DeSCENT: Deconvolutional Single-Cell RNA-seq Enhances Transcriptome-based Cancer Survival Analysis

MOTIVATION: Single-cell RNA-seq captures tumor heterogeneity, but it is rarely available together with patient survival outcomes. Bulk RNA-seq cohorts provide survival data but lack direct measurements of cellular expression. RESULTS: DeSCENT generates reference-informed cellular profiles from bulk RNA-seq and combines both representations for survival prediction. We evaluated DeSCENT with three survival models on eight TCGA cancer cohorts. Compared with Bulk, DeSCENT improved average C-index and generally improved time-dependent AUC, while integrated Brier score results were mixed. External validation showed higher average C-index than all three baselines, although performance was lower than in internal evaluation. These findings support the use of cellular representations in the evaluated transcriptome-only setting. AVAILABILITY AND IMPLEMENTATION: Code: https://github.com/YonghaoZhao722/DeSCENT. Archival snapshot: doi:10.5281/zenodo.22073099. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.