SurvBoard: standardized benchmarking for multi-omics cancer survival models.

Abstract

Multi-omics data, which include genomic, transcriptomic, epigenetic, and proteomic data, are gaining increasing importance for determining the clinical outcomes of cancer patients. Several recent studies have evaluated various multimodal integration strategies for cancer survival prediction, highlighting the need for standardizing model performance results. Addressing this issue, we introduce SurvBoard, a benchmark framework that standardizes key experimental design choices. SurvBoard enables comparisons between single-cancer and pan-cancer data models and assesses the benefits of using patient data with missing modalities. We also address common pitfalls in preprocessing and validating multi-omics cancer survival models. We apply SurvBoard to several exemplary use cases, further confirming that statistical models tend to outperform deep learning methods, especially for metrics measuring survival function calibration. Moreover, most models exhibit better performance when trained in a pan-cancer context and can benefit from leveraging samples for which data of some omics modalities are missing. We provide a web service for model evaluation and to make our benchmark results easily accessible and viewable: https://www.survboard.science/. All code is available on GitHub: https://github.com/BoevaLab/survboard/. All benchmark outputs are available on Zenodo: 10.5281/zenodo.11066226. A video tutorial on how to use the Survboard leaderboard is available on YouTube at https://youtu.be/HJrdpJP8Vvk.