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@Adames4 Adames4 commented May 8, 2026

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@Adames4 Adames4 self-assigned this May 8, 2026
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Adames4 requested review from a team, JakubPekar and ejdam87 May 8, 2026 17:07
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  • .ruff.toml
  • README.md
  • configs/base.yaml
  • configs/checkpoints/experiment_i_baseline_classification/fold_1.yaml
  • configs/checkpoints/experiment_i_baseline_classification/fold_2.yaml
  • configs/checkpoints/experiment_i_baseline_classification/fold_3.yaml
  • configs/checkpoints/experiment_i_baseline_classification/fold_4.yaml
  • configs/checkpoints/experiment_i_baseline_classification/fold_5.yaml
  • configs/checkpoints/experiment_ii_ordered_regression/fold_1.yaml
  • configs/checkpoints/experiment_ii_ordered_regression/fold_2.yaml
  • configs/checkpoints/experiment_ii_ordered_regression/fold_3.yaml
  • configs/checkpoints/experiment_ii_ordered_regression/fold_4.yaml
  • configs/checkpoints/experiment_ii_ordered_regression/fold_5.yaml
  • configs/checkpoints/experiment_iii_pathology_foundation_model/fold_1.yaml
  • configs/checkpoints/experiment_iii_pathology_foundation_model/fold_2.yaml
  • configs/checkpoints/experiment_iii_pathology_foundation_model/fold_3.yaml
  • configs/checkpoints/experiment_iii_pathology_foundation_model/fold_4.yaml
  • configs/checkpoints/experiment_iii_pathology_foundation_model/fold_5.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_high/fold_1.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_high/fold_2.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_high/fold_3.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_high/fold_4.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_high/fold_5.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_low/fold_1.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_low/fold_2.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_low/fold_3.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_low/fold_4.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/nancy_low/fold_5.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/neutrophils/fold_1.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/neutrophils/fold_2.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/neutrophils/fold_3.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/neutrophils/fold_4.yaml
  • configs/checkpoints/experiment_iv_mil_and_hierarchical_modeling/neutrophils/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_uni2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_uni2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_uni2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_uni2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_uni2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_virchow2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_virchow2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_virchow2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_virchow2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/1_virchow2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/2_virchow2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/2_virchow2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/2_virchow2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/2_virchow2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_high/2_virchow2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_uni2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_uni2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_uni2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_uni2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_uni2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_virchow2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_virchow2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_virchow2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_virchow2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/1_virchow2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/2_virchow2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/2_virchow2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/2_virchow2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/2_virchow2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/nancy_low/2_virchow2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_uni2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_uni2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_uni2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_uni2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_uni2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_virchow2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_virchow2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_virchow2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_virchow2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/1_virchow2/fold_5.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/2_virchow2/fold_1.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/2_virchow2/fold_2.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/2_virchow2/fold_3.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/2_virchow2/fold_4.yaml
  • configs/checkpoints/experiment_v_more_foundation_models/neutrophils/2_virchow2/fold_5.yaml
  • configs/checkpoints/final/nancy_high.yaml
  • configs/checkpoints/final/nancy_low.yaml
  • configs/checkpoints/final/neutrophils.yaml
  • configs/dataset/embeddings/ftn/1_prov-gigapath.yaml
  • configs/dataset/embeddings/ftn/1_uni2.yaml
  • configs/dataset/embeddings/ftn/1_virchow2.yaml
  • configs/dataset/embeddings/ftn/2_virchow2.yaml
  • configs/dataset/embeddings/ikem/1_prov-gigapath.yaml
  • configs/dataset/embeddings/ikem/1_uni2.yaml
  • configs/dataset/embeddings/ikem/1_virchow2.yaml
  • configs/dataset/embeddings/ikem/2_virchow2.yaml
  • configs/dataset/embeddings/knl_patos/1_prov-gigapath.yaml
  • configs/dataset/embeddings/knl_patos/1_uni2.yaml
  • configs/dataset/embeddings/knl_patos/1_virchow2.yaml
  • configs/dataset/embeddings/knl_patos/2_virchow2.yaml
  • configs/dataset/neutrophils/all.yaml
  • configs/dataset/neutrophils/ftn.yaml
  • configs/dataset/neutrophils/ikem.yaml
  • configs/dataset/neutrophils/knl_patos.yaml
  • configs/dataset/processed/ftn.yaml
  • configs/dataset/processed/ikem.yaml
  • configs/dataset/processed/knl_patos.yaml
  • configs/dataset/processed_w_masks/ftn.yaml
  • configs/dataset/processed_w_masks/ikem.yaml
  • configs/dataset/processed_w_masks/knl_patos.yaml
  • configs/dataset/tiled/ftn.yaml
  • configs/dataset/tiled/ftn/0_320.yaml
  • configs/dataset/tiled/ftn/0_512.yaml
  • configs/dataset/tiled/ftn/1_224.yaml
  • configs/dataset/tiled/ftn/2_224.yaml
  • configs/dataset/tiled/ikem.yaml
  • configs/dataset/tiled/ikem/0_320.yaml
  • configs/dataset/tiled/ikem/0_512.yaml
  • configs/dataset/tiled/ikem/1_224.yaml
  • configs/dataset/tiled/ikem/2_224.yaml
  • configs/dataset/tiled/knl_patos.yaml
  • configs/dataset/tiled/knl_patos/0_320.yaml
  • configs/dataset/tiled/knl_patos/0_512.yaml
  • configs/dataset/tiled/knl_patos/1_224.yaml
  • configs/dataset/tiled/knl_patos/2_224.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/test/fold_1.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/test/fold_2.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/test/fold_3.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/test/fold_4.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/test/fold_5.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/train/fold_1.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/train/fold_2.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/train/fold_3.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/train/fold_4.yaml
  • configs/experiment/ml/experiment_i_baseline_classification/train/fold_5.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/test/fold_1.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/test/fold_2.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/test/fold_3.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/test/fold_4.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/test/fold_5.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/train/fold_1.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/train/fold_2.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/train/fold_3.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/train/fold_4.yaml
  • configs/experiment/ml/experiment_ii_ordered_regression/train/fold_5.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/test/fold_1.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/test/fold_2.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/test/fold_3.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/test/fold_4.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/test/fold_5.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/train/fold_1.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/train/fold_2.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/train/fold_3.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/train/fold_4.yaml
  • configs/experiment/ml/experiment_iii_pathology_foundation_model/train/fold_5.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/test/fold_1.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/test/fold_2.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/test/fold_3.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/test/fold_4.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/test/fold_5.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/train/fold_1.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/train/fold_2.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/train/fold_3.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/train/fold_4.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_high/train/fold_5.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/test/fold_1.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/test/fold_2.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/test/fold_3.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/test/fold_4.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/test/fold_5.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/train/fold_1.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/train/fold_2.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/train/fold_3.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/train/fold_4.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/nancy_low/train/fold_5.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/test/fold_1.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/test/fold_2.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/test/fold_3.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/test/fold_4.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/test/fold_5.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/train/fold_1.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/train/fold_2.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/train/fold_3.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/train/fold_4.yaml
  • configs/experiment/ml/experiment_iv_mil_and_hierarchical_modeling/neutrophils/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_prov-gigapath/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_uni2/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/1_virchow2/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_high/2_virchow2/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_prov-gigapath/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_uni2/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/1_virchow2/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/nancy_low/2_virchow2/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_prov-gigapath/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/train/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/train/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/train/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_uni2/train/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_virchow2/test/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_virchow2/test/fold_2.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_virchow2/test/fold_3.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_virchow2/test/fold_4.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_virchow2/test/fold_5.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_virchow2/train/fold_1.yaml
  • configs/experiment/ml/experiment_v_more_foundation_models/neutrophils/1_virchow2/train/fold_2.yaml

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Summary of Changes

Hello, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request performs a significant expansion and reorganization of the project's configuration system. By adding numerous YAML files for checkpoints, datasets, and experiment definitions, the changes establish a modular framework for managing complex machine learning workflows. Additionally, existing dataset configurations were updated to use placeholders for MLflow URIs, likely to facilitate environment-specific configuration management.

Highlights

  • Configuration Restructuring: Added a comprehensive set of configuration files for checkpoints, datasets, and experiments to support a structured research workflow.
  • Project Directory Update: Updated the base configuration to include a specific project directory path.
  • MLflow URI Reset: Replaced hardcoded MLflow artifact URIs with placeholders across multiple dataset configuration files.
  • Experiment Setup: Implemented detailed training and testing configurations for various models and datasets, including classification, regression, and foundation model experiments.
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Code Review

This pull request updates the Hydra configuration files for the project. Key changes include the addition of a project_dir in the base configuration, the introduction of placeholder checkpoints for various experiments, and the creation of new dataset and experiment configurations for different models and folds. I have no feedback to provide.

@Adames4 Adames4 closed this May 13, 2026
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