Classification of Sarcoma Based on Genomic Data Using Machine Learning Models

Abstract

The proposed work provides a new machine-learnt classification approach for the various types of soft tissue sarcoma based on genomics data which addresses a considerable gap in sarcoma diagnostics. The previous studies have investigated various aspects of sarcoma but this study is unique in that it targets the predicting sarcoma variant types using genetic information, which has not been done before. Random Forest was used as the meta-estimator and a stacking ensemble model comprising of Random Forest, Extreme Gradient Boosting and LightGBM were used for this study. The model which was trained and validated on a complete dataset of 206 adult soft tissue sarcoma samples containing genomic alterations, transcriptomic, epigenomic and proteomic data achieved an accuracy of 89.44% at a precision level as high as 91%. Stratified k-fold cross validation is employed to ensure that class imbalance is not a hindrance to performance. This innovative approach outmatches single classifiers and traditional single model methods at great length hence making it possible and effective to use machine learning on genomic data for predicting sarcoma variants. Thus, the findings from this research could change cancer diagnosis forever; they promise more accurate classification as well as personalized treatment modalities while also providing a framework for analogous applications in other rare complex cancers.