Transfer learning project

This repository is the official implementation of Julian van Toledo's MSc Project.

Howto

• 1: TODO preprocessingscript.R/Preprocessing_icgc.R description
• 2: Run hyperparam_opt.py

Requirements

Python 3.7.12
R version 4.2.0
Keras - 2.9.0

See imports in nnetsurvivaltransfer.ipynb for further dependencies

Scripts

nnetsurvivaltransfer.ipynb - Jupyter Notebook containing the transfer learning model and various experiments that were performed
preprocessingscript.R - Preprocessing of the TCGA data broken
Preprocessing_icgc.R - Preprocessing of the ICGC data

TensorBoardNotebook.ipynb - Notebook containing a simple script to start TensorBoard which allows users to view training logs of their model
nnet_survival.py - Script of nnet_survival containing loss function, proportional hazards layer, and function to make survival matrices cox_nnet_v2.py - Script containing the Cox-nnet model which is used for comparison to our model