A laminar augmented cascading flexible neural forest model for classification of cancer subtypes based on gene expression data

Abstract

Abstract Background Correctly classifying the subtypes of cancer is of great significance for the in-depth study of cancer pathogenesis and the realization of personalized treatment for cancer patients. In recent years, classification of cancer subtypes using deep neural networks and gene expression data has gradually become a research hotspot. However, most classifiers may face overfitting and low classification accuracy when dealing with small sample size and high-dimensional biology data. Results In this paper, a laminar augmented cascading flexible neural forest (LACFNForest) model was proposed to complete the classification of cancer subtypes. This model is a cascading flexible neural forest using deep flexible neural forest (DFNForest) as the base classifier. A hierarchical broadening ensemble method was proposed, which ensures the robustness of classification results and avoids the waste of model structure and function as much as possible. We also introduced an output judgment mechanism to each layer of the forest to reduce the computational complexity of the model. The deep neural forest was extended to the densely connected deep neural forest to improve the prediction results. The experiments on RNA-seq gene expression data showed that LACFNForest has better performance in the classification of cancer subtypes compared to the conventional methods. Conclusion The LACFNForest model effectively improves the accuracy of cancer subtype classification with good robustness. It provides a new approach for the ensemble learning of classifiers in terms of structural design.

Keywords

• Cancer subtype
• Cascade forest
• Classification
• Deep learning
• Ensemble methods