RationAI · ejdam87 · Aug 4, 2026 · Mar 24, 2026 · Mar 25, 2026 · Mar 25, 2026
diff --git a/configs/datamodule/classic_bag_of_embeddings_datamodule.yaml b/configs/datamodule/classic_bag_of_embeddings_datamodule.yaml
@@ -0,0 +1,12 @@
+defaults:
+  - datasets@train: embeddings/bag_of_embeddings_sl_labeled
+  - datasets@val: embeddings/bag_of_embeddings_sl_labeled
+  - datasets@test: embeddings/bag_of_embeddings_labeled
+  - datasets@predict: embeddings/bag_of_embeddings_unlabeled
+
+  - samplers@sampler: bag_of_tiles_stratified_weighted_random
+
+_target_: prostate_cancer.datamodule.ClassicBagOfTilesDataModule
+
+batch_size: ???
+num_workers: ???
diff --git a/configs/datamodule/datasets/embeddings/bag_of_embeddings_sl_labeled.yaml b/configs/datamodule/datasets/embeddings/bag_of_embeddings_sl_labeled.yaml
@@ -0,0 +1,2 @@
+_target_: prostate_cancer.datamodule.datasets.SLLabeledBagOfEmbeddingsDataset
+uris: ???
diff --git a/configs/experiment/predict/bag_of_embeddings/base.yaml b/configs/experiment/predict/bag_of_embeddings/base.yaml
@@ -2,13 +2,12 @@
 
 defaults:
   - /experiment/predict/base
-  - /datamodule/bag_of_embeddings_datamodule@datamodule
   - _self_
 
 slide_threshold: ${model_data.slide_threshold}
 model:
   sl_threshold: ${slide_threshold}
 
 datamodule:
-  batch_size: 2
-  num_workers: 4
+  batch_size: 4
+  num_workers: 8
diff --git a/configs/experiment/predict/bag_of_embeddings/classic_base.yaml b/configs/experiment/predict/bag_of_embeddings/classic_base.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/base
+  - /datamodule/classic_bag_of_embeddings_datamodule@datamodule
+  - _self_
diff --git a/configs/experiment/predict/bag_of_embeddings/hybrid_base.yaml b/configs/experiment/predict/bag_of_embeddings/hybrid_base.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/base
+  - /datamodule/bag_of_embeddings_datamodule@datamodule
+  - _self_
diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/classic_base.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/classic_base.yaml
@@ -0,0 +1,12 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/classic_base
+  - /model/pgp_classic_mil_model@model
+  - /model/checkpoints/mmci_tl/pgp_classic_mil@model_data
+  - _self_
+
+datamodule:
+  predict:
+    uris:
+      - ${predict_data.tiles_filtered_w_pgp_uri_224}
diff --git a/...ag_of_embeddings/pgp/slide_threshold.yaml → ...beddings/pgp/classic_slide_threshold.yaml b/...ag_of_embeddings/pgp/slide_threshold.yaml → ...beddings/pgp/classic_slide_threshold.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/slide_threshold_mil@callbacks
-  - /experiment/predict/bag_of_embeddings/pgp/base
+  - /experiment/predict/bag_of_embeddings/pgp/classic_base
   - /data/mmci/sl_group_1@predict_data
   - _self_
 

diff --git a/...t/predict/bag_of_embeddings/pgp/base.yaml → ...ct/bag_of_embeddings/pgp/hybrid_base.yaml b/...t/predict/bag_of_embeddings/pgp/base.yaml → ...ct/bag_of_embeddings/pgp/hybrid_base.yaml
@@ -1,7 +1,7 @@
 # @package _global_
 
 defaults:
-  - /experiment/predict/bag_of_embeddings/base
+  - /experiment/predict/bag_of_embeddings/hybrid_base
   - /model/pgp_hybrid_mil_model@model
   - /model/checkpoints/mmci_tl/pgp_hybrid_mil@model_data
   - _self_

diff --git a/..._embeddings/virchow2/slide_threshold.yaml → ...mbeddings/pgp/hybrid_slide_threshold.yaml b/..._embeddings/virchow2/slide_threshold.yaml → ...mbeddings/pgp/hybrid_slide_threshold.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/slide_threshold_mil@callbacks
-  - /experiment/predict/bag_of_embeddings/virchow2/base
+  - /experiment/predict/bag_of_embeddings/pgp/hybrid_base
   - /data/mmci/sl_group_1@predict_data
   - _self_
 

diff --git a/..._embeddings/pgp/mil_predictions/base.yaml → ...ngs/pgp/mil_predictions/classic_base.yaml b/..._embeddings/pgp/mil_predictions/base.yaml → ...ngs/pgp/mil_predictions/classic_base.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/mil_prediction_callback@callbacks
-  - /experiment/predict/bag_of_embeddings/pgp/base
+  - /experiment/predict/bag_of_embeddings/pgp/classic_base
   - _self_
 
 use_case: "MIL predictions"
diff --git a/...igs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_sl_group_1.yaml b/...igs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_sl_group_1.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_base
+  - /data/mmci/sl_group_1@predict_data
+  - _self_
diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_tl_val.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_tl_val.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_base
+  - /data/mmci/tl_val@predict_data
+  - _self_
diff --git a/...ddings/virchow2/mil_predictions/base.yaml → ...ings/pgp/mil_predictions/hybrid_base.yaml b/...ddings/virchow2/mil_predictions/base.yaml → ...ings/pgp/mil_predictions/hybrid_base.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/mil_prediction_callback@callbacks
-  - /experiment/predict/bag_of_embeddings/virchow2/base
+  - /experiment/predict/bag_of_embeddings/pgp/hybrid_base
   - _self_
 
 use_case: "MIL predictions"
diff --git a/.../pgp/mil_predictions/mmci_sl_group_1.yaml → ...l_predictions/hybrid_mmci_sl_group_1.yaml b/.../pgp/mil_predictions/mmci_sl_group_1.yaml → ...l_predictions/hybrid_mmci_sl_group_1.yaml
@@ -1,6 +1,6 @@
 # @package _global_
 
 defaults:
-  - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/base
+  - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_base
   - /data/mmci/sl_group_1@predict_data
   - _self_
diff --git a/...ings/pgp/mil_predictions/mmci_tl_val.yaml → ...p/mil_predictions/hybrid_mmci_tl_val.yaml b/...ings/pgp/mil_predictions/mmci_tl_val.yaml → ...p/mil_predictions/hybrid_mmci_tl_val.yaml
@@ -1,6 +1,6 @@
 # @package _global_
 
 defaults:
-  - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/base
+  - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_base
   - /data/mmci/tl_val@predict_data
   - _self_
diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/classic_base.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/classic_base.yaml
@@ -0,0 +1,12 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/classic_base
+  - /model/virchow2_classic_mil_model@model
+  - /model/checkpoints/mmci_tl/virchow2_classic_mil@model_data
+  - _self_
+
+datamodule:
+  predict:
+    uris:
+      - ${predict_data.tiles_filtered_w_virchow2_uri_224}
diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/classic_slide_threshold.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/classic_slide_threshold.yaml
@@ -0,0 +1,10 @@
+# @package _global_
+
+defaults:
+  - /callbacks/slide_threshold_mil@callbacks
+  - /experiment/predict/bag_of_embeddings/virchow2/classic_base
+  - /data/mmci/sl_group_1@predict_data
+  - _self_
+
+slide_threshold: 0.99 # My estimate for other models
+use_case: "SL Threshold Estimation"
diff --git a/...dict/bag_of_embeddings/virchow2/base.yaml → ...g_of_embeddings/virchow2/hybrid_base.yaml b/...dict/bag_of_embeddings/virchow2/base.yaml → ...g_of_embeddings/virchow2/hybrid_base.yaml
@@ -1,7 +1,7 @@
 # @package _global_
 
 defaults:
-  - /experiment/predict/bag_of_embeddings/base
+  - /experiment/predict/bag_of_embeddings/hybrid_base
   - /model/virchow2_hybrid_mil_model@model
   - /model/checkpoints/mmci_tl/virchow2_hybrid_mil@model_data
   - _self_

diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_slide_threshold.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_slide_threshold.yaml
@@ -0,0 +1,10 @@
+# @package _global_
+
+defaults:
+  - /callbacks/slide_threshold_mil@callbacks
+  - /experiment/predict/bag_of_embeddings/virchow2/hybrid_base
+  - /data/mmci/sl_group_1@predict_data
+  - _self_
+
+slide_threshold: 0.99 # My estimate for other models
+use_case: "SL Threshold Estimation"
diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_base.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_base.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /callbacks/mil_prediction_callback@callbacks
+  - /experiment/predict/bag_of_embeddings/virchow2/classic_base
+  - _self_
+
+use_case: "MIL predictions"
diff --git a/...xperiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_sl_group_1.yaml b/...xperiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_sl_group_1.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_base
+  - /data/mmci/sl_group_1@predict_data
+  - _self_
diff --git a/...gs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_tl_val.yaml b/...gs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_tl_val.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_base
+  - /data/mmci/tl_val@predict_data
+  - _self_
diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_base.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_base.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /callbacks/mil_prediction_callback@callbacks
+  - /experiment/predict/bag_of_embeddings/virchow2/hybrid_base
+  - _self_
+
+use_case: "MIL predictions"
diff --git a/...how2/mil_predictions/mmci_sl_group_1.yaml → ...l_predictions/hybrid_mmci_sl_group_1.yaml b/...how2/mil_predictions/mmci_sl_group_1.yaml → ...l_predictions/hybrid_mmci_sl_group_1.yaml
@@ -1,6 +1,6 @@
 # @package _global_
 
 defaults:
-  - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/base
+  - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_base
   - /data/mmci/sl_group_1@predict_data
   - _self_
diff --git a/...virchow2/mil_predictions/mmci_tl_val.yaml → ...2/mil_predictions/hybrid_mmci_tl_val.yaml b/...virchow2/mil_predictions/mmci_tl_val.yaml → ...2/mil_predictions/hybrid_mmci_tl_val.yaml
@@ -1,6 +1,6 @@
 # @package _global_
 
 defaults:
-  - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/base
+  - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_base
   - /data/mmci/tl_val@predict_data
   - _self_
diff --git a/configs/experiment/test/bag_of_embeddings/base.yaml b/configs/experiment/test/bag_of_embeddings/base.yaml
@@ -2,7 +2,6 @@
 
 defaults:
   - /experiment/test/base
-  - /datamodule/bag_of_embeddings_datamodule@datamodule
   - _self_
 
 slide_threshold: ${model_data.slide_threshold}

diff --git a/configs/experiment/test/bag_of_embeddings/classic_base.yaml b/configs/experiment/test/bag_of_embeddings/classic_base.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/test/bag_of_embeddings/base
+  - /datamodule/classic_bag_of_embeddings_datamodule@datamodule
+  - _self_
diff --git a/configs/experiment/test/bag_of_embeddings/hybrid_base.yaml b/configs/experiment/test/bag_of_embeddings/hybrid_base.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/test/bag_of_embeddings/base
+  - /datamodule/bag_of_embeddings_datamodule@datamodule
+  - _self_
diff --git a/configs/experiment/test/bag_of_embeddings/pgp/classic_base.yaml b/configs/experiment/test/bag_of_embeddings/pgp/classic_base.yaml
@@ -0,0 +1,12 @@
+# @package _global_
+
+defaults:
+  - /experiment/test/bag_of_embeddings/classic_base
+  - /model/pgp_classic_mil_model@model
+  - /model/checkpoints/mmci_tl/pgp_classic_mil@model_data
+  - _self_
+
+datamodule:
+  test:
+    uris:
+      - ${test_data.tiles_filtered_w_pgp_uri_224}
diff --git a/...f_embeddings/virchow2/tile_threshold.yaml → ...mbeddings/pgp/classic_tile_threshold.yaml b/...f_embeddings/virchow2/tile_threshold.yaml → ...mbeddings/pgp/classic_tile_threshold.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/tile_threshold_mil@callbacks
-  - /experiment/test/bag_of_embeddings/virchow2/base
+  - /experiment/test/bag_of_embeddings/pgp/classic_base
   - /data/mmci/tl_val@test_data
   - _self_
 

diff --git a/...ment/test/bag_of_embeddings/pgp/base.yaml → ...st/bag_of_embeddings/pgp/hybrid_base.yaml b/...ment/test/bag_of_embeddings/pgp/base.yaml → ...st/bag_of_embeddings/pgp/hybrid_base.yaml
@@ -1,7 +1,7 @@
 # @package _global_
 
 defaults:
-  - /experiment/test/bag_of_embeddings/base
+  - /experiment/test/bag_of_embeddings/hybrid_base
   - /model/pgp_hybrid_mil_model@model
   - /model/checkpoints/mmci_tl/pgp_hybrid_mil@model_data
   - _self_

diff --git a/...bag_of_embeddings/pgp/tile_threshold.yaml → ...embeddings/pgp/hybrid_tile_threshold.yaml b/...bag_of_embeddings/pgp/tile_threshold.yaml → ...embeddings/pgp/hybrid_tile_threshold.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/tile_threshold_mil@callbacks
-  - /experiment/test/bag_of_embeddings/pgp/base
+  - /experiment/test/bag_of_embeddings/pgp/hybrid_base
   - /data/mmci/tl_val@test_data
   - _self_
 

diff --git a/..._embeddings/virchow2/test_suite/base.yaml → ...beddings/pgp/test_suite/classic_base.yaml b/..._embeddings/virchow2/test_suite/base.yaml → ...beddings/pgp/test_suite/classic_base.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/combined_test_suite_mil@callbacks
-  - /experiment/test/bag_of_embeddings/virchow2/base
+  - /experiment/test/bag_of_embeddings/pgp/classic_base
   - _self_
 
 use_case: "TL Test"
diff --git a/...ngs/virchow2/test_suite/mmci_tl_test.yaml → .../pgp/test_suite/classic_mmci_tl_test.yaml b/...ngs/virchow2/test_suite/mmci_tl_test.yaml → .../pgp/test_suite/classic_mmci_tl_test.yaml
@@ -1,6 +1,6 @@
 # @package _global_
 
 defaults:
-  - /experiment/test/bag_of_embeddings/virchow2/test_suite/base
+  - /experiment/test/bag_of_embeddings/pgp/test_suite/classic_base
   - /data/mmci/tl_test@test_data
   - _self_
diff --git a/...ag_of_embeddings/pgp/test_suite/base.yaml → ...mbeddings/pgp/test_suite/hybrid_base.yaml b/...ag_of_embeddings/pgp/test_suite/base.yaml → ...mbeddings/pgp/test_suite/hybrid_base.yaml
@@ -2,7 +2,7 @@
 
 defaults:
   - /callbacks/combined_test_suite_mil@callbacks
-  - /experiment/test/bag_of_embeddings/pgp/base
+  - /experiment/test/bag_of_embeddings/pgp/hybrid_base
   - _self_
 
 use_case: "TL Test"
diff --git a/...beddings/pgp/test_suite/mmci_tl_test.yaml → ...s/pgp/test_suite/hybrid_mmci_tl_test.yaml b/...beddings/pgp/test_suite/mmci_tl_test.yaml → ...s/pgp/test_suite/hybrid_mmci_tl_test.yaml
@@ -1,6 +1,6 @@
 # @package _global_
 
 defaults:
-  - /experiment/test/bag_of_embeddings/pgp/test_suite/base
+  - /experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_base
   - /data/mmci/tl_test@test_data
   - _self_
diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/classic_base.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/classic_base.yaml
@@ -0,0 +1,12 @@
+# @package _global_
+
+defaults:
+  - /experiment/test/bag_of_embeddings/classic_base
+  - /model/virchow2_classic_mil_model@model
+  - /model/checkpoints/mmci_tl/virchow2_classic_mil@model_data
+  - _self_
+
+datamodule:
+  test:
+    uris:
+      - ${test_data.tiles_filtered_w_virchow2_uri_224}
diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/classic_tile_threshold.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/classic_tile_threshold.yaml
@@ -0,0 +1,10 @@
+# @package _global_
+
+defaults:
+  - /callbacks/tile_threshold_mil@callbacks
+  - /experiment/test/bag_of_embeddings/virchow2/classic_base
+  - /data/mmci/tl_val@test_data
+  - _self_
+
+tile_threshold: 0.9 # Pathologist's estimate for other models
+use_case: "TL Threshold Estimation"
diff --git a/...test/bag_of_embeddings/virchow2/base.yaml → ...g_of_embeddings/virchow2/hybrid_base.yaml b/...test/bag_of_embeddings/virchow2/base.yaml → ...g_of_embeddings/virchow2/hybrid_base.yaml
@@ -1,7 +1,7 @@
 # @package _global_
 
 defaults:
-  - /experiment/test/bag_of_embeddings/base
+  - /experiment/test/bag_of_embeddings/hybrid_base
   - /model/virchow2_hybrid_mil_model@model
   - /model/checkpoints/mmci_tl/virchow2_hybrid_mil@model_data
   - _self_

diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_tile_threshold.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_tile_threshold.yaml
@@ -0,0 +1,10 @@
+# @package _global_
+
+defaults:
+  - /callbacks/tile_threshold_mil@callbacks
+  - /experiment/test/bag_of_embeddings/virchow2/hybrid_base
+  - /data/mmci/tl_val@test_data
+  - _self_
+
+tile_threshold: 0.9 # Pathologist's estimate for other models
+use_case: "TL Threshold Estimation"
diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_base.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_base.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /callbacks/combined_test_suite_mil@callbacks
+  - /experiment/test/bag_of_embeddings/virchow2/classic_base
+  - _self_
+
+use_case: "TL Test"
diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_mmci_tl_test.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_mmci_tl_test.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/test/bag_of_embeddings/virchow2/test_suite/classic_base
+  - /data/mmci/tl_test@test_data
+  - _self_
diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_base.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_base.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /callbacks/combined_test_suite_mil@callbacks
+  - /experiment/test/bag_of_embeddings/virchow2/hybrid_base
+  - _self_
+
+use_case: "TL Test"
diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_mmci_tl_test.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_mmci_tl_test.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_base
+  - /data/mmci/tl_test@test_data
+  - _self_
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		_target_: prostate_cancer.datamodule.datasets.SLLabeledBagOfEmbeddingsDataset
		uris: ???