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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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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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