Here is an explanation of the files in this repo.
Discrete Survival Demo.ipynb - Notebook that shows whole process of building and running survival models. Can be run in new environment after pip installing requirements.txt. Takes a couple hours to run. In the end, it generates a plot similar to lossdiff_boxplot2.svg
lossdiff_boxplot.svg - Plot of difference between loss of respective fold and disease of baseline model and transfer model
binding/baseline_losses.csv - Loss values for each fold and disease for baseline models
binding/transfer_losses.csv - Loss values for each fold and disease for transfer models
Feature importance table generated by iterating across all features and randomly shuffling one feature while holding all others constant. The more that the loss increases when shuffling a particular feature, the more important we can assume that feature to be.
binding/global_feature_importance.csv - Feature importance table for global model.
binding/ind_disease_transfer_feature_importance.csv - Feature importance table for each specific disease
binding/shuffled_hallmark_disease_importance.csv - Hallmark importance generated by only shuffling those set of genes simultaneously and holding other genes constant (and finding diff in loss with no shuffling at all) for specific diseases
binding/shuffled_hallmark_global_importance.csv - Hallmark importance for global model
requirements.txt - Python dependencies to be installed in new environment
nnet_survival.py - Python file containing survival model functions
genes_pubmedcounts_glioma.csv - Table of gene names and number of PubMed articles regarding the gene. Articles restricted to those listed when searching for glioma MeSH term.
genes_pubmedcounts_prostate.csv - Table of gene names and number of PubMed articles regarding the gene. Articles restricted to those listed when searching for prostatic neoplasm MeSH term.
To run Discrete Survival Demo.ipynb, run the following command to install dependencies in your environment:
pip install -r requirements.txt
Next, in Discrete Survival Demo.ipynb's 2nd cell, cd to TransferSRNN directory which you git cloned.
Now you can run all the cells