Add complete runnable BulkRNA-BERT TCGA survival example with all data #711

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Open

jlinecodes wants to merge 4 commits into sunlabuiuc:master from jlinecodes:add-bulkrna-bert-example

jlinecodes commented Dec 8, 2025

Fully self-contained BulkRNA-BERT reproduction example:

bulk_rna_bert_tcga_survival.py (complete script with model, ablations, plots)
All 8 required real TCGA files included in examples/
Runs immediately on free Google Colab or locally (<15 min)
Includes C-index, Kaplan-Meier, heatmaps, dendrograms, and required test
Zero setup needed — perfect reproducibility

jlinecodes added 4 commits

December 7, 2025 19:43


          Create bulk_rna_bert_tcga_survival.ipynb

cc20e1c


          Delete examples/bulk_rna_bert_tcga_survival.ipynb

3879eac


          Create bulk_rna_bert_tcga_survival.py

28d196e


          Add files via upload

dcab4a0

files needed to run the code, no setup needed

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet