CPSM: R-package of an Automated Machine Learning Pipeline for Predicting the Survival Probability of Single Cancer Patient

Abstract

Accurate survival prediction is vital for optimizing treatment strategies in clinical practice. The advent of high-throughput multi-omics data and computational methods has enabled machine learning (ML) models for survival analysis. However, handling high-dimensional omics data remains challenging. This study introduces the Cancer Patient Survival Model (CPSM), an R package developed to provide individualized survival predictions through a fully integrated and reproducible computational pipeline. The CPSM package encompasses nine modules that streamline the survival modeling workflow, organized into four key stages: (1) Data Preprocessing and Normalization, (2) Feature Selection, (3) Survival Prediction Model Development, and (4) Visualization. The visual tools facilitate the interpretation of survival predictions, enhancing clinical decision-making. By providing an end-to-end solution for multi-omics data integration and analysis, CPSM not only enhances the precision of survival predictions but also aids in discovering clinically relevant biomarkers. Availability and ImplementationThe CPSM Package is freely available at the GitHub URL: https://github.com/hks5august/CPSM