Hugging Face's logo

Datasets:
junidude14
/
PBISC-data

Modalities:
Tabular
Text
Formats:
parquet
Languages:
English
Size:
< 1K
Tags:
single-cell-rna-seq
bulk-rna-seq
diffusion
Libraries:
Datasets
pandas
Polars
Dataset card Data Studio Files
xet
 Community
1
junidude14 commited on
Commit
1ee769d
·
verified ·
1 Parent(s): d2784d2

Archive 4 checkpoints (1-4)

Browse files
Files changed (4) hide show
  1. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/data/liu2021/inner_val_donors.txt +4 -0
  2. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/splits/hoL_imperial_eskd.json +496 -0
  3. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/splits/hoL_ji2025_chili.json +541 -0
  4. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/splits/hoL_ye2026_sepsis.json +496 -0
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/data/liu2021/inner_val_donors.txt ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ HGR0000098
2
+ HGR0000115
3
+ HGR0000143
4
+ SHD1
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/splits/hoL_imperial_eskd.json ADDED
@@ -0,0 +1,496 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "pbisc_sdd.crosscohort.split.v1",
3
+ "split": "hoL_imperial_eskd",
4
+ "held_out": "imperial_eskd",
5
+ "held_out_bulk": "PBMC",
6
+ "training_cohorts": [
7
+ {
8
+ "cohort": "immicro",
9
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro",
10
+ "condition_npz": {
11
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/immicro/conditions_raw_K1000.npz",
12
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/immicro/conditions_raw_K2000.npz"
13
+ },
14
+ "train_sample_ids": [
15
+ "HS1",
16
+ "HS2",
17
+ "HS3",
18
+ "HS6",
19
+ "HS7",
20
+ "HS8",
21
+ "HS9",
22
+ "HS10",
23
+ "HS12",
24
+ "HS13",
25
+ "HS14",
26
+ "HS15",
27
+ "HS16",
28
+ "HS17",
29
+ "HS18",
30
+ "HS19",
31
+ "HS20",
32
+ "HS21",
33
+ "HS23",
34
+ "HS24",
35
+ "HS25",
36
+ "HS28",
37
+ "HS29",
38
+ "HS30",
39
+ "HS32",
40
+ "HS34",
41
+ "HS35",
42
+ "HS36",
43
+ "HS37",
44
+ "HS38",
45
+ "HS39",
46
+ "HS40",
47
+ "HS41",
48
+ "HS42",
49
+ "HS43",
50
+ "HS44",
51
+ "HS45",
52
+ "HS47",
53
+ "HS48",
54
+ "HS49",
55
+ "HS50",
56
+ "HS51",
57
+ "HS52",
58
+ "HS53",
59
+ "HS54",
60
+ "HS56",
61
+ "HS57",
62
+ "HS58",
63
+ "HS59",
64
+ "HS61",
65
+ "HS63",
66
+ "HS64",
67
+ "HS65",
68
+ "HS66",
69
+ "HS67",
70
+ "HS68",
71
+ "HS69",
72
+ "HS70",
73
+ "HS71",
74
+ "HS72",
75
+ "HS73",
76
+ "HS74",
77
+ "HS75",
78
+ "HS76",
79
+ "HS77",
80
+ "HS78",
81
+ "HS79",
82
+ "HS80",
83
+ "HS81",
84
+ "HS82",
85
+ "HS83",
86
+ "HS84",
87
+ "HS85",
88
+ "HS86",
89
+ "HS88",
90
+ "HS89",
91
+ "HS90",
92
+ "HS91",
93
+ "HS92",
94
+ "HS93",
95
+ "HS94",
96
+ "HS95",
97
+ "HS96",
98
+ "HS97",
99
+ "HS98",
100
+ "HS100",
101
+ "HS101",
102
+ "HS102",
103
+ "HS103",
104
+ "HS104",
105
+ "HS105",
106
+ "HS106",
107
+ "HS107",
108
+ "HS110",
109
+ "HS111"
110
+ ],
111
+ "inner_val_sample_ids": [
112
+ "HS4",
113
+ "HS11",
114
+ "HS26",
115
+ "HS27",
116
+ "HS31",
117
+ "HS46",
118
+ "HS55",
119
+ "HS60",
120
+ "HS62",
121
+ "HS87",
122
+ "HS108",
123
+ "HS109"
124
+ ]
125
+ },
126
+ {
127
+ "cohort": "ye2026_sepsis",
128
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
129
+ "condition_npz": {
130
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/conditions_raw_K1000.npz",
131
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/conditions_raw_K2000.npz"
132
+ },
133
+ "train_sample_ids": [
134
+ "Abd-PS04",
135
+ "Abd-PS05",
136
+ "Abd-PS07",
137
+ "Abd-PS19",
138
+ "Abd-PS20",
139
+ "Abd-PS27",
140
+ "Abd-S103",
141
+ "Abd-S120",
142
+ "Abd-S123",
143
+ "Abd-S156",
144
+ "Abd-S39",
145
+ "Abd-S42",
146
+ "Abd-S47",
147
+ "Abd-S51",
148
+ "Abd-S57",
149
+ "Abd-S66",
150
+ "Abd-S79",
151
+ "Abd-S83",
152
+ "HC05",
153
+ "HC07",
154
+ "HC09",
155
+ "HC12",
156
+ "HC13",
157
+ "HC16",
158
+ "IC10",
159
+ "IC15",
160
+ "IC16",
161
+ "IC22",
162
+ "IC23",
163
+ "PHC01",
164
+ "PHC02",
165
+ "PHC03",
166
+ "PHC05",
167
+ "PIC01",
168
+ "PIC02",
169
+ "PIC04",
170
+ "PIC05",
171
+ "Res-PS02",
172
+ "Res-PS03",
173
+ "Res-PS12",
174
+ "Res-PS21",
175
+ "Res-PS22",
176
+ "Res-PS25",
177
+ "Res-PS26",
178
+ "Res-S10",
179
+ "Res-S125",
180
+ "Res-S127",
181
+ "Res-S136",
182
+ "Res-S146",
183
+ "Res-S149",
184
+ "Res-S150",
185
+ "Res-S164",
186
+ "Res-S166",
187
+ "Res-S177",
188
+ "Res-S184",
189
+ "Res-S19",
190
+ "Res-S26",
191
+ "Res-S40",
192
+ "Res-S77",
193
+ "Res-S87",
194
+ "Skin-S140",
195
+ "Skin-S142",
196
+ "Skin-S152",
197
+ "Skin-S38",
198
+ "Skin-S43",
199
+ "Skin-S46",
200
+ "Skin-S52",
201
+ "Skin-S74",
202
+ "Uri-S134",
203
+ "Uri-S147",
204
+ "Uri-S157",
205
+ "Uri-S20",
206
+ "Uri-S93"
207
+ ],
208
+ "inner_val_sample_ids": [
209
+ "Abd-PS23",
210
+ "Abd-S102",
211
+ "Abd-S54",
212
+ "Abd-S98",
213
+ "HC01",
214
+ "IC19",
215
+ "Res-PS16",
216
+ "Res-S139",
217
+ "Res-S174"
218
+ ]
219
+ },
220
+ {
221
+ "cohort": "giroux2022",
222
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022",
223
+ "condition_npz": {
224
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/conditions_raw_K1000.npz",
225
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/conditions_raw_K2000.npz"
226
+ },
227
+ "train_sample_ids": [
228
+ "450905_d0",
229
+ "450905_d14",
230
+ "0B943B_d0",
231
+ "0B943B_d14",
232
+ "7085CA_d0",
233
+ "7085CA_d7",
234
+ "7085CA_d14",
235
+ "2AD75E_d0",
236
+ "2AD75E_d7",
237
+ "2AD75E_d14",
238
+ "B85D75_d0",
239
+ "B85D75_d7",
240
+ "180E1A_d0",
241
+ "180E1A_d7",
242
+ "180E1A_d14",
243
+ "82CCF5_d0",
244
+ "82CCF5_d7",
245
+ "82CCF5_d14",
246
+ "BAAF62_d0",
247
+ "BAAF62_d7",
248
+ "BAAF62_d14",
249
+ "0BF51C_d0",
250
+ "0BF51C_d7",
251
+ "0BF51C_d14"
252
+ ],
253
+ "inner_val_sample_ids": []
254
+ },
255
+ {
256
+ "cohort": "liu2021",
257
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/liu2021",
258
+ "condition_npz": {
259
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/liu2021/conditions_raw_K1000.npz",
260
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/liu2021/conditions_raw_K2000.npz"
261
+ },
262
+ "train_sample_ids": [
263
+ "AA220014_HC",
264
+ "AA220534_HC",
265
+ "AA220907_HC",
266
+ "HGR0000071_T0",
267
+ "HGR0000074_T0",
268
+ "HGR0000083_T1",
269
+ "HGR0000089_T1",
270
+ "HGR0000091_T0",
271
+ "HGR0000093_T0",
272
+ "HGR0000136_T0",
273
+ "HGR0000137_T0",
274
+ "HGR0000141_T0",
275
+ "IM000040_HC",
276
+ "HGR0000042_T1",
277
+ "HGR0000069_T0",
278
+ "HGR0000069_T1",
279
+ "HGR0000092_T0",
280
+ "HGR0000094_T0",
281
+ "HGR0000124_T0",
282
+ "HGR0000144_T2",
283
+ "HGR0000391_T0",
284
+ "HGR0000395_T0",
285
+ "HGR0000418_T1",
286
+ "SHD4_HC",
287
+ "SHD7_HC",
288
+ "HGR0000051_T0",
289
+ "HGR0000051_T1",
290
+ "HGR0000051_T3",
291
+ "HGR0000101_T1",
292
+ "HGR0000101_T3",
293
+ "HGR0000102_T0",
294
+ "HGR0000102_T1",
295
+ "HGR0000134_T0",
296
+ "HGR0000135_T0",
297
+ "HGR0000135_T1",
298
+ "HGR0000392_T0",
299
+ "HGR0000429_T1",
300
+ "HGR0000429_T2",
301
+ "SHD3_HC",
302
+ "SHD5_HC"
303
+ ],
304
+ "inner_val_sample_ids": [
305
+ "HGR0000098_T0",
306
+ "HGR0000143_T0",
307
+ "HGR0000115_T1",
308
+ "SHD1_HC"
309
+ ]
310
+ }
311
+ ],
312
+ "test": {
313
+ "cohort": "imperial_eskd",
314
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd",
315
+ "sample_ids": [
316
+ "C20_1004",
317
+ "C20_1404",
318
+ "C21_1004",
319
+ "C21_1704",
320
+ "C21_2504",
321
+ "C23_2204",
322
+ "C31_1304",
323
+ "C31_2004",
324
+ "C31_2704",
325
+ "C33_1401",
326
+ "C33_1601",
327
+ "C33_1901",
328
+ "C34_1404",
329
+ "C34_2104",
330
+ "C34_2504",
331
+ "C36_1504",
332
+ "C36_1704",
333
+ "C36_2104",
334
+ "C40_1504",
335
+ "C40_2204",
336
+ "C40_0105",
337
+ "C42_1504",
338
+ "C42_2204",
339
+ "C42_2704",
340
+ "C58_1604",
341
+ "C58_2501",
342
+ "C58_2901",
343
+ "C58_0102",
344
+ "C58_0402",
345
+ "C58_1003",
346
+ "C60_2504",
347
+ "C63_1704",
348
+ "C63_2404",
349
+ "C63_2904",
350
+ "C65_1704",
351
+ "C65_2104",
352
+ "C65_2504",
353
+ "C69_1804",
354
+ "C82_2504",
355
+ "C85_2004",
356
+ "C93_2104",
357
+ "C93_2704",
358
+ "C93_0405",
359
+ "C101_0601",
360
+ "C101_1101",
361
+ "C101_1301",
362
+ "C101_1801",
363
+ "C101_2001",
364
+ "C101_2502",
365
+ "C103_2204",
366
+ "C104_2204",
367
+ "C106_2204",
368
+ "C108_2204",
369
+ "C108_1501",
370
+ "C108_1801",
371
+ "C108_2201",
372
+ "C113_0605",
373
+ "C123_2404",
374
+ "C123_2904",
375
+ "C123_0505",
376
+ "C124_2404",
377
+ "C124_2704",
378
+ "C124_0105",
379
+ "C126_2504",
380
+ "C126_3004",
381
+ "C126_0605",
382
+ "C127_2504",
383
+ "C127_0405",
384
+ "C127_1105",
385
+ "C128_2504",
386
+ "C128_0405",
387
+ "C128_1105",
388
+ "C132_2804",
389
+ "C132_0205",
390
+ "C132_1105",
391
+ "C137_3004",
392
+ "C137_2502",
393
+ "C138_3004",
394
+ "C138_2301",
395
+ "C138_3001",
396
+ "C138_0202",
397
+ "C138_0402",
398
+ "C140_3004",
399
+ "C140_2801",
400
+ "C140_3001",
401
+ "C140_0202",
402
+ "C140_0402",
403
+ "C140_0602",
404
+ "C140_0902",
405
+ "C140_1103",
406
+ "C141_2001",
407
+ "C141_2201",
408
+ "C141_3001",
409
+ "C141_0202",
410
+ "C142_3004",
411
+ "C145_3004",
412
+ "C145_0701",
413
+ "C145_1201",
414
+ "C145_1401",
415
+ "C145_1901",
416
+ "C145_2301",
417
+ "C146_3004",
418
+ "C146_1201",
419
+ "C146_1401",
420
+ "C146_1601",
421
+ "C146_1901",
422
+ "C146_2301",
423
+ "C146_2701",
424
+ "C146_2502",
425
+ "C147_3004",
426
+ "C147_1401",
427
+ "C147_1901",
428
+ "C152_0405",
429
+ "C161_1105",
430
+ "C164_1105",
431
+ "C167_1205",
432
+ "C168_1205",
433
+ "C168_2001",
434
+ "C168_2301",
435
+ "C168_3001",
436
+ "C168_0202",
437
+ "C168_0403",
438
+ "C169_1205",
439
+ "C169_2001",
440
+ "C169_2301",
441
+ "C169_0202",
442
+ "C169_0403",
443
+ "C170_1205",
444
+ "C170_2301",
445
+ "C170_0202",
446
+ "C170_0402",
447
+ "C170_0403",
448
+ "C187_2605",
449
+ "C187_1201",
450
+ "C187_1401",
451
+ "C187_1901",
452
+ "C187_2301",
453
+ "C187_2502",
454
+ "C190_2605",
455
+ "C190_2901",
456
+ "C190_0102",
457
+ "C190_0302",
458
+ "C190_0502",
459
+ "C190_0802",
460
+ "C190_1002",
461
+ "C190_0903",
462
+ "C193_2605",
463
+ "C195_2605",
464
+ "C197_2605",
465
+ "C212_2705",
466
+ "C214_2705",
467
+ "C234_2805",
468
+ "C237_2805",
469
+ "C238_2905",
470
+ "C240_2905",
471
+ "C246_2905",
472
+ "C251_2905"
473
+ ],
474
+ "condition_npz": {
475
+ "1000": {
476
+ "raw": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/imperial_eskd/test_raw_K1000.npz",
477
+ "xcal": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_imperial_eskd/test_xcal_K1000.npz"
478
+ },
479
+ "2000": {
480
+ "raw": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/imperial_eskd/test_raw_K2000.npz",
481
+ "xcal": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_imperial_eskd/test_xcal_K2000.npz"
482
+ }
483
+ }
484
+ },
485
+ "xcal": {
486
+ "alpha": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_imperial_eskd/alpha_xcal.npy",
487
+ "genes_estimated": 11022,
488
+ "rule": "cohort-balanced mean CPM of the training cohorts' usable pairs"
489
+ },
490
+ "n_train_rows": 232,
491
+ "n_inner_val_rows": 25,
492
+ "extra_training_cohorts": [
493
+ "liu2021"
494
+ ],
495
+ "base_split": "ho_imperial_eskd"
496
+ }
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/splits/hoL_ji2025_chili.json ADDED
@@ -0,0 +1,541 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "pbisc_sdd.crosscohort.split.v1",
3
+ "split": "hoL_ji2025_chili",
4
+ "held_out": "ji2025_chili",
5
+ "held_out_bulk": "whole blood",
6
+ "training_cohorts": [
7
+ {
8
+ "cohort": "immicro",
9
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro",
10
+ "condition_npz": {
11
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/immicro/conditions_raw_K1000.npz",
12
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/immicro/conditions_raw_K2000.npz"
13
+ },
14
+ "train_sample_ids": [
15
+ "HS1",
16
+ "HS2",
17
+ "HS3",
18
+ "HS6",
19
+ "HS7",
20
+ "HS8",
21
+ "HS9",
22
+ "HS10",
23
+ "HS12",
24
+ "HS13",
25
+ "HS14",
26
+ "HS15",
27
+ "HS16",
28
+ "HS17",
29
+ "HS18",
30
+ "HS19",
31
+ "HS20",
32
+ "HS21",
33
+ "HS23",
34
+ "HS24",
35
+ "HS25",
36
+ "HS28",
37
+ "HS29",
38
+ "HS30",
39
+ "HS32",
40
+ "HS34",
41
+ "HS35",
42
+ "HS36",
43
+ "HS37",
44
+ "HS38",
45
+ "HS39",
46
+ "HS40",
47
+ "HS41",
48
+ "HS42",
49
+ "HS43",
50
+ "HS44",
51
+ "HS45",
52
+ "HS47",
53
+ "HS48",
54
+ "HS49",
55
+ "HS50",
56
+ "HS51",
57
+ "HS52",
58
+ "HS53",
59
+ "HS54",
60
+ "HS56",
61
+ "HS57",
62
+ "HS58",
63
+ "HS59",
64
+ "HS61",
65
+ "HS63",
66
+ "HS64",
67
+ "HS65",
68
+ "HS66",
69
+ "HS67",
70
+ "HS68",
71
+ "HS69",
72
+ "HS70",
73
+ "HS71",
74
+ "HS72",
75
+ "HS73",
76
+ "HS74",
77
+ "HS75",
78
+ "HS76",
79
+ "HS77",
80
+ "HS78",
81
+ "HS79",
82
+ "HS80",
83
+ "HS81",
84
+ "HS82",
85
+ "HS83",
86
+ "HS84",
87
+ "HS85",
88
+ "HS86",
89
+ "HS88",
90
+ "HS89",
91
+ "HS90",
92
+ "HS91",
93
+ "HS92",
94
+ "HS93",
95
+ "HS94",
96
+ "HS95",
97
+ "HS96",
98
+ "HS97",
99
+ "HS98",
100
+ "HS100",
101
+ "HS101",
102
+ "HS102",
103
+ "HS103",
104
+ "HS104",
105
+ "HS105",
106
+ "HS106",
107
+ "HS107",
108
+ "HS110",
109
+ "HS111"
110
+ ],
111
+ "inner_val_sample_ids": [
112
+ "HS4",
113
+ "HS11",
114
+ "HS26",
115
+ "HS27",
116
+ "HS31",
117
+ "HS46",
118
+ "HS55",
119
+ "HS60",
120
+ "HS62",
121
+ "HS87",
122
+ "HS108",
123
+ "HS109"
124
+ ]
125
+ },
126
+ {
127
+ "cohort": "ye2026_sepsis",
128
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
129
+ "condition_npz": {
130
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/conditions_raw_K1000.npz",
131
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/conditions_raw_K2000.npz"
132
+ },
133
+ "train_sample_ids": [
134
+ "Abd-PS04",
135
+ "Abd-PS05",
136
+ "Abd-PS07",
137
+ "Abd-PS19",
138
+ "Abd-PS20",
139
+ "Abd-PS27",
140
+ "Abd-S103",
141
+ "Abd-S120",
142
+ "Abd-S123",
143
+ "Abd-S156",
144
+ "Abd-S39",
145
+ "Abd-S42",
146
+ "Abd-S47",
147
+ "Abd-S51",
148
+ "Abd-S57",
149
+ "Abd-S66",
150
+ "Abd-S79",
151
+ "Abd-S83",
152
+ "HC05",
153
+ "HC07",
154
+ "HC09",
155
+ "HC12",
156
+ "HC13",
157
+ "HC16",
158
+ "IC10",
159
+ "IC15",
160
+ "IC16",
161
+ "IC22",
162
+ "IC23",
163
+ "PHC01",
164
+ "PHC02",
165
+ "PHC03",
166
+ "PHC05",
167
+ "PIC01",
168
+ "PIC02",
169
+ "PIC04",
170
+ "PIC05",
171
+ "Res-PS02",
172
+ "Res-PS03",
173
+ "Res-PS12",
174
+ "Res-PS21",
175
+ "Res-PS22",
176
+ "Res-PS25",
177
+ "Res-PS26",
178
+ "Res-S10",
179
+ "Res-S125",
180
+ "Res-S127",
181
+ "Res-S136",
182
+ "Res-S146",
183
+ "Res-S149",
184
+ "Res-S150",
185
+ "Res-S164",
186
+ "Res-S166",
187
+ "Res-S177",
188
+ "Res-S184",
189
+ "Res-S19",
190
+ "Res-S26",
191
+ "Res-S40",
192
+ "Res-S77",
193
+ "Res-S87",
194
+ "Skin-S140",
195
+ "Skin-S142",
196
+ "Skin-S152",
197
+ "Skin-S38",
198
+ "Skin-S43",
199
+ "Skin-S46",
200
+ "Skin-S52",
201
+ "Skin-S74",
202
+ "Uri-S134",
203
+ "Uri-S147",
204
+ "Uri-S157",
205
+ "Uri-S20",
206
+ "Uri-S93"
207
+ ],
208
+ "inner_val_sample_ids": [
209
+ "Abd-PS23",
210
+ "Abd-S102",
211
+ "Abd-S54",
212
+ "Abd-S98",
213
+ "HC01",
214
+ "IC19",
215
+ "Res-PS16",
216
+ "Res-S139",
217
+ "Res-S174"
218
+ ]
219
+ },
220
+ {
221
+ "cohort": "imperial_eskd",
222
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd",
223
+ "condition_npz": {
224
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/imperial_eskd/conditions_raw_K1000.npz",
225
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/imperial_eskd/conditions_raw_K2000.npz"
226
+ },
227
+ "train_sample_ids": [
228
+ "C20_1004",
229
+ "C20_1404",
230
+ "C21_1004",
231
+ "C21_1704",
232
+ "C21_2504",
233
+ "C23_2204",
234
+ "C31_1304",
235
+ "C31_2004",
236
+ "C31_2704",
237
+ "C33_1401",
238
+ "C33_1601",
239
+ "C33_1901",
240
+ "C34_1404",
241
+ "C34_2104",
242
+ "C34_2504",
243
+ "C36_1504",
244
+ "C36_1704",
245
+ "C36_2104",
246
+ "C40_1504",
247
+ "C40_2204",
248
+ "C40_0105",
249
+ "C42_1504",
250
+ "C42_2204",
251
+ "C42_2704",
252
+ "C58_1604",
253
+ "C58_2501",
254
+ "C58_2901",
255
+ "C58_0102",
256
+ "C58_0402",
257
+ "C58_1003",
258
+ "C60_2504",
259
+ "C65_1704",
260
+ "C65_2104",
261
+ "C65_2504",
262
+ "C69_1804",
263
+ "C82_2504",
264
+ "C85_2004",
265
+ "C93_2104",
266
+ "C93_2704",
267
+ "C93_0405",
268
+ "C101_0601",
269
+ "C101_1101",
270
+ "C101_1301",
271
+ "C101_1801",
272
+ "C101_2001",
273
+ "C101_2502",
274
+ "C103_2204",
275
+ "C104_2204",
276
+ "C106_2204",
277
+ "C108_2204",
278
+ "C108_1501",
279
+ "C108_1801",
280
+ "C108_2201",
281
+ "C113_0605",
282
+ "C123_2404",
283
+ "C123_2904",
284
+ "C123_0505",
285
+ "C124_2404",
286
+ "C124_2704",
287
+ "C124_0105",
288
+ "C126_2504",
289
+ "C126_3004",
290
+ "C126_0605",
291
+ "C127_2504",
292
+ "C127_0405",
293
+ "C127_1105",
294
+ "C132_2804",
295
+ "C132_0205",
296
+ "C132_1105",
297
+ "C137_3004",
298
+ "C137_2502",
299
+ "C138_3004",
300
+ "C138_2301",
301
+ "C138_3001",
302
+ "C138_0202",
303
+ "C138_0402",
304
+ "C140_3004",
305
+ "C140_2801",
306
+ "C140_3001",
307
+ "C140_0202",
308
+ "C140_0402",
309
+ "C140_0602",
310
+ "C140_0902",
311
+ "C140_1103",
312
+ "C141_2001",
313
+ "C141_2201",
314
+ "C141_3001",
315
+ "C141_0202",
316
+ "C145_3004",
317
+ "C145_0701",
318
+ "C145_1201",
319
+ "C145_1401",
320
+ "C145_1901",
321
+ "C145_2301",
322
+ "C146_3004",
323
+ "C146_1201",
324
+ "C146_1401",
325
+ "C146_1601",
326
+ "C146_1901",
327
+ "C146_2301",
328
+ "C146_2701",
329
+ "C146_2502",
330
+ "C152_0405",
331
+ "C161_1105",
332
+ "C164_1105",
333
+ "C167_1205",
334
+ "C168_1205",
335
+ "C168_2001",
336
+ "C168_2301",
337
+ "C168_3001",
338
+ "C168_0202",
339
+ "C168_0403",
340
+ "C169_1205",
341
+ "C169_2001",
342
+ "C169_2301",
343
+ "C169_0202",
344
+ "C169_0403",
345
+ "C170_1205",
346
+ "C170_2301",
347
+ "C170_0202",
348
+ "C170_0402",
349
+ "C170_0403",
350
+ "C187_2605",
351
+ "C187_1201",
352
+ "C187_1401",
353
+ "C187_1901",
354
+ "C187_2301",
355
+ "C187_2502",
356
+ "C190_2605",
357
+ "C190_2901",
358
+ "C190_0102",
359
+ "C190_0302",
360
+ "C190_0502",
361
+ "C190_0802",
362
+ "C190_1002",
363
+ "C190_0903",
364
+ "C193_2605",
365
+ "C195_2605",
366
+ "C197_2605",
367
+ "C212_2705",
368
+ "C214_2705",
369
+ "C237_2805",
370
+ "C238_2905",
371
+ "C240_2905",
372
+ "C246_2905",
373
+ "C251_2905"
374
+ ],
375
+ "inner_val_sample_ids": [
376
+ "C63_1704",
377
+ "C63_2404",
378
+ "C63_2904",
379
+ "C128_2504",
380
+ "C128_0405",
381
+ "C128_1105",
382
+ "C142_3004",
383
+ "C147_3004",
384
+ "C147_1401",
385
+ "C147_1901",
386
+ "C234_2805"
387
+ ]
388
+ },
389
+ {
390
+ "cohort": "giroux2022",
391
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022",
392
+ "condition_npz": {
393
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/conditions_raw_K1000.npz",
394
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/conditions_raw_K2000.npz"
395
+ },
396
+ "train_sample_ids": [
397
+ "450905_d0",
398
+ "450905_d14",
399
+ "0B943B_d0",
400
+ "0B943B_d14",
401
+ "7085CA_d0",
402
+ "7085CA_d7",
403
+ "7085CA_d14",
404
+ "2AD75E_d0",
405
+ "2AD75E_d7",
406
+ "2AD75E_d14",
407
+ "B85D75_d0",
408
+ "B85D75_d7",
409
+ "180E1A_d0",
410
+ "180E1A_d7",
411
+ "180E1A_d14",
412
+ "82CCF5_d0",
413
+ "82CCF5_d7",
414
+ "82CCF5_d14",
415
+ "BAAF62_d0",
416
+ "BAAF62_d7",
417
+ "BAAF62_d14",
418
+ "0BF51C_d0",
419
+ "0BF51C_d7",
420
+ "0BF51C_d14"
421
+ ],
422
+ "inner_val_sample_ids": []
423
+ },
424
+ {
425
+ "cohort": "liu2021",
426
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/liu2021",
427
+ "condition_npz": {
428
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/liu2021/conditions_raw_K1000.npz",
429
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/liu2021/conditions_raw_K2000.npz"
430
+ },
431
+ "train_sample_ids": [
432
+ "AA220014_HC",
433
+ "AA220534_HC",
434
+ "AA220907_HC",
435
+ "HGR0000071_T0",
436
+ "HGR0000074_T0",
437
+ "HGR0000083_T1",
438
+ "HGR0000089_T1",
439
+ "HGR0000091_T0",
440
+ "HGR0000093_T0",
441
+ "HGR0000136_T0",
442
+ "HGR0000137_T0",
443
+ "HGR0000141_T0",
444
+ "IM000040_HC",
445
+ "HGR0000042_T1",
446
+ "HGR0000069_T0",
447
+ "HGR0000069_T1",
448
+ "HGR0000092_T0",
449
+ "HGR0000094_T0",
450
+ "HGR0000124_T0",
451
+ "HGR0000144_T2",
452
+ "HGR0000391_T0",
453
+ "HGR0000395_T0",
454
+ "HGR0000418_T1",
455
+ "SHD4_HC",
456
+ "SHD7_HC",
457
+ "HGR0000051_T0",
458
+ "HGR0000051_T1",
459
+ "HGR0000051_T3",
460
+ "HGR0000101_T1",
461
+ "HGR0000101_T3",
462
+ "HGR0000102_T0",
463
+ "HGR0000102_T1",
464
+ "HGR0000134_T0",
465
+ "HGR0000135_T0",
466
+ "HGR0000135_T1",
467
+ "HGR0000392_T0",
468
+ "HGR0000429_T1",
469
+ "HGR0000429_T2",
470
+ "SHD3_HC",
471
+ "SHD5_HC"
472
+ ],
473
+ "inner_val_sample_ids": [
474
+ "HGR0000098_T0",
475
+ "HGR0000143_T0",
476
+ "HGR0000115_T1",
477
+ "SHD1_HC"
478
+ ]
479
+ }
480
+ ],
481
+ "test": {
482
+ "cohort": "ji2025_chili",
483
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili",
484
+ "sample_ids": [
485
+ "N064_TOL",
486
+ "N064_FU1",
487
+ "N032_AC",
488
+ "N038_BC",
489
+ "N038_AC",
490
+ "N055_AC",
491
+ "N136_TOL",
492
+ "N136_FU1",
493
+ "N138_TOL",
494
+ "N138_FU1",
495
+ "N128_BC",
496
+ "N128_AC",
497
+ "N129_BC",
498
+ "N129_AC",
499
+ "N147_TOL",
500
+ "N150_BC",
501
+ "N158_AC",
502
+ "N159_BC",
503
+ "N001_TOL",
504
+ "N001_FU1",
505
+ "N002_TOL",
506
+ "N002_FU1",
507
+ "N005_BC",
508
+ "N005_AC",
509
+ "N012_TOL",
510
+ "N012_FU1",
511
+ "N018_BC",
512
+ "N018_AC",
513
+ "N022_TOL",
514
+ "N022_FU1",
515
+ "N035_TOL",
516
+ "N043_TOL",
517
+ "N043_FU1"
518
+ ],
519
+ "condition_npz": {
520
+ "1000": {
521
+ "raw": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ji2025_chili/test_raw_K1000.npz",
522
+ "xcal": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ji2025_chili/test_xcal_K1000.npz"
523
+ },
524
+ "2000": {
525
+ "raw": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ji2025_chili/test_raw_K2000.npz",
526
+ "xcal": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ji2025_chili/test_xcal_K2000.npz"
527
+ }
528
+ }
529
+ },
530
+ "xcal": {
531
+ "alpha": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ji2025_chili/alpha_xcal.npy",
532
+ "genes_estimated": 11060,
533
+ "rule": "cohort-balanced mean CPM of the training cohorts' usable pairs"
534
+ },
535
+ "n_train_rows": 378,
536
+ "n_inner_val_rows": 36,
537
+ "extra_training_cohorts": [
538
+ "liu2021"
539
+ ],
540
+ "base_split": "ho_ji2025_chili"
541
+ }
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/splits/hoL_ye2026_sepsis.json ADDED
@@ -0,0 +1,496 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "pbisc_sdd.crosscohort.split.v1",
3
+ "split": "hoL_ye2026_sepsis",
4
+ "held_out": "ye2026_sepsis",
5
+ "held_out_bulk": "PBMC",
6
+ "training_cohorts": [
7
+ {
8
+ "cohort": "immicro",
9
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro",
10
+ "condition_npz": {
11
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/immicro/conditions_raw_K1000.npz",
12
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/immicro/conditions_raw_K2000.npz"
13
+ },
14
+ "train_sample_ids": [
15
+ "HS1",
16
+ "HS2",
17
+ "HS3",
18
+ "HS6",
19
+ "HS7",
20
+ "HS8",
21
+ "HS9",
22
+ "HS10",
23
+ "HS12",
24
+ "HS13",
25
+ "HS14",
26
+ "HS15",
27
+ "HS16",
28
+ "HS17",
29
+ "HS18",
30
+ "HS19",
31
+ "HS20",
32
+ "HS21",
33
+ "HS23",
34
+ "HS24",
35
+ "HS25",
36
+ "HS28",
37
+ "HS29",
38
+ "HS30",
39
+ "HS32",
40
+ "HS34",
41
+ "HS35",
42
+ "HS36",
43
+ "HS37",
44
+ "HS38",
45
+ "HS39",
46
+ "HS40",
47
+ "HS41",
48
+ "HS42",
49
+ "HS43",
50
+ "HS44",
51
+ "HS45",
52
+ "HS47",
53
+ "HS48",
54
+ "HS49",
55
+ "HS50",
56
+ "HS51",
57
+ "HS52",
58
+ "HS53",
59
+ "HS54",
60
+ "HS56",
61
+ "HS57",
62
+ "HS58",
63
+ "HS59",
64
+ "HS61",
65
+ "HS63",
66
+ "HS64",
67
+ "HS65",
68
+ "HS66",
69
+ "HS67",
70
+ "HS68",
71
+ "HS69",
72
+ "HS70",
73
+ "HS71",
74
+ "HS72",
75
+ "HS73",
76
+ "HS74",
77
+ "HS75",
78
+ "HS76",
79
+ "HS77",
80
+ "HS78",
81
+ "HS79",
82
+ "HS80",
83
+ "HS81",
84
+ "HS82",
85
+ "HS83",
86
+ "HS84",
87
+ "HS85",
88
+ "HS86",
89
+ "HS88",
90
+ "HS89",
91
+ "HS90",
92
+ "HS91",
93
+ "HS92",
94
+ "HS93",
95
+ "HS94",
96
+ "HS95",
97
+ "HS96",
98
+ "HS97",
99
+ "HS98",
100
+ "HS100",
101
+ "HS101",
102
+ "HS102",
103
+ "HS103",
104
+ "HS104",
105
+ "HS105",
106
+ "HS106",
107
+ "HS107",
108
+ "HS110",
109
+ "HS111"
110
+ ],
111
+ "inner_val_sample_ids": [
112
+ "HS4",
113
+ "HS11",
114
+ "HS26",
115
+ "HS27",
116
+ "HS31",
117
+ "HS46",
118
+ "HS55",
119
+ "HS60",
120
+ "HS62",
121
+ "HS87",
122
+ "HS108",
123
+ "HS109"
124
+ ]
125
+ },
126
+ {
127
+ "cohort": "imperial_eskd",
128
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd",
129
+ "condition_npz": {
130
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/imperial_eskd/conditions_raw_K1000.npz",
131
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/imperial_eskd/conditions_raw_K2000.npz"
132
+ },
133
+ "train_sample_ids": [
134
+ "C20_1004",
135
+ "C20_1404",
136
+ "C21_1004",
137
+ "C21_1704",
138
+ "C21_2504",
139
+ "C23_2204",
140
+ "C31_1304",
141
+ "C31_2004",
142
+ "C31_2704",
143
+ "C33_1401",
144
+ "C33_1601",
145
+ "C33_1901",
146
+ "C34_1404",
147
+ "C34_2104",
148
+ "C34_2504",
149
+ "C36_1504",
150
+ "C36_1704",
151
+ "C36_2104",
152
+ "C40_1504",
153
+ "C40_2204",
154
+ "C40_0105",
155
+ "C42_1504",
156
+ "C42_2204",
157
+ "C42_2704",
158
+ "C58_1604",
159
+ "C58_2501",
160
+ "C58_2901",
161
+ "C58_0102",
162
+ "C58_0402",
163
+ "C58_1003",
164
+ "C60_2504",
165
+ "C65_1704",
166
+ "C65_2104",
167
+ "C65_2504",
168
+ "C69_1804",
169
+ "C82_2504",
170
+ "C85_2004",
171
+ "C93_2104",
172
+ "C93_2704",
173
+ "C93_0405",
174
+ "C101_0601",
175
+ "C101_1101",
176
+ "C101_1301",
177
+ "C101_1801",
178
+ "C101_2001",
179
+ "C101_2502",
180
+ "C103_2204",
181
+ "C104_2204",
182
+ "C106_2204",
183
+ "C108_2204",
184
+ "C108_1501",
185
+ "C108_1801",
186
+ "C108_2201",
187
+ "C113_0605",
188
+ "C123_2404",
189
+ "C123_2904",
190
+ "C123_0505",
191
+ "C124_2404",
192
+ "C124_2704",
193
+ "C124_0105",
194
+ "C126_2504",
195
+ "C126_3004",
196
+ "C126_0605",
197
+ "C127_2504",
198
+ "C127_0405",
199
+ "C127_1105",
200
+ "C132_2804",
201
+ "C132_0205",
202
+ "C132_1105",
203
+ "C137_3004",
204
+ "C137_2502",
205
+ "C138_3004",
206
+ "C138_2301",
207
+ "C138_3001",
208
+ "C138_0202",
209
+ "C138_0402",
210
+ "C140_3004",
211
+ "C140_2801",
212
+ "C140_3001",
213
+ "C140_0202",
214
+ "C140_0402",
215
+ "C140_0602",
216
+ "C140_0902",
217
+ "C140_1103",
218
+ "C141_2001",
219
+ "C141_2201",
220
+ "C141_3001",
221
+ "C141_0202",
222
+ "C145_3004",
223
+ "C145_0701",
224
+ "C145_1201",
225
+ "C145_1401",
226
+ "C145_1901",
227
+ "C145_2301",
228
+ "C146_3004",
229
+ "C146_1201",
230
+ "C146_1401",
231
+ "C146_1601",
232
+ "C146_1901",
233
+ "C146_2301",
234
+ "C146_2701",
235
+ "C146_2502",
236
+ "C152_0405",
237
+ "C161_1105",
238
+ "C164_1105",
239
+ "C167_1205",
240
+ "C168_1205",
241
+ "C168_2001",
242
+ "C168_2301",
243
+ "C168_3001",
244
+ "C168_0202",
245
+ "C168_0403",
246
+ "C169_1205",
247
+ "C169_2001",
248
+ "C169_2301",
249
+ "C169_0202",
250
+ "C169_0403",
251
+ "C170_1205",
252
+ "C170_2301",
253
+ "C170_0202",
254
+ "C170_0402",
255
+ "C170_0403",
256
+ "C187_2605",
257
+ "C187_1201",
258
+ "C187_1401",
259
+ "C187_1901",
260
+ "C187_2301",
261
+ "C187_2502",
262
+ "C190_2605",
263
+ "C190_2901",
264
+ "C190_0102",
265
+ "C190_0302",
266
+ "C190_0502",
267
+ "C190_0802",
268
+ "C190_1002",
269
+ "C190_0903",
270
+ "C193_2605",
271
+ "C195_2605",
272
+ "C197_2605",
273
+ "C212_2705",
274
+ "C214_2705",
275
+ "C237_2805",
276
+ "C238_2905",
277
+ "C240_2905",
278
+ "C246_2905",
279
+ "C251_2905"
280
+ ],
281
+ "inner_val_sample_ids": [
282
+ "C63_1704",
283
+ "C63_2404",
284
+ "C63_2904",
285
+ "C128_2504",
286
+ "C128_0405",
287
+ "C128_1105",
288
+ "C142_3004",
289
+ "C147_3004",
290
+ "C147_1401",
291
+ "C147_1901",
292
+ "C234_2805"
293
+ ]
294
+ },
295
+ {
296
+ "cohort": "giroux2022",
297
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022",
298
+ "condition_npz": {
299
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/conditions_raw_K1000.npz",
300
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/conditions_raw_K2000.npz"
301
+ },
302
+ "train_sample_ids": [
303
+ "450905_d0",
304
+ "450905_d14",
305
+ "0B943B_d0",
306
+ "0B943B_d14",
307
+ "7085CA_d0",
308
+ "7085CA_d7",
309
+ "7085CA_d14",
310
+ "2AD75E_d0",
311
+ "2AD75E_d7",
312
+ "2AD75E_d14",
313
+ "B85D75_d0",
314
+ "B85D75_d7",
315
+ "180E1A_d0",
316
+ "180E1A_d7",
317
+ "180E1A_d14",
318
+ "82CCF5_d0",
319
+ "82CCF5_d7",
320
+ "82CCF5_d14",
321
+ "BAAF62_d0",
322
+ "BAAF62_d7",
323
+ "BAAF62_d14",
324
+ "0BF51C_d0",
325
+ "0BF51C_d7",
326
+ "0BF51C_d14"
327
+ ],
328
+ "inner_val_sample_ids": []
329
+ },
330
+ {
331
+ "cohort": "liu2021",
332
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/liu2021",
333
+ "condition_npz": {
334
+ "1000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/liu2021/conditions_raw_K1000.npz",
335
+ "2000": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/liu2021/conditions_raw_K2000.npz"
336
+ },
337
+ "train_sample_ids": [
338
+ "AA220014_HC",
339
+ "AA220534_HC",
340
+ "AA220907_HC",
341
+ "HGR0000071_T0",
342
+ "HGR0000074_T0",
343
+ "HGR0000083_T1",
344
+ "HGR0000089_T1",
345
+ "HGR0000091_T0",
346
+ "HGR0000093_T0",
347
+ "HGR0000136_T0",
348
+ "HGR0000137_T0",
349
+ "HGR0000141_T0",
350
+ "IM000040_HC",
351
+ "HGR0000042_T1",
352
+ "HGR0000069_T0",
353
+ "HGR0000069_T1",
354
+ "HGR0000092_T0",
355
+ "HGR0000094_T0",
356
+ "HGR0000124_T0",
357
+ "HGR0000144_T2",
358
+ "HGR0000391_T0",
359
+ "HGR0000395_T0",
360
+ "HGR0000418_T1",
361
+ "SHD4_HC",
362
+ "SHD7_HC",
363
+ "HGR0000051_T0",
364
+ "HGR0000051_T1",
365
+ "HGR0000051_T3",
366
+ "HGR0000101_T1",
367
+ "HGR0000101_T3",
368
+ "HGR0000102_T0",
369
+ "HGR0000102_T1",
370
+ "HGR0000134_T0",
371
+ "HGR0000135_T0",
372
+ "HGR0000135_T1",
373
+ "HGR0000392_T0",
374
+ "HGR0000429_T1",
375
+ "HGR0000429_T2",
376
+ "SHD3_HC",
377
+ "SHD5_HC"
378
+ ],
379
+ "inner_val_sample_ids": [
380
+ "HGR0000098_T0",
381
+ "HGR0000143_T0",
382
+ "HGR0000115_T1",
383
+ "SHD1_HC"
384
+ ]
385
+ }
386
+ ],
387
+ "test": {
388
+ "cohort": "ye2026_sepsis",
389
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
390
+ "sample_ids": [
391
+ "Abd-PS04",
392
+ "Abd-PS05",
393
+ "Abd-PS07",
394
+ "Abd-PS19",
395
+ "Abd-PS20",
396
+ "Abd-PS23",
397
+ "Abd-PS27",
398
+ "Abd-S102",
399
+ "Abd-S103",
400
+ "Abd-S120",
401
+ "Abd-S123",
402
+ "Abd-S156",
403
+ "Abd-S39",
404
+ "Abd-S42",
405
+ "Abd-S47",
406
+ "Abd-S51",
407
+ "Abd-S54",
408
+ "Abd-S57",
409
+ "Abd-S66",
410
+ "Abd-S79",
411
+ "Abd-S83",
412
+ "Abd-S98",
413
+ "HC01",
414
+ "HC05",
415
+ "HC07",
416
+ "HC09",
417
+ "HC12",
418
+ "HC13",
419
+ "HC16",
420
+ "IC10",
421
+ "IC15",
422
+ "IC16",
423
+ "IC19",
424
+ "IC22",
425
+ "IC23",
426
+ "PHC01",
427
+ "PHC02",
428
+ "PHC03",
429
+ "PHC05",
430
+ "PIC01",
431
+ "PIC02",
432
+ "PIC04",
433
+ "PIC05",
434
+ "Res-PS02",
435
+ "Res-PS03",
436
+ "Res-PS12",
437
+ "Res-PS16",
438
+ "Res-PS21",
439
+ "Res-PS22",
440
+ "Res-PS25",
441
+ "Res-PS26",
442
+ "Res-S10",
443
+ "Res-S125",
444
+ "Res-S127",
445
+ "Res-S136",
446
+ "Res-S139",
447
+ "Res-S146",
448
+ "Res-S149",
449
+ "Res-S150",
450
+ "Res-S164",
451
+ "Res-S166",
452
+ "Res-S174",
453
+ "Res-S177",
454
+ "Res-S184",
455
+ "Res-S19",
456
+ "Res-S26",
457
+ "Res-S40",
458
+ "Res-S77",
459
+ "Res-S87",
460
+ "Skin-S140",
461
+ "Skin-S142",
462
+ "Skin-S152",
463
+ "Skin-S38",
464
+ "Skin-S43",
465
+ "Skin-S46",
466
+ "Skin-S52",
467
+ "Skin-S74",
468
+ "Uri-S134",
469
+ "Uri-S147",
470
+ "Uri-S157",
471
+ "Uri-S20",
472
+ "Uri-S93"
473
+ ],
474
+ "condition_npz": {
475
+ "1000": {
476
+ "raw": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/test_raw_K1000.npz",
477
+ "xcal": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ye2026_sepsis/test_xcal_K1000.npz"
478
+ },
479
+ "2000": {
480
+ "raw": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/test_raw_K2000.npz",
481
+ "xcal": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ye2026_sepsis/test_xcal_K2000.npz"
482
+ }
483
+ }
484
+ },
485
+ "xcal": {
486
+ "alpha": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ye2026_sepsis/alpha_xcal.npy",
487
+ "genes_estimated": 10969,
488
+ "rule": "cohort-balanced mean CPM of the training cohorts' usable pairs"
489
+ },
490
+ "n_train_rows": 305,
491
+ "n_inner_val_rows": 27,
492
+ "extra_training_cohorts": [
493
+ "liu2021"
494
+ ],
495
+ "base_split": "ho_ye2026_sepsis"
496
+ }