsanity.com/paper/2201.12419/) (2022)

## Abstract (arXiv)

Generative models for molecules have shown considerable promise for use in computational chemistry, but remain difficult to use for non-experts. For this reason, we introduce open-source infrastructure for easily building generative molecular models into the widely used DeepChem [Ramsundar et al., 2019] library with the aim of creating a robust and reusable molecular generation pipeline. In particular, we add high quality PyTorch [Paszke et al., 2019] implementations of the Molecular Generative Adversarial Networks (MolGAN) [Cao and Kipf, 2022] and Normalizing Flows [Papamakarios et al., 2021]. Our implementations show strong performance comparable with past work [Kuznetsov and Polykovskiy, 2021, Cao and Kipf, 2022].