This repository contains the code and material to reproduce the results of the manuscript "Gradient-based Explanations for Deep Learning Survival Models". The paper is currently under review.
setup.R: R environment setup script that installs required packages, the necessary conda environmentSurvinng_paper, and sets global optionsSim_time_dependent.Rmd: Simulation for time-dependent features. The results used in the paper are stored in the notebookSim_time_dependent.htmland figures are saved in thefigures_paper/directory.Sim_time_independent.Rmd: Simulation for time-independent features. The results used in the paper are stored in the notebookSim_time_independent.htmland figures are saved in thefigures_paper/directory.Sim_GradSHAP: Simulation for comparing GradSHAP(t) and SurvSHAP(t) on time-independent features regarding runtime, local accuarcy and feature ranking.real_data/: Scripts for reproducing the results on the real data example.Survinng.zip: The corresponding R package for the paper.figures_paper/: Directory for storing the figures used in the paper.
-
To reproduce the results, from "TIME-INDEPENDENT EFFECTS" Section, run the RMarkdown file
Sim_time_independent.Rmdand the results will be storedSim_time_independent.htmland the figures in thefigures_paper/directory. -
To reproduce the results, from "TIME-DEPENDENT EFFECTS" Section, run the RMarkdown file
Sim_time_dependent.Rmdand the results will be storedSim_time_dependent.htmland the figures in thefigures_paper/directory. -
To reproduce the results, from "GRADSHAP(T) VS. SURVSHAP(T)" Section, run the R file
Sim_GradSHAP/Sim_GradSHAP.Rand the figures will be stored in thefigures_paper/directory. Note: This simulation is computationally expensive and conducts a simulation study usingbatchtools. -
To reproduce the results, from "REAL DATA EXAMPLE" Section, we refer to the README file in the folder
real_data/.
The script setup.R tries to install the necessary packages and the conda
environment Survinng_paper (see file env_survinng_paper.yml).
It installs the following R packages:
Survival packages
simsurvsurvivalsurvminerSurvMetricsSurvinng(from theSurvinng.zipfile)survexsurvivalmodelstorch(necessary for theSurvinngpackage)
Plotting and other useful packages
ggplot2cowplotviridisdplyrtidyrreticulatecallrheredata.tablebatchtools