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.gitattributes

@@ -57,3 +57,4 @@ 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
+parse_concat_full.h5ad filter=lfs diff=lfs merge=lfs -text

celltype.toml

@@ -0,0 +1,25 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."parse.B_Intermediate_Memory"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']
+
+[fewshot."parse.B_Naive"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']
+
+[fewshot."parse.Plasmablast"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']

celltype_zeroshot.toml

@@ -0,0 +1,17 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"parse.B_Intermediate_Memory" = "test"
+"parse.B_Naive" = "test"
+"parse.Plasmablast" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

donor.toml

@@ -0,0 +1,29 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."parse.Donor1"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']
+
+[fewshot."parse.Donor4"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']
+
+[fewshot."parse.Donor9"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']
+
+[fewshot."parse.Donor12"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']

donor_zeroshot.toml

@@ -0,0 +1,18 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"parse.Donor1" = "test"
+"parse.Donor4" = "test"
+"parse.Donor9" = "test"
+"parse.Donor12" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

parse_concat_full.h5ad

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2eeb42d1c8a028a826f84158d7bdf1124d68a0dc056096027399984e407219be
+size 367463139462

split_1.toml

@@ -0,0 +1,17 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."parse.B_Intermediate_Memory"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']

split_1_zeroshot.toml

@@ -0,0 +1,15 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"parse.B_Intermediate_Memory" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

split_2.toml

@@ -0,0 +1,17 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."parse.B_Naive"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']

split_2_zeroshot.toml

@@ -0,0 +1,15 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"parse.B_Naive" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

split_3.toml

@@ -0,0 +1,17 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."parse.Plasmablast"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']

split_3_zeroshot.toml

@@ -0,0 +1,15 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"parse.Plasmablast" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

split_4.toml

@@ -0,0 +1,17 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."parse.CD4_Memory"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']

split_4_zeroshot.toml

@@ -0,0 +1,15 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"parse.CD4_Memory" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]

split_5.toml

@@ -0,0 +1,17 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]
+[fewshot."parse.CD14_Mono"]
+val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']
+test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']

split_5_zeroshot.toml

@@ -0,0 +1,15 @@
+# Dataset paths - maps dataset names to their directories
+[datasets]
+parse = "/data/parse_final_concat"
+
+# Training specifications
+# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)
+[training]
+parse = "train"
+
+# Zeroshot specifications - entire cell types go to val or test
+[zeroshot]
+"parse.CD14_Mono" = "test"
+
+# Fewshot specifications - explicit perturbation lists
+[fewshot]