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fb33c97
chore: rename project folder to ml
Adames4 81f4f06
chore: dependencies
Adames4 e028c01
feat: dataset
Adames4 45b92ea
feat: embeddings
Adames4 1929804
feat: configs
Adames4 ec4f222
feat: update tiling uris
Adames4 0baa04d
feat: script and confs
Adames4 d04afab
feat: update conf
Adames4 cafc29e
fix: datamodule
Adames4 1b32f1d
feat: confs
Adames4 9ec51f0
fix: typo
Adames4 06f204f
feat: conf
Adames4 4b039f4
feat: confs
Adames4 1340dbf
feat: confs
Adames4 70ea97c
feat: confs
Adames4 9a9cc4d
feat: confs
Adames4 6c59386
feat: confs
Adames4 c6ce394
feat: reusing already generated embeddings
Adames4 0e62539
feat: artifacts logging at the end
Adames4 b394f82
fix: typo
Adames4 8826dc1
feat: new found models
Adames4 9a54054
chore: Merge branch 'feature/tiling' into feature/embeddings
Adames4 33de3cd
feat: confs
Adames4 8b1553f
chore: remove comments
Adames4 a3fdb24
fix: PR
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.17 | ||
| tile_extent: 320 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/bbbe4603bc30495d85ac99093fc9269a/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/bbbe4603bc30495d85ac99093fc9269a/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/bbbe4603bc30495d85ac99093fc9269a/artifacts/test final - ftn" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.17 | ||
| tile_extent: 430 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/de450f835f0d4462a91b35f4a79a500f/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/de450f835f0d4462a91b35f4a79a500f/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/de450f835f0d4462a91b35f4a79a500f/artifacts/test final - ftn" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.52 | ||
| tile_extent: 224 | ||
| level: 1 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/f85b64a7f96c41e38f86d84956e2dbe9/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/f85b64a7f96c41e38f86d84956e2dbe9/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/f85b64a7f96c41e38f86d84956e2dbe9/artifacts/test final - ftn" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 1.55 | ||
| tile_extent: 224 | ||
| level: 2 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/5814484b6cd7467e9d712889655479af/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/5814484b6cd7467e9d712889655479af/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/5814484b6cd7467e9d712889655479af/artifacts/test final - ftn" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.17 | ||
| tile_extent: 320 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/4486e598446d412d926ac66dadb35e51/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/4486e598446d412d926ac66dadb35e51/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/4486e598446d412d926ac66dadb35e51/artifacts/test final - ikem" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.17 | ||
| tile_extent: 430 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/fd112e63819c49d999502542b35bfce1/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/fd112e63819c49d999502542b35bfce1/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/fd112e63819c49d999502542b35bfce1/artifacts/test final - ikem" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.52 | ||
| tile_extent: 224 | ||
| level: 1 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/ece822e7c0e3416f97212267c773c8ac/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/ece822e7c0e3416f97212267c773c8ac/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/ece822e7c0e3416f97212267c773c8ac/artifacts/test final - ikem" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 1.55 | ||
| tile_extent: 224 | ||
| level: 2 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/0c09e1c61d294fa3877b6b21703bab2f/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/0c09e1c61d294fa3877b6b21703bab2f/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/0c09e1c61d294fa3877b6b21703bab2f/artifacts/test final - ikem" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.17 | ||
| tile_extent: 320 | ||
| level: 0 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/7b9a446145b14965981bbac88e8e2c8b/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/7b9a446145b14965981bbac88e8e2c8b/artifacts/test final - knl_patos" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.17 | ||
| tile_extent: 430 | ||
| level: 0 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/eb29255c944d4dad926160a7cb102ad9/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/eb29255c944d4dad926160a7cb102ad9/artifacts/test final - knl_patos" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.52 | ||
| tile_extent: 224 | ||
| level: 1 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/6782155362d54ecc9f1beccb4362d359/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/6782155362d54ecc9f1beccb4362d359/artifacts/test final - knl_patos" # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 1.55 | ||
| tile_extent: 224 | ||
| level: 2 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/d7486bb6b667433989c3ce1c8ce31d60/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/d7486bb6b667433989c3ce1c8ce31d60/artifacts/test final - knl_patos" # TODO update URI |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ftn_1_prov_gigapath.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/prov_gigapath | ||
| - _self_ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni | ||
| - _self_ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ftn_1_virchow.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ftn_1_virchow2.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ftn_2_virchow2.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ftn/2_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ikem_1_prov_gigapath.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ikem/1_224@dataset | ||
| - /preprocessing/tile_encoder/prov_gigapath | ||
| - _self_ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ikem/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni | ||
| - _self_ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ikem/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ikem_1_virchow.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ikem/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ikem_1_virchow2.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ikem/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/ikem_2_virchow2.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/ikem/2_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/knl_patos_1_prov_gigapath.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/knl_patos/1_224@dataset | ||
| - /preprocessing/tile_encoder/prov_gigapath | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/knl_patos_1_uni.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/knl_patos/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/knl_patos_1_uni2.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/knl_patos/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/knl_patos_1_virchow.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/knl_patos/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/knl_patos_1_virchow2.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/knl_patos/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/preprocessing/embeddings/knl_patos_2_virchow2.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/tiled/knl_patos/2_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| # @package _global_ | ||
|
|
||
| output_dir: ${project_dir}/embeddings/${dataset.institution}/${dataset.level}/${tile_encoder.name} | ||
|
|
||
| dataloader: | ||
| batch_size: 2048 # 2048 for H100, 1024 for A40, 512 for mig-2g.20gb | ||
| num_workers: 8 | ||
| persistent_workers: True | ||
|
|
||
| metadata: | ||
| run_name: '📂 Embeddings: ${dataset.institution} - ${dataset.level} - ${tile_encoder.name}' | ||
| description: Embeddings preprocessing for ${dataset.institution} institution with ${tile_encoder.name} tile encoder. | ||
| hyperparams: | ||
| tile_encoder: ${tile_encoder.name} | ||
| level: ${dataset.level} | ||
| batch_size: ${dataloader.batch_size} | ||
| num_workers: ${dataloader.num_workers} |
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| # @package _global_ | ||
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| tile_encoder: | ||
| _target_: preprocessing.embeddings.ProvGigaPath | ||
| name: prov_gigapath |
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| # @package _global_ | ||
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| tile_encoder: | ||
| _target_: preprocessing.embeddings.UNI | ||
| name: uni |
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| # @package _global_ | ||
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| tile_encoder: | ||
| _target_: preprocessing.embeddings.UNI2 | ||
| name: uni2 |
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| # @package _global_ | ||
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| tile_encoder: | ||
| _target_: preprocessing.embeddings.Virchow | ||
| name: virchow |
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| # @package _global_ | ||
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| tile_encoder: | ||
| _target_: preprocessing.embeddings.Virchow2 | ||
| name: virchow2 |
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| from ml.data.data_module import DataModule | ||
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| __all__ = ["DataModule"] |
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These MLFlow artifact URIs appear to be placeholders and are marked with
# TODO update URI. Committing placeholder values can lead to runtime errors or incorrect data being used if not updated. Please replace them with the final URIs or use a more dynamic configuration approach to avoid hardcoding them. This comment applies to all similar new dataset configuration files in this pull request.There was a problem hiding this comment.
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Waiting for #5