Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data.

Bo Yang, Chenxi Cui, Meng Wang, Hong Ji, Feiyue Gao
Author Information
  1. Bo Yang: School of Computer Science & The Shaanxi Key Laboratory of Clothing Intelligence, Xi'an Polytechnic University, Xi'an 710048, China. ORCID
  2. Chenxi Cui: School of Computer Science & The Shaanxi Key Laboratory of Clothing Intelligence, Xi'an Polytechnic University, Xi'an 710048, China. ORCID
  3. Meng Wang: School of Computer Science & The Shaanxi Key Laboratory of Clothing Intelligence, Xi'an Polytechnic University, Xi'an 710048, China. ORCID
  4. Hong Ji: School of Computer Science & The Shaanxi Key Laboratory of Clothing Intelligence, Xi'an Polytechnic University, Xi'an 710048, China.
  5. Feiyue Gao: School of Computer Science & The Shaanxi Key Laboratory of Clothing Intelligence, Xi'an Polytechnic University, Xi'an 710048, China.

Abstract

Cancer is a highly diverse group of diseases, and each type of cancer can be further divided into various subtypes according to specific characteristics, cellular origins, and molecular markers. Subtyping helps in tailoring treatment and prognosis accuracy. However, the existing studies are more concerned with integrating different omics data to discover potential connections, but ignoring the relationships between consensus information and individual information within each omics level during the integration process. To this end, we propose a novel fusion-free method called multi-view multi-level contrastive graph convolutional network (M$^{2}$CGCN) for cancer subtyping. M$^{2}$CGCN learns multi-level features, i.e. high-level and low-level features, respectively. The low-level features from each view capture the intrinsic information in each omics by reconstruction of node attribute and graph structures. The high-level features achieve cancer subtyping via contrastive learning. Comprehensive experiments were performed on 34 multi-omics cancer datasets. The findings indicate that M$^{2}$CGCN achieves results comparable to or surpassing many state-of-the-art methods.

Keywords

References

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Grants

  1. 2024JCYBMS-473/Natural Science Basic Research Program of Shaanxi
  2. 24YJA880034/Humanities and Social Science Foundation of Ministry of Education of China
  3. 61972312/National Natural Science Foundation of China
  4. 22JS019/Scientific Research Program Funded by Shaanxi Provincial Education Department

MeSH Term

Humans
Neoplasms
Computational Biology
Neural Networks, Computer
Genomics
Algorithms
Biomarkers, Tumor
Multiomics

Chemicals

Biomarkers, Tumor

Word Cloud

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