# Infusing Linguistic Knowledge of SMILES into Chemical Language Models

arXiv: https://arxiv.org/abs/2205.00084 · HTML: https://mlsanity.com/paper/2205.00084/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 39 references that are in the map.
- First posted on arXiv 20 Apr 2022.

## Builds on (most cited first, 14 of 14)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [A Primer in BERTology: What we know about how BERT works](https://mlsanity.com/paper/2002.12327/) (2020)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [K-Adapter: Infusing Knowledge into Pre-Trained Models with Adapters](https://mlsanity.com/paper/2002.01808/) (2020)
- [A Multiscale Visualization of Attention in the Transformer Model](https://mlsanity.com/paper/1906.05714/) (2019)
- [Simple, Scalable Adaptation for Neural Machine Translation](https://mlsanity.com/paper/1909.08478/) (2019)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [Discriminative Embeddings of Latent Variable Models for Structured Data](https://mlsanity.com/paper/1603.05629/) (2016)
- [MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction](https://mlsanity.com/paper/2004.11424/) (2020)

## Abstract (arXiv)

The simplified molecular-input line-entry system (SMILES) is the most popular representation of chemical compounds. Therefore, many SMILES-based molecular property prediction models have been developed. In particular, transformer-based models show promising performance because the model utilizes a massive chemical dataset for self-supervised learning. However, there is no transformer-based model to overcome the inherent limitations of SMILES, which result from the generation process of SMILES. In this study, we grammatically parsed SMILES to obtain connectivity between substructures and their type, which is called the grammatical knowledge of SMILES. First, we pretrained the transformers with substructural tokens, which were parsed from SMILES. Then, we used the training strategy 'same compound model' to better understand SMILES grammar. In addition, we injected knowledge of connectivity and type into the transformer with knowledge adapters. As a result, our representation model outperformed previous compound representations for the prediction of molecular properties. Finally, we analyzed the attention of the transformer model and adapters, demonstrating that the proposed model understands the grammar of SMILES.