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<b>Background</b> <p>Identifying drug–target interactions (DTIs) is essential in drug discovery and repositioning. Recently, deep learning has become the mainstream methodology for DTI prediction. However, the scarcity of three-dimensional structural data has forced almost all methods to predict drug-target interactions with low-dimensional data, thereby constraining their overall performance.</p> <b>Methods</b> <p>In tackling this challenge, we introduce a novel approach, CLSF-DTI. CLSF-DTI incorporates high-dimensional structural and functional information into the drug and protein features through contrastive learning during the feature extraction stage. This ensures that the model no longer solely focuses on sequence information, leading to a more precise modeling outcome.</p> <b>Results</b> <p>Experiments on five benchmark datasets demonstrate that CLSF-DTI achieves the best overall performance among five state-of-the-art baselines. Through ablation studies, we further prove that the contrastive module enhances the predictive performance and generalization ability of CLSF-DTI. Moreover, CLSF-DTI successfully identified some ligands for the protein PKA-C<InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(\alpha \)</EquationSource> </InlineEquation> in drug screening experiments.</p> <b>Conclusions</b> <p>This study proposed a contrastive learning model CLSF-DTI that integrates structural and functional similarity. It outperforms existing methods in drug-target interaction prediction and has stronger generalization ability. However, the handling of unbalanced data and long-distance dependencies still needs to be improved in the future. The data and source code are available at <a href="https://github.com/ZhangLab312/CLSF_DTI">https://github.com/ZhangLab312/CLSF_DTI</a>.</p>

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Contrastive learning in both structure and function spaces improve drug-target interaction prediction

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月2日

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  • Yongqing Zhang,
  • Le Chen,
  • Hong Luo,
  • Tianhao Li,
  • Shuwen Xiong,
  • Zixuan Wang,
  • Quan Zou,
  • Wenqian Zhang

摘要

Background

Identifying drug–target interactions (DTIs) is essential in drug discovery and repositioning. Recently, deep learning has become the mainstream methodology for DTI prediction. However, the scarcity of three-dimensional structural data has forced almost all methods to predict drug-target interactions with low-dimensional data, thereby constraining their overall performance.

Methods

In tackling this challenge, we introduce a novel approach, CLSF-DTI. CLSF-DTI incorporates high-dimensional structural and functional information into the drug and protein features through contrastive learning during the feature extraction stage. This ensures that the model no longer solely focuses on sequence information, leading to a more precise modeling outcome.

Results

Experiments on five benchmark datasets demonstrate that CLSF-DTI achieves the best overall performance among five state-of-the-art baselines. Through ablation studies, we further prove that the contrastive module enhances the predictive performance and generalization ability of CLSF-DTI. Moreover, CLSF-DTI successfully identified some ligands for the protein PKA-C \(\alpha \) in drug screening experiments.

Conclusions

This study proposed a contrastive learning model CLSF-DTI that integrates structural and functional similarity. It outperforms existing methods in drug-target interaction prediction and has stronger generalization ability. However, the handling of unbalanced data and long-distance dependencies still needs to be improved in the future. The data and source code are available at https://github.com/ZhangLab312/CLSF_DTI.