HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association Prediction
Accumulating scientific evidence highlights the pivotal role of miRNA–disease association research in elucidating disease pathogenesis and developing innovative diagnostics. Consequently, accurately identifying disease-associated miRNAs has emerged as a prominent research topic in bioinformatics. Ad...
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| Formaat: | Artikel |
| Taal: | English |
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MDPI AG
2024-07-01
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| Reeks: | Bioengineering |
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| Online toegang: | https://www.mdpi.com/2306-5354/11/7/680 |
| _version_ | 1827178887650476032 |
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| author | Daying Lu Jian Li Chunhou Zheng Jinxing Liu Qi Zhang |
| author_facet | Daying Lu Jian Li Chunhou Zheng Jinxing Liu Qi Zhang |
| author_sort | Daying Lu |
| collection | DOAJ |
| description | Accumulating scientific evidence highlights the pivotal role of miRNA–disease association research in elucidating disease pathogenesis and developing innovative diagnostics. Consequently, accurately identifying disease-associated miRNAs has emerged as a prominent research topic in bioinformatics. Advances in graph neural networks (GNNs) have catalyzed methodological breakthroughs in this field. However, existing methods are often plagued by data noise and struggle to effectively integrate local and global information, which hinders their predictive performance. To address this, we introduce HGTMDA, an innovative hypergraph learning framework that incorporates random walk with restart-based association masking and an enhanced GCN-Transformer model to infer miRNA–disease associations. HGTMDA starts by constructing multiple homogeneous similarity networks. A novel enhancement of our approach is the introduction of a restart-based random walk association masking strategy. By stochastically masking a subset of association data and integrating it with a GCN enhanced by an attention mechanism, this strategy enables better capture of key information, leading to improved information utilization and reduced impact of noisy data. Next, we build an miRNA–disease heterogeneous hypergraph and adopt an improved GCN-Transformer encoder to effectively solve the effective extraction of local and global information. Lastly, we utilize a combined Dice cross-entropy (DCE) loss function to guide the model training and optimize its performance. To evaluate the performance of HGTMDA, comprehensive comparisons were conducted with state-of-the-art methods. Additionally, in-depth case studies on lung cancer and colorectal cancer were performed. The results demonstrate HGTMDA’s outstanding performance across various metrics and its exceptional effectiveness in real-world application scenarios, highlighting the advantages and value of this method. |
| first_indexed | 2025-03-21T05:06:16Z |
| format | Article |
| id | doaj.art-bc6afdda97794b38be425d9fb8229f3b |
| institution | Directory Open Access Journal |
| issn | 2306-5354 |
| language | English |
| last_indexed | 2025-03-21T05:06:16Z |
| publishDate | 2024-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Bioengineering |
| spelling | doaj.art-bc6afdda97794b38be425d9fb8229f3b2024-07-26T12:34:18ZengMDPI AGBioengineering2306-53542024-07-0111768010.3390/bioengineering11070680HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association PredictionDaying Lu0Jian Li1Chunhou Zheng2Jinxing Liu3Qi Zhang4School of Cyber Science and Engineering, Qufu Normal University, Qufu 273165, ChinaSchool of Cyber Science and Engineering, Qufu Normal University, Qufu 273165, ChinaSchool of Cyber Science and Engineering, Qufu Normal University, Qufu 273165, ChinaSchool of Cyber Science and Engineering, Qufu Normal University, Qufu 273165, ChinaSchool of Cyber Science and Engineering, Qufu Normal University, Qufu 273165, ChinaAccumulating scientific evidence highlights the pivotal role of miRNA–disease association research in elucidating disease pathogenesis and developing innovative diagnostics. Consequently, accurately identifying disease-associated miRNAs has emerged as a prominent research topic in bioinformatics. Advances in graph neural networks (GNNs) have catalyzed methodological breakthroughs in this field. However, existing methods are often plagued by data noise and struggle to effectively integrate local and global information, which hinders their predictive performance. To address this, we introduce HGTMDA, an innovative hypergraph learning framework that incorporates random walk with restart-based association masking and an enhanced GCN-Transformer model to infer miRNA–disease associations. HGTMDA starts by constructing multiple homogeneous similarity networks. A novel enhancement of our approach is the introduction of a restart-based random walk association masking strategy. By stochastically masking a subset of association data and integrating it with a GCN enhanced by an attention mechanism, this strategy enables better capture of key information, leading to improved information utilization and reduced impact of noisy data. Next, we build an miRNA–disease heterogeneous hypergraph and adopt an improved GCN-Transformer encoder to effectively solve the effective extraction of local and global information. Lastly, we utilize a combined Dice cross-entropy (DCE) loss function to guide the model training and optimize its performance. To evaluate the performance of HGTMDA, comprehensive comparisons were conducted with state-of-the-art methods. Additionally, in-depth case studies on lung cancer and colorectal cancer were performed. The results demonstrate HGTMDA’s outstanding performance across various metrics and its exceptional effectiveness in real-world application scenarios, highlighting the advantages and value of this method.https://www.mdpi.com/2306-5354/11/7/680miRNA–disease associationGCN-Transformerrandom walk with restarthypergraph learning |
| spellingShingle | Daying Lu Jian Li Chunhou Zheng Jinxing Liu Qi Zhang HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association Prediction Bioengineering miRNA–disease association GCN-Transformer random walk with restart hypergraph learning |
| title | HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association Prediction |
| title_full | HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association Prediction |
| title_fullStr | HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association Prediction |
| title_full_unstemmed | HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association Prediction |
| title_short | HGTMDA: A Hypergraph Learning Approach with Improved GCN-Transformer for miRNA–Disease Association Prediction |
| title_sort | hgtmda a hypergraph learning approach with improved gcn transformer for mirna disease association prediction |
| topic | miRNA–disease association GCN-Transformer random walk with restart hypergraph learning |
| url | https://www.mdpi.com/2306-5354/11/7/680 |
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