Enhanced directed random walk for the identification of breast cancer prognostic markers from multiclass expression data

Abstract

Artificial intelligence in healthcare can potentially identify the probability of contracting a particular disease more accurately. There are five common molecular subtypes of breast cancer: luminal A, luminal B, basal, ERBB2, and normal‐like. Previous investigations showed that pathway-based microarray analysis could help in the identification of prognostic markers from gene expres-sions. For example, directed random walk (DRW) can infer a greater reproducibility power of the pathway activity between two classes of samples with a higher classification accuracy. However, most of the existing methods (including DRW) ignored the characteristics of different cancer sub-types and considered all of the pathways to contribute equally to the analysis. Therefore, an enhanced DRW (eDRW+) is proposed to identify breast cancer prognostic markers from multiclass expression data. An improved weight strategy using one‐way ANOVA (F‐test) and pathway selection based on the greatest reproducibility power is proposed in eDRW+. The experimental results show that the eDRW+ exceeds other methods in terms of AUC. Besides this, the eDRW+ identifies 294 gene markers and 45 pathway markers from the breast cancer datasets with better AUC. There-fore, the prognostic markers (pathway markers and gene markers) can identify drug targets and look for cancer subtypes with clinically distinct outcomes.