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

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jlinecodes wants to merge 4 commits intosunlabuiuc:masterfrom
jlinecodes:add-bulkrna-bert-example
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Add complete runnable BulkRNA-BERT TCGA survival example with all data#711
jlinecodes wants to merge 4 commits intosunlabuiuc:masterfrom
jlinecodes:add-bulkrna-bert-example

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@jlinecodes
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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

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github-actions Bot commented Mar 9, 2026

This PR has been automatically marked as stale because it has not had recent activity. It will be closed in 7 days if no further activity occurs.

@github-actions github-actions Bot added the stale label Mar 9, 2026
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This PR has been automatically closed due to inactivity. Please re-open it if you think it is still relevant.

@github-actions github-actions Bot closed this Mar 16, 2026
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