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6e1d4b9
chore: replace pdm with uv
Adames4 d7a1ef3
feat: configs
Adames4 34abac4
feat: dataset creation
Adames4 80eca85
fix: configs
Adames4 97335ef
fix: configs
Adames4 727c729
feat: add scripts
Adames4 fa9f581
fix: invalid job name
Adames4 fd978b3
fix: set slide_id as index and ensure nancy is an integer
Adames4 2869916
chore: dependencies
Adames4 725e17d
feat: processed data
Adames4 f7026b3
feat: tissue masks
Adames4 ed49c42
feat: script
Adames4 87113e1
feat: script
Adames4 de98fef
fix: job name
Adames4 929d298
fix: exclude .git folder from ray env
Adames4 81d4df3
fix: exclude .venv folder from ray env
Adames4 3f0321f
fix: typo
Adames4 2ecde13
feat: job script
Adames4 6cae5d0
feat: config
Adames4 616ed48
feat: job script
Adames4 700f916
chore: dependencies
Adames4 65e86db
feat: quality control
Adames4 59965a4
feat: add dataset configuration files for ftn, ikem, and knl_patos
Adames4 234d611
fix: output dir
Adames4 4930434
fix: typo
Adames4 180afe7
chore: Merge branch 'feature/tissue-masks' into feature/tiling
Adames4 456d4ae
chore: add tiling libs
Adames4 e88bfd8
fix: naming
Adames4 b91d36d
feat: confs
Adames4 413db4f
feat: tiling
Adames4 f5b4045
fix: confs
Adames4 2a578d1
fix: typo
Adames4 9262f3e
fix: typo
Adames4 b852be9
fix: typo
Adames4 bd8ca9f
fix: dataset index
Adames4 08d3320
feat: update tiling to latest ratiopath
Adames4 3ab6d5a
fix: use tile overlay overlap as udfexpr
Adames4 06e957e
chore: ratiopath from github
Adames4 de0fd75
fix: WIP
Adames4 e56216b
fix: None in overlap
Adames4 95cc81c
feat: confs
Adames4 754698f
chore: dependencies
Adames4 fb33c97
chore: rename project folder to ml
Adames4 81f4f06
chore: dependencies
Adames4 e028c01
feat: dataset
Adames4 45b92ea
feat: embeddings
Adames4 178f294
feat: tile = stride
Adames4 1929804
feat: configs
Adames4 e4d2499
fix: typo
Adames4 acfbf19
fix: glob over changing dir
Adames4 659f505
fix: finish the run
Adames4 45ac3b3
fix: rever last commit
Adames4 3c7a5fc
feat: conf
Adames4 774f24a
fix: splits
Adames4 076ba93
feat: tweaking resources
Adames4 2788656
feat: confs
Adames4 25bec6e
chore: dependecies
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 5faa224
fix: add paths
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 eb96f56
fix: conf
Adames4 89a4582
fix: typo
Adames4 18c556d
chore: dependencies
Adames4 35cfb5c
fix: group splitting
Adames4 bd0c6ac
fix: PR comments
Adames4 9ffea96
chore: dependencies
Adames4 0db7d08
chore: Merge branch 'feature/dataset' into feature/tissue-masks
Adames4 b833059
feat: refactor configs
Adames4 3300341
fix: PR comments
Adames4 c98608e
chore: Merge branch 'feature/dataset' into feature/quality-control
Adames4 bc71668
feat: configs
Adames4 6647d0d
chore: Merge branch 'feature/tissue-masks' into feature/tiling
Adames4 2dfb32b
chore: Merge branch 'feature/quality-control' into feature/tiling
Adames4 30d4494
feat: configs
Adames4 88eb5dc
fix: conf
Adames4 b394f82
fix: typo
Adames4 8826dc1
feat: new found models
Adames4 4269a3a
fix: PR
Adames4 a9615ed
fix: repo
Adames4 3b7f95c
chore: Merge branch 'feature/quality-control' into feature/tiling
Adames4 659910e
fix: repo
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 |
|---|---|---|
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@@ -180,3 +180,4 @@ lightning_logs/ | |
|
|
||
| # Project | ||
| /data | ||
| playground.ipynb | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| defaults: | ||
| - hydra: default | ||
| - logger: mlflow | ||
| - _self_ | ||
|
|
||
| metadata: | ||
| experiment_name: Ulcerative Colitis |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| defaults: | ||
| - /dataset/raw/ftn@_here_ | ||
| - _self_ | ||
|
|
||
| uri: mlflow-artifacts:/86/142642fc780f4a96800c691168b5c2c3/artifacts/dataset.csv # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| defaults: | ||
| - /dataset/raw/ikem@_here_ | ||
| - _self_ | ||
|
|
||
| uri: mlflow-artifacts:/86/52d0081d60ba4585a16a3bd341d5ab09/artifacts/dataset.csv # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| defaults: | ||
| - /dataset/raw/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| uri: mlflow-artifacts:/86/afbcfd43cb3c4fd0b1e9b5dbe7327d91/artifacts/dataset.csv # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| defaults: | ||
| - /dataset/processed/ftn@_here_ | ||
| - _self_ | ||
|
|
||
| tissue_mask_uri: mlflow-artifacts:/86/04778b10de254572b69ce0a101c1eee4/artifacts/tissue_masks # TODO update URI | ||
| qc_mask_uri: mlflow-artifacts:/86/c8edfb2541e84b44b1a28be3540c1a35/artifacts # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| defaults: | ||
| - /dataset/processed/ikem@_here_ | ||
| - _self_ | ||
|
|
||
| tissue_mask_uri: mlflow-artifacts:/86/13359cdd5d1a47ddabc352b9aa0d7635/artifacts/tissue_masks # TODO update URI | ||
| qc_mask_uri: mlflow-artifacts:/86/98443fe2b67445d5a56598bff15b7f27/artifacts # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| defaults: | ||
| - /dataset/processed/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| tissue_mask_uri: mlflow-artifacts:/86/8ef6d6f0c9af4f35a087596960f675aa/artifacts/tissue_masks # TODO update URI | ||
| qc_mask_uri: mlflow-artifacts:/86/75fc3e53112f4634ae5238777d87e88c/artifacts # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| institution: ftn | ||
| folder: /mnt/data/FTN/colon/IBD_AI | ||
| labels: | ||
| - IBD_AI_FTN.xlsx | ||
| - IBD_AI_FTN_doplnek.xlsx |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| institution: ikem | ||
| folder: /mnt/data/IKEM/colon/IBD_AI/20x | ||
| labels: | ||
| - Fab_IBD_AI_12_2024.csv | ||
| - IBD_AI_2.xlsx | ||
| - missing.xlsx |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| institution: knl_patos | ||
| folder: /mnt/data/KNL_PATOS/colon/IBD_AI | ||
| labels: | ||
| - IBD_AI_Liberec.xlsx | ||
| - IBD_AI_Liberec_02.xlsx | ||
| - IBD_AI_Liberec_10_2025.xlsx | ||
| - IBD_AI_Liberec_28_10_2025.xlsx |
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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 |
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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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| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni2 | ||
| - _self_ |
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configs/experiment/preprocessing/embeddings/ftn_1_virchow.yaml
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| # @package _global_ | ||
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| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow | ||
| - _self_ |
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configs/experiment/preprocessing/embeddings/ftn_1_virchow2.yaml
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| # @package _global_ | ||
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| defaults: | ||
| - /dataset/tiled/ftn/1_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
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configs/experiment/preprocessing/embeddings/ftn_2_virchow2.yaml
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| # @package _global_ | ||
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| defaults: | ||
| - /dataset/tiled/ftn/2_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
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configs/experiment/preprocessing/embeddings/ikem_1_prov_gigapath.yaml
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| # @package _global_ | ||
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| 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 |
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| # @package _global_ | ||
|
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| 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 |
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| # @package _global_ | ||
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| defaults: | ||
| - /dataset/tiled/ikem/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni2 | ||
| - _self_ |
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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
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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
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configs/experiment/preprocessing/embeddings/ikem_2_virchow2.yaml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
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| defaults: | ||
| - /dataset/tiled/ikem/2_224@dataset | ||
| - /preprocessing/tile_encoder/virchow2 | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
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configs/experiment/preprocessing/embeddings/knl_patos_1_prov_gigapath.yaml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
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| defaults: | ||
| - /dataset/tiled/knl_patos/1_224@dataset | ||
| - /preprocessing/tile_encoder/prov_gigapath | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
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configs/experiment/preprocessing/embeddings/knl_patos_1_uni.yaml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
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| defaults: | ||
| - /dataset/tiled/knl_patos/1_224@dataset | ||
| - /preprocessing/tile_encoder/uni | ||
| - _self_ |
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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