A repository that contains some code related to my Dissertation, focused on feature engineering in large oncology data.
Pre- and post-processing of DAE-constructed features.
Holdout data selection using a continuous stratification approach.
Monte carlo simulations for empirical validation of the continuous stratification approach; including generation of simulated mRNAseq data, simulated outcomes using Weibull survival time generators, and evaluation of extra-sample performance estimation approaches with multiple survival model types and metrics.
This script is designed to run in parallel on SGE, so it is called with a command-line parameter indicating whether to: a) generate simulated data, b) run a specific simulation and write the results to a file, or c) aggregate output files of all completed simulations for analysis.
Script for downloading TCGA-HNSC data.