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Fix prediction mask names and background value - #16

Merged

vojtech-cifka merged 133 commits into

masterfrom

fix/mug-prediction-masks

May 20, 2026

Merged

Fix prediction mask names and background value#16
vojtech-cifka merged 133 commits into
masterfrom
fix/mug-prediction-masks

Commits on May 7, 2026
- feat: create ml pipeline for linear probe
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- refactor(ml): switch DataModule to HF datasets with fold-based split
  
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- feat(ml): wire up linear probe training with k-fold CV on cached embeddings
  
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- fix(configs): use override for class_mapping in experiment yaml
  
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- fix(scripts): drop duplicate +ml= from linear-probe submit command
  
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- fix(ml): register random_seed/len resolvers and unflatten class_mapping refs
  
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Commits on May 8, 2026
- fix(ml): accept already-canonical labels in datamodule label map
  
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- feat(ml): class-weighted CE, raise class_coverage_min to 0.5
  
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- fix: sort only tiles parquet
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- fix: log join types of tile keys
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- fix: remove embeddings from the join
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- fix: remove label column
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- fix: prevent overflow
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- Merge remote-tracking branch 'origin/master' into feature/linear-probe
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- feat: add embedding dataset build pipeline
  
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- feat: add class tresholds and run ids
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- fix: wrong run id
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Commits on May 9, 2026
- Merge remote-tracking branch 'origin/master' into feature/embedding-dataset
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- feat: add timing
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- refactor: use pyarrow to avoid to pandas conversion
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- fix: join on keys only
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- fix: typing
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- fix: add prints
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- refactor: use combine chunks
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- fix: lazy-cast embeddings to large_list and stay in Arrow during join
  
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- fix: validate label/tissue_prop columns when derive=False
  
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- chore: remove time
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Commits on May 10, 2026
- feat: add timing
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  8df47aa
- chore: revert to the previous state
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- feat: add prints
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Commits on May 11, 2026
- refactor: use discusssed thresholds
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- refactor: use different labeling strategy
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- feat: implement training pipeline
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- feat: add class weights
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- refactor: join embeddings with metadata while loading the dataset
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- feat: add prints
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- fix: use chunks
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- fix: use numpy chunks
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- fix: call end at the end of the main
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- chore: remove prints
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- chore: remove debug prints, stale TODO, and unused preprocessing pipeline
  
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- chore: remove markdown file
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Commits on May 12, 2026
- fix: edge cases
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  6b7d1e8
- feat: normalize the confusion matrix rows per class recall
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- fix: format
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- feat: use stratified k fold run
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- fix: remove criterion
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- fix: remove criterion from configs
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Commits on May 13, 2026
- feat: implement test pipeline
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- fix: Hydra unreached
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- fix: set weights only to false
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- fix: criterion weight
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- Merge branch 'master' into feature/ml-linear-classifier
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- feat: add option to use different kfold strategies
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- feat: add training without validation
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- feat: implement final test run
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- fix: lower LR and patience
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Commits on May 14, 2026
- fix: use f1 macro as a monitor
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  efde82a
- fix: rever back to validation loss
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  c8102de
- fix: add weight decay 1e-3 to linear classifier
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- Revert "fix: add weight decay 1e-3 to linear classifier"
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- feat: add logistic regression
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- feat: polish and add two distinct submission scripts
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- fix: submission scripts
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- feat: implement knn
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  ff8d0bf
- refactor: focus on convergence
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- Remove kNN sklearn baseline
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- fix: change monitor to focus on train losss
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- feat: add run name
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Commits on May 15, 2026
Commits on May 16, 2026
- feat: implement prediction maps
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- fix: change the adamw checkpoint dir name to last
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- fix: lower the batch so the compute does not hang
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- fix: put num workers to 0
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- feat: add prints
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- Merge branch 'master' into feature/ml-test-mode
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- feat: add diagnostic prints
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- fix: use numpy buffer
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- refactor: use HeatmapAssembler
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- chore: clean config structure
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- fix: prediction maps class indices
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- fix: format and mypy
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Commits on May 17, 2026
- feat: add posibility to predict the whole slide with tissue area
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- feat: add embeddings for whole slide
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- refactor: compute grayscale mask per each class
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- feat: add the provgigapath train and test runs
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- feat: set final weight decay for train
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Commits on May 18, 2026
- feat: turn on prediction maps for the test runs over the annotated regions only
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- refactor: do not generate error masks
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- chore: config cleanup
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- feat: add prints to the prediction maps writer
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- feat: add embeddings run id for the whole tissue tiles run
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- feat: add prediction maps in configs
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- chore: deduplicate, apply safety nets
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- Merge branch 'feature/ml-test-mode' into feature/provgigapath-metrics-test
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- fix: pytorch checkpoint loading
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- chore: remove redundancy, rename variables
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- chore: remove username and branch
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- refactor: rename configs
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  847c3cc
- Merge branch 'feature/ml-test-mode' into feature/provgigapath-metrics-test
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- chore: remove pgp test prediction maps
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- fix: keep criterion.weight in state_dict for strict checkpoint load
  
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  2ba0562
- fix: criterion weight
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  e370417
- fix: keep space in MUG prediction masks names
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- fix: log test accuracy as jsons
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- chore: remove username from the submission script
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- fix: force the entering of the write phase of the prediction maps
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- fix: surface why prediction-map write phase skips
  
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- fix: remove username
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- feat: generate embeddings up to a budget
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- Merge branch 'feature/ml-test-mode' into feature/provgigapath-metrics-test
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Commits on May 19, 2026
- Merge branch 'master' into feature/provgigapath-metrics-test
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- chore: rename ml experiments for clarity
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  b3d803a
- feat: add original slide name in the per slide statistics
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- Merge remote-tracking branch 'origin/master' into feature/provgigapath-metrics-test
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- refactor: simplify the preprocessing name scripts
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- fix: commnets, generate safer filenames
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  cd4b19a
- fix: remove erorr masks
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- fix: remove rendundant column selection
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- feat: lower the worker consumption
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- fix: change the background color
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- feat: preserve original filename
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- Merge origin/master into fix/mug-prediction-masks
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  142f9cb
- Remove embedding preprocessing changes from PR
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  ab1c90a

Commits

Commits on May 7, 2026

Commits on May 8, 2026

Commits on May 9, 2026

Commits on May 10, 2026

Commits on May 11, 2026

Commits on May 12, 2026

Commits on May 13, 2026

Commits on May 14, 2026

Commits on May 15, 2026

Commits on May 16, 2026

Commits on May 17, 2026

Commits on May 18, 2026

Commits on May 19, 2026