Deep learning-based cancer survival prognosis from RNA-seq data: Approaches and evaluations

Zhi Huang, Travis S. Johnson, Zhi Han, Bryan Helm, Sha Cao, Chi Zhang, Paul Salama, Maher Rizkalla, Christina Y. Yu, Jun Cheng, Shunian Xiang, Xiaohui Zhan, Jie Zhang, Kun Huang

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

Background: Recent advances in kernel-based Deep Learning models have introduced a new era in medical research. Originally designed for pattern recognition and image processing, Deep Learning models are now applied to survival prognosis of cancer patients. Specifically, Deep Learning versions of the Cox proportional hazards models are trained with transcriptomic data to predict survival outcomes in cancer patients. Methods: In this study, a broad analysis was performed on TCGA cancers using a variety of Deep Learning-based models, including Cox-nnet, DeepSurv, and a method proposed by our group named AECOX (AutoEncoder with Cox regression network). Concordance index and p-value of the log-rank test are used to evaluate the model performances. Results: All models show competitive results across 12 cancer types. The last hidden layers of the Deep Learning approaches are lower dimensional representations of the input data that can be used for feature reduction and visualization. Furthermore, the prognosis performances reveal a negative correlation between model accuracy, overall survival time statistics, and tumor mutation burden (TMB), suggesting an association among overall survival time, TMB, and prognosis prediction accuracy. Conclusions: Deep Learning based algorithms demonstrate superior performances than traditional machine learning based models. The cancer prognosis results measured in concordance index are indistinguishable across models while are highly variable across cancers. These findings shedding some light into the relationships between patient characteristics and survival learnability on a pan-cancer level.

Original languageEnglish (US)
Article number41
JournalBMC Medical Genomics
Volume13
DOIs
StatePublished - Apr 3 2020

Keywords

  • Cancer prognosis
  • Cox regression
  • Deep learning
  • Survival analysis
  • Tumor mutation burden

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Huang, Z., Johnson, T. S., Han, Z., Helm, B., Cao, S., Zhang, C., Salama, P., Rizkalla, M., Yu, C. Y., Cheng, J., Xiang, S., Zhan, X., Zhang, J., & Huang, K. (2020). Deep learning-based cancer survival prognosis from RNA-seq data: Approaches and evaluations. BMC Medical Genomics, 13, [41]. https://doi.org/10.1186/s12920-020-0686-1