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2 changes: 1 addition & 1 deletion configs/aggregator/span.yaml
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@@ -1,4 +1,4 @@
_target_: prostate_cancer.aggregators.span.SpanAggregator
_target_: ml.aggregators.span.SpanAggregator
extent_tile: ???
stride_tile: ???
k: ???
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2 changes: 1 addition & 1 deletion configs/callbacks/aggregator.yaml
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@@ -1,3 +1,3 @@
aggregator_callback:
_target_: prostate_cancer.callbacks.AggregatorCallback
_target_: ml.callbacks.AggregatorCallback
aggregator: ${aggregator}
2 changes: 1 addition & 1 deletion configs/callbacks/aggregator_estimation.yaml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
estimation_callback:
_target_: prostate_cancer.callbacks.EstimationCallback
_target_: ml.callbacks.EstimationCallback
aggregator_cls_path: ???
to_estimate: ???
static: ???
2 changes: 1 addition & 1 deletion configs/callbacks/cam.yaml
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
cam_callback:
_target_: prostate_cancer.callbacks.CAMExplainer
_target_: ml.callbacks.CAMExplainer
resize_shape: [512, 512]
2 changes: 1 addition & 1 deletion configs/callbacks/carcinoma_prediction_table.yaml
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@@ -1,3 +1,3 @@
carcinoma_table_callback:
_target_: prostate_cancer.callbacks.CarcinomaPredictionTableCallback
_target_: ml.callbacks.CarcinomaPredictionTableCallback
threshold: ???
2 changes: 1 addition & 1 deletion configs/callbacks/curves.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
curves_callback:
_target_: prostate_cancer.callbacks.CurvesCallbackTile
_target_: ml.callbacks.CurvesCallbackTile
threshold: ${tile_threshold}
optimal_seek: false
2 changes: 1 addition & 1 deletion configs/callbacks/curves_mil.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
curves_callback:
_target_: prostate_cancer.callbacks.CurvesCallbackMIL
_target_: ml.callbacks.CurvesCallbackMIL
threshold: ${tile_threshold}
optimal_seek: false
2 changes: 1 addition & 1 deletion configs/callbacks/curves_sl.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
curves_callback:
_target_: prostate_cancer.callbacks.CurvesCallbackSL
_target_: ml.callbacks.CurvesCallbackSL
threshold: ${slide_threshold}
optimal_seek: false
2 changes: 1 addition & 1 deletion configs/callbacks/heatmap.yaml
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@@ -1,2 +1,2 @@
heatmap_callback:
_target_: prostate_cancer.callbacks.HeatmapCallback
_target_: ml.callbacks.HeatmapCallback
2 changes: 1 addition & 1 deletion configs/callbacks/mil_prediction_callback.yaml
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@@ -1,2 +1,2 @@
mil_prediction_callback:
_target_: prostate_cancer.callbacks.MILPredictionCallback
_target_: ml.callbacks.MILPredictionCallback
2 changes: 1 addition & 1 deletion configs/callbacks/multi_aggregator_eval.yaml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
multi_aggregator_eval_callback:
_target_: prostate_cancer.callbacks.MultiAggregatorEvalCallback
_target_: ml.callbacks.MultiAggregatorEvalCallback
max_aggregator: ${max_aggregator}
mean_pool_max_aggregator: ${mean_pool_max_aggregator}
top_k_aggregator: ${top_k_aggregator}
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2 changes: 1 addition & 1 deletion configs/callbacks/nested_metrics.yaml
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
nested_metrics_callback:
_target_: prostate_cancer.callbacks.NestedMetricsCallback
_target_: ml.callbacks.NestedMetricsCallback
threshold: ${tile_threshold}
2 changes: 1 addition & 1 deletion configs/callbacks/nested_metrics_mil.yaml
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
nested_metrics_callback:
_target_: prostate_cancer.callbacks.NestedMetricsCallbackMIL
_target_: ml.callbacks.NestedMetricsCallbackMIL
threshold: ${tile_threshold}
2 changes: 1 addition & 1 deletion configs/callbacks/slide_histograms_mil.yaml
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
slide_histograms_callback:
_target_: prostate_cancer.callbacks.SlideHistogramsCallbackMIL
_target_: ml.callbacks.SlideHistogramsCallbackMIL
2 changes: 1 addition & 1 deletion configs/callbacks/tile_histograms.yaml
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
tile_histograms_callback:
_target_: prostate_cancer.callbacks.TileHistogramsCallbackTile
_target_: ml.callbacks.TileHistogramsCallbackTile
2 changes: 1 addition & 1 deletion configs/callbacks/tile_histograms_mil.yaml
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
tile_histograms_callback:
_target_: prostate_cancer.callbacks.TileHistogramsCallbackMIL
_target_: ml.callbacks.TileHistogramsCallbackMIL
6 changes: 6 additions & 0 deletions configs/data/prostate/base.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# @package _global_

carcinoma_artifacts: /mnt/projects/prostate_cancer/cancer

metadata:
experiment_name: Prostate
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@@ -1,3 +1,7 @@
defaults:
- /data/prostate/base@_global_
- _self_

thresholds:
tissue_roi_t: 0.5
residual_t: 0.25
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
defaults:
- /data/prostate/base@_global_
- _self_

thresholds:
tissue_roi_t: 0.5
residual_t: 0.25
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
defaults:
- /data/prostate/base@_global_
- _self_

thresholds:
tissue_roi_t: 0.5
residual_t: 0.25
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
defaults:
- stats
- /data/prostate/base@_global_
- _self_

thresholds:
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
defaults:
- /data/prostate/base@_global_
- _self_

thresholds:
tissue_roi_t: 0.5
residual_t: 0.25
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
defaults:
- stats
- /data/prostate/base@_global_
- _self_

# point to public mlflow
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2 changes: 1 addition & 1 deletion configs/datamodule/bag_of_embeddings_datamodule.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ defaults:

- samplers@sampler: bag_of_tiles_stratified_weighted_random

_target_: prostate_cancer.datamodule.BagOfTilesDataModule
_target_: ml.datamodule.BagOfTilesDataModule

batch_size: ???
num_workers: ???
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ defaults:

- samplers@sampler: bag_of_tiles_stratified_weighted_random

_target_: prostate_cancer.datamodule.ClassicBagOfTilesDataModule
_target_: ml.datamodule.ClassicBagOfTilesDataModule

batch_size: ???
num_workers: ???
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
_target_: prostate_cancer.datamodule.datasets.LabeledBagOfEmbeddingsDataset
_target_: ml.datamodule.datasets.LabeledBagOfEmbeddingsDataset
uris: ???
carcinoma_roi_t: ${carcinoma_roi_t}
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
_target_: prostate_cancer.datamodule.datasets.SLLabeledBagOfEmbeddingsDataset
_target_: ml.datamodule.datasets.SLLabeledBagOfEmbeddingsDataset
uris: ???
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
_target_: prostate_cancer.datamodule.datasets.UnlabeledBagOfEmbeddingsDataset
_target_: ml.datamodule.datasets.UnlabeledBagOfEmbeddingsDataset
uris: ???
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
_target_: prostate_cancer.datamodule.datasets.LabeledEmbeddingsDataset
_target_: ml.datamodule.datasets.LabeledEmbeddingsDataset
uris: ???
stratified_filter: ???
carcinoma_roi_t: ${carcinoma_roi_t}
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
_target_: prostate_cancer.datamodule.datasets.UnlabeledEmbeddingsDataset
_target_: ml.datamodule.datasets.UnlabeledEmbeddingsDataset
uris: ???
2 changes: 1 addition & 1 deletion configs/datamodule/datasets/images/labeled.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
_target_: prostate_cancer.datamodule.datasets.LabeledTilesDataset
_target_: ml.datamodule.datasets.LabeledTilesDataset
uris: ???
transforms: ???
carcinoma_roi_t: ${carcinoma_roi_t}
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2 changes: 1 addition & 1 deletion configs/datamodule/datasets/images/unlabeled.yaml
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
_target_: prostate_cancer.datamodule.datasets.UnlabeledTilesDataset
_target_: ml.datamodule.datasets.UnlabeledTilesDataset
uris: ???
transforms: ???
2 changes: 1 addition & 1 deletion configs/datamodule/embeddings_datamodule.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ defaults:

- samplers@sampler: tile_stratified_weighted_random

_target_: prostate_cancer.datamodule.TileDataModule
_target_: ml.datamodule.TileDataModule

train:
stratified_filter: true
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2 changes: 1 addition & 1 deletion configs/datamodule/images_datamodule.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ defaults:
- transforms@default_transform: normalize
- samplers@sampler: tile_stratified_weighted_random

_target_: prostate_cancer.datamodule.TileDataModule
_target_: ml.datamodule.TileDataModule

train:
transforms: ??? # specified during the training (stain / non-stain augmentations)
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
_partial_: true
_target_: prostate_cancer.datamodule.samplers.BagOfTilesStratifiedWeightedRandomSampler
_target_: ml.datamodule.samplers.BagOfTilesStratifiedWeightedRandomSampler
replacement: true
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
_partial_: true
_target_: prostate_cancer.datamodule.samplers.TileStratifiedWeightedRandomSampler
_target_: ml.datamodule.samplers.TileStratifiedWeightedRandomSampler
replacement: true
3 changes: 0 additions & 3 deletions configs/default.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,6 @@ defaults:
- _self_


prostate_cancer_artifacts: /mnt/projects/prostate_cancer/cancer

metadata:
experiment_name: Prostate
run_name: ???
description: ???
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# @package _global_

defaults:
- /data/mmci/sl_group_1@data
- /data/prostate/mmci/sl_group_1@data
- _self_

source_of_truth: ${data.metadata_table}
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# @package _global_

defaults:
- /data/mmci/sl_group_2@data
- /data/prostate/mmci/sl_group_2@data
- _self_

source_of_truth: ${data.metadata_table}
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# @package _global_

defaults:
- /data/mmci/sl_group_1@data
- /data/prostate/mmci/sl_group_1@data
- _self_

source_of_truth: ${data.metadata_table}
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# @package _global_

defaults:
- /data/mmci/sl_group_1@data
- /data/prostate/mmci/sl_group_1@data
- _self_

source_of_truth: ${data.metadata_table}
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# @package _global_

defaults:
- /data/mmci/sl_group_2@data
- /data/prostate/mmci/sl_group_2@data
- _self_

source_of_truth: ${data.metadata_table}
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# @package _global_

defaults:
- /data/mmci/sl_group_2@data
- /data/prostate/mmci/sl_group_2@data
- _self_

source_of_truth: ${data.metadata_table}
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/google_vit@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/google_vit@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/google_vit_stain@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/google_vit_stain@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/pgp@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/pgp@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/pgp_stain@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/pgp_stain@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/resnet50@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/resnet50@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/resnet50_224@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/resnet50_224@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/resnet50_stain@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/resnet50_stain@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/resnet50_stain_224@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/resnet50_stain_224@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/vgg16@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/vgg16@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/vgg16_224@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/vgg16_224@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/vgg16_stain@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/vgg16_stain@model_data
- _self_
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@

defaults:
- /experiment/postprocessing/eval_estimation/mpm/base
- /data/mmci/sl_group_1@data
- /model/checkpoints/mmci_tl/vgg16_stain_224@model_data
- /data/prostate/mmci/sl_group_1@data
- /model/checkpoints/prostate/vgg16_stain_224@model_data
- _self_
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