RationAI · ejdam87 · Aug 4, 2026 · May 16, 2026 · May 16, 2026 · May 16, 2026
diff --git a/configs/data/radboud/test.yaml b/configs/data/radboud/test.yaml
@@ -4,6 +4,13 @@ defaults:
 
 
 metadata_table: "mlflow-artifacts:/38/1a718a849be3412ab4621b6772daf049/artifacts/PANDA - Radboud_test.csv"
-tiles_uri_512: "mlflow-artifacts:/38/7bfcfeeaa29a4745943ac8556a63de4b/artifacts/PANDA - Radboud test"
+
+tiles_uri_512: "mlflow-artifacts:/38/197410ccc71c443bb8b1d8eb517c53fa/artifacts/PANDA - Radboud test"
+tiles_filtered_uri_512: "mlflow-artifacts:/38/0525b745d0954fb6ace98ead20042faf/artifacts/PANDA - Radboud test_512"
+
+tiles_uri_224: "mlflow-artifacts:/38/4cab0908f7eb4d0aba64407af072f08c/artifacts/PANDA - Radboud test"
+tiles_filtered_uri_224: "mlflow-artifacts:/38/0525b745d0954fb6ace98ead20042faf/artifacts/PANDA - Radboud test_224"
+tiles_filtered_w_virchow2_uri_224: "mlflow-artifacts:/38/a63457454feb49ecb362af00ad5e2320/artifacts/PANDA - Radboud test"
+tiles_filtered_w_pgp_uri_224: "mlflow-artifacts:/38/11c6715b9d1445a9aa59e9d0e0294c4c/artifacts/PANDA - Radboud test"
 
 data_name: "PANDA - Radboud test"
diff --git a/configs/data/radboud/train.yaml b/configs/data/radboud/train.yaml
@@ -4,7 +4,10 @@ defaults:
 
 # points to the public mlflow
 metadata_table: "mlflow-artifacts:/38/25b0e9ead22e44908f74d23b4efcaa62/artifacts/PANDA - Radboud train + val_train.csv"
-tiles_uri_512: "mlflow-artifacts:/38/fc5ea991725d4066bddeb31090aae463/artifacts/PANDA - Radboud train"
-tiles_uri_224: "mlflow-artifacts:/38/71423731ba2a45099f28892733667386/artifacts/PANDA - Radboud train"
+tiles_uri_512: "mlflow-artifacts:/38/02b36c4f7e544436b0bd2f81146676c5/artifacts/PANDA - Radboud train"
+tiles_filtered_uri_512: "mlflow-artifacts:/38/e1ef2698c62541e4a5e92a65ecb36fa5/artifacts/PANDA - Radboud train_512"
+
+tiles_uri_224: "mlflow-artifacts:/38/d658d0c339844eec8b425b403657f086/artifacts/PANDA - Radboud train"
+tiles_filtered_uri_224: "mlflow-artifacts:/38/e1ef2698c62541e4a5e92a65ecb36fa5/artifacts/PANDA - Radboud train_224"
 
 data_name: "PANDA - Radboud train"
diff --git a/configs/data/radboud/val.yaml b/configs/data/radboud/val.yaml
@@ -3,6 +3,11 @@ defaults:
   - _self_
 
 tiles_uri_512: "mlflow-artifacts:/38/4e3b31f87a8a46df9f911a69206d6a1d/artifacts/PANDA - Radboud val"
-tiles_uri_224: "mlflow-artifacts:/38/fae8eacf77a24fce808de83cb8ec3edd/artifacts/PANDA - Radboud val"
+tiles_filtered_uri_512: "mlflow-artifacts:/38/b38ca47d6fd4422a9f8d5a32fcae221c/artifacts/PANDA - Radboud val_512"
+
+tiles_uri_224: "mlflow-artifacts:/38/33ad08ab5f9845809fb48b2b7d2aa643/artifacts/PANDA - Radboud val"
+tiles_filtered_uri_224: "mlflow-artifacts:/38/b38ca47d6fd4422a9f8d5a32fcae221c/artifacts/PANDA - Radboud val_224"
+tiles_filtered_w_virchow2_uri_224: "mlflow-artifacts:/38/e0376ffbbc894cb5862011e7f79c03f9/artifacts/PANDA - Radboud val"
+tiles_filtered_w_pgp_uri_224: "mlflow-artifacts:/38/1ffee8c4b2c841879a25aa3781a271ff/artifacts/PANDA - Radboud val"
 
 data_name: "PANDA - Radboud val"
diff --git a/configs/data/radboud/val_heuristic_normalized.yaml b/configs/data/radboud/val_heuristic_normalized.yaml
@@ -2,7 +2,7 @@ defaults:
   - base_val
   - _self_
 
-tiles_uri_512: "mlflow-artifacts:/38/4ced588761614abda73d2f447284d6ce/artifacts/PANDA - Radboud val512_normalized"
-tiles_uri_224: "mlflow-artifacts:/38/4ced588761614abda73d2f447284d6ce/artifacts/PANDA - Radboud val224_normalized"
+tiles_uri_512: "mlflow-artifacts:/38/4ced588761614abda73d2f447284d6ce/artifacts/PANDA - Radboud val512_normalized" # invalid QC
+tiles_uri_224: "mlflow-artifacts:/38/4ced588761614abda73d2f447284d6ce/artifacts/PANDA - Radboud val224_normalized" # invalid QC
 
 data_name: "PANDA - Radboud val (Heuristic Normalized)"
diff --git a/configs/data/radboud/val_ml_normalized.yaml b/configs/data/radboud/val_ml_normalized.yaml
@@ -2,7 +2,7 @@ defaults:
   - base_val
   - _self_
 
-tiles_uri_512: "mlflow-artifacts:/38/c0a9e22016924940880188d6e111f150/artifacts/PANDA - Radboud val512_normalized"
-tiles_uri_224: "mlflow-artifacts:/38/c0a9e22016924940880188d6e111f150/artifacts/PANDA - Radboud val224_normalized"
+tiles_uri_512: "mlflow-artifacts:/38/c0a9e22016924940880188d6e111f150/artifacts/PANDA - Radboud val512_normalized" # invalid QC
+tiles_uri_224: "mlflow-artifacts:/38/c0a9e22016924940880188d6e111f150/artifacts/PANDA - Radboud val224_normalized" # invalid QC
 
 data_name: "PANDA - Radboud val (ML Normalized)"
diff --git a/configs/datamodule/datasets/images/labeled.yaml b/configs/datamodule/datasets/images/labeled.yaml
@@ -1,4 +1,5 @@
 _target_: prostate_cancer.datamodule.datasets.LabeledTilesDataset
 uris: ???
+transforms: ???
 carcinoma_roi_t: ${carcinoma_roi_t}
 stratified_filter: ???
diff --git a/configs/datamodule/datasets/images/unlabeled.yaml b/configs/datamodule/datasets/images/unlabeled.yaml
@@ -1,2 +1,3 @@
 _target_: prostate_cancer.datamodule.datasets.UnlabeledTilesDataset
 uris: ???
+transforms: ???
diff --git a/configs/datamodule/transforms/augmentations.yaml b/configs/datamodule/transforms/augmentations.yaml
diff --git a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/embeddings/pgp/multi_aggregator_eval/base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/google_vit/multi_aggregator_eval/base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/google_vit/multi_aggregator_eval/stain_base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/radboud_test.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/radboud_test.yaml
@@ -0,0 +1,6 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/base
+  - /data/radboud/test@predict_data
+  - _self_
diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/resnet50/multi_aggregator_eval/base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test_224.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test_224.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/resnet50/multi_aggregator_eval/base_224
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test_224.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test_224.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base_224
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/vgg16/multi_aggregator_eval/base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test_224.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test_224.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/vgg16/multi_aggregator_eval/base_224
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/vgg16/multi_aggregator_eval/stain_base
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test_224.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test_224.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/predict/images/vgg16/multi_aggregator_eval/stain_base_224
+  - /data/radboud/test@predict_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}
diff --git a/configs/experiment/preprocessing/filter_tiles/radboud_test.yaml b/configs/experiment/preprocessing/filter_tiles/radboud_test.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/test@data
+  - _self_
diff --git a/configs/experiment/preprocessing/filter_tiles/radboud_train.yaml b/configs/experiment/preprocessing/filter_tiles/radboud_train.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/train@data
+  - _self_
diff --git a/configs/experiment/preprocessing/filter_tiles/radboud_val.yaml b/configs/experiment/preprocessing/filter_tiles/radboud_val.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/val@data
+  - _self_
diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/pgp/base.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/pgp/base.yaml
@@ -1,3 +1,3 @@
 # @package _global_
 
-encoder: "provgigapath"
+encoder: "prov-gigapath"
diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_test.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_test.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+defaults:
+  - /experiment/preprocessing/tile_embeddings_v2/pgp/base
+  - /data/radboud/test@data
diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_val.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_val.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+defaults:
+  - /experiment/preprocessing/tile_embeddings_v2/pgp/base
+  - /data/radboud/val@data
diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_test.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_test.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+defaults:
+  - /experiment/preprocessing/tile_embeddings_v2/virchow2/base
+  - /data/radboud/test@data
diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_val.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_val.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+defaults:
+  - /experiment/preprocessing/tile_embeddings_v2/virchow2/base
+  - /data/radboud/val@data
diff --git a/configs/experiment/preprocessing/tile_masks/radboud_test_224.yaml b/configs/experiment/preprocessing/tile_masks/radboud_test_224.yaml
@@ -0,0 +1,15 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/test@data
+  - _self_
+
+tile_uris:
+  - ${data.tiles_filtered_uri_224}
+
+percentage_cols:
+  - "tissue_roi_percentage"
+  - "carcinoma_roi_percentage"
+  - "residual_percentage"
+  - "blur_percentage"
+  - "folding_percentage"
diff --git a/configs/experiment/preprocessing/tile_masks/radboud_test_512.yaml b/configs/experiment/preprocessing/tile_masks/radboud_test_512.yaml
@@ -0,0 +1,15 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/test@data
+  - _self_
+
+tile_uris:
+  - ${data.tiles_filtered_uri_512}
+
+percentage_cols:
+  - "tissue_roi_percentage"
+  - "carcinoma_roi_percentage"
+  - "residual_percentage"
+  - "blur_percentage"
+  - "folding_percentage"
diff --git a/configs/experiment/preprocessing/tile_masks/radboud_train_224.yaml b/configs/experiment/preprocessing/tile_masks/radboud_train_224.yaml
@@ -0,0 +1,15 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/train@data
+  - _self_
+
+tile_uris:
+  - ${data.tiles_filtered_uri_224}
+
+percentage_cols:
+  - "tissue_roi_percentage"
+  - "carcinoma_roi_percentage"
+  - "residual_percentage"
+  - "blur_percentage"
+  - "folding_percentage"
diff --git a/configs/experiment/preprocessing/tile_masks/radboud_train_512.yaml b/configs/experiment/preprocessing/tile_masks/radboud_train_512.yaml
@@ -0,0 +1,15 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/train@data
+  - _self_
+
+tile_uris:
+  - ${data.tiles_filtered_uri_512}
+
+percentage_cols:
+  - "tissue_roi_percentage"
+  - "carcinoma_roi_percentage"
+  - "residual_percentage"
+  - "blur_percentage"
+  - "folding_percentage"
diff --git a/configs/experiment/preprocessing/tile_masks/radboud_val_224.yaml b/configs/experiment/preprocessing/tile_masks/radboud_val_224.yaml
@@ -0,0 +1,15 @@
+# @package _global_
+
+defaults:
+  - /data/radboud/val@data
+  - _self_
+
+tile_uris:
+  - ${data.tiles_filtered_uri_224}
+
+percentage_cols:
+  - "tissue_roi_percentage"
+  - "carcinoma_roi_percentage"
+  - "residual_percentage"
+  - "blur_percentage"
+  - "folding_percentage"
diff --git a/configs/experiment/preprocessing/tile_masks/radboud_val_512.yaml b/configs/experiment/preprocessing/tile_masks/radboud_val_512.yaml
@@ -5,8 +5,11 @@ defaults:
   - _self_
 
 tile_uris:
-  - ${data.tiles_uri_512}
+  - ${data.tiles_filtered_uri_512}
 
 percentage_cols:
   - "tissue_roi_percentage"
   - "carcinoma_roi_percentage"
+  - "residual_percentage"
+  - "blur_percentage"
+  - "folding_percentage"
diff --git a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_radboud_test.yaml b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_radboud_test.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+defaults:
+  - /experiment/test/bag_of_embeddings/pgp/test_suite/classic_base
+  - /data/radboud/test@test_data
+  - _self_
+
+checkpoint: ${model_data.public_checkpoint}