Cancer survival prediction by learning comprehensive deep feature representation for multiple types of genetic data

• Published in: BMC bioinformatics Vol. 24; no. 1; p. 267
• Main Authors: Hao, Yaru, Jing, Xiao-Yuan, Sun, Qixing
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 28.06.2023; BioMed Central; BMC
• Subjects: Biomarkers; Cancer; Cancer survival prediction; Comprehensive representation; Consensus; Deep learning; DNA Methylation; Electronic data processing; Gene expression; Genetic aspects; Heterogeneity; Humans; Machine learning; Methods; MicroRNA; MicroRNAs; miRNA; Neoplasms - genetics; Neural networks; Oncology, Experimental; Patients; Predictions; Prognosis; Ribonucleic acid; RNA; Shared information; Specific information; Survival; Survival analysis; China; Shared information; Comprehensive representation; Cancer survival prediction; Specific information
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05392-z

Cancer is one of the leading death causes around the world. Accurate prediction of its survival time is significant, which can help clinicians make appropriate therapeutic schemes. Cancer data can be characterized by varied molecular features, clinical behaviors and morphological appearances. However, the cancer heterogeneity problem usually makes patient samples with different risks (i.e., short and long survival time) inseparable, thereby causing unsatisfactory prediction results. Clinical studies have shown that genetic data tends to contain more molecular biomarkers associated with cancer, and hence integrating multi-type genetic data may be a feasible way to deal with cancer heterogeneity. Although multi-type gene data have been used in the existing work, how to learn more effective features for cancer survival prediction has not been well studied. To this end, we propose a deep learning approach to reduce the negative impact of cancer heterogeneity and improve the cancer survival prediction effect. It represents each type of genetic data as the shared and specific features, which can capture the consensus and complementary information among all types of data. We collect mRNA expression, DNA methylation and microRNA expression data for four cancers to conduct experiments. Experimental results demonstrate that our approach substantially outperforms established integrative methods and is effective for cancer survival prediction. https://github.com/githyr/ComprehensiveSurvival .