CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction
Abstract The process of new drug development is complex, whereas drug-disease association (DDA) prediction aims to identify new therapeutic uses for existing medications. However, existing graph contrastive learning approaches typically rely on single-view contrastive learning, which struggle to ful...
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BMC
2025-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-024-06032-w |
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| author | Xianfang Tang Yawen Hou Yajie Meng Zhaojing Wang Changcheng Lu Juan Lv Xinrong Hu Junlin Xu Jialiang Yang |
| author_facet | Xianfang Tang Yawen Hou Yajie Meng Zhaojing Wang Changcheng Lu Juan Lv Xinrong Hu Junlin Xu Jialiang Yang |
| author_sort | Xianfang Tang |
| collection | DOAJ |
| description | Abstract The process of new drug development is complex, whereas drug-disease association (DDA) prediction aims to identify new therapeutic uses for existing medications. However, existing graph contrastive learning approaches typically rely on single-view contrastive learning, which struggle to fully capture drug-disease relationships. Subsequently, we introduce a novel multi-view contrastive learning framework, named CDPMF-DDA, which enhances the model's ability to capture drug-disease associations by incorporating diverse information representations from different views. First, we decompose the original drug-disease association matrix into drug and disease feature matrices, which are then used to reconstruct the drug-disease association network, as well as the drug-drug and disease-disease similarity networks. This process effectively reduces noise in the data, establishing a reliable foundation for the networks produced. Next, we generate multiple contrastive views from both the original and generated networks. These views effectively capture hidden feature associations, significantly enhancing the model's ability to represent complex relationships. Extensive cross-validation experiments on three standard datasets show that CDPMF-DDA achieves an average AUC of 0.9475 and an AUPR of 0.5009, outperforming existing models. Additionally, case studies on Alzheimer’s disease and epilepsy further validate the model’s effectiveness, demonstrating its high accuracy and robustness in drug-disease association prediction. Based on a multi-view contrastive learning framework, CDPMF-DDA is capable of integrating multi-source information and effectively capturing complex drug-disease associations, making it a powerful tool for drug repositioning and the discovery of new therapeutic strategies. |
| format | Article |
| id | doaj-art-3555c4f76c7a40f282e5bd1820252e0b |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-3555c4f76c7a40f282e5bd1820252e0b2025-01-12T12:41:53ZengBMCBMC Bioinformatics1471-21052025-01-0126111810.1186/s12859-024-06032-wCDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association predictionXianfang Tang0Yawen Hou1Yajie Meng2Zhaojing Wang3Changcheng Lu4Juan Lv5Xinrong Hu6Junlin Xu7Jialiang Yang8School of Computer Science and Artificial Intelligence, Wuhan Textile UniversitySchool of Computer Science and Artificial Intelligence, Wuhan Textile UniversitySchool of Computer Science and Artificial Intelligence, Wuhan Textile UniversitySchool of Computer Science and Artificial Intelligence, Wuhan Textile UniversityCollege of Computer Science and Electronic Engineering, Hunan UniversityCollege of Traditional Chinese Medicine, Changsha Medical UniversitySchool of Computer Science and Artificial Intelligence, Wuhan Textile UniversitySchool of Computer Science and Technology, Wuhan University of Science and TechnologyGeneis Beijing Co., LtdAbstract The process of new drug development is complex, whereas drug-disease association (DDA) prediction aims to identify new therapeutic uses for existing medications. However, existing graph contrastive learning approaches typically rely on single-view contrastive learning, which struggle to fully capture drug-disease relationships. Subsequently, we introduce a novel multi-view contrastive learning framework, named CDPMF-DDA, which enhances the model's ability to capture drug-disease associations by incorporating diverse information representations from different views. First, we decompose the original drug-disease association matrix into drug and disease feature matrices, which are then used to reconstruct the drug-disease association network, as well as the drug-drug and disease-disease similarity networks. This process effectively reduces noise in the data, establishing a reliable foundation for the networks produced. Next, we generate multiple contrastive views from both the original and generated networks. These views effectively capture hidden feature associations, significantly enhancing the model's ability to represent complex relationships. Extensive cross-validation experiments on three standard datasets show that CDPMF-DDA achieves an average AUC of 0.9475 and an AUPR of 0.5009, outperforming existing models. Additionally, case studies on Alzheimer’s disease and epilepsy further validate the model’s effectiveness, demonstrating its high accuracy and robustness in drug-disease association prediction. Based on a multi-view contrastive learning framework, CDPMF-DDA is capable of integrating multi-source information and effectively capturing complex drug-disease associations, making it a powerful tool for drug repositioning and the discovery of new therapeutic strategies.https://doi.org/10.1186/s12859-024-06032-wDrug-disease association predictionContrastive learningMatrix factorizationMultiple contrastive views |
| spellingShingle | Xianfang Tang Yawen Hou Yajie Meng Zhaojing Wang Changcheng Lu Juan Lv Xinrong Hu Junlin Xu Jialiang Yang CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction BMC Bioinformatics Drug-disease association prediction Contrastive learning Matrix factorization Multiple contrastive views |
| title | CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction |
| title_full | CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction |
| title_fullStr | CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction |
| title_full_unstemmed | CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction |
| title_short | CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction |
| title_sort | cdpmf dda contrastive deep probabilistic matrix factorization for drug disease association prediction |
| topic | Drug-disease association prediction Contrastive learning Matrix factorization Multiple contrastive views |
| url | https://doi.org/10.1186/s12859-024-06032-w |
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