Unsupervised Learning of Cross-Modal Mappings in Multi-Omics data for Survival Stratification of Gastric Cancer

Abstract

Aims: This study presents a survival stratification model based on multi-omics integration using bidirectional deep neural networks (BiDNNs) in gastric cancer. Methods: Based on the survival-related representation features yielded by BiDNNs through integrating transcriptomics and epigenomics data, K-means clustering analysis was performed to cluster tumor samples into different survival subgroups. The BiDNNs-based model was validated using tenfold cross-validation and in two independent confirmation cohorts. Results: Using the BiDNNs-based survival stratification model, patients were grouped into two survival subgroups with log-rank p-value = 9.05E-05. The subgroups classification was robustly validated in tenfold cross-validation (C-index = 0.65 ± 0.02) and in two confirmation cohorts (E-GEOD-26253, C-index = 0.609; E-GEOD-62254, C-index = 0.706). Conclusion: We propose and validate a robust and stable BiDNN-based survival stratification model in gastric cancer.

Keywords::

• BiDNNs
• cross-modal mappings
• disease modeling
• gastric cancer
• machine learning
• multi-omics integration
• patient stratification
• risk assessment

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/fon-2021-1059

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.