C2M-Mamba: drug-drug interaction prediction based on cross-modal cross-Mamba

Accurately predicting potential drug-drug interactions (DDIs) from multimodal data is critical for medication safety and adverse drug reaction prevention. Existing methods face challenges in modeling long-range dependencies and effectively integrating heterogeneous features from structured molecular data and unstructured text. To address these limitations, we propose C2M-Mamba, a cross-modal framework that integrates convolutional neural networks, Mamba, and cross-Mamba (CroMamba) to capture discriminative features from drug descriptions, SMILES sequences, and social media texts. The model efficiently handles long-range dependencies through state space models while enabling effective cross-modal fusion. Comprehensive evaluations on the DDIExtraction2013 dataset demonstrate that C2M-Mamba outperforms 10 state-of-the-art baselines, achieving 82.37% precision, 80.98% F1-score, and 88.73% AUC. The proposed approach also exhibits robust performance in handling class imbalance and provides interpretable predictions, offering a reliable solution for multimodal DDI prediction with potential applications in pharmacovigilance and personalized medicine.

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Publication Details

Journal
BMC Bioinformatics
Published
2026-03-11
DOI
https://doi.org/10.1186/s12859-026-06420-4
Primary Topic
Computational Drug Discovery Methods
Type
article
Field-Weighted Citation Impact
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article

C2M-Mamba: drug-drug interaction prediction based on cross-modal cross-Mamba

Shimin Zhang, Dengwu Wang, Chuanlei Zhang
BMC Bioinformatics
Computational Drug Discovery Methods
article

C2M-Mamba: drug-drug interaction prediction based on cross-modal cross-Mamba

Shimin Zhang, Dengwu Wang, Chuanlei Zhang
article en

Abstract

Accurately predicting potential drug-drug interactions (DDIs) from multimodal data is critical for medication safety and adverse drug reaction prevention. Existing methods face challenges in modeling long-range dependencies and effectively integrating heterogeneous features from structured molecular data and unstructured text. To address these limitations, we propose C2M-Mamba, a cross-modal framework that integrates convolutional neural networks, Mamba, and cross-Mamba (CroMamba) to capture discriminative features from drug descriptions, SMILES sequences, and social media texts. The model efficiently handles long-range dependencies through state space models while enabling effective cross-modal fusion. Comprehensive evaluations on the DDIExtraction2013 dataset demonstrate that C2M-Mamba outperforms 10 state-of-the-art baselines, achieving 82.37% precision, 80.98% F1-score, and 88.73% AUC. The proposed approach also exhibits robust performance in handling class imbalance and provides interpretable predictions, offering a reliable solution for multimodal DDI prediction with potential applications in pharmacovigilance and personalized medicine.

BMC Bioinformatics
Tianjin University of Science and Technology (CN), Tianjin University of Technology (CN), Xijing University (CN)
Reduced inequalities
Openalex Percentile: Top 25%
Computational Drug Discovery Methods
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