# A Transformer-based Generative Model for De Novo Molecular Design

arXiv: https://arxiv.org/abs/2210.08749 · HTML: https://mlsanity.com/paper/2210.08749/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 25 of its 58 references that are in the map.
- First posted on arXiv 17 Oct 2022.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Neural Machine Translation by Jointly Learning to Align and Translate](https://mlsanity.com/paper/1409.0473/) (2014)
- [Pointer Sentinel Mixture Models](https://mlsanity.com/paper/1609.07843/) (2016)
- [Sequence to Sequence Learning with Neural Networks](https://mlsanity.com/paper/1409.3215/) (2014)
- [Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling](https://mlsanity.com/paper/1412.3555/) (2014)
- [Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation](https://mlsanity.com/paper/1609.08144/) (2016)
- [Pointer Networks](https://mlsanity.com/paper/1506.03134/) (2015)
- [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)
- [Enhancing the Locality and Breaking the Memory Bottleneck of Transformer on Time Series Forecasting](https://mlsanity.com/paper/1907.00235/) (2019)
- [Generating Sequences With Recurrent Neural Networks](https://mlsanity.com/paper/1308.0850/) (2013)
- [A Neural Attention Model for Abstractive Sentence Summarization](https://mlsanity.com/paper/1509.00685/) (2015)
- [Adversarial Autoencoders](https://mlsanity.com/paper/1511.05644/) (2015)
- [Generating Wikipedia by Summarizing Long Sequences](https://mlsanity.com/paper/1801.10198/) (2018)
- [GuacaMol: Benchmarking Models for De Novo Molecular Design](https://mlsanity.com/paper/1811.09621/) (2018)
- [Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models](https://mlsanity.com/paper/1811.12823/) (2018)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)
- [A Network-based End-to-End Trainable Task-oriented Dialogue System](https://mlsanity.com/paper/1604.04562/) (2016)
- [Incorporating Copying Mechanism in Sequence-to-Sequence Learning](https://mlsanity.com/paper/1603.06393/) (2016)
- [Deep Reinforcement Learning for De-Novo Drug Design](https://mlsanity.com/paper/1711.10907/) (2017)
- [A 3D Generative Model for Structure-Based Drug Design](https://mlsanity.com/paper/2203.10446/) (2022)
- [Multi-Objective De Novo Drug Design with Conditional Graph Generative Model](https://mlsanity.com/paper/1801.07299/) (2018)
- [Molecular generative model based on conditional variational autoencoder for de novo molecular design](https://mlsanity.com/paper/1806.05805/) (2018)
- [Molecular Generation with Recurrent Neural Networks (RNNs)](https://mlsanity.com/paper/1705.04612/) (2017)

## Abstract (arXiv)

In the scope of drug discovery, the molecular design aims to identify novel compounds from the chemical space where the potential drug-like molecules are estimated to be in the order of 10^60 - 10^100. Since this search task is computationally intractable due to the unbounded search space, deep learning draws a lot of attention as a new way of generating unseen molecules. As we seek compounds with specific target proteins, we propose a Transformer-based deep model for de novo target-specific molecular design. The proposed method is capable of generating both drug-like compounds (without specified targets) and target-specific compounds. The latter are generated by enforcing different keys and values of the multi-head attention for each target. In this way, we allow the generation of SMILES strings to be conditional on the specified target. Experimental results demonstrate that our method is capable of generating both valid drug-like compounds and target-specific compounds. Moreover, the sampled compounds from conditional model largely occupy the real target-specific molecules' chemical space and also cover a significant fraction of novel compounds.