# Dual-Modality Representation Learning for Molecular Property Prediction

arXiv: https://arxiv.org/abs/2501.06608 · HTML: https://mlsanity.com/paper/2501.06608/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 26 of its 44 references that are in the map.
- First posted on arXiv 11 Jan 2025.

## Builds on (most cited first, 26 of 26)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Scaling Up Visual and Vision-Language Representation Learning With Noisy Text Supervision](https://mlsanity.com/paper/2102.05918/) (2021)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Align before Fuse: Vision and Language Representation Learning with Momentum Distillation](https://mlsanity.com/paper/2107.07651/) (2021)
- [ViLT: Vision-and-Language Transformer Without Convolution or Region Supervision](https://mlsanity.com/paper/2102.03334/) (2021)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Multimodal Machine Learning: A Survey and Taxonomy](https://mlsanity.com/paper/1705.09406/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [VLMo: Unified Vision-Language Pre-Training with Mixture-of-Modality-Experts](https://mlsanity.com/paper/2111.02358/) (2021)
- [Multimodal Learning with Transformers: A Survey](https://mlsanity.com/paper/2206.06488/) (2022)
- [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)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [Molecular representation learning with language models and domain-relevant auxiliary tasks](https://mlsanity.com/paper/2011.13230/) (2020)
- [SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery](https://mlsanity.com/paper/1911.04738/) (2019)
- [Dual-view Molecule Pre-training](https://mlsanity.com/paper/2106.10234/) (2021)
- [Multilingual Molecular Representation Learning via Contrastive Pre-training](https://mlsanity.com/paper/2109.08830/) (2021)
- [Molecular Joint Representation Learning via Multi-modal Information](https://mlsanity.com/paper/2211.14042/) (2022)

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

- [LastOPD: Taming Collapse in Latent On-Policy Distillation](https://mlsanity.com/paper/2609.28845/) (2026)

## Abstract (arXiv)

Molecular property prediction has attracted substantial attention recently. Accurate prediction of drug properties relies heavily on effective molecular representations. The structures of chemical compounds are commonly represented as graphs or SMILES sequences. Recent advances in learning drug properties commonly employ Graph Neural Networks (GNNs) based on the graph representation. For the SMILES representation, Transformer-based architectures have been adopted by treating each SMILES string as a sequence of tokens. Because each representation has its own advantages and disadvantages, combining both representations in learning drug properties is a promising direction. We propose a method named Dual-Modality Cross-Attention (DMCA) that can effectively combine the strengths of two representations by employing the cross-attention mechanism. DMCA was evaluated across eight datasets including both classification and regression tasks. Results show that our method achieves the best overall performance, highlighting its effectiveness in leveraging the complementary information from both graph and SMILES modalities.