# MolCAP: Molecular Chemical reActivity pretraining and prompted-finetuning enhanced molecular representation learning

arXiv: https://arxiv.org/abs/2306.09187 · HTML: https://mlsanity.com/paper/2306.09187/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 34 references that are in the map.
- First posted on arXiv 13 Jun 2023.

## Builds on (most cited first, 12 of 12)

- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [AutoPrompt: Eliciting Knowledge from Language Models with Automatically Generated Prompts](https://mlsanity.com/paper/2010.15980/) (2020)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [ChemBERTa-2: Towards Chemical Foundation Models](https://mlsanity.com/paper/2209.01712/) (2022)
- [N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules](https://mlsanity.com/paper/1806.09206/) (2018)
- [Label Verbalization and Entailment for Effective Zero- and Few-Shot Relation Extraction](https://mlsanity.com/paper/2109.03659/) (2021)
- [Chemical-Reaction-Aware Molecule Representation Learning](https://mlsanity.com/paper/2109.09888/) (2021)
- [Multi-task Joint Strategies of Self-supervised Representation Learning on Biomedical Networks for Drug Discovery](https://mlsanity.com/paper/2201.04437/) (2022)
- [Can NLI Provide Proper Indirect Supervision for Low-resource Biomedical Relation Extraction?](https://mlsanity.com/paper/2212.10784/) (2022)

## Built on by (most cited first, 2 of 2)

- [Graph Neural Networks in Modern AI-aided Drug Discovery](https://mlsanity.com/paper/2506.06915/) (2025)
- [Graph AI in Medicine](https://mlsanity.com/paper/2310.13767/) (2023)

## Abstract (arXiv)

Molecular representation learning (MRL) is a fundamental task for drug discovery. However, previous deep-learning (DL) methods focus excessively on learning robust inner-molecular representations by mask-dominated pretraining framework, neglecting abundant chemical reactivity molecular relationships that have been demonstrated as the determining factor for various molecular property prediction tasks. Here, we present MolCAP to promote MRL, a graph pretraining Transformer based on chemical reactivity (IMR) knowledge with prompted finetuning. Results show that MolCAP outperforms comparative methods based on traditional molecular pretraining framework, in 13 publicly available molecular datasets across a diversity of biomedical tasks. Prompted by MolCAP, even basic graph neural networks are capable of achieving surprising performance that outperforms previous models, indicating the promising prospect of applying reactivity information for MRL. In addition, manual designed molecular templets are potential to uncover the dataset bias. All in all, we expect our MolCAP to gain more chemical meaningful insights for the entire process of drug discovery.