Diagnostic classification of cancers using extreme gradient boosting algorithm and multi-omics data

Accurate diagnostic classification of cancers can greatly help physicians to choose surveillance and treatment strategies for patients. Following the explosive growth of huge amounts of biological data, the shift from traditional biostatistical methods to computer-aided means has made machine-learning methods as an integral part of today's cancer prognosis prediction. In this work, we proposed a classification model by leveraging the power of extreme gradient boosting (XGBoost) and using increasingly complex multi-omics data with the aim to separate early stage and late stage cancers. We applied XGBoost model to four kinds of cancer data downloaded from TCGA and compared its performance with other popular machine-learning methods. The experimental results showed that our method obtained statistically significantly better or comparable predictive performance. The results of this study also revealed that DNA methylation outperforms other molecular data (mRNA expression and miRNA expression) in terms of accuracy and stability for discriminating between early stage and late stage groups. Furthermore, integration of multi-omics data by autoencoder can enhance the classification accuracy of cancer stage. Finally, we conducted bioinformatics analyses to assess the medical utility of the significant genes ranked by their importance using XGBoost algorithm. Extensively comparative experiments demonstrated that the XGBoost method has a remarkable performance in predicting the stage of cancer patients with multi-omics data. Moreover, identification of novel candidate genes associated with cancer stages would contribute to further elucidate disease pathogenesis and develop novel therapeutics.