# ProtoMol: Enhancing Molecular Property Prediction via Prototype-Guided Multimodal Learning

arXiv: https://arxiv.org/abs/2510.16824 · HTML: https://mlsanity.com/paper/2510.16824/

## Key facts

- Cited by 11 papers in the map (data through 14 Oct 2026).
- Builds on 51 of its 93 references that are in the map.
- First posted on arXiv 19 Oct 2025.

## Builds on (most cited first, 30 of 51)

- [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)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Prototypical Networks for Few-shot Learning](https://mlsanity.com/paper/1703.05175/) (2017)
- [Matching Networks for One Shot Learning](https://mlsanity.com/paper/1606.04080/) (2016)
- [ViLBERT: Pretraining Task-Agnostic Visiolinguistic Representations for Vision-and-Language Tasks](https://mlsanity.com/paper/1908.02265/) (2019)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [This Looks Like That: Deep Learning for Interpretable Image Recognition](https://mlsanity.com/paper/1806.10574/) (2018)
- [Prototypical Contrastive Learning of Unsupervised Representations](https://mlsanity.com/paper/2005.04966/) (2020)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [Graph Contrastive Learning Automated](https://mlsanity.com/paper/2106.07594/) (2021)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [Motif-based Graph Self-Supervised Learning for Molecular Property Prediction](https://mlsanity.com/paper/2110.00987/) (2021)
- [Self-supervised Graph-level Representation Learning with Local and Global Structure](https://mlsanity.com/paper/2106.04113/) (2021)
- [Accurate Learning of Graph Representations with Graph Multiset Pooling](https://mlsanity.com/paper/2102.11533/) (2021)
- [PMR: Prototypical Modal Rebalance for Multimodal Learning](https://mlsanity.com/paper/2211.07089/) (2022)
- [A Survey of Graph Neural Networks in Real world: Imbalance, Noise, Privacy and OOD Challenges](https://mlsanity.com/paper/2403.04468/) (2024)

## Built on by (most cited first, 11 of 11)

- [USBD: Universal Structural Basis Distillation for Source-Free Graph Domain Adaptation](https://mlsanity.com/paper/2602.08431/) (2026)
- [PIME: Prototype-based Interpretable MCTS-Enhanced Brain Network Analysis for Disorder Diagnosis](https://mlsanity.com/paper/2602.21046/) (2026)
- [DSBD: Dual-Aligned Structural Basis Distillation for Graph Domain Adaptation](https://mlsanity.com/paper/2604.03154/) (2026)
- [Learning beyond Site Bias for OOD Generalization in Brain Networks](https://mlsanity.com/paper/2605.06050/) (2026)
- [EVA-Net: Interpretable Anomaly Detection for Brain Health via Learning Continuous Aging Prototypes from One-Class EEG Cohorts](https://mlsanity.com/paper/2511.15393/) (2025)
- [MOLAR: Learning Multimodal Molecular Representations from Noisy Labels](https://mlsanity.com/paper/2606.18390/) (2026)
- [Cross-Resolution Semantic Learning for Graph Domain Adaptation](https://mlsanity.com/paper/2607.29365/) (2026)
- [Hierarchical Dual-Strategy Unlearning for Biomedical and Healthcare Intelligence Using Imperfect and Privacy-Sensitive Medical Data](https://mlsanity.com/paper/2511.19498/) (2025)
- [Data-Efficient Agentic Graph Domain Adaptation via Reliability-Aware Prototype Learning](https://mlsanity.com/paper/2609.14045/) (2026)
- [Beyond Site Agreement: Re-estimation for Brain Network Generalization](https://mlsanity.com/paper/2609.34611/) (2026)
- [Learning Propagation Geometry from Message-Passing Feedback](https://mlsanity.com/paper/2609.34711/) (2026)

## Abstract (arXiv)

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity, bioactivity, and physicochemical properties through the integration of structural and semantic information. However, existing multimodal methods suffer from two key limitations: (1) they typically perform cross-modal interaction only at the final encoder layer, thus overlooking hierarchical semantic dependencies; (2) they lack a unified prototype space for robust alignment between modalities. To address these limitations, we propose ProtoMol, a prototype-guided multimodal framework that enables fine-grained integration and consistent semantic alignment between molecular graphs and textual descriptions. ProtoMol incorporates dual-branch hierarchical encoders, utilizing Graph Neural Networks to process structured molecular graphs and Transformers to encode unstructured texts, resulting in comprehensive layer-wise representations. Then, ProtoMol introduces a layer-wise bidirectional cross-modal attention mechanism that progressively aligns semantic features across layers. Furthermore, a shared prototype space with learnable, class-specific anchors is constructed to guide both modalities toward coherent and discriminative representations. Extensive experiments on multiple benchmark datasets demonstrate that ProtoMol consistently outperforms state-of-the-art baselines across a variety of molecular property prediction tasks.