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@@ -58,3 +58,10 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+aml/aml.h5ad filter=lfs diff=lfs merge=lfs -text
+aml/aml_pretraining.h5ad filter=lfs diff=lfs merge=lfs -text
+bmmc/bmmc.h5ad filter=lfs diff=lfs merge=lfs -text
+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

aml/aml.h5ad

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+size 6933085

aml/aml_pretraining.h5ad

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+size 39569412

aml/aml_table.csv

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+,CD19,CD4,CD8,CD34,CD20,CD45,CD123,CD11C,CD7,CD16,CD38,CD3,HLADR,CD64
+Basophils,-1,,-1.0,-1,-1.0,,1,-1,-1.0,-1.0,,-1,-1.0,-1.0
+CD4 T cells,-1,1.0,-1.0,-1,-1.0,,-1,-1,,-1.0,,1,-1.0,-1.0
+CD8 T cells,-1,-1.0,1.0,-1,-1.0,,-1,-1,1.0,-1.0,,1,-1.0,-1.0
+CD16- NK cells,-1,,,-1,-1.0,,-1,-1,1.0,-1.0,,-1,-1.0,-1.0
+CD16+ NK cells,-1,,,-1,,,-1,-1,1.0,1.0,,-1,-1.0,-1.0
+CD34+CD38+CD123- HSPCs,-1,,-1.0,1,-1.0,-1.0,-1,-1,-1.0,-1.0,1.0,-1,,-1.0
+CD34+CD38+CD123+ HSPCs,-1,,-1.0,1,-1.0,-1.0,1,-1,-1.0,-1.0,1.0,-1,,-1.0
+CD34+CD38lo HSCs,-1,,-1.0,1,-1.0,-1.0,-1,-1,-1.0,-1.0,-1.0,-1,,-1.0
+Mature B cells,1,,-1.0,-1,,,-1,-1,-1.0,-1.0,-1.0,-1,,
+Plasma B cells,1,,-1.0,-1,,,-1,-1,-1.0,-1.0,1.0,-1,-1.0,
+Pre B cells,1,,-1.0,-1,,,-1,-1,-1.0,-1.0,1.0,-1,1.0,-1.0
+Pro B cells,1,,-1.0,1,,-1.0,-1,-1,-1.0,-1.0,1.0,-1,,-1.0
+Monocytes,-1,,-1.0,-1,-1.0,,-1,1,-1.0,,,-1,1.0,
+pDCs,-1,,-1.0,-1,-1.0,,1,-1,-1.0,,,-1,1.0,-1.0

bmmc/bmmc.h5ad

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bmmc/bmmc_pretraining.h5ad

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+version https://git-lfs.github.com/spec/v1
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+size 6526216

bmmc/bmmc_table.csv

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+,CD45,CD45RA,CD19,CD11B,CD4,CD8,CD34,CD20,CD33,CD123,CD38,CD90,CD3
+Mature CD4+ T,1.0,-1.0,-1,,1,-1,,,-1,,-1.0,,1
+Mature CD8+ T,1.0,-1.0,-1,,-1,1,,,-1,,-1.0,,1
+Naive CD4+ T,1.0,1.0,-1,,1,-1,,,-1,,-1.0,,1
+Naive CD8+ T,1.0,1.0,-1,,-1,1,,,-1,,-1.0,,1
+CD11bhi Monocyte,1.0,,-1,1.0,-1,-1,-1.0,,1,,,,-1
+CD11b- Monocyte,1.0,,-1,-1.0,-1,-1,-1.0,,1,,,,-1
+Pre-B I,,,1,,-1,-1,1.0,-1.0,-1,,1.0,,-1
+Pre-B II,,,1,,-1,-1,-1.0,-1.0,-1,,1.0,,-1
+Immature B,,,1,,-1,-1,-1.0,-1.0,-1,,-1.0,,-1
+Mature CD38lo B,,,1,,-1,-1,-1.0,1.0,-1,,-1.0,,-1
+Mature CD38mid B,,,1,,-1,-1,-1.0,1.0,-1,,1.0,,-1
+NK,1.0,1.0,-1,,-1,-1,,,-1,,1.0,,-1
+Plasmacytoid DC,1.0,1.0,-1,,-1,-1,-1.0,,-1,1.0,1.0,,-1
+CMP,,-1.0,-1,,-1,-1,1.0,,-1,-1.0,1.0,,-1
+GMP,,1.0,-1,,-1,-1,1.0,,-1,-1.0,1.0,,-1
+HSC,,-1.0,-1,,-1,-1,1.0,,-1,,-1.0,1.0,-1
+MEP,,-1.0,-1,,-1,-1,1.0,,-1,1.0,1.0,,-1
+MPP,,-1.0,-1,,-1,-1,1.0,,-1,,-1.0,-1.0,-1
+Plasma cell,,,1,,-1,-1,,-1.0,-1,,1.0,,-1

config_dataset.yaml

@@ -0,0 +1,53 @@
+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/poised.h5ad

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+version https://git-lfs.github.com/spec/v1
+oid sha256:46ef054ca4898a9dc1fbc61eee4ebf96a47797621b8f68b9d200a48d7882d55d
+size 1023275

poised/poised_table.csv

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+,CD19,CD20,CD3,CD4,CD8,TCRGD,CD16,CD56,CD25,CD127,CD45RA,CCR7,HLADR,CD14,CD11C,CD123,CD27,CD69,CD40L
+B Naive,1,1.0,-1,-1.0,-1.0,-1,,-1,,,,,1,-1.0,,,-1.0,,
+B Mem,1,1.0,-1,-1.0,-1.0,-1,,-1,,,,,1,-1.0,,,1.0,,
+pDCs,-1,,-1,,-1.0,-1,-1.0,-1,,,,,1,-1.0,-1.0,1.0,,,
+mDC1,-1,,-1,,-1.0,-1,-1.0,-1,,,,,1,-1.0,1.0,1.0,,,
+mDC2,-1,,-1,,-1.0,-1,-1.0,-1,,,,,1,-1.0,0.5,-1.0,,,
+DC others,-1,,-1,,-1.0,-1,-1.0,-1,,,,,1,-1.0,-1.0,,,,
+cMonocytes,-1,,-1,,-1.0,-1,,-1,,,,,1,1.0,1.0,1.0,,,
+Classical_mono CD14low,-1,,-1,,-1.0,-1,-1.0,-1,,,,,1,-0.5,1.0,1.0,,,
+iMonocytes,-1,,-1,,-1.0,-1,1.0,-1,,,,,1,-0.5,1.0,1.0,,,
+ncMonocytes,-1,,-1,,-1.0,-1,1.0,-1,,,,,1,-1.0,1.0,1.0,,,
+gdTCR Mem,-1,-1.0,1,-1.0,-1.0,1,,-1,-1.0,,-1.0,,-1,-1.0,-1.0,-1.0,,-1.0,
+gdTCR Naive,-1,-1.0,1,-1.0,-1.0,1,,-1,-1.0,,1.0,,-1,-1.0,-1.0,-1.0,,-1.0,
+TCD4 EM,-1,-1.0,1,1.0,-1.0,-1,,-1,-1.0,1.0,-1.0,-1.0,-1,-1.0,-1.0,-1.0,,-1.0,-1.0
+TCD4 CM,-1,-1.0,1,1.0,-1.0,-1,,-1,-1.0,1.0,-1.0,1.0,-1,-1.0,-1.0,-1.0,,-1.0,-1.0
+TCD4 Naive,-1,-1.0,1,1.0,-1.0,-1,,-1,-1.0,1.0,1.0,1.0,-1,-1.0,-1.0,-1.0,,-1.0,-1.0
+TCD4 PeaReactive,-1,-1.0,1,1.0,-1.0,-1,,-1,-1.0,1.0,,,-1,-1.0,-1.0,-1.0,,1.0,1.0
+Treg Mem,-1,-1.0,1,1.0,-1.0,-1,,-1,1.0,-1.0,-1.0,,-1,-1.0,-1.0,-1.0,,-1.0,-1.0
+Treg Naive,-1,-1.0,1,1.0,-1.0,-1,,-1,1.0,-1.0,1.0,,-1,-1.0,-1.0,-1.0,,-1.0,-1.0
+TCD8 EM,-1,-1.0,1,-1.0,1.0,-1,,-1,,,-1.0,-1.0,-1,-1.0,-1.0,-1.0,,-1.0,
+TCD8 CM,-1,-1.0,1,-1.0,1.0,-1,,-1,,,-1.0,1.0,-1,-1.0,-1.0,-1.0,,-1.0,
+TCD8 Naive,-1,-1.0,1,-1.0,1.0,-1,,-1,,,1.0,1.0,-1,-1.0,-1.0,-1.0,,-1.0,
+TCD8 PeaReactive,-1,-1.0,1,-1.0,1.0,-1,,-1,,,,,-1,-1.0,-1.0,-1.0,,1.0,
+NK,-1,,-1,,-1.0,-1,,1,,,,,-1,-1.0,,,,,
+NKT,-1,,1,,,-1,-1.0,1,,,,,-1,-1.0,-1.0,-1.0,,,

top1501/top1501.h5ad

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+size 61316992

top1501/top1501_pretraining.h5ad

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