Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions

• Published in: PloS one 2022-09, Vol.17 (9)
• Main Author: Li-Pang Chen
• Format: Article
• Language: English
• ISSN: 1932-6203
• DOI: 10.1371/journal.pone.0274440

Analysis of gene expression data is an attractive topic in the field of bioinformatics, and a typical application is to classify and predict individuals’ diseases or tumors by treating gene expression values as predictors. A primary challenge of this study comes from ultrahigh-dimensionality, which makes that (i) many predictors in the dataset might be non-informative, (ii) pairwise dependence structures possibly exist among high-dimensional predictors, yielding the network structure. While many supervised learning methods have been developed, it is expected that the prediction performance would be affected if impacts of ultrahigh-dimensionality were not carefully addressed. In this paper, we propose a new statistical learning algorithm to deal with multi-classification subject to ultrahigh-dimensional gene expressions. In the proposed algorithm, we employ the model-free feature screening method to retain informative gene expression values from ultrahigh-dimensional data, and then construct predictive models with network structures of selected gene expression accommodated. Different from existing supervised learning methods that build predictive models based on entire dataset, our approach is able to identify informative predictors and dependence structures for gene expression. Throughout analysis of a real dataset, we find that the proposed algorithm gives precise classification as well as accurate prediction, and outperforms some commonly used supervised learning methods.