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Merged
mducducd merged 87 commits into from
Nov 26, 2025
Merged

Dev/multitask - STAMP extended for regression and survival analysis (v2.4 update) #132

mducducd merged 87 commits into from
Nov 26, 2025

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@mducducd mducducd commented Oct 20, 2025 •
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Stamp v2.4

  • Add support for regression and survival analysis tasks.
    • Regression with MAE loss.
    • Cox-based survival analysis, currently supporting title-level training.
  • Add TransMIL (NeurIPS 2021) as a new attention-based model.
  • Training now supports optional backbones: Attention (ViT), TransMIL, and MLP.
  • All backbone types can perform tile-level or patient-level modeling by automatic ModelClass initialization based on feature type and task.
  • Add new statistics: Regression → R², Pearson r, Pearson p, MAE, RMSE. Survival → Kaplan–Meier curve, log-rank p-value, C-index.
  • Added probability heatmaps for regression and survival analysis.

mducducd and others added 30 commits August 22, 2025 09:05
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reconstruct classifiers in modeling
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reconstruct modeling
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set seed
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add ctranformer
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clean
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fix model register in heatmap
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clean
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format
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remove redundant
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class remake to not touch current heatmap and tests
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fix test model
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format
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fix deploy model
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add base class
cfe8bd4
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add base class
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.
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Merge branch 'KatherLab:main' into feature/regression
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deploy regression
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Merge remote-tracking branch 'origin/feature/regression' into feature…
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…/regression
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add l1 cc statistics
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add l1 cc statistics
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update statistics
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update
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refine construction
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refine construction
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add task and supported ft hparams to model
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fix warning
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survival dev
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reconstruct
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Update config schema
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mducducd commented Oct 28, 2025

I found that regression and survival heatmaps are meaningless without determining gradient range.
So min and max prediction values from training need to be saved to the model, serving for heatmap and especially getting the cut_off for survival statistics.

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mducducd commented Nov 6, 2025

I’ve added both slide-level and patient-level support for regression and survival tasks (only mlp can be trained). Just a few more steps are needed to add tests.

s1787956
s1787956 reviewed Nov 6, 2025
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I am very happy, great job Duc! I think we can merge tomorrow.

AsierRabasco
AsierRabasco reviewed Nov 16, 2025
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src/stamp/modeling/train.py
# Sample count for training
log_total_class_summary(patient_to_data, categories)

# Stratified split
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The stratified split is also needed for survival, the variable for the StratifiedKFold should be the event marker. I did not see it in the code, make sure that the stratification variable for survival is set

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@mducducd mducducd Nov 17, 2025

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Thanks for pointing it out. I have just added it and also strengthened event labels handling.

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mducducd commented Nov 18, 2025

Can we merge it today? I will release it as 2.4 :)

@mducducd mducducd merged commit 95e6a10 into main Nov 26, 2025
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@mducducd @s1787956 @AsierRabasco