Datasets:
Upload results/experiments/exp_9/results.json with huggingface_hub
Browse files- results/experiments/exp_9/results.json +2952 -45
results/experiments/exp_9/results.json
CHANGED
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@@ -1,41 +1,51 @@
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{
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"rank_sensitivity": {
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"4": {
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"best_epoch": 31
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},
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"8": {
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"best_epoch": 4
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},
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"16": {
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"best_epoch": 9
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},
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"32": {
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"best_epoch": 41
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},
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"64": {
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"best_epoch": 11
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}
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},
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"topk_sensitivity": {
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"25": {
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"mean_spearman_vs_50":
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"per_celltype": {
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"Astrocyte":
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"Endothel":
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"Excitatory neuron":
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"Inhibitory neuron":
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"Lymphocyte":
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"Malignant":
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"OPC":
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"Oligodendrocyte":
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"Other":
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"Pericyte":
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"TAM":
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}
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},
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"50": {
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}
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},
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"100": {
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"mean_spearman_vs_50":
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"per_celltype": {
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"Astrocyte":
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"Endothel":
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"Excitatory neuron":
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"Inhibitory neuron":
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"Lymphocyte":
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"Malignant":
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"OPC":
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"Oligodendrocyte":
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"Other":
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"Pericyte":
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"TAM":
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}
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},
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"200": {
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-
"mean_spearman_vs_50":
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"per_celltype": {
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"Astrocyte":
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"Endothel":
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"Excitatory neuron":
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"Inhibitory neuron":
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"Lymphocyte":
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"Malignant":
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"OPC":
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"Oligodendrocyte":
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"Other":
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"Pericyte":
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"TAM":
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| 87 |
}
|
| 88 |
}
|
| 89 |
},
|
| 90 |
"cell_subsampling": {
|
| 91 |
"0.5": {
|
| 92 |
-
"mean_spearman": 0.
|
| 93 |
"n_celltypes": 11
|
| 94 |
},
|
| 95 |
"0.25": {
|
| 96 |
-
"mean_spearman": 0.
|
| 97 |
"n_celltypes": 11
|
| 98 |
},
|
| 99 |
"0.1": {
|
| 100 |
-
"mean_spearman": 0.
|
| 101 |
"n_celltypes": 11
|
| 102 |
}
|
| 103 |
},
|
|
@@ -111,5 +2985,38 @@
|
|
| 111 |
"CDK8",
|
| 112 |
"NDUFV2",
|
| 113 |
"PKM"
|
| 114 |
-
]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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|
| 115 |
}
|
|
|
|
| 1 |
{
|
| 2 |
"rank_sensitivity": {
|
| 3 |
"4": {
|
| 4 |
+
"pooled_auroc": 0.8544,
|
| 5 |
+
"macro_auroc": 0.589,
|
| 6 |
+
"n_groups": 8,
|
| 7 |
"best_epoch": 31
|
| 8 |
},
|
| 9 |
"8": {
|
| 10 |
+
"pooled_auroc": 0.8504,
|
| 11 |
+
"macro_auroc": 0.5685,
|
| 12 |
+
"n_groups": 8,
|
| 13 |
"best_epoch": 4
|
| 14 |
},
|
| 15 |
"16": {
|
| 16 |
+
"pooled_auroc": 0.8423,
|
| 17 |
+
"macro_auroc": 0.4754,
|
| 18 |
+
"n_groups": 8,
|
| 19 |
"best_epoch": 9
|
| 20 |
},
|
| 21 |
"32": {
|
| 22 |
+
"pooled_auroc": 0.851,
|
| 23 |
+
"macro_auroc": 0.5657,
|
| 24 |
+
"n_groups": 8,
|
| 25 |
"best_epoch": 41
|
| 26 |
},
|
| 27 |
"64": {
|
| 28 |
+
"pooled_auroc": 0.8436,
|
| 29 |
+
"macro_auroc": 0.5486,
|
| 30 |
+
"n_groups": 8,
|
| 31 |
"best_epoch": 11
|
| 32 |
}
|
| 33 |
},
|
| 34 |
"topk_sensitivity": {
|
| 35 |
"25": {
|
| 36 |
+
"mean_spearman_vs_50": 0.9996,
|
| 37 |
"per_celltype": {
|
| 38 |
+
"Astrocyte": 0.9996,
|
| 39 |
+
"Endothel": 0.9996,
|
| 40 |
+
"Excitatory neuron": 0.9995,
|
| 41 |
+
"Inhibitory neuron": 0.9994,
|
| 42 |
+
"Lymphocyte": 0.9997,
|
| 43 |
+
"Malignant": 0.9997,
|
| 44 |
+
"OPC": 0.9995,
|
| 45 |
+
"Oligodendrocyte": 0.9997,
|
| 46 |
+
"Other": 0.9996,
|
| 47 |
+
"Pericyte": 0.9995,
|
| 48 |
+
"TAM": 0.9997
|
| 49 |
}
|
| 50 |
},
|
| 51 |
"50": {
|
|
|
|
| 65 |
}
|
| 66 |
},
|
| 67 |
"100": {
|
| 68 |
+
"mean_spearman_vs_50": 0.9995,
|
| 69 |
"per_celltype": {
|
| 70 |
+
"Astrocyte": 0.9996,
|
| 71 |
+
"Endothel": 0.9995,
|
| 72 |
+
"Excitatory neuron": 0.9995,
|
| 73 |
+
"Inhibitory neuron": 0.9995,
|
| 74 |
+
"Lymphocyte": 0.9996,
|
| 75 |
+
"Malignant": 0.9996,
|
| 76 |
+
"OPC": 0.9996,
|
| 77 |
+
"Oligodendrocyte": 0.9997,
|
| 78 |
+
"Other": 0.9994,
|
| 79 |
+
"Pericyte": 0.9994,
|
| 80 |
+
"TAM": 0.9994
|
| 81 |
}
|
| 82 |
},
|
| 83 |
"200": {
|
| 84 |
+
"mean_spearman_vs_50": 0.9979,
|
| 85 |
"per_celltype": {
|
| 86 |
+
"Astrocyte": 0.9982,
|
| 87 |
+
"Endothel": 0.9979,
|
| 88 |
+
"Excitatory neuron": 0.9983,
|
| 89 |
+
"Inhibitory neuron": 0.9982,
|
| 90 |
+
"Lymphocyte": 0.9979,
|
| 91 |
+
"Malignant": 0.9985,
|
| 92 |
+
"OPC": 0.9979,
|
| 93 |
+
"Oligodendrocyte": 0.9986,
|
| 94 |
+
"Other": 0.9977,
|
| 95 |
+
"Pericyte": 0.9971,
|
| 96 |
+
"TAM": 0.9972
|
| 97 |
+
}
|
| 98 |
+
}
|
| 99 |
+
},
|
| 100 |
+
"bootstrap_stability": {
|
| 101 |
+
"per_celltype": {
|
| 102 |
+
"Astrocyte": {
|
| 103 |
+
"n_cells": 8281,
|
| 104 |
+
"sample_size": 5000,
|
| 105 |
+
"n_replicates": 20,
|
| 106 |
+
"mean_spearman": 0.9716,
|
| 107 |
+
"mean_top20_jaccard": 0.1802,
|
| 108 |
+
"replicates": [
|
| 109 |
+
{
|
| 110 |
+
"replicate": 1,
|
| 111 |
+
"spearman_rho": 0.9653,
|
| 112 |
+
"top20_jaccard": 0.0526
|
| 113 |
+
},
|
| 114 |
+
{
|
| 115 |
+
"replicate": 2,
|
| 116 |
+
"spearman_rho": 0.9692,
|
| 117 |
+
"top20_jaccard": 0.0811
|
| 118 |
+
},
|
| 119 |
+
{
|
| 120 |
+
"replicate": 3,
|
| 121 |
+
"spearman_rho": 0.9721,
|
| 122 |
+
"top20_jaccard": 0.2903
|
| 123 |
+
},
|
| 124 |
+
{
|
| 125 |
+
"replicate": 4,
|
| 126 |
+
"spearman_rho": 0.9678,
|
| 127 |
+
"top20_jaccard": 0.1429
|
| 128 |
+
},
|
| 129 |
+
{
|
| 130 |
+
"replicate": 5,
|
| 131 |
+
"spearman_rho": 0.9704,
|
| 132 |
+
"top20_jaccard": 0.2903
|
| 133 |
+
},
|
| 134 |
+
{
|
| 135 |
+
"replicate": 6,
|
| 136 |
+
"spearman_rho": 0.9704,
|
| 137 |
+
"top20_jaccard": 0.25
|
| 138 |
+
},
|
| 139 |
+
{
|
| 140 |
+
"replicate": 7,
|
| 141 |
+
"spearman_rho": 0.9771,
|
| 142 |
+
"top20_jaccard": 0.0526
|
| 143 |
+
},
|
| 144 |
+
{
|
| 145 |
+
"replicate": 8,
|
| 146 |
+
"spearman_rho": 0.9732,
|
| 147 |
+
"top20_jaccard": 0.25
|
| 148 |
+
},
|
| 149 |
+
{
|
| 150 |
+
"replicate": 9,
|
| 151 |
+
"spearman_rho": 0.9715,
|
| 152 |
+
"top20_jaccard": 0.25
|
| 153 |
+
},
|
| 154 |
+
{
|
| 155 |
+
"replicate": 10,
|
| 156 |
+
"spearman_rho": 0.9796,
|
| 157 |
+
"top20_jaccard": 0.0526
|
| 158 |
+
},
|
| 159 |
+
{
|
| 160 |
+
"replicate": 11,
|
| 161 |
+
"spearman_rho": 0.9747,
|
| 162 |
+
"top20_jaccard": 0.1765
|
| 163 |
+
},
|
| 164 |
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{
|
| 165 |
+
"replicate": 12,
|
| 166 |
+
"spearman_rho": 0.9661,
|
| 167 |
+
"top20_jaccard": 0.1765
|
| 168 |
+
},
|
| 169 |
+
{
|
| 170 |
+
"replicate": 13,
|
| 171 |
+
"spearman_rho": 0.9671,
|
| 172 |
+
"top20_jaccard": 0.1765
|
| 173 |
+
},
|
| 174 |
+
{
|
| 175 |
+
"replicate": 14,
|
| 176 |
+
"spearman_rho": 0.9735,
|
| 177 |
+
"top20_jaccard": 0.2121
|
| 178 |
+
},
|
| 179 |
+
{
|
| 180 |
+
"replicate": 15,
|
| 181 |
+
"spearman_rho": 0.9781,
|
| 182 |
+
"top20_jaccard": 0.1111
|
| 183 |
+
},
|
| 184 |
+
{
|
| 185 |
+
"replicate": 16,
|
| 186 |
+
"spearman_rho": 0.9675,
|
| 187 |
+
"top20_jaccard": 0.1429
|
| 188 |
+
},
|
| 189 |
+
{
|
| 190 |
+
"replicate": 17,
|
| 191 |
+
"spearman_rho": 0.9784,
|
| 192 |
+
"top20_jaccard": 0.25
|
| 193 |
+
},
|
| 194 |
+
{
|
| 195 |
+
"replicate": 18,
|
| 196 |
+
"spearman_rho": 0.975,
|
| 197 |
+
"top20_jaccard": 0.2121
|
| 198 |
+
},
|
| 199 |
+
{
|
| 200 |
+
"replicate": 19,
|
| 201 |
+
"spearman_rho": 0.9659,
|
| 202 |
+
"top20_jaccard": 0.1429
|
| 203 |
+
},
|
| 204 |
+
{
|
| 205 |
+
"replicate": 20,
|
| 206 |
+
"spearman_rho": 0.969,
|
| 207 |
+
"top20_jaccard": 0.2903
|
| 208 |
+
}
|
| 209 |
+
]
|
| 210 |
+
},
|
| 211 |
+
"Endothel": {
|
| 212 |
+
"n_cells": 5426,
|
| 213 |
+
"sample_size": 5000,
|
| 214 |
+
"n_replicates": 20,
|
| 215 |
+
"mean_spearman": 0.9787,
|
| 216 |
+
"mean_top20_jaccard": 0.2211,
|
| 217 |
+
"replicates": [
|
| 218 |
+
{
|
| 219 |
+
"replicate": 1,
|
| 220 |
+
"spearman_rho": 0.9794,
|
| 221 |
+
"top20_jaccard": 0.2121
|
| 222 |
+
},
|
| 223 |
+
{
|
| 224 |
+
"replicate": 2,
|
| 225 |
+
"spearman_rho": 0.9811,
|
| 226 |
+
"top20_jaccard": 0.2121
|
| 227 |
+
},
|
| 228 |
+
{
|
| 229 |
+
"replicate": 3,
|
| 230 |
+
"spearman_rho": 0.9772,
|
| 231 |
+
"top20_jaccard": 0.3793
|
| 232 |
+
},
|
| 233 |
+
{
|
| 234 |
+
"replicate": 4,
|
| 235 |
+
"spearman_rho": 0.9701,
|
| 236 |
+
"top20_jaccard": 0.25
|
| 237 |
+
},
|
| 238 |
+
{
|
| 239 |
+
"replicate": 5,
|
| 240 |
+
"spearman_rho": 0.9812,
|
| 241 |
+
"top20_jaccard": 0.1429
|
| 242 |
+
},
|
| 243 |
+
{
|
| 244 |
+
"replicate": 6,
|
| 245 |
+
"spearman_rho": 0.979,
|
| 246 |
+
"top20_jaccard": 0.2903
|
| 247 |
+
},
|
| 248 |
+
{
|
| 249 |
+
"replicate": 7,
|
| 250 |
+
"spearman_rho": 0.9851,
|
| 251 |
+
"top20_jaccard": 0.2903
|
| 252 |
+
},
|
| 253 |
+
{
|
| 254 |
+
"replicate": 8,
|
| 255 |
+
"spearman_rho": 0.9787,
|
| 256 |
+
"top20_jaccard": 0.25
|
| 257 |
+
},
|
| 258 |
+
{
|
| 259 |
+
"replicate": 9,
|
| 260 |
+
"spearman_rho": 0.9761,
|
| 261 |
+
"top20_jaccard": 0.1765
|
| 262 |
+
},
|
| 263 |
+
{
|
| 264 |
+
"replicate": 10,
|
| 265 |
+
"spearman_rho": 0.9796,
|
| 266 |
+
"top20_jaccard": 0.2121
|
| 267 |
+
},
|
| 268 |
+
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| 1401 |
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| 1407 |
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| 1439 |
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| 1446 |
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| 1448 |
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| 1449 |
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| 1455 |
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| 1461 |
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| 1477 |
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| 1840 |
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| 1841 |
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| 1847 |
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| 1848 |
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| 1859 |
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| 1870 |
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| 1876 |
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| 1877 |
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| 1881 |
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| 1882 |
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| 1883 |
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| 1888 |
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| 1895 |
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| 1907 |
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| 1913 |
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| 1915 |
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| 1917 |
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| 1918 |
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| 1919 |
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| 1920 |
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| 1923 |
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| 1924 |
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| 1926 |
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| 1927 |
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| 1928 |
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| 1929 |
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| 1930 |
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| 1931 |
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| 1932 |
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| 1933 |
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| 1934 |
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| 1935 |
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| 1936 |
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| 1937 |
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| 1938 |
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| 1939 |
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| 1940 |
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| 1941 |
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| 1942 |
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| 1943 |
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| 1944 |
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| 1945 |
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| 1946 |
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| 1947 |
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| 1948 |
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| 1949 |
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| 1955 |
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| 1956 |
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| 1957 |
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| 1958 |
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| 1960 |
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| 1961 |
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| 1978 |
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| 1984 |
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| 1987 |
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| 1989 |
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| 1995 |
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| 2000 |
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| 2001 |
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| 2002 |
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| 2007 |
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| 2008 |
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| 2013 |
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| 2020 |
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| 2110 |
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| 2119 |
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| 2125 |
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| 2126 |
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| 2128 |
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| 2131 |
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| 2133 |
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| 2134 |
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| 2135 |
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| 2137 |
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| 2138 |
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| 2139 |
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| 2140 |
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| 2141 |
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| 2142 |
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| 2143 |
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| 2144 |
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| 2145 |
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| 2146 |
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| 2147 |
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| 2149 |
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| 2150 |
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| 2151 |
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| 2152 |
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| 2155 |
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| 2156 |
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| 2157 |
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| 2158 |
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| 2159 |
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| 2160 |
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| 2161 |
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| 2162 |
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| 2164 |
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| 2165 |
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| 2166 |
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| 2167 |
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| 2168 |
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| 2169 |
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| 2170 |
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| 2171 |
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| 2172 |
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| 2173 |
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| 2174 |
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| 2175 |
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| 2176 |
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| 2177 |
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| 2178 |
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| 2179 |
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| 2180 |
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| 2181 |
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| 2182 |
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| 2183 |
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| 2184 |
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| 2185 |
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| 2187 |
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| 2188 |
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| 2189 |
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| 2191 |
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| 2192 |
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| 2193 |
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| 2194 |
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| 2195 |
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| 2196 |
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| 2197 |
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| 2198 |
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| 2199 |
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| 2830 |
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| 2850 |
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| 2865 |
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| 2873 |
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| 2886 |
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| 2887 |
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| 2890 |
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| 2920 |
+
},
|
| 2921 |
+
"Inhibitory neuron": {
|
| 2922 |
+
"n_overlap_tfs": 1146,
|
| 2923 |
+
"spearman_rho": 0.7795,
|
| 2924 |
+
"top20_jaccard": 0.1429
|
| 2925 |
+
},
|
| 2926 |
+
"Lymphocyte": {
|
| 2927 |
+
"n_overlap_tfs": 1146,
|
| 2928 |
+
"spearman_rho": 0.7956,
|
| 2929 |
+
"top20_jaccard": 0.2121
|
| 2930 |
+
},
|
| 2931 |
+
"Malignant": {
|
| 2932 |
+
"n_overlap_tfs": 1146,
|
| 2933 |
+
"spearman_rho": 0.7112,
|
| 2934 |
+
"top20_jaccard": 0.0811
|
| 2935 |
+
},
|
| 2936 |
+
"OPC": {
|
| 2937 |
+
"n_overlap_tfs": 1146,
|
| 2938 |
+
"spearman_rho": 0.7474,
|
| 2939 |
+
"top20_jaccard": 0.2121
|
| 2940 |
+
},
|
| 2941 |
+
"Oligodendrocyte": {
|
| 2942 |
+
"n_overlap_tfs": 1146,
|
| 2943 |
+
"spearman_rho": 0.7482,
|
| 2944 |
+
"top20_jaccard": 0.0811
|
| 2945 |
+
},
|
| 2946 |
+
"Other": {
|
| 2947 |
+
"n_overlap_tfs": 1146,
|
| 2948 |
+
"spearman_rho": 0.7741,
|
| 2949 |
+
"top20_jaccard": 0.1111
|
| 2950 |
+
},
|
| 2951 |
+
"Pericyte": {
|
| 2952 |
+
"n_overlap_tfs": 1146,
|
| 2953 |
+
"spearman_rho": 0.7854,
|
| 2954 |
+
"top20_jaccard": 0.1765
|
| 2955 |
+
},
|
| 2956 |
+
"TAM": {
|
| 2957 |
+
"n_overlap_tfs": 1146,
|
| 2958 |
+
"spearman_rho": 0.7624,
|
| 2959 |
+
"top20_jaccard": 0.1765
|
| 2960 |
+
}
|
| 2961 |
}
|
| 2962 |
}
|
| 2963 |
},
|
| 2964 |
"cell_subsampling": {
|
| 2965 |
"0.5": {
|
| 2966 |
+
"mean_spearman": 0.9754,
|
| 2967 |
"n_celltypes": 11
|
| 2968 |
},
|
| 2969 |
"0.25": {
|
| 2970 |
+
"mean_spearman": 0.9543,
|
| 2971 |
"n_celltypes": 11
|
| 2972 |
},
|
| 2973 |
"0.1": {
|
| 2974 |
+
"mean_spearman": 0.916,
|
| 2975 |
"n_celltypes": 11
|
| 2976 |
}
|
| 2977 |
},
|
|
|
|
| 2985 |
"CDK8",
|
| 2986 |
"NDUFV2",
|
| 2987 |
"PKM"
|
| 2988 |
+
],
|
| 2989 |
+
"input_inspection": {
|
| 2990 |
+
"gene_universe_size": 18716,
|
| 2991 |
+
"n_tf_in_gene_universe": 1617,
|
| 2992 |
+
"microglia_labels": {
|
| 2993 |
+
"n_edges_total": 319581,
|
| 2994 |
+
"n_positive": 2724,
|
| 2995 |
+
"n_negative": 316857,
|
| 2996 |
+
"n_train_edges": 251792,
|
| 2997 |
+
"n_eval_edges": 67789
|
| 2998 |
+
},
|
| 2999 |
+
"bootstrap_cell_counts": {
|
| 3000 |
+
"Astrocyte": 8281,
|
| 3001 |
+
"Endothel": 5426,
|
| 3002 |
+
"Excitatory neuron": 14439,
|
| 3003 |
+
"Inhibitory neuron": 5502,
|
| 3004 |
+
"Lymphocyte": 5740,
|
| 3005 |
+
"Malignant": 239954,
|
| 3006 |
+
"OPC": 7078,
|
| 3007 |
+
"Oligodendrocyte": 55160,
|
| 3008 |
+
"Other": 13255,
|
| 3009 |
+
"Pericyte": 1918,
|
| 3010 |
+
"TAM": 62080
|
| 3011 |
+
},
|
| 3012 |
+
"lopo_compartments": [
|
| 3013 |
+
"Malignant",
|
| 3014 |
+
"TAM"
|
| 3015 |
+
]
|
| 3016 |
+
},
|
| 3017 |
+
"computation_logic": {
|
| 3018 |
+
"bootstrap": "Per cell type, sample 5,000 cells with replacement for 20 replicates, compute mean expression, run threshold-gated Stage C ranking, compare to full-data ranking via Spearman and top-20 TF Jaccard.",
|
| 3019 |
+
"lopo": "For Malignant and TAM, leave one patient/timepoint out using annotation ID labels, recompute compartment mean expression, and compare TF rankings to the full-compartment baseline.",
|
| 3020 |
+
"gene_dropout": "Randomly remove 10/20/30% genes from G*, filter perturbation labels to retained regulators/targets, retrain Stage B on the reduced universe, rerun Stage C ranking, and compare to full rankings on overlapping TFs."
|
| 3021 |
+
}
|
| 3022 |
}
|