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48d2aab
feat: correction tiles
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feat: correct metadata
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feat: add docstring
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feat: rebase
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fix: lm notes
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feat: prepare modules
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feat: prepare for training
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fix: add unlabeled processor
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fix: prefix
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fix: import
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fix: typo
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feat: google vit inference configs
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feat: different Lr
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feat: warmuup
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fix: add imports
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feat: basic augments
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feat: use standard decomposition
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fix: import
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feat: module hierarchy
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feat: classifier hierarchy
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fix: add pooling
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feat: clean dataset configs
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feat: rebase
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feat: new staining augmentation
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feat: fix param name
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fix: do not include backbone in embedding models
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fix: importing old model
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feat: use just backbone directly
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feat: add new checkpoint
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feat: ruff
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fix: mypy
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feat: new checkpoint
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feat: set estimated tl threshold
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feat: rebase
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feat: MIL module
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feat: mil forward
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feat: datamodule strucutre
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feat: datamodule configs
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feat: prepare training mil
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feat: use uris
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feat: update embeds
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fix: index
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fix: collate
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feat: increase epochs
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feat: replace linear with embedding classifier
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feat: mil pred callback
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feat: mil callback configs
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feat: rebase
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feat: nest model
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fix: path
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chore: debug
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feat: another debug
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feat: custom collate
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feat: tl sl train
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feat: tl sl tran
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feat: train data
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fix: add tl th
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feat: do not use series
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feat: extended mil model
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fix: add tl threshold
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feat: generalize
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feat: show also attention
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feat: rescale attn
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feat: rebase
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feat: add sl
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feat: training
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feat: per task loss
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feat: weighted tl loss
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feat: drop dropout
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feat: add partial losses log
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fix: lint
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feat: models
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feat: tile filtering
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feat: filtering
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fix: apply fixes
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feat: fixed dim
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feat: filtered uris
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fix: not filter carcinoma
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feat: new uris
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feat: mergig
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feat: merged parquets
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fix: tl macro avg
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feat: rebase
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feat: remove filtering
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feat: HF dataset
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fix: downgrade mlkit
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fix: datasets
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fix: proper glob
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fix: proper glob
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fix: type
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fix: rem comment
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feat: classic
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feat: rebase
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feat: replace log table
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fix: setup
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feat: replace log table
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fix: meta
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fix: filtering
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feat: freeze
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fix: filter
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fix: missing import
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fix: sampler bag
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fix: lint
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fix: patch mlflow
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fix: lint
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feat: resolve comments
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feat: try builtin
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fix: lint and indexing
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feat: try gene
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feat: invoke check
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feat: my filter
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feat: stricter typing
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feat: pgp augmented training
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fix: model path
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fix: freeze
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feat: light checkpoint
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feat: pgp stain model
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feat: try preds
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fix: nest
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feat: prepare virchow2 training
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feat: redesign
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feat: add full stain trained variant
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feat: fix mlkit
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feat: move to embeds
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feat: heatmaps
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feat: tl test
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feat: v2stain heat and amx
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fix: last slide
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feat: use main mlkit
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feat: update lock
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feat: loader
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feat: ps
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feat: pgp tl t
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feat: max aggr
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feat: estimations
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feat: up to topk
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feat: span
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feat: evals
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feat: sl test tl test
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feat: mmci tl eval
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feat: update non inferiority
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feat: rebase
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feat: remove full fine tune
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fix: checkpoint loading
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feat: test non strict load
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fix: header
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fix: lint
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feat: remove test pgp
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feat: smaller patch size
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feat: rebase
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feat: rename
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feat: TL thresholds
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feat: add new est. runs
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feat: rename to 224x224
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feat: revert to 512x512
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feat: 224 traning configs
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feat: resnet configs
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feat: bring back 512 models
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feat: test add 224
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feat: estimations nest
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feat: restructure and delete
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feat: aggr eval
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feat: mmci sl group 1 work
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feat: non inferiority
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feat: tl val heatmaps
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feat: resnet50
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feat: rebase
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feat: tl test
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fix: mmci tl
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feat: eval script
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feat: multi aggregate sl eval
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feat: add test set
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feat: fix hyperparams
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feat: fix typos
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feat: rebase
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feat: fix kernel size
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feat: new threshold
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feat: rebase
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feat: preds sl group 1
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feat: revert
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feat: rebase
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fix: lint
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fix: advanced lint
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| multi_aggregator_eval_callback: | ||
| _target_: prostate_cancer.callbacks.MultiAggregatorEvalCallback | ||
| max_aggregator: ${max_aggregator} | ||
| mean_pool_max_aggregator: ${mean_pool_max_aggregator} | ||
| top_k_aggregator: ${top_k_aggregator} | ||
| max_threshold: ${model_data.slide_max_threshold} | ||
| mean_pool_max_threshold: ${model_data.slide_mpm_threshold} | ||
| top_k_threshold: ${model_data.slide_top_k_threshold} |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/embeddings/pgp/base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/embeddings/pgp/multi_aggregator_eval/base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/embeddings/pgp/stain_base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 3 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 2 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/embeddings/virchow2/base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 2 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 2 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 3 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/embeddings/virchow2/stain_base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 2 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 2 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 2 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
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21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/google_vit/multi_aggregator_eval/base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/google_vit/base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 2 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/google_vit/multi_aggregator_eval/mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/google_vit/multi_aggregator_eval/base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/google_vit/stain_base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 6 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 2 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/google_vit/multi_aggregator_eval/stain_base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/resnet50/multi_aggregator_eval/base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/resnet50/base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 5 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| top_k_aggregator: | ||
| kernel_size: 4 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/resnet50/multi_aggregator_eval/base_224.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/resnet50/base_224 | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 6 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 5 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/resnet50/multi_aggregator_eval/base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test_224.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/resnet50/multi_aggregator_eval/base_224 | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/resnet50/stain_base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 3 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| top_k_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" | ||
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_base_224.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/resnet50/stain_base_224 | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 2 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test_224.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base_224 | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/vgg16/multi_aggregator_eval/base.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/vgg16/base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| top_k_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/vgg16/multi_aggregator_eval/base_224.yaml
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/vgg16/base_224 | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 7 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| top_k_aggregator: | ||
| kernel_size: 5 | ||
| extent_tile: 224 | ||
| stride_tile: 112 | ||
| k: 4 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test.yaml
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/vgg16/multi_aggregator_eval/base | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
6 changes: 6 additions & 0 deletions
6
configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test_224.yaml
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /experiment/predict/images/vgg16/multi_aggregator_eval/base_224 | ||
| - /data/mmci/tl_test@predict_data | ||
| - _self_ |
21 changes: 21 additions & 0 deletions
21
configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_base.yaml
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /callbacks/multi_aggregator_eval@callbacks | ||
| - /aggregator/max@max_aggregator | ||
| - /aggregator/mean_pool_max@mean_pool_max_aggregator | ||
| - /aggregator/top_k@top_k_aggregator | ||
| - /experiment/predict/images/vgg16/stain_base | ||
| - _self_ | ||
|
|
||
| mean_pool_max_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| top_k_aggregator: | ||
| kernel_size: 1 | ||
| extent_tile: 512 | ||
| stride_tile: 256 | ||
| k: 2 | ||
|
|
||
| use_case: "Multi-Aggregator SL Evaluation" |
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