GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing
Abstract Background The main focus of in silico drug repurposing, which is a promising area for using artificial intelligence in drug discovery, is the prediction of drug–disease relationships. Although many computational models have been proposed recently, it is still difficult to reliably predict...
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| Format: | Article |
| Language: | English |
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BMC
2022-09-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-022-04911-8 |
| _version_ | 1828148189258055680 |
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| author | Fan Zhang Wei Hu Yirong Liu |
| author_facet | Fan Zhang Wei Hu Yirong Liu |
| author_sort | Fan Zhang |
| collection | DOAJ |
| description | Abstract Background The main focus of in silico drug repurposing, which is a promising area for using artificial intelligence in drug discovery, is the prediction of drug–disease relationships. Although many computational models have been proposed recently, it is still difficult to reliably predict drug–disease associations from a variety of sources of data. Results In order to identify potential drug–disease associations, this paper introduces a novel end-to-end model called Graph convolution network based on a multimodal attention mechanism (GCMM). In particular, GCMM incorporates known drug–disease relations, drug–drug chemical similarity, drug–drug therapeutic similarity, disease–disease semantic similarity, and disease–disease target-based similarity into a heterogeneous network. A Graph Convolution Network encoder is used to learn how diseases and drugs are embedded in various perspectives. Additionally, GCMM can enhance performance by applying a multimodal attention layer to assign various levels of value to various features and the inputting of multi-source information. Conclusion 5 fold cross-validation evaluations show that the GCMM outperforms four recently proposed deep-learning models on the majority of the criteria. It shows that GCMM can predict drug–disease relationships reliably and suggests improvement in the desired metrics. Hyper-parameter analysis and exploratory ablation experiments are also provided to demonstrate the necessity of each module of the model and the highest possible level of prediction performance. Additionally, a case study on Alzheimer’s disease (AD). Four of the five medications indicated by GCMM to have the highest potential correlation coefficient with AD have been demonstrated through literature or experimental research, demonstrating the viability of GCMM. All of these results imply that GCMM can provide a strong and effective tool for drug development and repositioning. |
| first_indexed | 2024-04-11T21:11:30Z |
| format | Article |
| id | doaj.art-ea98624d1cdd4e31a37fd9a964fea7cb |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-11T21:11:30Z |
| publishDate | 2022-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-ea98624d1cdd4e31a37fd9a964fea7cb2022-12-22T04:03:00ZengBMCBMC Bioinformatics1471-21052022-09-0123111710.1186/s12859-022-04911-8GCMM: graph convolution network based on multimodal attention mechanism for drug repurposingFan Zhang0Wei Hu1Yirong Liu2School of Information Science and Technology, University of Science and Technology of ChinaSchool of Information Science and Technology, University of Science and Technology of ChinaSchool of Information Science and Technology, University of Science and Technology of ChinaAbstract Background The main focus of in silico drug repurposing, which is a promising area for using artificial intelligence in drug discovery, is the prediction of drug–disease relationships. Although many computational models have been proposed recently, it is still difficult to reliably predict drug–disease associations from a variety of sources of data. Results In order to identify potential drug–disease associations, this paper introduces a novel end-to-end model called Graph convolution network based on a multimodal attention mechanism (GCMM). In particular, GCMM incorporates known drug–disease relations, drug–drug chemical similarity, drug–drug therapeutic similarity, disease–disease semantic similarity, and disease–disease target-based similarity into a heterogeneous network. A Graph Convolution Network encoder is used to learn how diseases and drugs are embedded in various perspectives. Additionally, GCMM can enhance performance by applying a multimodal attention layer to assign various levels of value to various features and the inputting of multi-source information. Conclusion 5 fold cross-validation evaluations show that the GCMM outperforms four recently proposed deep-learning models on the majority of the criteria. It shows that GCMM can predict drug–disease relationships reliably and suggests improvement in the desired metrics. Hyper-parameter analysis and exploratory ablation experiments are also provided to demonstrate the necessity of each module of the model and the highest possible level of prediction performance. Additionally, a case study on Alzheimer’s disease (AD). Four of the five medications indicated by GCMM to have the highest potential correlation coefficient with AD have been demonstrated through literature or experimental research, demonstrating the viability of GCMM. All of these results imply that GCMM can provide a strong and effective tool for drug development and repositioning.https://doi.org/10.1186/s12859-022-04911-8Computational drug repurposingGraph convolutional networkAttention mechanismHeterogeneous information |
| spellingShingle | Fan Zhang Wei Hu Yirong Liu GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing BMC Bioinformatics Computational drug repurposing Graph convolutional network Attention mechanism Heterogeneous information |
| title | GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing |
| title_full | GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing |
| title_fullStr | GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing |
| title_full_unstemmed | GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing |
| title_short | GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing |
| title_sort | gcmm graph convolution network based on multimodal attention mechanism for drug repurposing |
| topic | Computational drug repurposing Graph convolutional network Attention mechanism Heterogeneous information |
| url | https://doi.org/10.1186/s12859-022-04911-8 |
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