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results/experiments/exp_6/results.json
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| 1 |
+
{
|
| 2 |
+
"per_celltype": {
|
| 3 |
+
"Astrocyte": {
|
| 4 |
+
"full": {
|
| 5 |
+
"chipatlas_median_fe": 0.888,
|
| 6 |
+
"canonical_recovered": 2,
|
| 7 |
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"canonical_total": 3,
|
| 8 |
+
"dorothea_recovery": 0.002115,
|
| 9 |
+
"trrust_recovery": 0.000309,
|
| 10 |
+
"rank_corr_with_full": 1.0
|
| 11 |
+
},
|
| 12 |
+
"base_only": {
|
| 13 |
+
"chipatlas_median_fe": 0.227,
|
| 14 |
+
"canonical_recovered": 0,
|
| 15 |
+
"canonical_total": 3,
|
| 16 |
+
"dorothea_recovery": 0.000569,
|
| 17 |
+
"trrust_recovery": 0.000482,
|
| 18 |
+
"rank_corr_with_full": -0.1374
|
| 19 |
+
},
|
| 20 |
+
"expression_only": {
|
| 21 |
+
"chipatlas_median_fe": 1.043,
|
| 22 |
+
"canonical_recovered": 2,
|
| 23 |
+
"canonical_total": 3,
|
| 24 |
+
"dorothea_recovery": 0.003129,
|
| 25 |
+
"trrust_recovery": 0.000223,
|
| 26 |
+
"rank_corr_with_full": 0.9872
|
| 27 |
+
},
|
| 28 |
+
"random_base_expr": {
|
| 29 |
+
"chipatlas_median_fe": 1.032,
|
| 30 |
+
"canonical_recovered": 2,
|
| 31 |
+
"canonical_total": 3,
|
| 32 |
+
"dorothea_recovery": 0.002968,
|
| 33 |
+
"trrust_recovery": 0.00021,
|
| 34 |
+
"rank_corr_with_full": 0.9862
|
| 35 |
+
}
|
| 36 |
+
},
|
| 37 |
+
"Endothel": {
|
| 38 |
+
"full": {
|
| 39 |
+
"chipatlas_median_fe": 1.031,
|
| 40 |
+
"canonical_recovered": 0,
|
| 41 |
+
"canonical_total": 4,
|
| 42 |
+
"dorothea_recovery": 0.002857,
|
| 43 |
+
"trrust_recovery": 0.000544,
|
| 44 |
+
"rank_corr_with_full": 1.0
|
| 45 |
+
},
|
| 46 |
+
"base_only": {
|
| 47 |
+
"chipatlas_median_fe": 0.227,
|
| 48 |
+
"canonical_recovered": 0,
|
| 49 |
+
"canonical_total": 4,
|
| 50 |
+
"dorothea_recovery": 0.000569,
|
| 51 |
+
"trrust_recovery": 0.000482,
|
| 52 |
+
"rank_corr_with_full": -0.128
|
| 53 |
+
},
|
| 54 |
+
"expression_only": {
|
| 55 |
+
"chipatlas_median_fe": 1.076,
|
| 56 |
+
"canonical_recovered": 2,
|
| 57 |
+
"canonical_total": 4,
|
| 58 |
+
"dorothea_recovery": 0.004923,
|
| 59 |
+
"trrust_recovery": 0.000519,
|
| 60 |
+
"rank_corr_with_full": 0.9901
|
| 61 |
+
},
|
| 62 |
+
"random_base_expr": {
|
| 63 |
+
"chipatlas_median_fe": 1.088,
|
| 64 |
+
"canonical_recovered": 2,
|
| 65 |
+
"canonical_total": 4,
|
| 66 |
+
"dorothea_recovery": 0.004564,
|
| 67 |
+
"trrust_recovery": 0.000544,
|
| 68 |
+
"rank_corr_with_full": 0.9895
|
| 69 |
+
}
|
| 70 |
+
},
|
| 71 |
+
"Excitatory neuron": {
|
| 72 |
+
"full": {
|
| 73 |
+
"chipatlas_median_fe": 0.858,
|
| 74 |
+
"canonical_recovered": 0,
|
| 75 |
+
"canonical_total": 3,
|
| 76 |
+
"dorothea_recovery": 0.001497,
|
| 77 |
+
"trrust_recovery": 8.7e-05,
|
| 78 |
+
"rank_corr_with_full": 1.0
|
| 79 |
+
},
|
| 80 |
+
"base_only": {
|
| 81 |
+
"chipatlas_median_fe": 0.227,
|
| 82 |
+
"canonical_recovered": 0,
|
| 83 |
+
"canonical_total": 3,
|
| 84 |
+
"dorothea_recovery": 0.000569,
|
| 85 |
+
"trrust_recovery": 0.000482,
|
| 86 |
+
"rank_corr_with_full": -0.1552
|
| 87 |
+
},
|
| 88 |
+
"expression_only": {
|
| 89 |
+
"chipatlas_median_fe": 0.971,
|
| 90 |
+
"canonical_recovered": 0,
|
| 91 |
+
"canonical_total": 3,
|
| 92 |
+
"dorothea_recovery": 0.002041,
|
| 93 |
+
"trrust_recovery": 3.7e-05,
|
| 94 |
+
"rank_corr_with_full": 0.9884
|
| 95 |
+
},
|
| 96 |
+
"random_base_expr": {
|
| 97 |
+
"chipatlas_median_fe": 1.065,
|
| 98 |
+
"canonical_recovered": 0,
|
| 99 |
+
"canonical_total": 3,
|
| 100 |
+
"dorothea_recovery": 0.002016,
|
| 101 |
+
"trrust_recovery": 9.9e-05,
|
| 102 |
+
"rank_corr_with_full": 0.9865
|
| 103 |
+
}
|
| 104 |
+
},
|
| 105 |
+
"Inhibitory neuron": {
|
| 106 |
+
"full": {
|
| 107 |
+
"chipatlas_median_fe": 0.847,
|
| 108 |
+
"canonical_recovered": 0,
|
| 109 |
+
"canonical_total": 3,
|
| 110 |
+
"dorothea_recovery": 0.001583,
|
| 111 |
+
"trrust_recovery": 9.9e-05,
|
| 112 |
+
"rank_corr_with_full": 1.0
|
| 113 |
+
},
|
| 114 |
+
"base_only": {
|
| 115 |
+
"chipatlas_median_fe": 0.227,
|
| 116 |
+
"canonical_recovered": 0,
|
| 117 |
+
"canonical_total": 3,
|
| 118 |
+
"dorothea_recovery": 0.000569,
|
| 119 |
+
"trrust_recovery": 0.000482,
|
| 120 |
+
"rank_corr_with_full": -0.117
|
| 121 |
+
},
|
| 122 |
+
"expression_only": {
|
| 123 |
+
"chipatlas_median_fe": 0.98,
|
| 124 |
+
"canonical_recovered": 0,
|
| 125 |
+
"canonical_total": 3,
|
| 126 |
+
"dorothea_recovery": 0.002387,
|
| 127 |
+
"trrust_recovery": 0.000111,
|
| 128 |
+
"rank_corr_with_full": 0.9893
|
| 129 |
+
},
|
| 130 |
+
"random_base_expr": {
|
| 131 |
+
"chipatlas_median_fe": 1.042,
|
| 132 |
+
"canonical_recovered": 0,
|
| 133 |
+
"canonical_total": 3,
|
| 134 |
+
"dorothea_recovery": 0.00235,
|
| 135 |
+
"trrust_recovery": 9.9e-05,
|
| 136 |
+
"rank_corr_with_full": 0.9881
|
| 137 |
+
}
|
| 138 |
+
},
|
| 139 |
+
"Lymphocyte": {
|
| 140 |
+
"full": {
|
| 141 |
+
"chipatlas_median_fe": 1.008,
|
| 142 |
+
"canonical_recovered": 0,
|
| 143 |
+
"canonical_total": 5,
|
| 144 |
+
"dorothea_recovery": 0.001905,
|
| 145 |
+
"trrust_recovery": 0.000507,
|
| 146 |
+
"rank_corr_with_full": 1.0
|
| 147 |
+
},
|
| 148 |
+
"base_only": {
|
| 149 |
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"chipatlas_median_fe": 0.227,
|
| 150 |
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"canonical_recovered": 0,
|
| 151 |
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"canonical_total": 5,
|
| 152 |
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"dorothea_recovery": 0.000569,
|
| 153 |
+
"trrust_recovery": 0.000482,
|
| 154 |
+
"rank_corr_with_full": -0.0993
|
| 155 |
+
},
|
| 156 |
+
"expression_only": {
|
| 157 |
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"chipatlas_median_fe": 1.122,
|
| 158 |
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"canonical_recovered": 1,
|
| 159 |
+
"canonical_total": 5,
|
| 160 |
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"dorothea_recovery": 0.004292,
|
| 161 |
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"trrust_recovery": 0.00068,
|
| 162 |
+
"rank_corr_with_full": 0.9878
|
| 163 |
+
},
|
| 164 |
+
"random_base_expr": {
|
| 165 |
+
"chipatlas_median_fe": 1.122,
|
| 166 |
+
"canonical_recovered": 1,
|
| 167 |
+
"canonical_total": 5,
|
| 168 |
+
"dorothea_recovery": 0.003575,
|
| 169 |
+
"trrust_recovery": 0.000569,
|
| 170 |
+
"rank_corr_with_full": 0.9879
|
| 171 |
+
}
|
| 172 |
+
},
|
| 173 |
+
"Malignant": {
|
| 174 |
+
"full": {
|
| 175 |
+
"chipatlas_median_fe": 1.024,
|
| 176 |
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"canonical_recovered": 0,
|
| 177 |
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"canonical_total": 0,
|
| 178 |
+
"dorothea_recovery": 0.002325,
|
| 179 |
+
"trrust_recovery": 0.000346,
|
| 180 |
+
"rank_corr_with_full": 1.0
|
| 181 |
+
},
|
| 182 |
+
"base_only": {
|
| 183 |
+
"chipatlas_median_fe": 0.227,
|
| 184 |
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"canonical_recovered": 0,
|
| 185 |
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"canonical_total": 0,
|
| 186 |
+
"dorothea_recovery": 0.000569,
|
| 187 |
+
"trrust_recovery": 0.000482,
|
| 188 |
+
"rank_corr_with_full": -0.1457
|
| 189 |
+
},
|
| 190 |
+
"expression_only": {
|
| 191 |
+
"chipatlas_median_fe": 1.093,
|
| 192 |
+
"canonical_recovered": 0,
|
| 193 |
+
"canonical_total": 0,
|
| 194 |
+
"dorothea_recovery": 0.004045,
|
| 195 |
+
"trrust_recovery": 0.000594,
|
| 196 |
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"rank_corr_with_full": 0.9843
|
| 197 |
+
},
|
| 198 |
+
"random_base_expr": {
|
| 199 |
+
"chipatlas_median_fe": 1.027,
|
| 200 |
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"canonical_recovered": 0,
|
| 201 |
+
"canonical_total": 0,
|
| 202 |
+
"dorothea_recovery": 0.003698,
|
| 203 |
+
"trrust_recovery": 0.000581,
|
| 204 |
+
"rank_corr_with_full": 0.982
|
| 205 |
+
}
|
| 206 |
+
},
|
| 207 |
+
"OPC": {
|
| 208 |
+
"full": {
|
| 209 |
+
"chipatlas_median_fe": 0.975,
|
| 210 |
+
"canonical_recovered": 0,
|
| 211 |
+
"canonical_total": 3,
|
| 212 |
+
"dorothea_recovery": 0.001682,
|
| 213 |
+
"trrust_recovery": 0.000198,
|
| 214 |
+
"rank_corr_with_full": 1.0
|
| 215 |
+
},
|
| 216 |
+
"base_only": {
|
| 217 |
+
"chipatlas_median_fe": 0.227,
|
| 218 |
+
"canonical_recovered": 0,
|
| 219 |
+
"canonical_total": 3,
|
| 220 |
+
"dorothea_recovery": 0.000569,
|
| 221 |
+
"trrust_recovery": 0.000482,
|
| 222 |
+
"rank_corr_with_full": -0.1189
|
| 223 |
+
},
|
| 224 |
+
"expression_only": {
|
| 225 |
+
"chipatlas_median_fe": 0.991,
|
| 226 |
+
"canonical_recovered": 0,
|
| 227 |
+
"canonical_total": 3,
|
| 228 |
+
"dorothea_recovery": 0.002016,
|
| 229 |
+
"trrust_recovery": 0.00021,
|
| 230 |
+
"rank_corr_with_full": 0.9856
|
| 231 |
+
},
|
| 232 |
+
"random_base_expr": {
|
| 233 |
+
"chipatlas_median_fe": 1.032,
|
| 234 |
+
"canonical_recovered": 0,
|
| 235 |
+
"canonical_total": 3,
|
| 236 |
+
"dorothea_recovery": 0.001967,
|
| 237 |
+
"trrust_recovery": 0.000198,
|
| 238 |
+
"rank_corr_with_full": 0.9842
|
| 239 |
+
}
|
| 240 |
+
},
|
| 241 |
+
"Oligodendrocyte": {
|
| 242 |
+
"full": {
|
| 243 |
+
"chipatlas_median_fe": 0.858,
|
| 244 |
+
"canonical_recovered": 1,
|
| 245 |
+
"canonical_total": 4,
|
| 246 |
+
"dorothea_recovery": 0.001596,
|
| 247 |
+
"trrust_recovery": 0.000247,
|
| 248 |
+
"rank_corr_with_full": 1.0
|
| 249 |
+
},
|
| 250 |
+
"base_only": {
|
| 251 |
+
"chipatlas_median_fe": 0.227,
|
| 252 |
+
"canonical_recovered": 0,
|
| 253 |
+
"canonical_total": 4,
|
| 254 |
+
"dorothea_recovery": 0.000569,
|
| 255 |
+
"trrust_recovery": 0.000482,
|
| 256 |
+
"rank_corr_with_full": -0.1465
|
| 257 |
+
},
|
| 258 |
+
"expression_only": {
|
| 259 |
+
"chipatlas_median_fe": 1.077,
|
| 260 |
+
"canonical_recovered": 1,
|
| 261 |
+
"canonical_total": 4,
|
| 262 |
+
"dorothea_recovery": 0.002684,
|
| 263 |
+
"trrust_recovery": 0.000111,
|
| 264 |
+
"rank_corr_with_full": 0.99
|
| 265 |
+
},
|
| 266 |
+
"random_base_expr": {
|
| 267 |
+
"chipatlas_median_fe": 1.054,
|
| 268 |
+
"canonical_recovered": 1,
|
| 269 |
+
"canonical_total": 4,
|
| 270 |
+
"dorothea_recovery": 0.002362,
|
| 271 |
+
"trrust_recovery": 0.000173,
|
| 272 |
+
"rank_corr_with_full": 0.9889
|
| 273 |
+
}
|
| 274 |
+
},
|
| 275 |
+
"Other": {
|
| 276 |
+
"full": {
|
| 277 |
+
"chipatlas_median_fe": 0.91,
|
| 278 |
+
"canonical_recovered": 0,
|
| 279 |
+
"canonical_total": 0,
|
| 280 |
+
"dorothea_recovery": 0.002622,
|
| 281 |
+
"trrust_recovery": 0.000371,
|
| 282 |
+
"rank_corr_with_full": 1.0
|
| 283 |
+
},
|
| 284 |
+
"base_only": {
|
| 285 |
+
"chipatlas_median_fe": 0.227,
|
| 286 |
+
"canonical_recovered": 0,
|
| 287 |
+
"canonical_total": 0,
|
| 288 |
+
"dorothea_recovery": 0.000569,
|
| 289 |
+
"trrust_recovery": 0.000482,
|
| 290 |
+
"rank_corr_with_full": -0.1707
|
| 291 |
+
},
|
| 292 |
+
"expression_only": {
|
| 293 |
+
"chipatlas_median_fe": 1.09,
|
| 294 |
+
"canonical_recovered": 0,
|
| 295 |
+
"canonical_total": 0,
|
| 296 |
+
"dorothea_recovery": 0.004181,
|
| 297 |
+
"trrust_recovery": 0.000421,
|
| 298 |
+
"rank_corr_with_full": 0.9873
|
| 299 |
+
},
|
| 300 |
+
"random_base_expr": {
|
| 301 |
+
"chipatlas_median_fe": 0.978,
|
| 302 |
+
"canonical_recovered": 0,
|
| 303 |
+
"canonical_total": 0,
|
| 304 |
+
"dorothea_recovery": 0.003908,
|
| 305 |
+
"trrust_recovery": 0.000445,
|
| 306 |
+
"rank_corr_with_full": 0.9853
|
| 307 |
+
}
|
| 308 |
+
},
|
| 309 |
+
"Pericyte": {
|
| 310 |
+
"full": {
|
| 311 |
+
"chipatlas_median_fe": 1.03,
|
| 312 |
+
"canonical_recovered": 0,
|
| 313 |
+
"canonical_total": 1,
|
| 314 |
+
"dorothea_recovery": 0.002721,
|
| 315 |
+
"trrust_recovery": 0.000396,
|
| 316 |
+
"rank_corr_with_full": 1.0
|
| 317 |
+
},
|
| 318 |
+
"base_only": {
|
| 319 |
+
"chipatlas_median_fe": 0.227,
|
| 320 |
+
"canonical_recovered": 0,
|
| 321 |
+
"canonical_total": 1,
|
| 322 |
+
"dorothea_recovery": 0.000569,
|
| 323 |
+
"trrust_recovery": 0.000482,
|
| 324 |
+
"rank_corr_with_full": -0.0963
|
| 325 |
+
},
|
| 326 |
+
"expression_only": {
|
| 327 |
+
"chipatlas_median_fe": 0.99,
|
| 328 |
+
"canonical_recovered": 0,
|
| 329 |
+
"canonical_total": 1,
|
| 330 |
+
"dorothea_recovery": 0.004156,
|
| 331 |
+
"trrust_recovery": 0.00047,
|
| 332 |
+
"rank_corr_with_full": 0.9899
|
| 333 |
+
},
|
| 334 |
+
"random_base_expr": {
|
| 335 |
+
"chipatlas_median_fe": 0.977,
|
| 336 |
+
"canonical_recovered": 0,
|
| 337 |
+
"canonical_total": 1,
|
| 338 |
+
"dorothea_recovery": 0.004007,
|
| 339 |
+
"trrust_recovery": 0.000445,
|
| 340 |
+
"rank_corr_with_full": 0.9891
|
| 341 |
+
}
|
| 342 |
+
},
|
| 343 |
+
"TAM": {
|
| 344 |
+
"full": {
|
| 345 |
+
"chipatlas_median_fe": 0.997,
|
| 346 |
+
"canonical_recovered": 1,
|
| 347 |
+
"canonical_total": 4,
|
| 348 |
+
"dorothea_recovery": 0.002338,
|
| 349 |
+
"trrust_recovery": 0.000581,
|
| 350 |
+
"rank_corr_with_full": 1.0
|
| 351 |
+
},
|
| 352 |
+
"base_only": {
|
| 353 |
+
"chipatlas_median_fe": 0.227,
|
| 354 |
+
"canonical_recovered": 1,
|
| 355 |
+
"canonical_total": 4,
|
| 356 |
+
"dorothea_recovery": 0.000569,
|
| 357 |
+
"trrust_recovery": 0.000482,
|
| 358 |
+
"rank_corr_with_full": -0.1794
|
| 359 |
+
},
|
| 360 |
+
"expression_only": {
|
| 361 |
+
"chipatlas_median_fe": 1.017,
|
| 362 |
+
"canonical_recovered": 0,
|
| 363 |
+
"canonical_total": 4,
|
| 364 |
+
"dorothea_recovery": 0.003302,
|
| 365 |
+
"trrust_recovery": 0.000359,
|
| 366 |
+
"rank_corr_with_full": 0.9848
|
| 367 |
+
},
|
| 368 |
+
"random_base_expr": {
|
| 369 |
+
"chipatlas_median_fe": 1.016,
|
| 370 |
+
"canonical_recovered": 0,
|
| 371 |
+
"canonical_total": 4,
|
| 372 |
+
"dorothea_recovery": 0.003253,
|
| 373 |
+
"trrust_recovery": 0.000346,
|
| 374 |
+
"rank_corr_with_full": 0.9834
|
| 375 |
+
}
|
| 376 |
+
}
|
| 377 |
+
},
|
| 378 |
+
"aggregate": {
|
| 379 |
+
"full": {
|
| 380 |
+
"mean_chipatlas_fe": 0.948,
|
| 381 |
+
"mean_dorothea_recovery": 0.00211,
|
| 382 |
+
"canonical_total_recovered": 4,
|
| 383 |
+
"canonical_total": 30,
|
| 384 |
+
"mean_rank_corr": 1.0
|
| 385 |
+
},
|
| 386 |
+
"base_only": {
|
| 387 |
+
"mean_chipatlas_fe": 0.227,
|
| 388 |
+
"mean_dorothea_recovery": 0.00057,
|
| 389 |
+
"canonical_total_recovered": 1,
|
| 390 |
+
"canonical_total": 30,
|
| 391 |
+
"mean_rank_corr": -0.1359
|
| 392 |
+
},
|
| 393 |
+
"expression_only": {
|
| 394 |
+
"mean_chipatlas_fe": 1.041,
|
| 395 |
+
"mean_dorothea_recovery": 0.00338,
|
| 396 |
+
"canonical_total_recovered": 6,
|
| 397 |
+
"canonical_total": 30,
|
| 398 |
+
"mean_rank_corr": 0.9877
|
| 399 |
+
},
|
| 400 |
+
"random_base_expr": {
|
| 401 |
+
"mean_chipatlas_fe": 1.039,
|
| 402 |
+
"mean_dorothea_recovery": 0.00315,
|
| 403 |
+
"canonical_total_recovered": 6,
|
| 404 |
+
"canonical_total": 30,
|
| 405 |
+
"mean_rank_corr": 0.9865
|
| 406 |
+
}
|
| 407 |
+
},
|
| 408 |
+
"embedding_source": "geneformer",
|
| 409 |
+
"top_k": 50,
|
| 410 |
+
"config_descriptions": {
|
| 411 |
+
"full": "Trained W + expression gating (complete scRegNet)",
|
| 412 |
+
"base_only": "Trained W, no expression gating",
|
| 413 |
+
"expression_only": "Uniform base (all=1) + expression gating",
|
| 414 |
+
"random_base_expr": "Random W + expression gating"
|
| 415 |
+
}
|
| 416 |
+
}
|