Cancer subtype identification by multi-omics clustering based on interpretable feature and latent subspace learning.
Methods
; 231: 144-153, 2024 Sep 24.
Article
em En
| MEDLINE
| ID: mdl-39326482
ABSTRACT
In recent years, multi-omics clustering has become a powerful tool in cancer research, offering a comprehensive perspective on the diverse molecular characteristics inherent to various cancer subtypes. However, most existing multi-omics clustering methods directly integrate heterogeneous features from different omics, which may struggle to deal with the noise or redundancy of multi-omics data and lead to poor clustering results. Therefore, we propose a novel multi-omics clustering method to extract interpretable and discriminative features from various omics before data integration. The clinical information is used to supervise the process of feature extraction based on SHAP (SHapley Additive exPlanation) values. Singular value decomposition (SVD) is then applied to integrate the extracted features of different omics by constructing a latent subspace. Finally, we utilize shared nearest neighbor-based spectral clustering on the latent representation to obtain the clustering result. The proposed method is evaluated on several cancer datasets across three levels of omics, in comparison to several state-of-the-art multi-omics clustering methods. The comparison results demonstrate the superior performance of the proposed method in multi-omics data analysis for cancer subtyping. Additionally, experiments reveal the efficacy of utilizing clinical information based on SHAP values for feature extraction, enhancing the performance of clustering analyses. Moreover, enrichment analysis of the identified gene signatures in different subtypes is also performed to further demonstrate the effectiveness of the proposed method. Availability:
The proposed method can be freely accessible at https//github.com/Tianyi-Shi-Tsukuba/Multi-omics-clustering-based-on-SHAP. Data will be made available on request.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Idioma:
En
Revista:
Methods
/
Methods (S. Diego)
/
Methods (San Diego)
Assunto da revista:
BIOQUIMICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Japão
País de publicação:
Estados Unidos