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
08c6b69
·
verified ·
1 Parent(s): ec08ab5

Archive 4 checkpoints (1-4)

Browse files
Files changed (4) hide show
  1. paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/2d37d963fd4b3e48/score.json +52 -0
  2. paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/5caccf592c78d502/summary.json +540 -0
  3. paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/7336fa367195565c/summary.json +2143 -0
  4. paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/aba3f711c4e558ba/summary.json +751 -0
paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/2d37d963fd4b3e48/score.json ADDED
@@ -0,0 +1,52 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "state": "completed",
3
+ "stage": "score",
4
+ "at": "2026-10-15T12:00:39.460971+00:00",
5
+ "outputs": [
6
+ {
7
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold1/n20/lora/score/arms/lora/generated_cells.parquet",
8
+ "sha256": "64daae6a1a58f093295212eef69f381cc86cf14ffe958e278df898ee6760cc0a",
9
+ "bytes": 289100
10
+ },
11
+ {
12
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold1/n20/lora/score/arms/lora/labels/labels.manifest.json",
13
+ "sha256": "aa33562771545c55608c1f154d231a80d0c818e2d64d4c8a99af4848d4f50ffc",
14
+ "bytes": 5112
15
+ },
16
+ {
17
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold1/n20/lora/score/arms/lora/labels/labels.parquet",
18
+ "sha256": "a61da5ced24a1b21309741da04bb1d85a44ad21dc84d6ed7cf1e0c31d2aceba4",
19
+ "bytes": 816529
20
+ },
21
+ {
22
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold1/n20/lora/score/per_donor.csv",
23
+ "sha256": "d4ff74d3711a834cee869e19a8a27b87cacedc5e36bcbbf87dc78540210cfa07",
24
+ "bytes": 9369
25
+ },
26
+ {
27
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold1/n20/lora/score/summary.json",
28
+ "sha256": "4322af20fb8695f4f092354252d6dfa563ab2d1559194a4b7f20e54696e33d2c",
29
+ "bytes": 7562
30
+ },
31
+ {
32
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold1/n20/lora/scoring_support.json",
33
+ "sha256": "1f649890b0363cd1958649c98f9cd586baebbf54a84af1e47ac1953801ee9673",
34
+ "bytes": 2098
35
+ }
36
+ ],
37
+ "support_sha256": "e8d557be6f2e1d807f043f68ed8c2ff803dd04fe18f928167741079279d57ae6",
38
+ "binding": {
39
+ "arm": "lora",
40
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold1/n20/lora.npz",
41
+ "npz_sha256": "8d28a5c114dbf6a4a5075438bc212fc5871ef6c4a1ead7b87c75e32e46aca4bc",
42
+ "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold1/n20/lora.log",
43
+ "receipt_sha256": "09ba2e60323a62d4bd0015f700accc92002bd12cec65906095f422ede62264bc",
44
+ "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/immicro/healthy/fold1/n20/lora/RUN.json",
45
+ "source_binding_sha256": "f223827782b12a208ee7955ef27062c4cb42093a135edd945bda2812f8c3f8d7",
46
+ "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/immicro/healthy/fold1/n20/test_raw.npz",
47
+ "condition_sha256": "f64c30e0d9cd130f95402573ee1b53826b57447fb3d7e8de727481c86f243d9d",
48
+ "checkpoint_sha256": "080147b5e9eb9c60723f4d91d259235bb059550c9588fa90e0f814c1a95ce14c",
49
+ "support_sha256": "e8d557be6f2e1d807f043f68ed8c2ff803dd04fe18f928167741079279d57ae6"
50
+ },
51
+ "reuse": {}
52
+ }
paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/5caccf592c78d502/summary.json ADDED
@@ -0,0 +1,540 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "paired_ft_scores.v1",
3
+ "dataset": "ji2025_chili",
4
+ "written_utc": "2026-10-15T11:37:05.178017+00:00",
5
+ "command": [
6
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
7
+ "--dataset",
8
+ "ji2025_chili",
9
+ "--out",
10
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw3/score",
11
+ "--arm",
12
+ "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/disease/draw3/lora.npz",
13
+ "--condition",
14
+ "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw3/test_raw.npz",
15
+ "--donors",
16
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw3/test_samples.txt",
17
+ "--threads",
18
+ "2",
19
+ "--case-groups",
20
+ "TOL,FU1",
21
+ "--control-groups",
22
+ "BC,AC"
23
+ ],
24
+ "arms": [
25
+ "lora"
26
+ ],
27
+ "donors": [
28
+ "N064_TOL",
29
+ "N064_FU1",
30
+ "N032_AC",
31
+ "N055_AC",
32
+ "N136_TOL",
33
+ "N136_FU1",
34
+ "N138_TOL",
35
+ "N138_FU1",
36
+ "N128_BC",
37
+ "N128_AC",
38
+ "N129_BC",
39
+ "N129_AC",
40
+ "N158_AC",
41
+ "N159_BC",
42
+ "N002_TOL",
43
+ "N002_FU1",
44
+ "N005_BC",
45
+ "N005_AC",
46
+ "N012_TOL",
47
+ "N012_FU1",
48
+ "N022_TOL",
49
+ "N022_FU1",
50
+ "N035_TOL",
51
+ "N043_TOL",
52
+ "N043_FU1"
53
+ ],
54
+ "n_donors": 25,
55
+ "reference": {
56
+ "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili",
57
+ "reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
58
+ "features_sha256": "049795e3a2470a223347015c0c965f56ca90c21143aad6f72d12e39f3e95e58b",
59
+ "n_r1_cells": 3750,
60
+ "pca": {
61
+ "n_components": 50,
62
+ "explained_variance_ratio_sum": 0.28761026263237,
63
+ "n_fit_cells": 3750
64
+ },
65
+ "r2_control": {
66
+ "precision": 0.9965333333333334,
67
+ "coverage": 1.0,
68
+ "density": 2.5364533333333332,
69
+ "n_query": 3750,
70
+ "depth_matched": {
71
+ "precision": 0.9962666666666666,
72
+ "coverage": 1.0,
73
+ "density": 2.48704
74
+ }
75
+ },
76
+ "observed_l1_loo_null_mean": 0.480736250006395
77
+ },
78
+ "contrast_definition": {
79
+ "enabled": true,
80
+ "rule": "explicit --case-groups / --control-groups",
81
+ "group_source": "features groups",
82
+ "case_groups": [
83
+ "TOL",
84
+ "FU1"
85
+ ],
86
+ "control_groups": [
87
+ "BC",
88
+ "AC"
89
+ ],
90
+ "n_case_donors": 15,
91
+ "n_control_donors": 10,
92
+ "n_donors_in_neither": 0,
93
+ "case": [
94
+ true,
95
+ true,
96
+ false,
97
+ false,
98
+ true,
99
+ true,
100
+ true,
101
+ true,
102
+ false,
103
+ false,
104
+ false,
105
+ false,
106
+ false,
107
+ false,
108
+ true,
109
+ true,
110
+ false,
111
+ false,
112
+ true,
113
+ true,
114
+ true,
115
+ true,
116
+ true,
117
+ true,
118
+ true
119
+ ],
120
+ "ctrl": [
121
+ false,
122
+ false,
123
+ true,
124
+ true,
125
+ false,
126
+ false,
127
+ false,
128
+ false,
129
+ true,
130
+ true,
131
+ true,
132
+ true,
133
+ true,
134
+ true,
135
+ false,
136
+ false,
137
+ true,
138
+ true,
139
+ false,
140
+ false,
141
+ false,
142
+ false,
143
+ false,
144
+ false,
145
+ false
146
+ ],
147
+ "groups": [
148
+ "TOL",
149
+ "FU1",
150
+ "AC",
151
+ "AC",
152
+ "TOL",
153
+ "FU1",
154
+ "TOL",
155
+ "FU1",
156
+ "BC",
157
+ "AC",
158
+ "BC",
159
+ "AC",
160
+ "AC",
161
+ "BC",
162
+ "TOL",
163
+ "FU1",
164
+ "BC",
165
+ "AC",
166
+ "TOL",
167
+ "FU1",
168
+ "TOL",
169
+ "FU1",
170
+ "TOL",
171
+ "TOL",
172
+ "FU1"
173
+ ]
174
+ },
175
+ "deg_definition": {
176
+ "enabled": true,
177
+ "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
178
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
179
+ "functions": [
180
+ "welch_bh_deg",
181
+ "top_deg_genes",
182
+ "jaccard"
183
+ ],
184
+ "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
185
+ "top_n": 50,
186
+ "fdr": 0.05,
187
+ "n_genes": 5752,
188
+ "types": [
189
+ "T cell",
190
+ "B cell",
191
+ "Monocyte",
192
+ "NK cell",
193
+ "DC"
194
+ ],
195
+ "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili/deg_reference.npz",
196
+ "aggregates_sha256": "4f5eb8c8389ef1308ce3ec44be8be024cedb97de37351d109d9070c818df5a9e",
197
+ "aggregates_note": null,
198
+ "types_not_scored_observed": [],
199
+ "observed": {
200
+ "T cell": {
201
+ "n_significant": 813,
202
+ "n_tested": 5667,
203
+ "n_case_donors": 15,
204
+ "n_control_donors": 10,
205
+ "n_cells": 44374,
206
+ "top_list_size": 50
207
+ },
208
+ "B cell": {
209
+ "n_significant": 8,
210
+ "n_tested": 5377,
211
+ "n_case_donors": 15,
212
+ "n_control_donors": 10,
213
+ "n_cells": 6285,
214
+ "top_list_size": 8
215
+ },
216
+ "Monocyte": {
217
+ "n_significant": 0,
218
+ "n_tested": 5684,
219
+ "n_case_donors": 15,
220
+ "n_control_donors": 10,
221
+ "n_cells": 26936,
222
+ "top_list_size": 0
223
+ },
224
+ "NK cell": {
225
+ "n_significant": 14,
226
+ "n_tested": 5460,
227
+ "n_case_donors": 15,
228
+ "n_control_donors": 10,
229
+ "n_cells": 13603,
230
+ "top_list_size": 14
231
+ },
232
+ "DC": {
233
+ "n_significant": 3,
234
+ "n_tested": 4970,
235
+ "n_case_donors": 13,
236
+ "n_control_donors": 10,
237
+ "n_cells": 1144,
238
+ "top_list_size": 3
239
+ }
240
+ },
241
+ "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
242
+ },
243
+ "headline": {
244
+ "lora": {
245
+ "comp_l1": 0.4494866933153665,
246
+ "comp_l1_obs_loo_null": 0.480736250006395,
247
+ "precision": 0.98,
248
+ "coverage": 0.7421333333333333,
249
+ "precision_dm": 0.9813333333333333,
250
+ "coverage_dm": 0.932,
251
+ "pb_r_median": 0.8700788382131606,
252
+ "pb_top1": 0.12,
253
+ "mono_pct_gen": 29.61333333333333,
254
+ "mono_pct_obs": 26.78051547525648,
255
+ "median_umi_gen": 1013.0,
256
+ "median_umi_obs": 1052.0,
257
+ "contrast_mean_cp10k_r_gen": 0.40606651714837955,
258
+ "contrast_pseudobulk_log1p_cpm_r_gen": 0.2286809976632689,
259
+ "contrast_mean_cp10k_r_broadcast": 0.2577780039471977,
260
+ "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.2082425017470386,
261
+ "deg_top50_T": 0,
262
+ "deg_top50_B": 0,
263
+ "deg_top50_Mono": 0,
264
+ "deg_top50_NK": 0,
265
+ "deg_top50_DC": 0,
266
+ "deg_top50_sum": 0,
267
+ "deg_top50_max": 75,
268
+ "deg_top50_sum_4type": 0,
269
+ "deg_top50_sum_broadcast": 0,
270
+ "seconds": 7.8
271
+ }
272
+ },
273
+ "per_arm": {
274
+ "lora": {
275
+ "arm": "lora",
276
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/disease/draw3/lora.npz",
277
+ "npz_sha256": "93d0325b0c3e5e5102759dc73042e7c7ab28af1e1310f7f267cde2785a4f1078",
278
+ "receipt_verified": true,
279
+ "generation": {
280
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/ji2025_chili/disease/draw3/lora/checkpoint_ft.pt",
281
+ "checkpoint_sha256": "0222709692b267072116b62b180cb1004d79bf71c8a01c31f4c1d6764ffc605c",
282
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw3/test_raw.npz",
283
+ "input_condition_sha256": "3d69ce8b1625cfe1b516085caf6444e49d8db5580f4ccdc4452526401b7018cb",
284
+ "seed": 20260928,
285
+ "steps": 50,
286
+ "support_readout": "bernoulli",
287
+ "weights": "ema"
288
+ },
289
+ "condition_for_broadcast": {
290
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw3/test_raw.npz",
291
+ "sha256": "3d69ce8b1625cfe1b516085caf6444e49d8db5580f4ccdc4452526401b7018cb"
292
+ },
293
+ "poisson": {
294
+ "seed": 20260916,
295
+ "rule": "whole NPZ, rows in NPZ order",
296
+ "nnz_whole_npz": 9441406,
297
+ "median_library_whole_npz_panel": 1014.0,
298
+ "n_rows_whole_npz": 37500
299
+ },
300
+ "annotation": {
301
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
302
+ "zero_padded_model_genes": 1,
303
+ "label_counts": {
304
+ "T cell": 18924,
305
+ "Monocyte": 11105,
306
+ "NK cell": 4770,
307
+ "B cell": 1166,
308
+ "Other": 775,
309
+ "DC": 760
310
+ },
311
+ "mean_l2_max_prob": 0.9257009138631821,
312
+ "predict_seconds": 3.2
313
+ },
314
+ "n_donors": 25,
315
+ "n_generated_cells": 37500,
316
+ "composition": {
317
+ "l1_mean": 0.4494866933153665,
318
+ "l1_median": 0.4519786373693446,
319
+ "l1_obs_loo_null_mean": 0.480736250006395,
320
+ "l1_generated_loo_mean_vs_observed_mean": 0.46206770439544587,
321
+ "composition_top1": 0.0,
322
+ "mean_fraction_generated": {
323
+ "T cell": 0.50464,
324
+ "B cell": 0.031093,
325
+ "Monocyte": 0.296133,
326
+ "NK cell": 0.1272,
327
+ "DC": 0.020267,
328
+ "Other": 0.020667
329
+ },
330
+ "mean_fraction_observed": {
331
+ "T cell": 0.46404,
332
+ "B cell": 0.064326,
333
+ "Monocyte": 0.267805,
334
+ "NK cell": 0.157739,
335
+ "DC": 0.011256,
336
+ "Other": 0.034834
337
+ }
338
+ },
339
+ "pseudobulk": {
340
+ "n_genes": 5752,
341
+ "r_median": 0.8700788382131606,
342
+ "r_mean": 0.868618104406674,
343
+ "top1": 0.12,
344
+ "n_top1": 3,
345
+ "own_rank_median": 6.0,
346
+ "chance_top1": 0.04
347
+ },
348
+ "precision_coverage": {
349
+ "precision": 0.98,
350
+ "coverage": 0.7421333333333333,
351
+ "density": 1.4152799999999999,
352
+ "n_query": 3750,
353
+ "n_reference": 3750
354
+ },
355
+ "precision_coverage_depth_matched": {
356
+ "precision": 0.9813333333333333,
357
+ "coverage": 0.932,
358
+ "density": 1.5097866666666666,
359
+ "detected_median_before": {
360
+ "R1": 367.0,
361
+ "Q": 236.0
362
+ },
363
+ "detected_median_after": {
364
+ "R1": 235.0,
365
+ "Q": 235.0
366
+ }
367
+ },
368
+ "monocyte_pct": {
369
+ "generated_mean_over_donors": 29.61333333333333,
370
+ "observed_mean_over_donors": 26.78051547525648,
371
+ "generated_pooled_cells": 29.613333333333337
372
+ },
373
+ "median_umi_per_cell_scoring_genes": {
374
+ "generated_pooled": 1013.0,
375
+ "observed_pooled": 1052.0,
376
+ "generated_mean_of_donor_medians": 1035.4000244140625,
377
+ "observed_mean_of_donor_medians": 1160.72
378
+ },
379
+ "contrast": {
380
+ "mean_cp10k": {
381
+ "per_type": {
382
+ "T cell": {
383
+ "r_generated": 0.48238503095049146,
384
+ "r_broadcast": 0.2368920077117674,
385
+ "partial_r_generated_given_broadcast": 0.448571731401243,
386
+ "r_generated_vs_broadcast": 0.25981116516883196,
387
+ "n_genes": 3028
388
+ },
389
+ "B cell": {
390
+ "r_generated": 0.19905424900530452,
391
+ "r_broadcast": 0.16221245678147309,
392
+ "partial_r_generated_given_broadcast": 0.1809419160106288,
393
+ "r_generated_vs_broadcast": 0.13677565903737743,
394
+ "n_genes": 3238
395
+ },
396
+ "Monocyte": {
397
+ "r_generated": 0.5530945374995733,
398
+ "r_broadcast": 0.4012426962403039,
399
+ "partial_r_generated_given_broadcast": 0.4682125343099418,
400
+ "r_generated_vs_broadcast": 0.3978204242826742,
401
+ "n_genes": 3132
402
+ },
403
+ "NK cell": {
404
+ "r_generated": 0.3897322511381489,
405
+ "r_broadcast": 0.23076485505524633,
406
+ "partial_r_generated_given_broadcast": 0.35201746764043473,
407
+ "r_generated_vs_broadcast": 0.2528280586993432,
408
+ "n_genes": 3064
409
+ }
410
+ },
411
+ "mean_r_generated": 0.40606651714837955,
412
+ "mean_r_broadcast": 0.2577780039471977,
413
+ "mean_partial_r": 0.36243591234056216
414
+ },
415
+ "pseudobulk_log1p_cpm": {
416
+ "per_type": {
417
+ "T cell": {
418
+ "r_generated": 0.3751926313127488,
419
+ "r_broadcast": 0.30559676102300276,
420
+ "partial_r_generated_given_broadcast": 0.33930563563718014,
421
+ "r_generated_vs_broadcast": 0.18975618205162745,
422
+ "n_genes": 3028
423
+ },
424
+ "B cell": {
425
+ "r_generated": 0.041917778584511206,
426
+ "r_broadcast": 0.047548729682353,
427
+ "partial_r_generated_given_broadcast": 0.04025439931277354,
428
+ "r_generated_vs_broadcast": 0.036503790454867256,
429
+ "n_genes": 3238
430
+ },
431
+ "Monocyte": {
432
+ "r_generated": 0.4028058779634047,
433
+ "r_broadcast": 0.36057989165867327,
434
+ "partial_r_generated_given_broadcast": 0.33904266970906016,
435
+ "r_generated_vs_broadcast": 0.2735368350859839,
436
+ "n_genes": 3132
437
+ },
438
+ "NK cell": {
439
+ "r_generated": 0.09480770279241091,
440
+ "r_broadcast": 0.11924462462412533,
441
+ "partial_r_generated_given_broadcast": 0.08343518061671204,
442
+ "r_generated_vs_broadcast": 0.1041412156985704,
443
+ "n_genes": 3064
444
+ }
445
+ },
446
+ "mean_r_generated": 0.2286809976632689,
447
+ "mean_r_broadcast": 0.2082425017470386,
448
+ "mean_partial_r": 0.20050947131893146
449
+ }
450
+ },
451
+ "deg_top50": {
452
+ "types_scored": [
453
+ "T cell",
454
+ "B cell",
455
+ "Monocyte",
456
+ "NK cell",
457
+ "DC"
458
+ ],
459
+ "types_not_scored": {},
460
+ "per_type": {
461
+ "T cell": {
462
+ "deg_scored": true,
463
+ "top50_overlap": 0,
464
+ "top50_jaccard": 0.0,
465
+ "obs_top_list_size": 50,
466
+ "gen_top_list_size": 1,
467
+ "top50_overlap_broadcast": 0,
468
+ "top50_jaccard_broadcast": 0.0,
469
+ "n_cells_obs": 44374,
470
+ "n_cells_gen": 18924
471
+ },
472
+ "B cell": {
473
+ "deg_scored": true,
474
+ "top50_overlap": 0,
475
+ "top50_jaccard": 0.0,
476
+ "obs_top_list_size": 8,
477
+ "gen_top_list_size": 0,
478
+ "top50_overlap_broadcast": 0,
479
+ "top50_jaccard_broadcast": 0.0,
480
+ "n_cells_obs": 6285,
481
+ "n_cells_gen": 1166
482
+ },
483
+ "Monocyte": {
484
+ "deg_scored": true,
485
+ "top50_overlap": 0,
486
+ "top50_jaccard": 0.0,
487
+ "obs_top_list_size": 0,
488
+ "gen_top_list_size": 3,
489
+ "top50_overlap_broadcast": 0,
490
+ "top50_jaccard_broadcast": 0.0,
491
+ "n_cells_obs": 26936,
492
+ "n_cells_gen": 11105
493
+ },
494
+ "NK cell": {
495
+ "deg_scored": true,
496
+ "top50_overlap": 0,
497
+ "top50_jaccard": 0.0,
498
+ "obs_top_list_size": 14,
499
+ "gen_top_list_size": 0,
500
+ "top50_overlap_broadcast": 0,
501
+ "top50_jaccard_broadcast": 0.0,
502
+ "n_cells_obs": 13603,
503
+ "n_cells_gen": 4770
504
+ },
505
+ "DC": {
506
+ "deg_scored": true,
507
+ "top50_overlap": 0,
508
+ "top50_jaccard": 0.0,
509
+ "obs_top_list_size": 3,
510
+ "gen_top_list_size": 0,
511
+ "top50_overlap_broadcast": 0,
512
+ "top50_jaccard_broadcast": 0.0,
513
+ "n_cells_obs": 1144,
514
+ "n_cells_gen": 760
515
+ }
516
+ },
517
+ "sum": 0,
518
+ "sum_4type": 0,
519
+ "max": 75,
520
+ "mean": 0.0,
521
+ "sum_broadcast": 0,
522
+ "sum_broadcast_4type": 0,
523
+ "broadcast_n_significant": 1,
524
+ "seconds": 0.07
525
+ },
526
+ "seconds": 7.8
527
+ }
528
+ },
529
+ "code_sha256": {
530
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
531
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
532
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
533
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
534
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
535
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
536
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
537
+ },
538
+ "seconds": 9.7,
539
+ "core_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw3/score"
540
+ }
paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/7336fa367195565c/summary.json ADDED
@@ -0,0 +1,2143 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "paired_ft_scores.v1",
3
+ "dataset": "imperial_eskd",
4
+ "written_utc": "2026-10-13T10:04:58.778133+00:00",
5
+ "command": [
6
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
7
+ "--dataset",
8
+ "imperial_eskd",
9
+ "--out",
10
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw2/score",
11
+ "--donors",
12
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw2/test_sample_ids.txt",
13
+ "--threads",
14
+ "4",
15
+ "--arm",
16
+ "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw2/lora.npz",
17
+ "--arm",
18
+ "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw2/pairedcal.npz",
19
+ "--arm",
20
+ "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw2/scsemi.npz",
21
+ "--arm",
22
+ "raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/imperial_eskd/raw.npz",
23
+ "--arm",
24
+ "refcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/imperial_eskd/refcal.npz",
25
+ "--case-groups",
26
+ "covid_positive",
27
+ "--control-groups",
28
+ "covid_negative"
29
+ ],
30
+ "arms": [
31
+ "lora",
32
+ "pairedcal",
33
+ "scsemi",
34
+ "raw",
35
+ "refcal"
36
+ ],
37
+ "donors": [
38
+ "C20_1004",
39
+ "C20_1404",
40
+ "C21_1004",
41
+ "C21_1704",
42
+ "C21_2504",
43
+ "C23_2204",
44
+ "C31_1304",
45
+ "C31_2004",
46
+ "C31_2704",
47
+ "C33_1401",
48
+ "C33_1601",
49
+ "C33_1901",
50
+ "C34_1404",
51
+ "C34_2104",
52
+ "C34_2504",
53
+ "C36_1504",
54
+ "C36_1704",
55
+ "C36_2104",
56
+ "C40_1504",
57
+ "C40_2204",
58
+ "C40_0105",
59
+ "C42_1504",
60
+ "C42_2204",
61
+ "C42_2704",
62
+ "C58_1604",
63
+ "C58_2501",
64
+ "C58_2901",
65
+ "C58_0102",
66
+ "C58_0402",
67
+ "C58_1003",
68
+ "C63_1704",
69
+ "C63_2404",
70
+ "C63_2904",
71
+ "C65_1704",
72
+ "C65_2104",
73
+ "C65_2504",
74
+ "C69_1804",
75
+ "C82_2504",
76
+ "C93_2104",
77
+ "C93_2704",
78
+ "C93_0405",
79
+ "C103_2204",
80
+ "C104_2204",
81
+ "C106_2204",
82
+ "C108_2204",
83
+ "C108_1501",
84
+ "C108_1801",
85
+ "C108_2201",
86
+ "C113_0605",
87
+ "C123_2404",
88
+ "C123_2904",
89
+ "C123_0505",
90
+ "C124_2404",
91
+ "C124_2704",
92
+ "C124_0105",
93
+ "C126_2504",
94
+ "C126_3004",
95
+ "C126_0605",
96
+ "C127_2504",
97
+ "C127_0405",
98
+ "C127_1105",
99
+ "C128_2504",
100
+ "C128_0405",
101
+ "C128_1105",
102
+ "C132_2804",
103
+ "C132_0205",
104
+ "C132_1105",
105
+ "C137_3004",
106
+ "C137_2502",
107
+ "C138_3004",
108
+ "C138_2301",
109
+ "C138_3001",
110
+ "C138_0202",
111
+ "C138_0402",
112
+ "C140_3004",
113
+ "C140_2801",
114
+ "C140_3001",
115
+ "C140_0202",
116
+ "C140_0402",
117
+ "C140_0602",
118
+ "C140_0902",
119
+ "C140_1103",
120
+ "C141_2001",
121
+ "C141_2201",
122
+ "C141_3001",
123
+ "C141_0202",
124
+ "C142_3004",
125
+ "C145_3004",
126
+ "C145_0701",
127
+ "C145_1201",
128
+ "C145_1401",
129
+ "C145_1901",
130
+ "C145_2301",
131
+ "C146_3004",
132
+ "C146_1201",
133
+ "C146_1401",
134
+ "C146_1601",
135
+ "C146_1901",
136
+ "C146_2301",
137
+ "C146_2701",
138
+ "C146_2502",
139
+ "C147_3004",
140
+ "C147_1401",
141
+ "C147_1901",
142
+ "C152_0405",
143
+ "C161_1105",
144
+ "C167_1205",
145
+ "C168_1205",
146
+ "C168_2001",
147
+ "C168_2301",
148
+ "C168_3001",
149
+ "C168_0202",
150
+ "C168_0403",
151
+ "C169_1205",
152
+ "C169_2001",
153
+ "C169_2301",
154
+ "C169_0202",
155
+ "C169_0403",
156
+ "C170_1205",
157
+ "C170_2301",
158
+ "C170_0202",
159
+ "C170_0402",
160
+ "C170_0403",
161
+ "C190_2605",
162
+ "C190_2901",
163
+ "C190_0102",
164
+ "C190_0302",
165
+ "C190_0502",
166
+ "C190_0802",
167
+ "C190_1002",
168
+ "C190_0903",
169
+ "C193_2605",
170
+ "C195_2605",
171
+ "C197_2605",
172
+ "C212_2705",
173
+ "C214_2705",
174
+ "C234_2805",
175
+ "C237_2805",
176
+ "C238_2905",
177
+ "C240_2905",
178
+ "C246_2905",
179
+ "C251_2905"
180
+ ],
181
+ "n_donors": 142,
182
+ "reference": {
183
+ "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd",
184
+ "reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
185
+ "features_sha256": "e46e5bb1a24eae045efe75125d20e3accaa8f68a1006eb2f60d24159013d4aa7",
186
+ "n_r1_cells": 21232,
187
+ "pca": {
188
+ "n_components": 50,
189
+ "explained_variance_ratio_sum": 0.25841519236564636,
190
+ "n_fit_cells": 21232
191
+ },
192
+ "r2_control": {
193
+ "precision": 0.9693858327053504,
194
+ "coverage": 0.9998116051243406,
195
+ "density": 1.2866569329314241,
196
+ "n_query": 21232,
197
+ "depth_matched": {
198
+ "precision": 0.9689619442351168,
199
+ "coverage": 0.9996703089675961,
200
+ "density": 1.28150433308214
201
+ }
202
+ },
203
+ "observed_l1_loo_null_mean": 0.47851633327026316
204
+ },
205
+ "contrast_definition": {
206
+ "enabled": true,
207
+ "rule": "explicit --case-groups / --control-groups",
208
+ "group_source": "features groups",
209
+ "case_groups": [
210
+ "covid_positive"
211
+ ],
212
+ "control_groups": [
213
+ "covid_negative"
214
+ ],
215
+ "n_case_donors": 103,
216
+ "n_control_donors": 31,
217
+ "n_donors_in_neither": 8,
218
+ "case": [
219
+ true,
220
+ true,
221
+ true,
222
+ true,
223
+ true,
224
+ true,
225
+ true,
226
+ true,
227
+ true,
228
+ true,
229
+ true,
230
+ true,
231
+ true,
232
+ true,
233
+ true,
234
+ true,
235
+ true,
236
+ true,
237
+ true,
238
+ true,
239
+ true,
240
+ true,
241
+ true,
242
+ true,
243
+ false,
244
+ true,
245
+ true,
246
+ true,
247
+ true,
248
+ false,
249
+ true,
250
+ true,
251
+ true,
252
+ true,
253
+ true,
254
+ true,
255
+ false,
256
+ true,
257
+ true,
258
+ true,
259
+ true,
260
+ false,
261
+ false,
262
+ false,
263
+ false,
264
+ true,
265
+ true,
266
+ true,
267
+ true,
268
+ true,
269
+ true,
270
+ true,
271
+ true,
272
+ true,
273
+ true,
274
+ true,
275
+ true,
276
+ true,
277
+ true,
278
+ true,
279
+ true,
280
+ true,
281
+ true,
282
+ true,
283
+ true,
284
+ true,
285
+ true,
286
+ false,
287
+ false,
288
+ false,
289
+ true,
290
+ true,
291
+ true,
292
+ true,
293
+ false,
294
+ true,
295
+ true,
296
+ true,
297
+ true,
298
+ true,
299
+ true,
300
+ false,
301
+ true,
302
+ true,
303
+ true,
304
+ true,
305
+ false,
306
+ false,
307
+ true,
308
+ true,
309
+ true,
310
+ true,
311
+ true,
312
+ false,
313
+ true,
314
+ true,
315
+ true,
316
+ true,
317
+ true,
318
+ true,
319
+ false,
320
+ false,
321
+ true,
322
+ true,
323
+ false,
324
+ false,
325
+ false,
326
+ false,
327
+ true,
328
+ true,
329
+ true,
330
+ true,
331
+ false,
332
+ false,
333
+ true,
334
+ true,
335
+ true,
336
+ false,
337
+ false,
338
+ true,
339
+ true,
340
+ true,
341
+ false,
342
+ false,
343
+ true,
344
+ true,
345
+ true,
346
+ true,
347
+ true,
348
+ true,
349
+ false,
350
+ false,
351
+ false,
352
+ false,
353
+ false,
354
+ false,
355
+ false,
356
+ false,
357
+ false,
358
+ false,
359
+ false,
360
+ false
361
+ ],
362
+ "ctrl": [
363
+ false,
364
+ false,
365
+ false,
366
+ false,
367
+ false,
368
+ false,
369
+ false,
370
+ false,
371
+ false,
372
+ false,
373
+ false,
374
+ false,
375
+ false,
376
+ false,
377
+ false,
378
+ false,
379
+ false,
380
+ false,
381
+ false,
382
+ false,
383
+ false,
384
+ false,
385
+ false,
386
+ false,
387
+ true,
388
+ false,
389
+ false,
390
+ false,
391
+ false,
392
+ false,
393
+ false,
394
+ false,
395
+ false,
396
+ false,
397
+ false,
398
+ false,
399
+ true,
400
+ false,
401
+ false,
402
+ false,
403
+ false,
404
+ true,
405
+ true,
406
+ true,
407
+ true,
408
+ false,
409
+ false,
410
+ false,
411
+ false,
412
+ false,
413
+ false,
414
+ false,
415
+ false,
416
+ false,
417
+ false,
418
+ false,
419
+ false,
420
+ false,
421
+ false,
422
+ false,
423
+ false,
424
+ false,
425
+ false,
426
+ false,
427
+ false,
428
+ false,
429
+ false,
430
+ true,
431
+ false,
432
+ true,
433
+ false,
434
+ false,
435
+ false,
436
+ false,
437
+ true,
438
+ false,
439
+ false,
440
+ false,
441
+ false,
442
+ false,
443
+ false,
444
+ false,
445
+ false,
446
+ false,
447
+ false,
448
+ false,
449
+ true,
450
+ true,
451
+ false,
452
+ false,
453
+ false,
454
+ false,
455
+ false,
456
+ true,
457
+ false,
458
+ false,
459
+ false,
460
+ false,
461
+ false,
462
+ false,
463
+ false,
464
+ true,
465
+ false,
466
+ false,
467
+ true,
468
+ true,
469
+ true,
470
+ true,
471
+ false,
472
+ false,
473
+ false,
474
+ false,
475
+ false,
476
+ true,
477
+ false,
478
+ false,
479
+ false,
480
+ false,
481
+ true,
482
+ false,
483
+ false,
484
+ false,
485
+ false,
486
+ true,
487
+ false,
488
+ false,
489
+ false,
490
+ false,
491
+ false,
492
+ false,
493
+ false,
494
+ true,
495
+ true,
496
+ true,
497
+ true,
498
+ true,
499
+ true,
500
+ true,
501
+ true,
502
+ true,
503
+ true,
504
+ true
505
+ ],
506
+ "groups": [
507
+ "covid_positive",
508
+ "covid_positive",
509
+ "covid_positive",
510
+ "covid_positive",
511
+ "covid_positive",
512
+ "covid_positive",
513
+ "covid_positive",
514
+ "covid_positive",
515
+ "covid_positive",
516
+ "covid_positive",
517
+ "covid_positive",
518
+ "covid_positive",
519
+ "covid_positive",
520
+ "covid_positive",
521
+ "covid_positive",
522
+ "covid_positive",
523
+ "covid_positive",
524
+ "covid_positive",
525
+ "covid_positive",
526
+ "covid_positive",
527
+ "covid_positive",
528
+ "covid_positive",
529
+ "covid_positive",
530
+ "covid_positive",
531
+ "covid_negative",
532
+ "covid_positive",
533
+ "covid_positive",
534
+ "covid_positive",
535
+ "covid_positive",
536
+ "recovery",
537
+ "covid_positive",
538
+ "covid_positive",
539
+ "covid_positive",
540
+ "covid_positive",
541
+ "covid_positive",
542
+ "covid_positive",
543
+ "covid_negative",
544
+ "covid_positive",
545
+ "covid_positive",
546
+ "covid_positive",
547
+ "covid_positive",
548
+ "covid_negative",
549
+ "covid_negative",
550
+ "covid_negative",
551
+ "covid_negative",
552
+ "covid_positive",
553
+ "covid_positive",
554
+ "covid_positive",
555
+ "covid_positive",
556
+ "covid_positive",
557
+ "covid_positive",
558
+ "covid_positive",
559
+ "covid_positive",
560
+ "covid_positive",
561
+ "covid_positive",
562
+ "covid_positive",
563
+ "covid_positive",
564
+ "covid_positive",
565
+ "covid_positive",
566
+ "covid_positive",
567
+ "covid_positive",
568
+ "covid_positive",
569
+ "covid_positive",
570
+ "covid_positive",
571
+ "covid_positive",
572
+ "covid_positive",
573
+ "covid_positive",
574
+ "covid_negative",
575
+ "recovery",
576
+ "covid_negative",
577
+ "covid_positive",
578
+ "covid_positive",
579
+ "covid_positive",
580
+ "covid_positive",
581
+ "covid_negative",
582
+ "covid_positive",
583
+ "covid_positive",
584
+ "covid_positive",
585
+ "covid_positive",
586
+ "covid_positive",
587
+ "covid_positive",
588
+ "recovery",
589
+ "covid_positive",
590
+ "covid_positive",
591
+ "covid_positive",
592
+ "covid_positive",
593
+ "covid_negative",
594
+ "covid_negative",
595
+ "covid_positive",
596
+ "covid_positive",
597
+ "covid_positive",
598
+ "covid_positive",
599
+ "covid_positive",
600
+ "covid_negative",
601
+ "covid_positive",
602
+ "covid_positive",
603
+ "covid_positive",
604
+ "covid_positive",
605
+ "covid_positive",
606
+ "covid_positive",
607
+ "recovery",
608
+ "covid_negative",
609
+ "covid_positive",
610
+ "covid_positive",
611
+ "covid_negative",
612
+ "covid_negative",
613
+ "covid_negative",
614
+ "covid_negative",
615
+ "covid_positive",
616
+ "covid_positive",
617
+ "covid_positive",
618
+ "covid_positive",
619
+ "recovery",
620
+ "covid_negative",
621
+ "covid_positive",
622
+ "covid_positive",
623
+ "covid_positive",
624
+ "recovery",
625
+ "covid_negative",
626
+ "covid_positive",
627
+ "covid_positive",
628
+ "covid_positive",
629
+ "recovery",
630
+ "covid_negative",
631
+ "covid_positive",
632
+ "covid_positive",
633
+ "covid_positive",
634
+ "covid_positive",
635
+ "covid_positive",
636
+ "covid_positive",
637
+ "recovery",
638
+ "covid_negative",
639
+ "covid_negative",
640
+ "covid_negative",
641
+ "covid_negative",
642
+ "covid_negative",
643
+ "covid_negative",
644
+ "covid_negative",
645
+ "covid_negative",
646
+ "covid_negative",
647
+ "covid_negative",
648
+ "covid_negative"
649
+ ]
650
+ },
651
+ "deg_definition": {
652
+ "enabled": true,
653
+ "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
654
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
655
+ "functions": [
656
+ "welch_bh_deg",
657
+ "top_deg_genes",
658
+ "jaccard"
659
+ ],
660
+ "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
661
+ "top_n": 50,
662
+ "fdr": 0.05,
663
+ "n_genes": 5927,
664
+ "types": [
665
+ "T cell",
666
+ "B cell",
667
+ "Monocyte",
668
+ "NK cell",
669
+ "DC"
670
+ ],
671
+ "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd/deg_reference.npz",
672
+ "aggregates_sha256": "8fada1ace7530b79bfc5c5201b9cb60399ff77d083dd8b53b13cfbe900cda55c",
673
+ "aggregates_note": null,
674
+ "types_not_scored_observed": [],
675
+ "observed": {
676
+ "T cell": {
677
+ "n_significant": 655,
678
+ "n_tested": 5752,
679
+ "n_case_donors": 103,
680
+ "n_control_donors": 31,
681
+ "n_cells": 249798,
682
+ "top_list_size": 50
683
+ },
684
+ "B cell": {
685
+ "n_significant": 240,
686
+ "n_tested": 5639,
687
+ "n_case_donors": 103,
688
+ "n_control_donors": 31,
689
+ "n_cells": 46668,
690
+ "top_list_size": 50
691
+ },
692
+ "Monocyte": {
693
+ "n_significant": 235,
694
+ "n_tested": 5620,
695
+ "n_case_donors": 102,
696
+ "n_control_donors": 31,
697
+ "n_cells": 75478,
698
+ "top_list_size": 50
699
+ },
700
+ "NK cell": {
701
+ "n_significant": 359,
702
+ "n_tested": 5582,
703
+ "n_case_donors": 103,
704
+ "n_control_donors": 31,
705
+ "n_cells": 66389,
706
+ "top_list_size": 50
707
+ },
708
+ "DC": {
709
+ "n_significant": 214,
710
+ "n_tested": 5418,
711
+ "n_case_donors": 103,
712
+ "n_control_donors": 31,
713
+ "n_cells": 12425,
714
+ "top_list_size": 50
715
+ }
716
+ },
717
+ "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
718
+ },
719
+ "headline": {
720
+ "lora": {
721
+ "comp_l1": 0.49690465056354277,
722
+ "comp_l1_obs_loo_null": 0.47851633327026316,
723
+ "precision": 0.8489073097211756,
724
+ "coverage": 0.6606066314996232,
725
+ "precision_dm": 0.8850320271288621,
726
+ "coverage_dm": 0.849707987942728,
727
+ "pb_r_median": 0.867501639721653,
728
+ "pb_top1": 0.035211267605633804,
729
+ "mono_pct_gen": 13.994366197183098,
730
+ "mono_pct_obs": 16.205826518972017,
731
+ "median_umi_gen": 1219.0,
732
+ "median_umi_obs": 1372.0,
733
+ "contrast_mean_cp10k_r_gen": 0.7342266929000006,
734
+ "contrast_pseudobulk_log1p_cpm_r_gen": 0.546928308603402,
735
+ "contrast_mean_cp10k_r_broadcast": 0.6433613217171205,
736
+ "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5930746251539698,
737
+ "deg_top50_T": 37,
738
+ "deg_top50_B": 16,
739
+ "deg_top50_Mono": 23,
740
+ "deg_top50_NK": 24,
741
+ "deg_top50_DC": 20,
742
+ "deg_top50_sum": 120,
743
+ "deg_top50_max": 250,
744
+ "deg_top50_sum_4type": 100,
745
+ "deg_top50_sum_broadcast": 65,
746
+ "seconds": 30.9
747
+ },
748
+ "pairedcal": {
749
+ "comp_l1": 0.48690416697398886,
750
+ "comp_l1_obs_loo_null": 0.47851633327026316,
751
+ "precision": 0.8537584777694047,
752
+ "coverage": 0.6304634513941221,
753
+ "precision_dm": 0.8811228334589299,
754
+ "coverage_dm": 0.6784099472494348,
755
+ "pb_r_median": 0.8659267793839085,
756
+ "pb_top1": 0.04929577464788732,
757
+ "mono_pct_gen": 14.293896713615023,
758
+ "mono_pct_obs": 16.205826518972017,
759
+ "median_umi_gen": 1604.0,
760
+ "median_umi_obs": 1372.0,
761
+ "contrast_mean_cp10k_r_gen": 0.6618291543402255,
762
+ "contrast_pseudobulk_log1p_cpm_r_gen": 0.4989552748391821,
763
+ "contrast_mean_cp10k_r_broadcast": 0.6956050424812483,
764
+ "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5982473667330177,
765
+ "deg_top50_T": 25,
766
+ "deg_top50_B": 16,
767
+ "deg_top50_Mono": 25,
768
+ "deg_top50_NK": 19,
769
+ "deg_top50_DC": 7,
770
+ "deg_top50_sum": 92,
771
+ "deg_top50_max": 250,
772
+ "deg_top50_sum_4type": 85,
773
+ "deg_top50_sum_broadcast": 89,
774
+ "seconds": 30.8
775
+ },
776
+ "scsemi": {
777
+ "comp_l1": 0.6903180999715937,
778
+ "comp_l1_obs_loo_null": 0.47851633327026316,
779
+ "precision": 0.24156932931424266,
780
+ "coverage": 0.04130557648831952,
781
+ "precision_dm": 0.4188489073097212,
782
+ "coverage_dm": 0.15674453654860587,
783
+ "pb_r_median": 0.5951250403361148,
784
+ "pb_top1": 0.02112676056338028,
785
+ "mono_pct_gen": 8.207042253521125,
786
+ "mono_pct_obs": 16.205826518972017,
787
+ "median_umi_gen": 1357.0,
788
+ "median_umi_obs": 1372.0,
789
+ "contrast_mean_cp10k_r_gen": 0.5112172444204303,
790
+ "contrast_pseudobulk_log1p_cpm_r_gen": 0.27707471223810287,
791
+ "contrast_mean_cp10k_r_broadcast": 0.6433613217171205,
792
+ "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5930746251539698,
793
+ "deg_top50_T": 16,
794
+ "deg_top50_B": 7,
795
+ "deg_top50_Mono": 8,
796
+ "deg_top50_NK": 11,
797
+ "deg_top50_DC": 7,
798
+ "deg_top50_sum": 49,
799
+ "deg_top50_max": 250,
800
+ "deg_top50_sum_4type": 42,
801
+ "deg_top50_sum_broadcast": 65,
802
+ "seconds": 27.9
803
+ },
804
+ "raw": {
805
+ "comp_l1": 0.7913025138195902,
806
+ "comp_l1_obs_loo_null": 0.47851633327026316,
807
+ "precision": 0.48930859080633005,
808
+ "coverage": 0.11412019593067069,
809
+ "precision_dm": 0.5175207234363225,
810
+ "coverage_dm": 0.15321213262999248,
811
+ "pb_r_median": 0.8853890205964849,
812
+ "pb_top1": 0.028169014084507043,
813
+ "mono_pct_gen": 50.68685446009389,
814
+ "mono_pct_obs": 16.205826518972017,
815
+ "median_umi_gen": 1295.0,
816
+ "median_umi_obs": 1372.0,
817
+ "contrast_mean_cp10k_r_gen": 0.6341200084949812,
818
+ "contrast_pseudobulk_log1p_cpm_r_gen": 0.4579676533253675,
819
+ "contrast_mean_cp10k_r_broadcast": 0.6433613217171205,
820
+ "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5930746251539698,
821
+ "deg_top50_T": 30,
822
+ "deg_top50_B": 18,
823
+ "deg_top50_Mono": 25,
824
+ "deg_top50_NK": 18,
825
+ "deg_top50_DC": 8,
826
+ "deg_top50_sum": 99,
827
+ "deg_top50_max": 250,
828
+ "deg_top50_sum_4type": 91,
829
+ "deg_top50_sum_broadcast": 65,
830
+ "seconds": 38.1
831
+ },
832
+ "refcal": {
833
+ "comp_l1": 0.5035736748554334,
834
+ "comp_l1_obs_loo_null": 0.47851633327026316,
835
+ "precision": 0.8204596834966089,
836
+ "coverage": 0.36379050489826675,
837
+ "precision_dm": 0.8311981914091937,
838
+ "coverage_dm": 0.5074415975885456,
839
+ "pb_r_median": 0.8521668347812354,
840
+ "pb_top1": 0.028169014084507043,
841
+ "mono_pct_gen": 26.317840375586854,
842
+ "mono_pct_obs": 16.205826518972017,
843
+ "median_umi_gen": 1518.0,
844
+ "median_umi_obs": 1372.0,
845
+ "contrast_mean_cp10k_r_gen": 0.4973273614440279,
846
+ "contrast_pseudobulk_log1p_cpm_r_gen": 0.3856152478713802,
847
+ "contrast_mean_cp10k_r_broadcast": 0.5820354953035813,
848
+ "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5896018838201683,
849
+ "deg_top50_T": 17,
850
+ "deg_top50_B": 14,
851
+ "deg_top50_Mono": 18,
852
+ "deg_top50_NK": 7,
853
+ "deg_top50_DC": 6,
854
+ "deg_top50_sum": 62,
855
+ "deg_top50_max": 250,
856
+ "deg_top50_sum_4type": 56,
857
+ "deg_top50_sum_broadcast": 88,
858
+ "seconds": 33.1
859
+ }
860
+ },
861
+ "per_arm": {
862
+ "lora": {
863
+ "arm": "lora",
864
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw2/lora.npz",
865
+ "npz_sha256": "fe71c96458b85d14f7a6836bc45aeff99599ec91fd367f9fb373c9d60fb96793",
866
+ "receipt_verified": true,
867
+ "generation": {
868
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/imperial_eskd/disease/draw2/lora/checkpoint_ft.pt",
869
+ "checkpoint_sha256": "43397459bc083fdc9493a77f80c8f8f28bcc0346acc06d1633be74486a61b804",
870
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw2/test_raw.npz",
871
+ "input_condition_sha256": "11ba7c4e0f734b8eeab115536093d16205a1f592833e54115aa10cafd131e466",
872
+ "seed": 20260928,
873
+ "steps": 50,
874
+ "support_readout": "bernoulli",
875
+ "weights": "ema"
876
+ },
877
+ "condition_for_broadcast": {
878
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw2/test_raw.npz",
879
+ "sha256": "11ba7c4e0f734b8eeab115536093d16205a1f592833e54115aa10cafd131e466"
880
+ },
881
+ "poisson": {
882
+ "seed": 20260916,
883
+ "rule": "whole NPZ, rows in NPZ order",
884
+ "nnz_whole_npz": 51544418,
885
+ "median_library_whole_npz_panel": 1219.0,
886
+ "n_rows_whole_npz": 213000
887
+ },
888
+ "annotation": {
889
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
890
+ "zero_padded_model_genes": 0,
891
+ "label_counts": {
892
+ "T cell": 137442,
893
+ "Monocyte": 29808,
894
+ "NK cell": 25038,
895
+ "B cell": 12132,
896
+ "DC": 5716,
897
+ "Other": 2864
898
+ },
899
+ "mean_l2_max_prob": 0.9232385695843209,
900
+ "predict_seconds": 5.2
901
+ },
902
+ "n_donors": 142,
903
+ "n_generated_cells": 213000,
904
+ "composition": {
905
+ "l1_mean": 0.49690465056354277,
906
+ "l1_median": 0.45615288401267573,
907
+ "l1_obs_loo_null_mean": 0.47851633327026316,
908
+ "l1_generated_loo_mean_vs_observed_mean": 0.4967381244797774,
909
+ "composition_top1": 0.014084507042253521,
910
+ "mean_fraction_generated": {
911
+ "T cell": 0.645268,
912
+ "B cell": 0.056958,
913
+ "Monocyte": 0.139944,
914
+ "NK cell": 0.117549,
915
+ "DC": 0.026836,
916
+ "Other": 0.013446
917
+ },
918
+ "mean_fraction_observed": {
919
+ "T cell": 0.50954,
920
+ "B cell": 0.123023,
921
+ "Monocyte": 0.162058,
922
+ "NK cell": 0.163853,
923
+ "DC": 0.028277,
924
+ "Other": 0.013248
925
+ }
926
+ },
927
+ "pseudobulk": {
928
+ "n_genes": 5927,
929
+ "r_median": 0.867501639721653,
930
+ "r_mean": 0.8640208477957554,
931
+ "top1": 0.035211267605633804,
932
+ "n_top1": 5,
933
+ "own_rank_median": 36.0,
934
+ "chance_top1": 0.007042253521126761
935
+ },
936
+ "precision_coverage": {
937
+ "precision": 0.8489073097211756,
938
+ "coverage": 0.6606066314996232,
939
+ "density": 0.6656038055764883,
940
+ "n_query": 21232,
941
+ "n_reference": 21232
942
+ },
943
+ "precision_coverage_depth_matched": {
944
+ "precision": 0.8850320271288621,
945
+ "coverage": 0.849707987942728,
946
+ "density": 0.910663149962321,
947
+ "detected_median_before": {
948
+ "R1": 347.0,
949
+ "Q": 238.0
950
+ },
951
+ "detected_median_after": {
952
+ "R1": 238.0,
953
+ "Q": 238.0
954
+ }
955
+ },
956
+ "monocyte_pct": {
957
+ "generated_mean_over_donors": 13.994366197183098,
958
+ "observed_mean_over_donors": 16.205826518972017,
959
+ "generated_pooled_cells": 13.994366197183098
960
+ },
961
+ "median_umi_per_cell_scoring_genes": {
962
+ "generated_pooled": 1219.0,
963
+ "observed_pooled": 1372.0,
964
+ "generated_mean_of_donor_medians": 1233.79931640625,
965
+ "observed_mean_of_donor_medians": 1311.5598591549297
966
+ },
967
+ "contrast": {
968
+ "mean_cp10k": {
969
+ "per_type": {
970
+ "T cell": {
971
+ "r_generated": 0.823245507919071,
972
+ "r_broadcast": 0.6311553277299028,
973
+ "partial_r_generated_given_broadcast": 0.7668456033044245,
974
+ "r_generated_vs_broadcast": 0.47507571602287574,
975
+ "n_genes": 3036
976
+ },
977
+ "B cell": {
978
+ "r_generated": 0.6970149354561576,
979
+ "r_broadcast": 0.6245632309702648,
980
+ "partial_r_generated_given_broadcast": 0.5712184139297037,
981
+ "r_generated_vs_broadcast": 0.49564022194637614,
982
+ "n_genes": 3187
983
+ },
984
+ "Monocyte": {
985
+ "r_generated": 0.6536284248598316,
986
+ "r_broadcast": 0.6837051334204964,
987
+ "partial_r_generated_given_broadcast": 0.39260390909950743,
988
+ "r_generated_vs_broadcast": 0.6308758757117082,
989
+ "n_genes": 2886
990
+ },
991
+ "NK cell": {
992
+ "r_generated": 0.7630179033649425,
993
+ "r_broadcast": 0.6340215947478178,
994
+ "partial_r_generated_given_broadcast": 0.6241093634984135,
995
+ "r_generated_vs_broadcast": 0.587400061645664,
996
+ "n_genes": 2961
997
+ }
998
+ },
999
+ "mean_r_generated": 0.7342266929000006,
1000
+ "mean_r_broadcast": 0.6433613217171205,
1001
+ "mean_partial_r": 0.5886943224580123
1002
+ },
1003
+ "pseudobulk_log1p_cpm": {
1004
+ "per_type": {
1005
+ "T cell": {
1006
+ "r_generated": 0.7193066514970855,
1007
+ "r_broadcast": 0.6350373450250355,
1008
+ "partial_r_generated_given_broadcast": 0.579638601606999,
1009
+ "r_generated_vs_broadcast": 0.5386289782291876,
1010
+ "n_genes": 3036
1011
+ },
1012
+ "B cell": {
1013
+ "r_generated": 0.37611253287893887,
1014
+ "r_broadcast": 0.4816610289030315,
1015
+ "partial_r_generated_given_broadcast": 0.24768872622334612,
1016
+ "r_generated_vs_broadcast": 0.3605135260262331,
1017
+ "n_genes": 3187
1018
+ },
1019
+ "Monocyte": {
1020
+ "r_generated": 0.5925941968736181,
1021
+ "r_broadcast": 0.6802082395314715,
1022
+ "partial_r_generated_given_broadcast": 0.32737940604935906,
1023
+ "r_generated_vs_broadcast": 0.5850875930410999,
1024
+ "n_genes": 2886
1025
+ },
1026
+ "NK cell": {
1027
+ "r_generated": 0.4996998531639657,
1028
+ "r_broadcast": 0.5753918871563406,
1029
+ "partial_r_generated_given_broadcast": 0.31755075571146085,
1030
+ "r_generated_vs_broadcast": 0.4700493020665799,
1031
+ "n_genes": 2961
1032
+ }
1033
+ },
1034
+ "mean_r_generated": 0.546928308603402,
1035
+ "mean_r_broadcast": 0.5930746251539698,
1036
+ "mean_partial_r": 0.3680643723977912
1037
+ }
1038
+ },
1039
+ "deg_top50": {
1040
+ "types_scored": [
1041
+ "T cell",
1042
+ "B cell",
1043
+ "Monocyte",
1044
+ "NK cell",
1045
+ "DC"
1046
+ ],
1047
+ "types_not_scored": {},
1048
+ "per_type": {
1049
+ "T cell": {
1050
+ "deg_scored": true,
1051
+ "top50_overlap": 37,
1052
+ "top50_jaccard": 0.5873015873015873,
1053
+ "obs_top_list_size": 50,
1054
+ "gen_top_list_size": 50,
1055
+ "top50_overlap_broadcast": 13,
1056
+ "top50_jaccard_broadcast": 0.14942528735632185,
1057
+ "n_cells_obs": 249798,
1058
+ "n_cells_gen": 128697
1059
+ },
1060
+ "B cell": {
1061
+ "deg_scored": true,
1062
+ "top50_overlap": 16,
1063
+ "top50_jaccard": 0.19047619047619047,
1064
+ "obs_top_list_size": 50,
1065
+ "gen_top_list_size": 50,
1066
+ "top50_overlap_broadcast": 10,
1067
+ "top50_jaccard_broadcast": 0.1111111111111111,
1068
+ "n_cells_obs": 46668,
1069
+ "n_cells_gen": 11571
1070
+ },
1071
+ "Monocyte": {
1072
+ "deg_scored": true,
1073
+ "top50_overlap": 23,
1074
+ "top50_jaccard": 0.2987012987012987,
1075
+ "obs_top_list_size": 50,
1076
+ "gen_top_list_size": 50,
1077
+ "top50_overlap_broadcast": 18,
1078
+ "top50_jaccard_broadcast": 0.21951219512195122,
1079
+ "n_cells_obs": 75478,
1080
+ "n_cells_gen": 28555
1081
+ },
1082
+ "NK cell": {
1083
+ "deg_scored": true,
1084
+ "top50_overlap": 24,
1085
+ "top50_jaccard": 0.3157894736842105,
1086
+ "obs_top_list_size": 50,
1087
+ "gen_top_list_size": 50,
1088
+ "top50_overlap_broadcast": 13,
1089
+ "top50_jaccard_broadcast": 0.14942528735632185,
1090
+ "n_cells_obs": 66389,
1091
+ "n_cells_gen": 23991
1092
+ },
1093
+ "DC": {
1094
+ "deg_scored": true,
1095
+ "top50_overlap": 20,
1096
+ "top50_jaccard": 0.25,
1097
+ "obs_top_list_size": 50,
1098
+ "gen_top_list_size": 50,
1099
+ "top50_overlap_broadcast": 11,
1100
+ "top50_jaccard_broadcast": 0.12359550561797752,
1101
+ "n_cells_obs": 12425,
1102
+ "n_cells_gen": 5428
1103
+ }
1104
+ },
1105
+ "sum": 120,
1106
+ "sum_4type": 100,
1107
+ "max": 250,
1108
+ "mean": 24.0,
1109
+ "sum_broadcast": 65,
1110
+ "sum_broadcast_4type": 54,
1111
+ "broadcast_n_significant": 2026,
1112
+ "seconds": 0.34
1113
+ },
1114
+ "seconds": 30.9
1115
+ },
1116
+ "pairedcal": {
1117
+ "arm": "pairedcal",
1118
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw2/pairedcal.npz",
1119
+ "npz_sha256": "0ec860c7ed9115b492ce77ab99663bf317b9267a67c962da688310efdacefab0",
1120
+ "receipt_verified": true,
1121
+ "generation": {
1122
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
1123
+ "checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
1124
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw2/test_cal.npz",
1125
+ "input_condition_sha256": "5183c668477b710b7fc8eb37e70010916e22d5387c20e50ac351e17b641c5e8b",
1126
+ "seed": 20260928,
1127
+ "steps": 50,
1128
+ "support_readout": "bernoulli",
1129
+ "weights": "ema"
1130
+ },
1131
+ "condition_for_broadcast": {
1132
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw2/test_cal.npz",
1133
+ "sha256": "5183c668477b710b7fc8eb37e70010916e22d5387c20e50ac351e17b641c5e8b"
1134
+ },
1135
+ "poisson": {
1136
+ "seed": 20260916,
1137
+ "rule": "whole NPZ, rows in NPZ order",
1138
+ "nnz_whole_npz": 58081648,
1139
+ "median_library_whole_npz_panel": 1604.0,
1140
+ "n_rows_whole_npz": 213000
1141
+ },
1142
+ "annotation": {
1143
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
1144
+ "zero_padded_model_genes": 0,
1145
+ "label_counts": {
1146
+ "T cell": 142013,
1147
+ "Monocyte": 30446,
1148
+ "NK cell": 23084,
1149
+ "B cell": 13103,
1150
+ "Other": 2633,
1151
+ "DC": 1721
1152
+ },
1153
+ "mean_l2_max_prob": 0.9346544865745474,
1154
+ "predict_seconds": 4.8
1155
+ },
1156
+ "n_donors": 142,
1157
+ "n_generated_cells": 213000,
1158
+ "composition": {
1159
+ "l1_mean": 0.48690416697398886,
1160
+ "l1_median": 0.4487813881945781,
1161
+ "l1_obs_loo_null_mean": 0.47851633327026316,
1162
+ "l1_generated_loo_mean_vs_observed_mean": 0.5119930352548303,
1163
+ "composition_top1": 0.007042253521126761,
1164
+ "mean_fraction_generated": {
1165
+ "T cell": 0.666728,
1166
+ "B cell": 0.061516,
1167
+ "Monocyte": 0.142939,
1168
+ "NK cell": 0.108376,
1169
+ "DC": 0.00808,
1170
+ "Other": 0.012362
1171
+ },
1172
+ "mean_fraction_observed": {
1173
+ "T cell": 0.50954,
1174
+ "B cell": 0.123023,
1175
+ "Monocyte": 0.162058,
1176
+ "NK cell": 0.163853,
1177
+ "DC": 0.028277,
1178
+ "Other": 0.013248
1179
+ }
1180
+ },
1181
+ "pseudobulk": {
1182
+ "n_genes": 5927,
1183
+ "r_median": 0.8659267793839085,
1184
+ "r_mean": 0.8640682590106017,
1185
+ "top1": 0.04929577464788732,
1186
+ "n_top1": 7,
1187
+ "own_rank_median": 40.0,
1188
+ "chance_top1": 0.007042253521126761
1189
+ },
1190
+ "precision_coverage": {
1191
+ "precision": 0.8537584777694047,
1192
+ "coverage": 0.6304634513941221,
1193
+ "density": 0.6800678221552373,
1194
+ "n_query": 21232,
1195
+ "n_reference": 21232
1196
+ },
1197
+ "precision_coverage_depth_matched": {
1198
+ "precision": 0.8811228334589299,
1199
+ "coverage": 0.6784099472494348,
1200
+ "density": 0.8120478522984176,
1201
+ "detected_median_before": {
1202
+ "R1": 347.0,
1203
+ "Q": 267.0
1204
+ },
1205
+ "detected_median_after": {
1206
+ "R1": 267.0,
1207
+ "Q": 267.0
1208
+ }
1209
+ },
1210
+ "monocyte_pct": {
1211
+ "generated_mean_over_donors": 14.293896713615023,
1212
+ "observed_mean_over_donors": 16.205826518972017,
1213
+ "generated_pooled_cells": 14.293896713615023
1214
+ },
1215
+ "median_umi_per_cell_scoring_genes": {
1216
+ "generated_pooled": 1604.0,
1217
+ "observed_pooled": 1372.0,
1218
+ "generated_mean_of_donor_medians": 1616.9964599609375,
1219
+ "observed_mean_of_donor_medians": 1311.5598591549297
1220
+ },
1221
+ "contrast": {
1222
+ "mean_cp10k": {
1223
+ "per_type": {
1224
+ "T cell": {
1225
+ "r_generated": 0.6925352275718538,
1226
+ "r_broadcast": 0.7166511391151084,
1227
+ "partial_r_generated_given_broadcast": 0.41177061002075677,
1228
+ "r_generated_vs_broadcast": 0.6682236325538528,
1229
+ "n_genes": 3036
1230
+ },
1231
+ "B cell": {
1232
+ "r_generated": 0.5855311326668361,
1233
+ "r_broadcast": 0.6878106153880695,
1234
+ "partial_r_generated_given_broadcast": 0.30298397402406557,
1235
+ "r_generated_vs_broadcast": 0.5940821153346622,
1236
+ "n_genes": 3187
1237
+ },
1238
+ "Monocyte": {
1239
+ "r_generated": 0.6775454104465839,
1240
+ "r_broadcast": 0.6850283120157358,
1241
+ "partial_r_generated_given_broadcast": 0.4042923564177836,
1242
+ "r_generated_vs_broadcast": 0.6698238165344448,
1243
+ "n_genes": 2886
1244
+ },
1245
+ "NK cell": {
1246
+ "r_generated": 0.6917048466756283,
1247
+ "r_broadcast": 0.6929301034060799,
1248
+ "partial_r_generated_given_broadcast": 0.43301663397031603,
1249
+ "r_generated_vs_broadcast": 0.6595715393449322,
1250
+ "n_genes": 2961
1251
+ }
1252
+ },
1253
+ "mean_r_generated": 0.6618291543402255,
1254
+ "mean_r_broadcast": 0.6956050424812483,
1255
+ "mean_partial_r": 0.3880158936082305
1256
+ },
1257
+ "pseudobulk_log1p_cpm": {
1258
+ "per_type": {
1259
+ "T cell": {
1260
+ "r_generated": 0.5281164703149163,
1261
+ "r_broadcast": 0.6424644595227534,
1262
+ "partial_r_generated_given_broadcast": 0.20749356552852213,
1263
+ "r_generated_vs_broadcast": 0.6297681438776512,
1264
+ "n_genes": 3036
1265
+ },
1266
+ "B cell": {
1267
+ "r_generated": 0.42824757941911384,
1268
+ "r_broadcast": 0.4849450656263207,
1269
+ "partial_r_generated_given_broadcast": 0.25400800682514696,
1270
+ "r_generated_vs_broadcast": 0.48164226690132106,
1271
+ "n_genes": 3187
1272
+ },
1273
+ "Monocyte": {
1274
+ "r_generated": 0.5609001579817517,
1275
+ "r_broadcast": 0.6825843812326946,
1276
+ "partial_r_generated_given_broadcast": 0.2694010313290736,
1277
+ "r_generated_vs_broadcast": 0.5885412309754801,
1278
+ "n_genes": 2886
1279
+ },
1280
+ "NK cell": {
1281
+ "r_generated": 0.4785568916409467,
1282
+ "r_broadcast": 0.5829955605503023,
1283
+ "partial_r_generated_given_broadcast": 0.23101063460126825,
1284
+ "r_generated_vs_broadcast": 0.5525205829933211,
1285
+ "n_genes": 2961
1286
+ }
1287
+ },
1288
+ "mean_r_generated": 0.4989552748391821,
1289
+ "mean_r_broadcast": 0.5982473667330177,
1290
+ "mean_partial_r": 0.24047830957100272
1291
+ }
1292
+ },
1293
+ "deg_top50": {
1294
+ "types_scored": [
1295
+ "T cell",
1296
+ "B cell",
1297
+ "Monocyte",
1298
+ "NK cell",
1299
+ "DC"
1300
+ ],
1301
+ "types_not_scored": {},
1302
+ "per_type": {
1303
+ "T cell": {
1304
+ "deg_scored": true,
1305
+ "top50_overlap": 25,
1306
+ "top50_jaccard": 0.3333333333333333,
1307
+ "obs_top_list_size": 50,
1308
+ "gen_top_list_size": 50,
1309
+ "top50_overlap_broadcast": 19,
1310
+ "top50_jaccard_broadcast": 0.2345679012345679,
1311
+ "n_cells_obs": 249798,
1312
+ "n_cells_gen": 133310
1313
+ },
1314
+ "B cell": {
1315
+ "deg_scored": true,
1316
+ "top50_overlap": 16,
1317
+ "top50_jaccard": 0.19047619047619047,
1318
+ "obs_top_list_size": 50,
1319
+ "gen_top_list_size": 50,
1320
+ "top50_overlap_broadcast": 15,
1321
+ "top50_jaccard_broadcast": 0.17647058823529413,
1322
+ "n_cells_obs": 46668,
1323
+ "n_cells_gen": 12290
1324
+ },
1325
+ "Monocyte": {
1326
+ "deg_scored": true,
1327
+ "top50_overlap": 25,
1328
+ "top50_jaccard": 0.3333333333333333,
1329
+ "obs_top_list_size": 50,
1330
+ "gen_top_list_size": 50,
1331
+ "top50_overlap_broadcast": 21,
1332
+ "top50_jaccard_broadcast": 0.26582278481012656,
1333
+ "n_cells_obs": 75478,
1334
+ "n_cells_gen": 29228
1335
+ },
1336
+ "NK cell": {
1337
+ "deg_scored": true,
1338
+ "top50_overlap": 19,
1339
+ "top50_jaccard": 0.2345679012345679,
1340
+ "obs_top_list_size": 50,
1341
+ "gen_top_list_size": 50,
1342
+ "top50_overlap_broadcast": 18,
1343
+ "top50_jaccard_broadcast": 0.21951219512195122,
1344
+ "n_cells_obs": 66389,
1345
+ "n_cells_gen": 22023
1346
+ },
1347
+ "DC": {
1348
+ "deg_scored": true,
1349
+ "top50_overlap": 7,
1350
+ "top50_jaccard": 0.08536585365853659,
1351
+ "obs_top_list_size": 50,
1352
+ "gen_top_list_size": 39,
1353
+ "top50_overlap_broadcast": 16,
1354
+ "top50_jaccard_broadcast": 0.19047619047619047,
1355
+ "n_cells_obs": 12425,
1356
+ "n_cells_gen": 1625
1357
+ }
1358
+ },
1359
+ "sum": 92,
1360
+ "sum_4type": 85,
1361
+ "max": 250,
1362
+ "mean": 18.4,
1363
+ "sum_broadcast": 89,
1364
+ "sum_broadcast_4type": 73,
1365
+ "broadcast_n_significant": 1765,
1366
+ "seconds": 0.36
1367
+ },
1368
+ "seconds": 30.8
1369
+ },
1370
+ "scsemi": {
1371
+ "arm": "scsemi",
1372
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw2/scsemi.npz",
1373
+ "npz_sha256": "ad2d37648e7f60e1179d1e912603085e44c15ae263f13b08c7d23dda07853bca",
1374
+ "receipt_verified": true,
1375
+ "generation": {
1376
+ "checkpoint": null,
1377
+ "checkpoint_sha256": null,
1378
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw2/test_raw.npz",
1379
+ "input_condition_sha256": "11ba7c4e0f734b8eeab115536093d16205a1f592833e54115aa10cafd131e466",
1380
+ "seed": 20260927,
1381
+ "steps": null,
1382
+ "support_readout": "upstream (values <= 10 normalized units zeroed by fast_semi)",
1383
+ "weights": null
1384
+ },
1385
+ "condition_for_broadcast": {
1386
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw2/test_raw.npz",
1387
+ "sha256": "11ba7c4e0f734b8eeab115536093d16205a1f592833e54115aa10cafd131e466"
1388
+ },
1389
+ "poisson": {
1390
+ "seed": 20260916,
1391
+ "rule": "whole NPZ, rows in NPZ order",
1392
+ "nnz_whole_npz": 26132102,
1393
+ "median_library_whole_npz_panel": 1357.0,
1394
+ "n_rows_whole_npz": 213000
1395
+ },
1396
+ "annotation": {
1397
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
1398
+ "zero_padded_model_genes": 0,
1399
+ "label_counts": {
1400
+ "T cell": 161194,
1401
+ "NK cell": 20426,
1402
+ "Monocyte": 17481,
1403
+ "DC": 5211,
1404
+ "B cell": 4828,
1405
+ "Other": 3860
1406
+ },
1407
+ "mean_l2_max_prob": 0.9081419917387022,
1408
+ "predict_seconds": 4.7
1409
+ },
1410
+ "n_donors": 142,
1411
+ "n_generated_cells": 213000,
1412
+ "composition": {
1413
+ "l1_mean": 0.6903180999715937,
1414
+ "l1_median": 0.6438657373708684,
1415
+ "l1_obs_loo_null_mean": 0.47851633327026316,
1416
+ "l1_generated_loo_mean_vs_observed_mean": 0.5955214663982105,
1417
+ "composition_top1": 0.007042253521126761,
1418
+ "mean_fraction_generated": {
1419
+ "T cell": 0.756779,
1420
+ "B cell": 0.022667,
1421
+ "Monocyte": 0.08207,
1422
+ "NK cell": 0.095897,
1423
+ "DC": 0.024465,
1424
+ "Other": 0.018122
1425
+ },
1426
+ "mean_fraction_observed": {
1427
+ "T cell": 0.50954,
1428
+ "B cell": 0.123023,
1429
+ "Monocyte": 0.162058,
1430
+ "NK cell": 0.163853,
1431
+ "DC": 0.028277,
1432
+ "Other": 0.013248
1433
+ }
1434
+ },
1435
+ "pseudobulk": {
1436
+ "n_genes": 5927,
1437
+ "r_median": 0.5951250403361148,
1438
+ "r_mean": 0.5994787862305065,
1439
+ "top1": 0.02112676056338028,
1440
+ "n_top1": 3,
1441
+ "own_rank_median": 46.5,
1442
+ "chance_top1": 0.007042253521126761
1443
+ },
1444
+ "precision_coverage": {
1445
+ "precision": 0.24156932931424266,
1446
+ "coverage": 0.04130557648831952,
1447
+ "density": 0.04066032403918614,
1448
+ "n_query": 21232,
1449
+ "n_reference": 21232
1450
+ },
1451
+ "precision_coverage_depth_matched": {
1452
+ "precision": 0.4188489073097212,
1453
+ "coverage": 0.15674453654860587,
1454
+ "density": 0.14232761868877167,
1455
+ "detected_median_before": {
1456
+ "R1": 347.0,
1457
+ "Q": 121.0
1458
+ },
1459
+ "detected_median_after": {
1460
+ "R1": 121.0,
1461
+ "Q": 121.0
1462
+ }
1463
+ },
1464
+ "monocyte_pct": {
1465
+ "generated_mean_over_donors": 8.207042253521125,
1466
+ "observed_mean_over_donors": 16.205826518972017,
1467
+ "generated_pooled_cells": 8.207042253521127
1468
+ },
1469
+ "median_umi_per_cell_scoring_genes": {
1470
+ "generated_pooled": 1357.0,
1471
+ "observed_pooled": 1372.0,
1472
+ "generated_mean_of_donor_medians": 1356.8626708984375,
1473
+ "observed_mean_of_donor_medians": 1311.5598591549297
1474
+ },
1475
+ "contrast": {
1476
+ "mean_cp10k": {
1477
+ "per_type": {
1478
+ "T cell": {
1479
+ "r_generated": 0.6042970449314204,
1480
+ "r_broadcast": 0.6311553277299028,
1481
+ "partial_r_generated_given_broadcast": 0.5497430792487825,
1482
+ "r_generated_vs_broadcast": 0.3165928058974416,
1483
+ "n_genes": 3036
1484
+ },
1485
+ "B cell": {
1486
+ "r_generated": 0.3654719302565729,
1487
+ "r_broadcast": 0.6245632309702648,
1488
+ "partial_r_generated_given_broadcast": 0.3334327711962793,
1489
+ "r_generated_vs_broadcast": 0.17463580433024403,
1490
+ "n_genes": 3187
1491
+ },
1492
+ "Monocyte": {
1493
+ "r_generated": 0.5175918034692244,
1494
+ "r_broadcast": 0.6837051334204964,
1495
+ "partial_r_generated_given_broadcast": 0.2542772503812919,
1496
+ "r_generated_vs_broadcast": 0.5262569433440974,
1497
+ "n_genes": 2886
1498
+ },
1499
+ "NK cell": {
1500
+ "r_generated": 0.5575081990245035,
1501
+ "r_broadcast": 0.6340215947478178,
1502
+ "partial_r_generated_given_broadcast": 0.41404892704385843,
1503
+ "r_generated_vs_broadcast": 0.4213152637937319,
1504
+ "n_genes": 2961
1505
+ }
1506
+ },
1507
+ "mean_r_generated": 0.5112172444204303,
1508
+ "mean_r_broadcast": 0.6433613217171205,
1509
+ "mean_partial_r": 0.387875506967553
1510
+ },
1511
+ "pseudobulk_log1p_cpm": {
1512
+ "per_type": {
1513
+ "T cell": {
1514
+ "r_generated": 0.39463840865700156,
1515
+ "r_broadcast": 0.6350373450250355,
1516
+ "partial_r_generated_given_broadcast": 0.29156729403447756,
1517
+ "r_generated_vs_broadcast": 0.281066114958644,
1518
+ "n_genes": 3036
1519
+ },
1520
+ "B cell": {
1521
+ "r_generated": 0.07452358118868478,
1522
+ "r_broadcast": 0.4816610289030315,
1523
+ "partial_r_generated_given_broadcast": -0.004241203809385688,
1524
+ "r_generated_vs_broadcast": 0.1623363444479944,
1525
+ "n_genes": 3187
1526
+ },
1527
+ "Monocyte": {
1528
+ "r_generated": 0.3362449283833411,
1529
+ "r_broadcast": 0.6802082395314715,
1530
+ "partial_r_generated_given_broadcast": 0.11233991986037101,
1531
+ "r_generated_vs_broadcast": 0.3824691202927535,
1532
+ "n_genes": 2886
1533
+ },
1534
+ "NK cell": {
1535
+ "r_generated": 0.302891930723384,
1536
+ "r_broadcast": 0.5753918871563406,
1537
+ "partial_r_generated_given_broadcast": 0.1733240975522633,
1538
+ "r_generated_vs_broadcast": 0.2906802599666514,
1539
+ "n_genes": 2961
1540
+ }
1541
+ },
1542
+ "mean_r_generated": 0.27707471223810287,
1543
+ "mean_r_broadcast": 0.5930746251539698,
1544
+ "mean_partial_r": 0.14324752690943154
1545
+ }
1546
+ },
1547
+ "deg_top50": {
1548
+ "types_scored": [
1549
+ "T cell",
1550
+ "B cell",
1551
+ "Monocyte",
1552
+ "NK cell",
1553
+ "DC"
1554
+ ],
1555
+ "types_not_scored": {},
1556
+ "per_type": {
1557
+ "T cell": {
1558
+ "deg_scored": true,
1559
+ "top50_overlap": 16,
1560
+ "top50_jaccard": 0.19047619047619047,
1561
+ "obs_top_list_size": 50,
1562
+ "gen_top_list_size": 50,
1563
+ "top50_overlap_broadcast": 13,
1564
+ "top50_jaccard_broadcast": 0.14942528735632185,
1565
+ "n_cells_obs": 249798,
1566
+ "n_cells_gen": 150986
1567
+ },
1568
+ "B cell": {
1569
+ "deg_scored": true,
1570
+ "top50_overlap": 7,
1571
+ "top50_jaccard": 0.07526881720430108,
1572
+ "obs_top_list_size": 50,
1573
+ "gen_top_list_size": 50,
1574
+ "top50_overlap_broadcast": 10,
1575
+ "top50_jaccard_broadcast": 0.1111111111111111,
1576
+ "n_cells_obs": 46668,
1577
+ "n_cells_gen": 4625
1578
+ },
1579
+ "Monocyte": {
1580
+ "deg_scored": true,
1581
+ "top50_overlap": 8,
1582
+ "top50_jaccard": 0.08695652173913043,
1583
+ "obs_top_list_size": 50,
1584
+ "gen_top_list_size": 50,
1585
+ "top50_overlap_broadcast": 18,
1586
+ "top50_jaccard_broadcast": 0.21951219512195122,
1587
+ "n_cells_obs": 75478,
1588
+ "n_cells_gen": 16776
1589
+ },
1590
+ "NK cell": {
1591
+ "deg_scored": true,
1592
+ "top50_overlap": 11,
1593
+ "top50_jaccard": 0.12359550561797752,
1594
+ "obs_top_list_size": 50,
1595
+ "gen_top_list_size": 50,
1596
+ "top50_overlap_broadcast": 13,
1597
+ "top50_jaccard_broadcast": 0.14942528735632185,
1598
+ "n_cells_obs": 66389,
1599
+ "n_cells_gen": 19951
1600
+ },
1601
+ "DC": {
1602
+ "deg_scored": true,
1603
+ "top50_overlap": 7,
1604
+ "top50_jaccard": 0.07526881720430108,
1605
+ "obs_top_list_size": 50,
1606
+ "gen_top_list_size": 50,
1607
+ "top50_overlap_broadcast": 11,
1608
+ "top50_jaccard_broadcast": 0.12359550561797752,
1609
+ "n_cells_obs": 12425,
1610
+ "n_cells_gen": 4948
1611
+ }
1612
+ },
1613
+ "sum": 49,
1614
+ "sum_4type": 42,
1615
+ "max": 250,
1616
+ "mean": 9.8,
1617
+ "sum_broadcast": 65,
1618
+ "sum_broadcast_4type": 54,
1619
+ "broadcast_n_significant": 2026,
1620
+ "seconds": 0.19
1621
+ },
1622
+ "seconds": 27.9
1623
+ },
1624
+ "raw": {
1625
+ "arm": "raw",
1626
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/imperial_eskd/raw.npz",
1627
+ "npz_sha256": "933d3797441cee599cc8da7a3df0a624edc71e71672f6f5bea877e88cbb53fb3",
1628
+ "receipt_verified": true,
1629
+ "generation": {
1630
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
1631
+ "checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
1632
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/imperial_eskd/conditions_raw.npz",
1633
+ "input_condition_sha256": "0ac35b61c09fb1d50ca64e314c62b1adb84f3759ae5b5b029a3496c7efade10f",
1634
+ "seed": 20260928,
1635
+ "steps": 50,
1636
+ "support_readout": "bernoulli",
1637
+ "weights": "ema"
1638
+ },
1639
+ "condition_for_broadcast": {
1640
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/imperial_eskd/conditions_raw.npz",
1641
+ "sha256": "0ac35b61c09fb1d50ca64e314c62b1adb84f3759ae5b5b029a3496c7efade10f"
1642
+ },
1643
+ "poisson": {
1644
+ "seed": 20260916,
1645
+ "rule": "whole NPZ, rows in NPZ order",
1646
+ "nnz_whole_npz": 97238557,
1647
+ "median_library_whole_npz_panel": 1294.0,
1648
+ "n_rows_whole_npz": 235500
1649
+ },
1650
+ "annotation": {
1651
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
1652
+ "zero_padded_model_genes": 0,
1653
+ "label_counts": {
1654
+ "Monocyte": 107963,
1655
+ "T cell": 64184,
1656
+ "NK cell": 19984,
1657
+ "B cell": 14432,
1658
+ "Other": 3567,
1659
+ "DC": 2870
1660
+ },
1661
+ "mean_l2_max_prob": 0.9468183402918594,
1662
+ "predict_seconds": 5.3
1663
+ },
1664
+ "n_donors": 142,
1665
+ "n_generated_cells": 213000,
1666
+ "composition": {
1667
+ "l1_mean": 0.7913025138195902,
1668
+ "l1_median": 0.7811376057160034,
1669
+ "l1_obs_loo_null_mean": 0.47851633327026316,
1670
+ "l1_generated_loo_mean_vs_observed_mean": 0.8037289234933391,
1671
+ "composition_top1": 0.014084507042253521,
1672
+ "mean_fraction_generated": {
1673
+ "T cell": 0.301333,
1674
+ "B cell": 0.067756,
1675
+ "Monocyte": 0.506869,
1676
+ "NK cell": 0.093822,
1677
+ "DC": 0.013474,
1678
+ "Other": 0.016746
1679
+ },
1680
+ "mean_fraction_observed": {
1681
+ "T cell": 0.50954,
1682
+ "B cell": 0.123023,
1683
+ "Monocyte": 0.162058,
1684
+ "NK cell": 0.163853,
1685
+ "DC": 0.028277,
1686
+ "Other": 0.013248
1687
+ }
1688
+ },
1689
+ "pseudobulk": {
1690
+ "n_genes": 5927,
1691
+ "r_median": 0.8853890205964849,
1692
+ "r_mean": 0.8796219205155791,
1693
+ "top1": 0.028169014084507043,
1694
+ "n_top1": 4,
1695
+ "own_rank_median": 42.5,
1696
+ "chance_top1": 0.007042253521126761
1697
+ },
1698
+ "precision_coverage": {
1699
+ "precision": 0.48930859080633005,
1700
+ "coverage": 0.11412019593067069,
1701
+ "density": 0.12208458929917106,
1702
+ "n_query": 21232,
1703
+ "n_reference": 21232
1704
+ },
1705
+ "precision_coverage_depth_matched": {
1706
+ "precision": 0.5175207234363225,
1707
+ "coverage": 0.15321213262999248,
1708
+ "density": 0.1351262245666918,
1709
+ "detected_median_before": {
1710
+ "R1": 347.0,
1711
+ "Q": 420.0
1712
+ },
1713
+ "detected_median_after": {
1714
+ "R1": 340.0,
1715
+ "Q": 340.0
1716
+ }
1717
+ },
1718
+ "monocyte_pct": {
1719
+ "generated_mean_over_donors": 50.68685446009389,
1720
+ "observed_mean_over_donors": 16.205826518972017,
1721
+ "generated_pooled_cells": 50.6868544600939
1722
+ },
1723
+ "median_umi_per_cell_scoring_genes": {
1724
+ "generated_pooled": 1295.0,
1725
+ "observed_pooled": 1372.0,
1726
+ "generated_mean_of_donor_medians": 1315.0528564453125,
1727
+ "observed_mean_of_donor_medians": 1311.5598591549297
1728
+ },
1729
+ "contrast": {
1730
+ "mean_cp10k": {
1731
+ "per_type": {
1732
+ "T cell": {
1733
+ "r_generated": 0.6298756968465996,
1734
+ "r_broadcast": 0.6311553277299028,
1735
+ "partial_r_generated_given_broadcast": 0.44706893742042214,
1736
+ "r_generated_vs_broadcast": 0.53314759474214,
1737
+ "n_genes": 3036
1738
+ },
1739
+ "B cell": {
1740
+ "r_generated": 0.6066447388831934,
1741
+ "r_broadcast": 0.6245632309702648,
1742
+ "partial_r_generated_given_broadcast": 0.4737860803638668,
1743
+ "r_generated_vs_broadcast": 0.4390181094162766,
1744
+ "n_genes": 3187
1745
+ },
1746
+ "Monocyte": {
1747
+ "r_generated": 0.6875859944317092,
1748
+ "r_broadcast": 0.6837051334204964,
1749
+ "partial_r_generated_given_broadcast": 0.40677949446468714,
1750
+ "r_generated_vs_broadcast": 0.6924166385338688,
1751
+ "n_genes": 2886
1752
+ },
1753
+ "NK cell": {
1754
+ "r_generated": 0.6123736038184224,
1755
+ "r_broadcast": 0.6340215947478178,
1756
+ "partial_r_generated_given_broadcast": 0.39483676030016474,
1757
+ "r_generated_vs_broadcast": 0.5702506072545342,
1758
+ "n_genes": 2961
1759
+ }
1760
+ },
1761
+ "mean_r_generated": 0.6341200084949812,
1762
+ "mean_r_broadcast": 0.6433613217171205,
1763
+ "mean_partial_r": 0.4306178181372852
1764
+ },
1765
+ "pseudobulk_log1p_cpm": {
1766
+ "per_type": {
1767
+ "T cell": {
1768
+ "r_generated": 0.43773924914616164,
1769
+ "r_broadcast": 0.6350373450250355,
1770
+ "partial_r_generated_given_broadcast": 0.16278864740041984,
1771
+ "r_generated_vs_broadcast": 0.5201922964575654,
1772
+ "n_genes": 3036
1773
+ },
1774
+ "B cell": {
1775
+ "r_generated": 0.3682117856392941,
1776
+ "r_broadcast": 0.4816610289030315,
1777
+ "partial_r_generated_given_broadcast": 0.23229543091621155,
1778
+ "r_generated_vs_broadcast": 0.3721748664424604,
1779
+ "n_genes": 3187
1780
+ },
1781
+ "Monocyte": {
1782
+ "r_generated": 0.6322319518162953,
1783
+ "r_broadcast": 0.6802082395314715,
1784
+ "partial_r_generated_given_broadcast": 0.3518205086638999,
1785
+ "r_generated_vs_broadcast": 0.6373006217702858,
1786
+ "n_genes": 2886
1787
+ },
1788
+ "NK cell": {
1789
+ "r_generated": 0.3936876266997188,
1790
+ "r_broadcast": 0.5753918871563406,
1791
+ "partial_r_generated_given_broadcast": 0.16689556038273892,
1792
+ "r_generated_vs_broadcast": 0.4755148090075675,
1793
+ "n_genes": 2961
1794
+ }
1795
+ },
1796
+ "mean_r_generated": 0.4579676533253675,
1797
+ "mean_r_broadcast": 0.5930746251539698,
1798
+ "mean_partial_r": 0.22845003684081755
1799
+ }
1800
+ },
1801
+ "deg_top50": {
1802
+ "types_scored": [
1803
+ "T cell",
1804
+ "B cell",
1805
+ "Monocyte",
1806
+ "NK cell",
1807
+ "DC"
1808
+ ],
1809
+ "types_not_scored": {},
1810
+ "per_type": {
1811
+ "T cell": {
1812
+ "deg_scored": true,
1813
+ "top50_overlap": 30,
1814
+ "top50_jaccard": 0.42857142857142855,
1815
+ "obs_top_list_size": 50,
1816
+ "gen_top_list_size": 50,
1817
+ "top50_overlap_broadcast": 13,
1818
+ "top50_jaccard_broadcast": 0.14942528735632185,
1819
+ "n_cells_obs": 249798,
1820
+ "n_cells_gen": 60015
1821
+ },
1822
+ "B cell": {
1823
+ "deg_scored": true,
1824
+ "top50_overlap": 18,
1825
+ "top50_jaccard": 0.21951219512195122,
1826
+ "obs_top_list_size": 50,
1827
+ "gen_top_list_size": 50,
1828
+ "top50_overlap_broadcast": 10,
1829
+ "top50_jaccard_broadcast": 0.1111111111111111,
1830
+ "n_cells_obs": 46668,
1831
+ "n_cells_gen": 13538
1832
+ },
1833
+ "Monocyte": {
1834
+ "deg_scored": true,
1835
+ "top50_overlap": 25,
1836
+ "top50_jaccard": 0.3333333333333333,
1837
+ "obs_top_list_size": 50,
1838
+ "gen_top_list_size": 50,
1839
+ "top50_overlap_broadcast": 18,
1840
+ "top50_jaccard_broadcast": 0.21951219512195122,
1841
+ "n_cells_obs": 75478,
1842
+ "n_cells_gen": 102736
1843
+ },
1844
+ "NK cell": {
1845
+ "deg_scored": true,
1846
+ "top50_overlap": 18,
1847
+ "top50_jaccard": 0.21951219512195122,
1848
+ "obs_top_list_size": 50,
1849
+ "gen_top_list_size": 50,
1850
+ "top50_overlap_broadcast": 13,
1851
+ "top50_jaccard_broadcast": 0.14942528735632185,
1852
+ "n_cells_obs": 66389,
1853
+ "n_cells_gen": 18654
1854
+ },
1855
+ "DC": {
1856
+ "deg_scored": true,
1857
+ "top50_overlap": 8,
1858
+ "top50_jaccard": 0.08695652173913043,
1859
+ "obs_top_list_size": 50,
1860
+ "gen_top_list_size": 50,
1861
+ "top50_overlap_broadcast": 11,
1862
+ "top50_jaccard_broadcast": 0.12359550561797752,
1863
+ "n_cells_obs": 12425,
1864
+ "n_cells_gen": 2685
1865
+ }
1866
+ },
1867
+ "sum": 99,
1868
+ "sum_4type": 91,
1869
+ "max": 250,
1870
+ "mean": 19.8,
1871
+ "sum_broadcast": 65,
1872
+ "sum_broadcast_4type": 54,
1873
+ "broadcast_n_significant": 2026,
1874
+ "seconds": 0.55
1875
+ },
1876
+ "seconds": 38.1
1877
+ },
1878
+ "refcal": {
1879
+ "arm": "refcal",
1880
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/imperial_eskd/refcal.npz",
1881
+ "npz_sha256": "ba80faf1dc9942da1935d4f73e780cc67289eadf6e4a8f51d6a9035de4d3fcff",
1882
+ "receipt_verified": true,
1883
+ "generation": {
1884
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
1885
+ "checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
1886
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/imperial_eskd/conditions_refcal.npz",
1887
+ "input_condition_sha256": "85e8a48cb6168da565b8e0d953774e29380ed142a9f0afdca93abf157cd8c35e",
1888
+ "seed": 20260928,
1889
+ "steps": 50,
1890
+ "support_readout": "bernoulli",
1891
+ "weights": "ema"
1892
+ },
1893
+ "condition_for_broadcast": {
1894
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/imperial_eskd/conditions_refcal.npz",
1895
+ "sha256": "85e8a48cb6168da565b8e0d953774e29380ed142a9f0afdca93abf157cd8c35e"
1896
+ },
1897
+ "poisson": {
1898
+ "seed": 20260916,
1899
+ "rule": "whole NPZ, rows in NPZ order",
1900
+ "nnz_whole_npz": 57316417,
1901
+ "median_library_whole_npz_panel": 1522.0,
1902
+ "n_rows_whole_npz": 235500
1903
+ },
1904
+ "annotation": {
1905
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
1906
+ "zero_padded_model_genes": 0,
1907
+ "label_counts": {
1908
+ "T cell": 116011,
1909
+ "Monocyte": 56057,
1910
+ "B cell": 16859,
1911
+ "NK cell": 14474,
1912
+ "Other": 6194,
1913
+ "DC": 3405
1914
+ },
1915
+ "mean_l2_max_prob": 0.9334809368386375,
1916
+ "predict_seconds": 5.1
1917
+ },
1918
+ "n_donors": 142,
1919
+ "n_generated_cells": 213000,
1920
+ "composition": {
1921
+ "l1_mean": 0.5035736748554334,
1922
+ "l1_median": 0.46096223902081124,
1923
+ "l1_obs_loo_null_mean": 0.47851633327026316,
1924
+ "l1_generated_loo_mean_vs_observed_mean": 0.5475948513714951,
1925
+ "composition_top1": 0.04929577464788732,
1926
+ "mean_fraction_generated": {
1927
+ "T cell": 0.544653,
1928
+ "B cell": 0.07915,
1929
+ "Monocyte": 0.263178,
1930
+ "NK cell": 0.067953,
1931
+ "DC": 0.015986,
1932
+ "Other": 0.02908
1933
+ },
1934
+ "mean_fraction_observed": {
1935
+ "T cell": 0.50954,
1936
+ "B cell": 0.123023,
1937
+ "Monocyte": 0.162058,
1938
+ "NK cell": 0.163853,
1939
+ "DC": 0.028277,
1940
+ "Other": 0.013248
1941
+ }
1942
+ },
1943
+ "pseudobulk": {
1944
+ "n_genes": 5927,
1945
+ "r_median": 0.8521668347812354,
1946
+ "r_mean": 0.8503389606705036,
1947
+ "top1": 0.028169014084507043,
1948
+ "n_top1": 4,
1949
+ "own_rank_median": 42.5,
1950
+ "chance_top1": 0.007042253521126761
1951
+ },
1952
+ "precision_coverage": {
1953
+ "precision": 0.8204596834966089,
1954
+ "coverage": 0.36379050489826675,
1955
+ "density": 0.48929917106254706,
1956
+ "n_query": 21232,
1957
+ "n_reference": 21232
1958
+ },
1959
+ "precision_coverage_depth_matched": {
1960
+ "precision": 0.8311981914091937,
1961
+ "coverage": 0.5074415975885456,
1962
+ "density": 0.5885220422004521,
1963
+ "detected_median_before": {
1964
+ "R1": 347.0,
1965
+ "Q": 233.0
1966
+ },
1967
+ "detected_median_after": {
1968
+ "R1": 233.0,
1969
+ "Q": 233.0
1970
+ }
1971
+ },
1972
+ "monocyte_pct": {
1973
+ "generated_mean_over_donors": 26.317840375586854,
1974
+ "observed_mean_over_donors": 16.205826518972017,
1975
+ "generated_pooled_cells": 26.317840375586854
1976
+ },
1977
+ "median_umi_per_cell_scoring_genes": {
1978
+ "generated_pooled": 1518.0,
1979
+ "observed_pooled": 1372.0,
1980
+ "generated_mean_of_donor_medians": 1540.1021728515625,
1981
+ "observed_mean_of_donor_medians": 1311.5598591549297
1982
+ },
1983
+ "contrast": {
1984
+ "mean_cp10k": {
1985
+ "per_type": {
1986
+ "T cell": {
1987
+ "r_generated": 0.5263710274560865,
1988
+ "r_broadcast": 0.6268336903883583,
1989
+ "partial_r_generated_given_broadcast": 0.3013883853759045,
1990
+ "r_generated_vs_broadcast": 0.5196603278351689,
1991
+ "n_genes": 3036
1992
+ },
1993
+ "B cell": {
1994
+ "r_generated": 0.42811602764030066,
1995
+ "r_broadcast": 0.5798515746562791,
1996
+ "partial_r_generated_given_broadcast": 0.22519454527912847,
1997
+ "r_generated_vs_broadcast": 0.4568610638404226,
1998
+ "n_genes": 3187
1999
+ },
2000
+ "Monocyte": {
2001
+ "r_generated": 0.5683658674310538,
2002
+ "r_broadcast": 0.5487400393061043,
2003
+ "partial_r_generated_given_broadcast": 0.37333116738493755,
2004
+ "r_generated_vs_broadcast": 0.567437652618543,
2005
+ "n_genes": 2886
2006
+ },
2007
+ "NK cell": {
2008
+ "r_generated": 0.4664565232486705,
2009
+ "r_broadcast": 0.5727166768635839,
2010
+ "partial_r_generated_given_broadcast": 0.2858297457619563,
2011
+ "r_generated_vs_broadcast": 0.44887559900968427,
2012
+ "n_genes": 2961
2013
+ }
2014
+ },
2015
+ "mean_r_generated": 0.4973273614440279,
2016
+ "mean_r_broadcast": 0.5820354953035813,
2017
+ "mean_partial_r": 0.2964359609504817
2018
+ },
2019
+ "pseudobulk_log1p_cpm": {
2020
+ "per_type": {
2021
+ "T cell": {
2022
+ "r_generated": 0.468684663900347,
2023
+ "r_broadcast": 0.6339482595091982,
2024
+ "partial_r_generated_given_broadcast": 0.1957447664467542,
2025
+ "r_generated_vs_broadcast": 0.5380222790572539,
2026
+ "n_genes": 3036
2027
+ },
2028
+ "B cell": {
2029
+ "r_generated": 0.3406871599758421,
2030
+ "r_broadcast": 0.48417800731897287,
2031
+ "partial_r_generated_given_broadcast": 0.16843227567912417,
2032
+ "r_generated_vs_broadcast": 0.4286427180955453,
2033
+ "n_genes": 3187
2034
+ },
2035
+ "Monocyte": {
2036
+ "r_generated": 0.45034730080606566,
2037
+ "r_broadcast": 0.6668646112573656,
2038
+ "partial_r_generated_given_broadcast": 0.11581618421987536,
2039
+ "r_generated_vs_broadcast": 0.5688855375109219,
2040
+ "n_genes": 2886
2041
+ },
2042
+ "NK cell": {
2043
+ "r_generated": 0.282741866803266,
2044
+ "r_broadcast": 0.5734166571951365,
2045
+ "partial_r_generated_given_broadcast": 0.10074317290842048,
2046
+ "r_generated_vs_broadcast": 0.35872685740830723,
2047
+ "n_genes": 2961
2048
+ }
2049
+ },
2050
+ "mean_r_generated": 0.3856152478713802,
2051
+ "mean_r_broadcast": 0.5896018838201683,
2052
+ "mean_partial_r": 0.14518409981354355
2053
+ }
2054
+ },
2055
+ "deg_top50": {
2056
+ "types_scored": [
2057
+ "T cell",
2058
+ "B cell",
2059
+ "Monocyte",
2060
+ "NK cell",
2061
+ "DC"
2062
+ ],
2063
+ "types_not_scored": {},
2064
+ "per_type": {
2065
+ "T cell": {
2066
+ "deg_scored": true,
2067
+ "top50_overlap": 17,
2068
+ "top50_jaccard": 0.20481927710843373,
2069
+ "obs_top_list_size": 50,
2070
+ "gen_top_list_size": 50,
2071
+ "top50_overlap_broadcast": 19,
2072
+ "top50_jaccard_broadcast": 0.2345679012345679,
2073
+ "n_cells_obs": 249798,
2074
+ "n_cells_gen": 108858
2075
+ },
2076
+ "B cell": {
2077
+ "deg_scored": true,
2078
+ "top50_overlap": 14,
2079
+ "top50_jaccard": 0.16279069767441862,
2080
+ "obs_top_list_size": 50,
2081
+ "gen_top_list_size": 50,
2082
+ "top50_overlap_broadcast": 16,
2083
+ "top50_jaccard_broadcast": 0.19047619047619047,
2084
+ "n_cells_obs": 46668,
2085
+ "n_cells_gen": 15819
2086
+ },
2087
+ "Monocyte": {
2088
+ "deg_scored": true,
2089
+ "top50_overlap": 18,
2090
+ "top50_jaccard": 0.21951219512195122,
2091
+ "obs_top_list_size": 50,
2092
+ "gen_top_list_size": 50,
2093
+ "top50_overlap_broadcast": 19,
2094
+ "top50_jaccard_broadcast": 0.2345679012345679,
2095
+ "n_cells_obs": 75478,
2096
+ "n_cells_gen": 53668
2097
+ },
2098
+ "NK cell": {
2099
+ "deg_scored": true,
2100
+ "top50_overlap": 7,
2101
+ "top50_jaccard": 0.07526881720430108,
2102
+ "obs_top_list_size": 50,
2103
+ "gen_top_list_size": 50,
2104
+ "top50_overlap_broadcast": 18,
2105
+ "top50_jaccard_broadcast": 0.21951219512195122,
2106
+ "n_cells_obs": 66389,
2107
+ "n_cells_gen": 13511
2108
+ },
2109
+ "DC": {
2110
+ "deg_scored": true,
2111
+ "top50_overlap": 6,
2112
+ "top50_jaccard": 0.06382978723404255,
2113
+ "obs_top_list_size": 50,
2114
+ "gen_top_list_size": 50,
2115
+ "top50_overlap_broadcast": 16,
2116
+ "top50_jaccard_broadcast": 0.19047619047619047,
2117
+ "n_cells_obs": 12425,
2118
+ "n_cells_gen": 3204
2119
+ }
2120
+ },
2121
+ "sum": 62,
2122
+ "sum_4type": 56,
2123
+ "max": 250,
2124
+ "mean": 12.4,
2125
+ "sum_broadcast": 88,
2126
+ "sum_broadcast_4type": 72,
2127
+ "broadcast_n_significant": 2186,
2128
+ "seconds": 0.35
2129
+ },
2130
+ "seconds": 33.1
2131
+ }
2132
+ },
2133
+ "code_sha256": {
2134
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
2135
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
2136
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
2137
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
2138
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
2139
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
2140
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
2141
+ },
2142
+ "seconds": 180.7
2143
+ }
paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/aba3f711c4e558ba/summary.json ADDED
@@ -0,0 +1,751 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "paired_ft_scores.v1",
3
+ "dataset": "giroux2022",
4
+ "written_utc": "2026-10-15T06:52:52.652114+00:00",
5
+ "command": [
6
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
7
+ "--dataset",
8
+ "giroux2022",
9
+ "--out",
10
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw4/score",
11
+ "--arm",
12
+ "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw4/lora.npz",
13
+ "--condition",
14
+ "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw4/test_raw.npz",
15
+ "--donors",
16
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw4/test_samples.txt",
17
+ "--threads",
18
+ "2",
19
+ "--case-groups",
20
+ "severe",
21
+ "--control-groups",
22
+ "mild",
23
+ "--exclude-genes",
24
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv"
25
+ ],
26
+ "arms": [
27
+ "lora"
28
+ ],
29
+ "donors": [
30
+ "450905_d0",
31
+ "450905_d14",
32
+ "7085CA_d0",
33
+ "7085CA_d7",
34
+ "7085CA_d14",
35
+ "B85D75_d0",
36
+ "B85D75_d7",
37
+ "180E1A_d0",
38
+ "180E1A_d7",
39
+ "180E1A_d14"
40
+ ],
41
+ "n_donors": 10,
42
+ "reference": {
43
+ "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
44
+ "reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
45
+ "features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
46
+ "n_r1_cells": 1500,
47
+ "pca": {
48
+ "n_components": 50,
49
+ "explained_variance_ratio_sum": 0.2558751106262207,
50
+ "n_fit_cells": 1500
51
+ },
52
+ "r2_control": {
53
+ "precision": 0.9993333333333333,
54
+ "coverage": 1.0,
55
+ "density": 6.356199999999999,
56
+ "n_query": 1500,
57
+ "depth_matched": {
58
+ "precision": 0.9986666666666667,
59
+ "coverage": 1.0,
60
+ "density": 6.294933333333334
61
+ }
62
+ },
63
+ "observed_l1_loo_null_mean": 0.4883353341880966
64
+ },
65
+ "contrast_definition": {
66
+ "enabled": true,
67
+ "rule": "explicit --case-groups / --control-groups",
68
+ "group_source": "features groups",
69
+ "case_groups": [
70
+ "severe"
71
+ ],
72
+ "control_groups": [
73
+ "mild"
74
+ ],
75
+ "n_case_donors": 5,
76
+ "n_control_donors": 5,
77
+ "n_donors_in_neither": 0,
78
+ "case": [
79
+ false,
80
+ false,
81
+ false,
82
+ false,
83
+ false,
84
+ true,
85
+ true,
86
+ true,
87
+ true,
88
+ true
89
+ ],
90
+ "ctrl": [
91
+ true,
92
+ true,
93
+ true,
94
+ true,
95
+ true,
96
+ false,
97
+ false,
98
+ false,
99
+ false,
100
+ false
101
+ ],
102
+ "groups": [
103
+ "mild",
104
+ "mild",
105
+ "mild",
106
+ "mild",
107
+ "mild",
108
+ "severe",
109
+ "severe",
110
+ "severe",
111
+ "severe",
112
+ "severe"
113
+ ]
114
+ },
115
+ "deg_definition": {
116
+ "enabled": true,
117
+ "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
118
+ "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
119
+ "functions": [
120
+ "welch_bh_deg",
121
+ "top_deg_genes",
122
+ "jaccard"
123
+ ],
124
+ "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
125
+ "top_n": 50,
126
+ "fdr": 0.05,
127
+ "n_genes": 5498,
128
+ "types": [
129
+ "T cell",
130
+ "B cell",
131
+ "Monocyte",
132
+ "NK cell",
133
+ "DC"
134
+ ],
135
+ "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022/deg_reference.npz",
136
+ "aggregates_sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e",
137
+ "aggregates_note": null,
138
+ "types_not_scored_observed": [],
139
+ "observed": {
140
+ "T cell": {
141
+ "n_significant": 0,
142
+ "n_tested": 5182,
143
+ "n_case_donors": 5,
144
+ "n_control_donors": 5,
145
+ "n_cells": 55877,
146
+ "top_list_size": 0
147
+ },
148
+ "B cell": {
149
+ "n_significant": 0,
150
+ "n_tested": 4807,
151
+ "n_case_donors": 5,
152
+ "n_control_donors": 5,
153
+ "n_cells": 4890,
154
+ "top_list_size": 0
155
+ },
156
+ "Monocyte": {
157
+ "n_significant": 1,
158
+ "n_tested": 5109,
159
+ "n_case_donors": 5,
160
+ "n_control_donors": 5,
161
+ "n_cells": 21294,
162
+ "top_list_size": 1
163
+ },
164
+ "NK cell": {
165
+ "n_significant": 0,
166
+ "n_tested": 4929,
167
+ "n_case_donors": 5,
168
+ "n_control_donors": 5,
169
+ "n_cells": 12579,
170
+ "top_list_size": 0
171
+ },
172
+ "DC": {
173
+ "n_significant": 0,
174
+ "n_tested": 4638,
175
+ "n_case_donors": 5,
176
+ "n_control_donors": 5,
177
+ "n_cells": 1773,
178
+ "top_list_size": 0
179
+ }
180
+ },
181
+ "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
182
+ },
183
+ "headline": {
184
+ "lora": {
185
+ "comp_l1": 0.2575259905456889,
186
+ "comp_l1_obs_loo_null": 0.4883353341880966,
187
+ "precision": 1.0,
188
+ "coverage": 0.9693333333333334,
189
+ "precision_dm": 0.9993333333333333,
190
+ "coverage_dm": 0.9933333333333333,
191
+ "pb_r_median": 0.8683118625307109,
192
+ "pb_top1": 0.2,
193
+ "mono_pct_gen": 18.519999999999996,
194
+ "mono_pct_obs": 21.511770225768277,
195
+ "median_umi_gen": 483.0,
196
+ "median_umi_obs": 447.0,
197
+ "contrast_mean_cp10k_r_gen": 0.4421883183219261,
198
+ "contrast_pseudobulk_log1p_cpm_r_gen": 0.20339089787597897,
199
+ "contrast_mean_cp10k_r_broadcast": 0.6280870820074911,
200
+ "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5956357335570572,
201
+ "deg_top50_T": 0,
202
+ "deg_top50_B": 0,
203
+ "deg_top50_Mono": 0,
204
+ "deg_top50_NK": 0,
205
+ "deg_top50_DC": 0,
206
+ "deg_top50_sum": 0,
207
+ "deg_top50_max": 1,
208
+ "deg_top50_sum_4type": 0,
209
+ "deg_top50_sum_broadcast": 0,
210
+ "seconds": 4.7
211
+ }
212
+ },
213
+ "per_arm": {
214
+ "lora": {
215
+ "arm": "lora",
216
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw4/lora.npz",
217
+ "npz_sha256": "7dc39e3963038c6e4c41d2681b5be1135bce425de1514732c4b91af899249afc",
218
+ "receipt_verified": true,
219
+ "generation": {
220
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw4/lora/checkpoint_ft.pt",
221
+ "checkpoint_sha256": "ccd39f782235579aae57cd576348a44f26f57e5c62d068b5d2554a6e87c68ea4",
222
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw4/test_raw.npz",
223
+ "input_condition_sha256": "1339e7631cd54c77bef770b2248bdc2ca560a6dc70e244ed61cd4d38a835bf3f",
224
+ "seed": 20260928,
225
+ "steps": 50,
226
+ "support_readout": "bernoulli",
227
+ "weights": "ema"
228
+ },
229
+ "condition_for_broadcast": {
230
+ "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw4/test_raw.npz",
231
+ "sha256": "1339e7631cd54c77bef770b2248bdc2ca560a6dc70e244ed61cd4d38a835bf3f"
232
+ },
233
+ "poisson": {
234
+ "seed": 20260916,
235
+ "rule": "whole NPZ, rows in NPZ order",
236
+ "nnz_whole_npz": 3706513,
237
+ "median_library_whole_npz_panel": 1449.5,
238
+ "n_rows_whole_npz": 15000
239
+ },
240
+ "annotation": {
241
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
242
+ "zero_padded_model_genes": 0,
243
+ "label_counts": {
244
+ "T cell": 9321,
245
+ "Monocyte": 2778,
246
+ "NK cell": 1322,
247
+ "B cell": 776,
248
+ "Other": 428,
249
+ "DC": 375
250
+ },
251
+ "mean_l2_max_prob": 0.8912148882766565,
252
+ "predict_seconds": 3.1
253
+ },
254
+ "n_donors": 10,
255
+ "n_generated_cells": 15000,
256
+ "composition": {
257
+ "l1_mean": 0.2575259905456889,
258
+ "l1_median": 0.23397108212507342,
259
+ "l1_obs_loo_null_mean": 0.4883353341880966,
260
+ "l1_generated_loo_mean_vs_observed_mean": 0.4169110929337795,
261
+ "composition_top1": 0.1,
262
+ "mean_fraction_generated": {
263
+ "T cell": 0.6214,
264
+ "B cell": 0.051733,
265
+ "Monocyte": 0.1852,
266
+ "NK cell": 0.088133,
267
+ "DC": 0.025,
268
+ "Other": 0.028533
269
+ },
270
+ "mean_fraction_observed": {
271
+ "T cell": 0.544094,
272
+ "B cell": 0.047144,
273
+ "Monocyte": 0.215118,
274
+ "NK cell": 0.125669,
275
+ "DC": 0.017383,
276
+ "Other": 0.050593
277
+ }
278
+ },
279
+ "pseudobulk": {
280
+ "n_genes": 5563,
281
+ "r_median": 0.8683118625307109,
282
+ "r_mean": 0.8703664967065722,
283
+ "top1": 0.2,
284
+ "n_top1": 2,
285
+ "own_rank_median": 2.0,
286
+ "chance_top1": 0.1
287
+ },
288
+ "precision_coverage": {
289
+ "precision": 1.0,
290
+ "coverage": 0.9693333333333334,
291
+ "density": 5.388133333333333,
292
+ "n_query": 1500,
293
+ "n_reference": 1500
294
+ },
295
+ "precision_coverage_depth_matched": {
296
+ "precision": 0.9993333333333333,
297
+ "coverage": 0.9933333333333333,
298
+ "density": 3.3584666666666663,
299
+ "detected_median_before": {
300
+ "R1": 252.0,
301
+ "Q": 170.0
302
+ },
303
+ "detected_median_after": {
304
+ "R1": 170.0,
305
+ "Q": 170.0
306
+ }
307
+ },
308
+ "monocyte_pct": {
309
+ "generated_mean_over_donors": 18.519999999999996,
310
+ "observed_mean_over_donors": 21.511770225768277,
311
+ "generated_pooled_cells": 18.52
312
+ },
313
+ "median_umi_per_cell_scoring_genes": {
314
+ "generated_pooled": 483.0,
315
+ "observed_pooled": 447.0,
316
+ "generated_mean_of_donor_medians": 489.6000061035156,
317
+ "observed_mean_of_donor_medians": 470.35
318
+ },
319
+ "contrast": {
320
+ "mean_cp10k": {
321
+ "per_type": {
322
+ "T cell": {
323
+ "r_generated": 0.6631265853728078,
324
+ "r_broadcast": 0.7344048019011988,
325
+ "partial_r_generated_given_broadcast": 0.46704952496141494,
326
+ "r_generated_vs_broadcast": 0.5395235474343575,
327
+ "n_genes": 2870
328
+ },
329
+ "B cell": {
330
+ "r_generated": 0.2925989610866921,
331
+ "r_broadcast": 0.565884313340693,
332
+ "partial_r_generated_given_broadcast": 0.1608945387708825,
333
+ "r_generated_vs_broadcast": 0.2929270554715147,
334
+ "n_genes": 3061
335
+ },
336
+ "Monocyte": {
337
+ "r_generated": 0.3657364980723787,
338
+ "r_broadcast": 0.5561945453231222,
339
+ "partial_r_generated_given_broadcast": 0.1509583855847481,
340
+ "r_generated_vs_broadcast": 0.4569352941809483,
341
+ "n_genes": 3017
342
+ },
343
+ "NK cell": {
344
+ "r_generated": 0.44729122875582594,
345
+ "r_broadcast": 0.6558646674649503,
346
+ "partial_r_generated_given_broadcast": 0.28422417103254227,
347
+ "r_generated_vs_broadcast": 0.3792998523868367,
348
+ "n_genes": 2940
349
+ }
350
+ },
351
+ "mean_r_generated": 0.4421883183219261,
352
+ "mean_r_broadcast": 0.6280870820074911,
353
+ "mean_partial_r": 0.26578165508739693
354
+ },
355
+ "pseudobulk_log1p_cpm": {
356
+ "per_type": {
357
+ "T cell": {
358
+ "r_generated": 0.371485040719346,
359
+ "r_broadcast": 0.6900634955326531,
360
+ "partial_r_generated_given_broadcast": 0.2527165207639843,
361
+ "r_generated_vs_broadcast": 0.28421214480261103,
362
+ "n_genes": 2870
363
+ },
364
+ "B cell": {
365
+ "r_generated": 0.11707659203544454,
366
+ "r_broadcast": 0.4704332503129004,
367
+ "partial_r_generated_given_broadcast": 0.06414563860145382,
368
+ "r_generated_vs_broadcast": 0.12955989535222984,
369
+ "n_genes": 3061
370
+ },
371
+ "Monocyte": {
372
+ "r_generated": 0.17028474662959694,
373
+ "r_broadcast": 0.6573550923248582,
374
+ "partial_r_generated_given_broadcast": 0.030778841960678104,
375
+ "r_generated_vs_broadcast": 0.22466293572298648,
376
+ "n_genes": 3017
377
+ },
378
+ "NK cell": {
379
+ "r_generated": 0.15471721211952835,
380
+ "r_broadcast": 0.5646910960578172,
381
+ "partial_r_generated_given_broadcast": 0.0772087764689645,
382
+ "r_generated_vs_broadcast": 0.16264663479990635,
383
+ "n_genes": 2940
384
+ }
385
+ },
386
+ "mean_r_generated": 0.20339089787597897,
387
+ "mean_r_broadcast": 0.5956357335570572,
388
+ "mean_partial_r": 0.10621244444877019
389
+ }
390
+ },
391
+ "deg_top50": {
392
+ "types_scored": [
393
+ "T cell",
394
+ "B cell",
395
+ "Monocyte",
396
+ "NK cell",
397
+ "DC"
398
+ ],
399
+ "types_not_scored": {},
400
+ "per_type": {
401
+ "T cell": {
402
+ "deg_scored": true,
403
+ "top50_overlap": 0,
404
+ "top50_jaccard": 0.0,
405
+ "obs_top_list_size": 0,
406
+ "gen_top_list_size": 3,
407
+ "top50_overlap_broadcast": 0,
408
+ "top50_jaccard_broadcast": 0.0,
409
+ "n_cells_obs": 55877,
410
+ "n_cells_gen": 9321
411
+ },
412
+ "B cell": {
413
+ "deg_scored": true,
414
+ "top50_overlap": 0,
415
+ "top50_jaccard": null,
416
+ "obs_top_list_size": 0,
417
+ "gen_top_list_size": 0,
418
+ "top50_overlap_broadcast": 0,
419
+ "top50_jaccard_broadcast": 0.0,
420
+ "n_cells_obs": 4890,
421
+ "n_cells_gen": 776
422
+ },
423
+ "Monocyte": {
424
+ "deg_scored": true,
425
+ "top50_overlap": 0,
426
+ "top50_jaccard": 0.0,
427
+ "obs_top_list_size": 1,
428
+ "gen_top_list_size": 0,
429
+ "top50_overlap_broadcast": 0,
430
+ "top50_jaccard_broadcast": 0.0,
431
+ "n_cells_obs": 21294,
432
+ "n_cells_gen": 2778
433
+ },
434
+ "NK cell": {
435
+ "deg_scored": true,
436
+ "top50_overlap": 0,
437
+ "top50_jaccard": null,
438
+ "obs_top_list_size": 0,
439
+ "gen_top_list_size": 0,
440
+ "top50_overlap_broadcast": 0,
441
+ "top50_jaccard_broadcast": 0.0,
442
+ "n_cells_obs": 12579,
443
+ "n_cells_gen": 1322
444
+ },
445
+ "DC": {
446
+ "deg_scored": true,
447
+ "top50_overlap": 0,
448
+ "top50_jaccard": null,
449
+ "obs_top_list_size": 0,
450
+ "gen_top_list_size": 0,
451
+ "top50_overlap_broadcast": 0,
452
+ "top50_jaccard_broadcast": 0.0,
453
+ "n_cells_obs": 1773,
454
+ "n_cells_gen": 375
455
+ }
456
+ },
457
+ "sum": 0,
458
+ "sum_4type": 0,
459
+ "max": 1,
460
+ "mean": 0.0,
461
+ "sum_broadcast": 0,
462
+ "sum_broadcast_4type": 0,
463
+ "broadcast_n_significant": 1,
464
+ "seconds": 0.03
465
+ },
466
+ "seconds": 4.7
467
+ }
468
+ },
469
+ "code_sha256": {
470
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
471
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
472
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
473
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
474
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
475
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
476
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
477
+ },
478
+ "seconds": 5.4,
479
+ "gene_exclusion": {
480
+ "file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv",
481
+ "sha256": "e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de",
482
+ "n_listed": 196,
483
+ "n_scoring_genes": 5563,
484
+ "n_dropped_from_scoring_genes": 65,
485
+ "n_scoring_genes_kept": 5498,
486
+ "dropped": [
487
+ {
488
+ "gene_id": "ENSG00000124343",
489
+ "symbol": "XG"
490
+ },
491
+ {
492
+ "gene_id": "ENSG00000183943",
493
+ "symbol": "PRKX"
494
+ },
495
+ {
496
+ "gene_id": "ENSG00000146938",
497
+ "symbol": "NLGN4X"
498
+ },
499
+ {
500
+ "gene_id": "ENSG00000130021",
501
+ "symbol": "PUDP"
502
+ },
503
+ {
504
+ "gene_id": "ENSG00000101846",
505
+ "symbol": "STS"
506
+ },
507
+ {
508
+ "gene_id": "ENSG00000011201",
509
+ "symbol": "ANOS1"
510
+ },
511
+ {
512
+ "gene_id": "ENSG00000177138",
513
+ "symbol": "FAM9B"
514
+ },
515
+ {
516
+ "gene_id": "ENSG00000101849",
517
+ "symbol": "TBL1X"
518
+ },
519
+ {
520
+ "gene_id": "ENSG00000146950",
521
+ "symbol": "SHROOM2"
522
+ },
523
+ {
524
+ "gene_id": "ENSG00000182287",
525
+ "symbol": "AP1S2"
526
+ },
527
+ {
528
+ "gene_id": "ENSG00000047230",
529
+ "symbol": "CTPS2"
530
+ },
531
+ {
532
+ "gene_id": "ENSG00000086712",
533
+ "symbol": "TXLNG"
534
+ },
535
+ {
536
+ "gene_id": "ENSG00000188158",
537
+ "symbol": "NHS"
538
+ },
539
+ {
540
+ "gene_id": "ENSG00000177324",
541
+ "symbol": "BEND2"
542
+ },
543
+ {
544
+ "gene_id": "ENSG00000086717",
545
+ "symbol": "PPEF1"
546
+ },
547
+ {
548
+ "gene_id": "ENSG00000149970",
549
+ "symbol": "CNKSR2"
550
+ },
551
+ {
552
+ "gene_id": "ENSG00000102174",
553
+ "symbol": "PHEX"
554
+ },
555
+ {
556
+ "gene_id": "ENSG00000165186",
557
+ "symbol": "PTCHD1"
558
+ },
559
+ {
560
+ "gene_id": "ENSG00000169306",
561
+ "symbol": "IL1RAPL1"
562
+ },
563
+ {
564
+ "gene_id": "ENSG00000147036",
565
+ "symbol": "LANCL3"
566
+ },
567
+ {
568
+ "gene_id": "ENSG00000047597",
569
+ "symbol": "XK"
570
+ },
571
+ {
572
+ "gene_id": "ENSG00000180182",
573
+ "symbol": "MED14"
574
+ },
575
+ {
576
+ "gene_id": "ENSG00000183690",
577
+ "symbol": "EFHC2"
578
+ },
579
+ {
580
+ "gene_id": "ENSG00000147050",
581
+ "symbol": "KDM6A"
582
+ },
583
+ {
584
+ "gene_id": "ENSG00000147117",
585
+ "symbol": "ZNF157"
586
+ },
587
+ {
588
+ "gene_id": "ENSG00000102265",
589
+ "symbol": "TIMP1"
590
+ },
591
+ {
592
+ "gene_id": "ENSG00000158423",
593
+ "symbol": "RIBC1"
594
+ },
595
+ {
596
+ "gene_id": "ENSG00000155659",
597
+ "symbol": "VSIG4"
598
+ },
599
+ {
600
+ "gene_id": "ENSG00000204165",
601
+ "symbol": "CXorf65"
602
+ },
603
+ {
604
+ "gene_id": "ENSG00000204131",
605
+ "symbol": "NHSL2"
606
+ },
607
+ {
608
+ "gene_id": "ENSG00000078589",
609
+ "symbol": "P2RY10"
610
+ },
611
+ {
612
+ "gene_id": "ENSG00000147138",
613
+ "symbol": "GPR174"
614
+ },
615
+ {
616
+ "gene_id": "ENSG00000198157",
617
+ "symbol": "HMGN5"
618
+ },
619
+ {
620
+ "gene_id": "ENSG00000147180",
621
+ "symbol": "ZNF711"
622
+ },
623
+ {
624
+ "gene_id": "ENSG00000124429",
625
+ "symbol": "POF1B"
626
+ },
627
+ {
628
+ "gene_id": "ENSG00000126733",
629
+ "symbol": "DACH2"
630
+ },
631
+ {
632
+ "gene_id": "ENSG00000102290",
633
+ "symbol": "PCDH11X"
634
+ },
635
+ {
636
+ "gene_id": "ENSG00000102362",
637
+ "symbol": "SYTL4"
638
+ },
639
+ {
640
+ "gene_id": "ENSG00000182489",
641
+ "symbol": "XKRX"
642
+ },
643
+ {
644
+ "gene_id": "ENSG00000166432",
645
+ "symbol": "ZMAT1"
646
+ },
647
+ {
648
+ "gene_id": "ENSG00000189108",
649
+ "symbol": "IL1RAPL2"
650
+ },
651
+ {
652
+ "gene_id": "ENSG00000198088",
653
+ "symbol": "NUP62CL"
654
+ },
655
+ {
656
+ "gene_id": "ENSG00000147234",
657
+ "symbol": "FRMPD3"
658
+ },
659
+ {
660
+ "gene_id": "ENSG00000080561",
661
+ "symbol": "MID2"
662
+ },
663
+ {
664
+ "gene_id": "ENSG00000197565",
665
+ "symbol": "COL4A6"
666
+ },
667
+ {
668
+ "gene_id": "ENSG00000072315",
669
+ "symbol": "TRPC5"
670
+ },
671
+ {
672
+ "gene_id": "ENSG00000187823",
673
+ "symbol": "RTL4"
674
+ },
675
+ {
676
+ "gene_id": "ENSG00000125675",
677
+ "symbol": "GRIA3"
678
+ },
679
+ {
680
+ "gene_id": "ENSG00000183918",
681
+ "symbol": "SH2D1A"
682
+ },
683
+ {
684
+ "gene_id": "ENSG00000056277",
685
+ "symbol": "ZNF280C"
686
+ },
687
+ {
688
+ "gene_id": "ENSG00000171004",
689
+ "symbol": "HS6ST2"
690
+ },
691
+ {
692
+ "gene_id": "ENSG00000170965",
693
+ "symbol": "PLAC1"
694
+ },
695
+ {
696
+ "gene_id": "ENSG00000022267",
697
+ "symbol": "FHL1"
698
+ },
699
+ {
700
+ "gene_id": "ENSG00000102245",
701
+ "symbol": "CD40LG"
702
+ },
703
+ {
704
+ "gene_id": "ENSG00000129682",
705
+ "symbol": "FGF13"
706
+ },
707
+ {
708
+ "gene_id": "ENSG00000155966",
709
+ "symbol": "AFF2"
710
+ },
711
+ {
712
+ "gene_id": "ENSG00000011677",
713
+ "symbol": "GABRA3"
714
+ },
715
+ {
716
+ "gene_id": "ENSG00000183837",
717
+ "symbol": "PNMA3"
718
+ },
719
+ {
720
+ "gene_id": "ENSG00000067646",
721
+ "symbol": "ZFY"
722
+ },
723
+ {
724
+ "gene_id": "ENSG00000099715",
725
+ "symbol": "PCDH11Y"
726
+ },
727
+ {
728
+ "gene_id": "ENSG00000114374",
729
+ "symbol": "USP9Y"
730
+ },
731
+ {
732
+ "gene_id": "ENSG00000067048",
733
+ "symbol": "DDX3Y"
734
+ },
735
+ {
736
+ "gene_id": "ENSG00000183878",
737
+ "symbol": "UTY"
738
+ },
739
+ {
740
+ "gene_id": "ENSG00000165246",
741
+ "symbol": "NLGN4Y"
742
+ },
743
+ {
744
+ "gene_id": "ENSG00000012817",
745
+ "symbol": "KDM5D"
746
+ }
747
+ ],
748
+ "applies_to": "group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene"
749
+ },
750
+ "core_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw4/score"
751
+ }