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@@ -65,3 +65,6 @@ bmmc/bmmc_pretraining.h5ad filter=lfs diff=lfs merge=lfs -text
 poised/poised.h5ad filter=lfs diff=lfs merge=lfs -text
 top1501/top1501.h5ad filter=lfs diff=lfs merge=lfs -text
 top1501/top1501_pretraining.h5ad filter=lfs diff=lfs merge=lfs -text
+krieg_antipd1/krieg_antipd1.h5ad filter=lfs diff=lfs merge=lfs -text
+nilsson_rare/nilsson_rare.h5ad filter=lfs diff=lfs merge=lfs -text
+nsclc_antipd1/nsclc_antipd1.h5ad filter=lfs diff=lfs merge=lfs -text

aml/aml.h5ad

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aml/aml_pretraining.h5ad

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bmmc/bmmc.h5ad

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bmmc/bmmc_pretraining.h5ad

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config_dataset.yaml

@@ -1,53 +1,77 @@
-path: ""
-
-cell_classification:
-  aml:
-    h5ad_path: "{path}/aml/aml.h5ad"
-    table_path: "{path}/aml/aml_table.csv"
-    h5ad_pretraining_path: "{path}/aml/aml_pretraining.h5ad"
-    label_key: cell_type
-    sample_key: Sample
-    batch_key: null
-    pretraining_sample_key: Sub_study
-    unknown_label: null
-    classification_level: cell
-    num_cls_label_finetuning: 14
-  bmmc:
-    h5ad_path: "{path}/bmmc/bmmc.h5ad"
-    table_path: "{path}/bmmc/bmmc_table.csv"
-    h5ad_pretraining_path: "{path}/bmmc/bmmc_pretraining.h5ad"
-    label_key: cell_type
-    sample_key: Sample
-    batch_key: null
-    pretraining_sample_key: Sub_study
-    unknown_label: null
-    classification_level: cell
-    num_cls_label_finetuning: 19
-
-sample_classification:
-  top1501:
-    h5ad_path: "{path}/top1501/top1501.h5ad"
-    table_path: null
-    h5ad_pretraining_path: "{path}/top1501/top1501_pretraining.h5ad"
-    label_key: Outcome
-    sample_key: Sample
-    batch_key: null
-    pretraining_sample_key: Sub_study
-    unknown_label: null
-    classification_level: sample
-    num_cls_label_finetuning: 2
-
-batch_integration:
-  poised:
-    h5ad_path: "{path}/poised/poised.h5ad"
-    table_path: "{path}/poised/poised_table.csv"
-    h5ad_pretraining_path: "{path}/aml/aml_pretraining.h5ad"
-    label_key: labels
-    sample_key: file
-    batch_key: batch
-    pretraining_sample_key: Sub_study
-    unknown_label: Unknown
-    classification_level: cell
-    num_cls_label_finetuning: 22
-
-
+poised:
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+  table_path: processed_datasets/poised/poised_table.csv
+  sample_key: file
+  batch_key: batch
+  cell_label_key: labels
+  nb_classes_cell_labels: 22
+  sample_label_key: null
+  nb_classes_sample_labels: null
+  unknown_label: Unknown
+  classification_level: cell
+aml:
+  h5ad_path: processed_datasets/aml/aml.h5ad
+  table_path: processed_datasets/aml/aml_table.csv
+  sample_key: Sample
+  batch_key: null
+  cell_label_key: cell_type
+  nb_classes_cell_labels: 14
+  sample_label_key: null
+  nb_classes_sample_labels: null
+  unknown_label: null
+  classification_level: cell
+bmmc:
+  h5ad_path: processed_datasets/bmmc/bmmc.h5ad
+  table_path: processed_datasets/bmmc/bmmc_table.csv
+  sample_key: Sample
+  batch_key: null
+  cell_label_key: cell_type
+  nb_classes_cell_labels: 19
+  sample_label_key: null
+  nb_classes_sample_labels: null
+  unknown_label: null
+  classification_level: cell
+nilsson_rare:
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+  table_path: null
+  sample_key: Sample
+  batch_key: null
+  cell_label_key: cell_type
+  nb_classes_cell_labels: 2
+  sample_label_key: null
+  nb_classes_sample_labels: null
+  unknown_label: null
+  classification_level: cell
+top1501:
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+  table_path: null
+  sample_key: Sample
+  batch_key: null
+  cell_label_key: null
+  nb_classes_cell_labels: null
+  sample_label_key: Outcome
+  nb_classes_sample_labels: 2
+  unknown_label: null
+  classification_level: sample
+krieg_antipd1:
+  h5ad_path: processed_datasets/krieg_antipd1/krieg_antipd1.h5ad
+  table_path: null
+  sample_key: Sample
+  batch_key: batch
+  cell_label_key: null
+  nb_classes_cell_labels: null
+  sample_label_key: Outcome
+  nb_classes_sample_labels: 2
+  unknown_label: null
+  classification_level: sample
+nsclc_antipd1:
+  h5ad_path: processed_datasets/nsclc_antipd1/nsclc_antipd1.h5ad
+  table_path: null
+  sample_key: Sample
+  batch_key: null
+  cell_label_key: null
+  nb_classes_cell_labels: null
+  sample_label_key: Outcome
+  nb_classes_sample_labels: 2
+  unknown_label: null
+  classification_level: sample

krieg_antipd1/krieg_antipd1.h5ad

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nilsson_rare/nilsson_rare.h5ad

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poised/poised.h5ad

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top1501/top1501.h5ad

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top1501/top1501_pretraining.h5ad

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