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ProtoMol: enhancing molecular property prediction via prototype-guided multimodal learning
Wang, Yingxu Zhang, Kunyu Huang, Jiaxin Yin, Nan Liu, Siwei Segal, Eran
Wang, Yingxu
Zhang, Kunyu
Huang, Jiaxin
Yin, Nan
Liu, Siwei
Segal, Eran
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bbaf629.pdf
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Department
Machine Learning
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Journal article
Date
2025
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English
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Abstract
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: (i) they typically perform cross-modal interaction only at the final encoder layer, thus overlooking hierarchical semantic dependencies; (ii) 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. Our source code is available at: https://github.com/zky04/Protomol.
Citation
Y. Wang, K. Zhang, J. Huang, N. Yin, S. Liu, and E. Segal, “ProtoMol: enhancing molecular property prediction via prototype-guided multimodal learning,” Brief Bioinform, vol. 26, no. 6, Nov. 2025, doi: 10.1093/BIB/BBAF629
Source
Briefings in Bioinformatics
Conference
Keywords
Molecular Property Prediction, Multimodal Learning, Molecular Graphs, Graph Neural Networks, Computational Chemistry
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Oxford University Press