Survival analysis in breast cancer: evaluating ensemble learning techniques for prediction

Abstract

Breast cancer is most commonly faced with form of cancer amongst women worldwide. In spite of the fact that the breast cancer research and awareness have gained considerable momentum, there is still no one treatment due to disease heterogeneity. Survival data may be of specific interest in breast cancer studies to understand its dynamic and complex trajectories. This study copes with the most important covariates affecting the disease progression. The study utilizes the German Breast Cancer Study Group 2 (GBSG2) and the Molecular Taxonomy of Breast Cancer International Consortium dataset (METABRIC) datasets. In both datasets, interests lie in relapse of the disease and the time when the relapse happens. The three models, namely the Cox proportional hazards (PH) model, random survival forest (RSF) and conditional inference forest (Cforest) were employed to analyse the breast cancer datasets. The goal of this study is to apply these methods in prediction of breast cancer progression and compare their performances based on two different estimation methods: the bootstrap estimation and the bootstrap .632 estimation. The model performance was evaluated in concordance index (C-index) and prediction error curves (pec) for discrimination. The Cox PH model has a lower C-index and bigger prediction error compared to the RSF and the Cforest approach for both datasets. The analysis results of GBSG2 and METABRIC datasets reveal that the RSF and the Cforest algorithms provide non-parametric alternatives to Cox PH model for estimation of the survival probability of breast cancer patients.

Keywords

• Conditional inference forest
• C-index
• Integrated Brier score
• Prediction error curve
• Random survival forest
• METABRIC