Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ji2025_chili/loco_lora16_K1000/summary.json +569 -0
- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ji2025_chili/zs_K1000/summary.json +569 -0
- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/loco_lora16_K1000/summary.json +767 -0
- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/zs_K1000/summary.json +767 -0
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ji2025_chili/loco_lora16_K1000/summary.json
ADDED
|
@@ -0,0 +1,569 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "ji2025_chili",
|
| 4 |
+
"written_utc": "2026-10-02T12:13:14.471762+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 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ji2025_chili/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"loco_lora16_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ji2025_chili/ho_ji2025_chili/K1000_lora16.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"TOL,FU1",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"BC,AC",
|
| 19 |
+
"--out",
|
| 20 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/ji2025_chili/loco_lora16_K1000"
|
| 21 |
+
],
|
| 22 |
+
"arms": [
|
| 23 |
+
"loco_lora16_K1000"
|
| 24 |
+
],
|
| 25 |
+
"donors": [
|
| 26 |
+
"N064_TOL",
|
| 27 |
+
"N064_FU1",
|
| 28 |
+
"N032_AC",
|
| 29 |
+
"N038_BC",
|
| 30 |
+
"N038_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 |
+
"N147_TOL",
|
| 41 |
+
"N150_BC",
|
| 42 |
+
"N158_AC",
|
| 43 |
+
"N159_BC",
|
| 44 |
+
"N001_TOL",
|
| 45 |
+
"N001_FU1",
|
| 46 |
+
"N002_TOL",
|
| 47 |
+
"N002_FU1",
|
| 48 |
+
"N005_BC",
|
| 49 |
+
"N005_AC",
|
| 50 |
+
"N012_TOL",
|
| 51 |
+
"N012_FU1",
|
| 52 |
+
"N018_BC",
|
| 53 |
+
"N018_AC",
|
| 54 |
+
"N022_TOL",
|
| 55 |
+
"N022_FU1",
|
| 56 |
+
"N035_TOL",
|
| 57 |
+
"N043_TOL",
|
| 58 |
+
"N043_FU1"
|
| 59 |
+
],
|
| 60 |
+
"n_donors": 33,
|
| 61 |
+
"reference": {
|
| 62 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili",
|
| 63 |
+
"reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
|
| 64 |
+
"features_sha256": "049795e3a2470a223347015c0c965f56ca90c21143aad6f72d12e39f3e95e58b",
|
| 65 |
+
"n_r1_cells": 4950,
|
| 66 |
+
"pca": {
|
| 67 |
+
"n_components": 50,
|
| 68 |
+
"explained_variance_ratio_sum": 0.2840818762779236,
|
| 69 |
+
"n_fit_cells": 4950
|
| 70 |
+
},
|
| 71 |
+
"r2_control": {
|
| 72 |
+
"precision": 0.9961616161616161,
|
| 73 |
+
"coverage": 1.0,
|
| 74 |
+
"density": 2.2093535353535354,
|
| 75 |
+
"n_query": 4950,
|
| 76 |
+
"depth_matched": {
|
| 77 |
+
"precision": 0.9967676767676767,
|
| 78 |
+
"coverage": 1.0,
|
| 79 |
+
"density": 2.1805656565656566
|
| 80 |
+
}
|
| 81 |
+
},
|
| 82 |
+
"observed_l1_loo_null_mean": 0.45223248248542647
|
| 83 |
+
},
|
| 84 |
+
"contrast_definition": {
|
| 85 |
+
"enabled": true,
|
| 86 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 87 |
+
"group_source": "features groups",
|
| 88 |
+
"case_groups": [
|
| 89 |
+
"TOL",
|
| 90 |
+
"FU1"
|
| 91 |
+
],
|
| 92 |
+
"control_groups": [
|
| 93 |
+
"BC",
|
| 94 |
+
"AC"
|
| 95 |
+
],
|
| 96 |
+
"n_case_donors": 18,
|
| 97 |
+
"n_control_donors": 15,
|
| 98 |
+
"n_donors_in_neither": 0,
|
| 99 |
+
"case": [
|
| 100 |
+
true,
|
| 101 |
+
true,
|
| 102 |
+
false,
|
| 103 |
+
false,
|
| 104 |
+
false,
|
| 105 |
+
false,
|
| 106 |
+
true,
|
| 107 |
+
true,
|
| 108 |
+
true,
|
| 109 |
+
true,
|
| 110 |
+
false,
|
| 111 |
+
false,
|
| 112 |
+
false,
|
| 113 |
+
false,
|
| 114 |
+
true,
|
| 115 |
+
false,
|
| 116 |
+
false,
|
| 117 |
+
false,
|
| 118 |
+
true,
|
| 119 |
+
true,
|
| 120 |
+
true,
|
| 121 |
+
true,
|
| 122 |
+
false,
|
| 123 |
+
false,
|
| 124 |
+
true,
|
| 125 |
+
true,
|
| 126 |
+
false,
|
| 127 |
+
false,
|
| 128 |
+
true,
|
| 129 |
+
true,
|
| 130 |
+
true,
|
| 131 |
+
true,
|
| 132 |
+
true
|
| 133 |
+
],
|
| 134 |
+
"ctrl": [
|
| 135 |
+
false,
|
| 136 |
+
false,
|
| 137 |
+
true,
|
| 138 |
+
true,
|
| 139 |
+
true,
|
| 140 |
+
true,
|
| 141 |
+
false,
|
| 142 |
+
false,
|
| 143 |
+
false,
|
| 144 |
+
false,
|
| 145 |
+
true,
|
| 146 |
+
true,
|
| 147 |
+
true,
|
| 148 |
+
true,
|
| 149 |
+
false,
|
| 150 |
+
true,
|
| 151 |
+
true,
|
| 152 |
+
true,
|
| 153 |
+
false,
|
| 154 |
+
false,
|
| 155 |
+
false,
|
| 156 |
+
false,
|
| 157 |
+
true,
|
| 158 |
+
true,
|
| 159 |
+
false,
|
| 160 |
+
false,
|
| 161 |
+
true,
|
| 162 |
+
true,
|
| 163 |
+
false,
|
| 164 |
+
false,
|
| 165 |
+
false,
|
| 166 |
+
false,
|
| 167 |
+
false
|
| 168 |
+
],
|
| 169 |
+
"groups": [
|
| 170 |
+
"TOL",
|
| 171 |
+
"FU1",
|
| 172 |
+
"AC",
|
| 173 |
+
"BC",
|
| 174 |
+
"AC",
|
| 175 |
+
"AC",
|
| 176 |
+
"TOL",
|
| 177 |
+
"FU1",
|
| 178 |
+
"TOL",
|
| 179 |
+
"FU1",
|
| 180 |
+
"BC",
|
| 181 |
+
"AC",
|
| 182 |
+
"BC",
|
| 183 |
+
"AC",
|
| 184 |
+
"TOL",
|
| 185 |
+
"BC",
|
| 186 |
+
"AC",
|
| 187 |
+
"BC",
|
| 188 |
+
"TOL",
|
| 189 |
+
"FU1",
|
| 190 |
+
"TOL",
|
| 191 |
+
"FU1",
|
| 192 |
+
"BC",
|
| 193 |
+
"AC",
|
| 194 |
+
"TOL",
|
| 195 |
+
"FU1",
|
| 196 |
+
"BC",
|
| 197 |
+
"AC",
|
| 198 |
+
"TOL",
|
| 199 |
+
"FU1",
|
| 200 |
+
"TOL",
|
| 201 |
+
"TOL",
|
| 202 |
+
"FU1"
|
| 203 |
+
]
|
| 204 |
+
},
|
| 205 |
+
"deg_definition": {
|
| 206 |
+
"enabled": true,
|
| 207 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
| 208 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
|
| 209 |
+
"functions": [
|
| 210 |
+
"welch_bh_deg",
|
| 211 |
+
"top_deg_genes",
|
| 212 |
+
"jaccard"
|
| 213 |
+
],
|
| 214 |
+
"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",
|
| 215 |
+
"top_n": 50,
|
| 216 |
+
"fdr": 0.05,
|
| 217 |
+
"n_genes": 5752,
|
| 218 |
+
"types": [
|
| 219 |
+
"T cell",
|
| 220 |
+
"B cell",
|
| 221 |
+
"Monocyte",
|
| 222 |
+
"NK cell",
|
| 223 |
+
"DC"
|
| 224 |
+
],
|
| 225 |
+
"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",
|
| 226 |
+
"aggregates_sha256": "4f5eb8c8389ef1308ce3ec44be8be024cedb97de37351d109d9070c818df5a9e",
|
| 227 |
+
"aggregates_note": null,
|
| 228 |
+
"types_not_scored_observed": [],
|
| 229 |
+
"observed": {
|
| 230 |
+
"T cell": {
|
| 231 |
+
"n_significant": 1897,
|
| 232 |
+
"n_tested": 5696,
|
| 233 |
+
"n_case_donors": 18,
|
| 234 |
+
"n_control_donors": 15,
|
| 235 |
+
"n_cells": 59396,
|
| 236 |
+
"top_list_size": 50
|
| 237 |
+
},
|
| 238 |
+
"B cell": {
|
| 239 |
+
"n_significant": 73,
|
| 240 |
+
"n_tested": 5418,
|
| 241 |
+
"n_case_donors": 18,
|
| 242 |
+
"n_control_donors": 15,
|
| 243 |
+
"n_cells": 7162,
|
| 244 |
+
"top_list_size": 50
|
| 245 |
+
},
|
| 246 |
+
"Monocyte": {
|
| 247 |
+
"n_significant": 346,
|
| 248 |
+
"n_tested": 5699,
|
| 249 |
+
"n_case_donors": 18,
|
| 250 |
+
"n_control_donors": 15,
|
| 251 |
+
"n_cells": 34457,
|
| 252 |
+
"top_list_size": 50
|
| 253 |
+
},
|
| 254 |
+
"NK cell": {
|
| 255 |
+
"n_significant": 396,
|
| 256 |
+
"n_tested": 5516,
|
| 257 |
+
"n_case_donors": 18,
|
| 258 |
+
"n_control_donors": 15,
|
| 259 |
+
"n_cells": 18147,
|
| 260 |
+
"top_list_size": 50
|
| 261 |
+
},
|
| 262 |
+
"DC": {
|
| 263 |
+
"n_significant": 138,
|
| 264 |
+
"n_tested": 5168,
|
| 265 |
+
"n_case_donors": 16,
|
| 266 |
+
"n_control_donors": 15,
|
| 267 |
+
"n_cells": 1755,
|
| 268 |
+
"top_list_size": 50
|
| 269 |
+
}
|
| 270 |
+
},
|
| 271 |
+
"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"
|
| 272 |
+
},
|
| 273 |
+
"headline": {
|
| 274 |
+
"loco_lora16_K1000": {
|
| 275 |
+
"comp_l1": 0.4942971856123803,
|
| 276 |
+
"comp_l1_obs_loo_null": 0.45223248248542647,
|
| 277 |
+
"precision": 0.8452525252525253,
|
| 278 |
+
"coverage": 0.31272727272727274,
|
| 279 |
+
"precision_dm": 0.7476767676767677,
|
| 280 |
+
"coverage_dm": 0.5208080808080808,
|
| 281 |
+
"pb_r_median": 0.8363609394362492,
|
| 282 |
+
"pb_top1": 0.06060606060606061,
|
| 283 |
+
"mono_pct_gen": 25.640404040404036,
|
| 284 |
+
"mono_pct_obs": 26.35512163470612,
|
| 285 |
+
"median_umi_gen": 705.0,
|
| 286 |
+
"median_umi_obs": 1056.0,
|
| 287 |
+
"contrast_mean_cp10k_r_gen": 0.08922685293161287,
|
| 288 |
+
"contrast_pseudobulk_log1p_cpm_r_gen": 0.08016613008212725,
|
| 289 |
+
"contrast_mean_cp10k_r_broadcast": 0.2398746224459366,
|
| 290 |
+
"contrast_pseudobulk_log1p_cpm_r_broadcast": 0.18795071850481,
|
| 291 |
+
"deg_top50_T": 8,
|
| 292 |
+
"deg_top50_B": 0,
|
| 293 |
+
"deg_top50_Mono": 1,
|
| 294 |
+
"deg_top50_NK": 0,
|
| 295 |
+
"deg_top50_DC": 0,
|
| 296 |
+
"deg_top50_sum": 9,
|
| 297 |
+
"deg_top50_max": 250,
|
| 298 |
+
"deg_top50_sum_4type": 9,
|
| 299 |
+
"deg_top50_sum_broadcast": 4,
|
| 300 |
+
"seconds": 13.1
|
| 301 |
+
}
|
| 302 |
+
},
|
| 303 |
+
"per_arm": {
|
| 304 |
+
"loco_lora16_K1000": {
|
| 305 |
+
"arm": "loco_lora16_K1000",
|
| 306 |
+
"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ji2025_chili/ho_ji2025_chili/K1000_lora16.npz",
|
| 307 |
+
"npz_sha256": "4990086e0077dc32a337a9523db3b05ad63c1b8a13d3a538b1a95ed06374f7c0",
|
| 308 |
+
"receipt_verified": true,
|
| 309 |
+
"generation": {
|
| 310 |
+
"checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/runs/ho_ji2025_chili/K1000/lora16/checkpoint_ft.pt",
|
| 311 |
+
"checkpoint_sha256": "e00f716f4a61ff5acf7f094007e68c40cab0da1aca64516942edc62dfa783a5f",
|
| 312 |
+
"input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ji2025_chili/test_raw_K1000.npz",
|
| 313 |
+
"input_condition_sha256": "78d8ac589dee9315807163c174fafde76bd890710e96c512773dfaf9151e5b86",
|
| 314 |
+
"seed": 20260927,
|
| 315 |
+
"steps": 50,
|
| 316 |
+
"support_readout": "bernoulli",
|
| 317 |
+
"weights": "ema"
|
| 318 |
+
},
|
| 319 |
+
"condition_for_broadcast": {
|
| 320 |
+
"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ji2025_chili/test_raw_K1000.npz",
|
| 321 |
+
"sha256": "78d8ac589dee9315807163c174fafde76bd890710e96c512773dfaf9151e5b86"
|
| 322 |
+
},
|
| 323 |
+
"poisson": {
|
| 324 |
+
"seed": 20260916,
|
| 325 |
+
"rule": "whole NPZ, rows in NPZ order",
|
| 326 |
+
"nnz_whole_npz": 8301562,
|
| 327 |
+
"median_library_whole_npz_panel": 705.0,
|
| 328 |
+
"n_rows_whole_npz": 49500
|
| 329 |
+
},
|
| 330 |
+
"annotation": {
|
| 331 |
+
"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 332 |
+
"zero_padded_model_genes": 1,
|
| 333 |
+
"label_counts": {
|
| 334 |
+
"T cell": 24372,
|
| 335 |
+
"Monocyte": 12692,
|
| 336 |
+
"Other": 6951,
|
| 337 |
+
"NK cell": 2645,
|
| 338 |
+
"B cell": 2114,
|
| 339 |
+
"DC": 726
|
| 340 |
+
},
|
| 341 |
+
"mean_l2_max_prob": 0.8394829567481171,
|
| 342 |
+
"predict_seconds": 5.7
|
| 343 |
+
},
|
| 344 |
+
"n_donors": 33,
|
| 345 |
+
"n_generated_cells": 49500,
|
| 346 |
+
"composition": {
|
| 347 |
+
"l1_mean": 0.4942971856123803,
|
| 348 |
+
"l1_median": 0.487086516720219,
|
| 349 |
+
"l1_obs_loo_null_mean": 0.45223248248542647,
|
| 350 |
+
"l1_generated_loo_mean_vs_observed_mean": 0.5484625486458352,
|
| 351 |
+
"composition_top1": 0.09090909090909091,
|
| 352 |
+
"mean_fraction_generated": {
|
| 353 |
+
"T cell": 0.492364,
|
| 354 |
+
"B cell": 0.042707,
|
| 355 |
+
"Monocyte": 0.256404,
|
| 356 |
+
"NK cell": 0.053434,
|
| 357 |
+
"DC": 0.014667,
|
| 358 |
+
"Other": 0.140424
|
| 359 |
+
},
|
| 360 |
+
"mean_fraction_observed": {
|
| 361 |
+
"T cell": 0.479517,
|
| 362 |
+
"B cell": 0.055487,
|
| 363 |
+
"Monocyte": 0.263551,
|
| 364 |
+
"NK cell": 0.155783,
|
| 365 |
+
"DC": 0.014105,
|
| 366 |
+
"Other": 0.031557
|
| 367 |
+
}
|
| 368 |
+
},
|
| 369 |
+
"pseudobulk": {
|
| 370 |
+
"n_genes": 5752,
|
| 371 |
+
"r_median": 0.8363609394362492,
|
| 372 |
+
"r_mean": 0.8362995535461151,
|
| 373 |
+
"top1": 0.06060606060606061,
|
| 374 |
+
"n_top1": 2,
|
| 375 |
+
"own_rank_median": 11.0,
|
| 376 |
+
"chance_top1": 0.030303030303030304
|
| 377 |
+
},
|
| 378 |
+
"precision_coverage": {
|
| 379 |
+
"precision": 0.8452525252525253,
|
| 380 |
+
"coverage": 0.31272727272727274,
|
| 381 |
+
"density": 0.5713939393939393,
|
| 382 |
+
"n_query": 4950,
|
| 383 |
+
"n_reference": 4950
|
| 384 |
+
},
|
| 385 |
+
"precision_coverage_depth_matched": {
|
| 386 |
+
"precision": 0.7476767676767677,
|
| 387 |
+
"coverage": 0.5208080808080808,
|
| 388 |
+
"density": 0.5071313131313131,
|
| 389 |
+
"detected_median_before": {
|
| 390 |
+
"R1": 358.5,
|
| 391 |
+
"Q": 162.0
|
| 392 |
+
},
|
| 393 |
+
"detected_median_after": {
|
| 394 |
+
"R1": 162.0,
|
| 395 |
+
"Q": 162.0
|
| 396 |
+
}
|
| 397 |
+
},
|
| 398 |
+
"monocyte_pct": {
|
| 399 |
+
"generated_mean_over_donors": 25.640404040404036,
|
| 400 |
+
"observed_mean_over_donors": 26.35512163470612,
|
| 401 |
+
"generated_pooled_cells": 25.640404040404043
|
| 402 |
+
},
|
| 403 |
+
"median_umi_per_cell_scoring_genes": {
|
| 404 |
+
"generated_pooled": 705.0,
|
| 405 |
+
"observed_pooled": 1056.0,
|
| 406 |
+
"generated_mean_of_donor_medians": 713.1060791015625,
|
| 407 |
+
"observed_mean_of_donor_medians": 1155.8030303030303
|
| 408 |
+
},
|
| 409 |
+
"contrast": {
|
| 410 |
+
"mean_cp10k": {
|
| 411 |
+
"per_type": {
|
| 412 |
+
"T cell": {
|
| 413 |
+
"r_generated": 0.20268425379511953,
|
| 414 |
+
"r_broadcast": 0.22039608693345034,
|
| 415 |
+
"partial_r_generated_given_broadcast": 0.1511904024065317,
|
| 416 |
+
"r_generated_vs_broadcast": 0.2766203595302527,
|
| 417 |
+
"n_genes": 3021
|
| 418 |
+
},
|
| 419 |
+
"B cell": {
|
| 420 |
+
"r_generated": -0.08770777753933644,
|
| 421 |
+
"r_broadcast": 0.13326750229861392,
|
| 422 |
+
"partial_r_generated_given_broadcast": -0.10752230631234073,
|
| 423 |
+
"r_generated_vs_broadcast": 0.13424739159474694,
|
| 424 |
+
"n_genes": 3245
|
| 425 |
+
},
|
| 426 |
+
"Monocyte": {
|
| 427 |
+
"r_generated": 0.1840120352525352,
|
| 428 |
+
"r_broadcast": 0.3983317004681723,
|
| 429 |
+
"partial_r_generated_given_broadcast": 0.09938397108607265,
|
| 430 |
+
"r_generated_vs_broadcast": 0.23978086463987353,
|
| 431 |
+
"n_genes": 3154
|
| 432 |
+
},
|
| 433 |
+
"NK cell": {
|
| 434 |
+
"r_generated": 0.05791890021813316,
|
| 435 |
+
"r_broadcast": 0.20750320008350984,
|
| 436 |
+
"partial_r_generated_given_broadcast": 0.0236086193501655,
|
| 437 |
+
"r_generated_vs_broadcast": 0.16943378211186588,
|
| 438 |
+
"n_genes": 3051
|
| 439 |
+
}
|
| 440 |
+
},
|
| 441 |
+
"mean_r_generated": 0.08922685293161287,
|
| 442 |
+
"mean_r_broadcast": 0.2398746224459366,
|
| 443 |
+
"mean_partial_r": 0.04166517163260728
|
| 444 |
+
},
|
| 445 |
+
"pseudobulk_log1p_cpm": {
|
| 446 |
+
"per_type": {
|
| 447 |
+
"T cell": {
|
| 448 |
+
"r_generated": 0.28859980605125096,
|
| 449 |
+
"r_broadcast": 0.27145331834905573,
|
| 450 |
+
"partial_r_generated_given_broadcast": 0.23653821031636865,
|
| 451 |
+
"r_generated_vs_broadcast": 0.2514539023684234,
|
| 452 |
+
"n_genes": 3021
|
| 453 |
+
},
|
| 454 |
+
"B cell": {
|
| 455 |
+
"r_generated": -0.11872687302095873,
|
| 456 |
+
"r_broadcast": 0.01993963216355321,
|
| 457 |
+
"partial_r_generated_given_broadcast": -0.12027451487579073,
|
| 458 |
+
"r_generated_vs_broadcast": 0.06403859054219135,
|
| 459 |
+
"n_genes": 3245
|
| 460 |
+
},
|
| 461 |
+
"Monocyte": {
|
| 462 |
+
"r_generated": 0.12283999073815398,
|
| 463 |
+
"r_broadcast": 0.35676796217145185,
|
| 464 |
+
"partial_r_generated_given_broadcast": 0.07648682820201043,
|
| 465 |
+
"r_generated_vs_broadcast": 0.1461850274488971,
|
| 466 |
+
"n_genes": 3154
|
| 467 |
+
},
|
| 468 |
+
"NK cell": {
|
| 469 |
+
"r_generated": 0.027951596560062818,
|
| 470 |
+
"r_broadcast": 0.10364196133517908,
|
| 471 |
+
"partial_r_generated_given_broadcast": 0.01962333979821144,
|
| 472 |
+
"r_generated_vs_broadcast": 0.08201002712556633,
|
| 473 |
+
"n_genes": 3051
|
| 474 |
+
}
|
| 475 |
+
},
|
| 476 |
+
"mean_r_generated": 0.08016613008212725,
|
| 477 |
+
"mean_r_broadcast": 0.18795071850481,
|
| 478 |
+
"mean_partial_r": 0.053093465860199945
|
| 479 |
+
}
|
| 480 |
+
},
|
| 481 |
+
"deg_top50": {
|
| 482 |
+
"types_scored": [
|
| 483 |
+
"T cell",
|
| 484 |
+
"B cell",
|
| 485 |
+
"Monocyte",
|
| 486 |
+
"NK cell",
|
| 487 |
+
"DC"
|
| 488 |
+
],
|
| 489 |
+
"types_not_scored": {},
|
| 490 |
+
"per_type": {
|
| 491 |
+
"T cell": {
|
| 492 |
+
"deg_scored": true,
|
| 493 |
+
"top50_overlap": 8,
|
| 494 |
+
"top50_jaccard": 0.08695652173913043,
|
| 495 |
+
"obs_top_list_size": 50,
|
| 496 |
+
"gen_top_list_size": 50,
|
| 497 |
+
"top50_overlap_broadcast": 0,
|
| 498 |
+
"top50_jaccard_broadcast": 0.0,
|
| 499 |
+
"n_cells_obs": 59396,
|
| 500 |
+
"n_cells_gen": 24372
|
| 501 |
+
},
|
| 502 |
+
"B cell": {
|
| 503 |
+
"deg_scored": true,
|
| 504 |
+
"top50_overlap": 0,
|
| 505 |
+
"top50_jaccard": 0.0,
|
| 506 |
+
"obs_top_list_size": 50,
|
| 507 |
+
"gen_top_list_size": 22,
|
| 508 |
+
"top50_overlap_broadcast": 1,
|
| 509 |
+
"top50_jaccard_broadcast": 0.015625,
|
| 510 |
+
"n_cells_obs": 7162,
|
| 511 |
+
"n_cells_gen": 2114
|
| 512 |
+
},
|
| 513 |
+
"Monocyte": {
|
| 514 |
+
"deg_scored": true,
|
| 515 |
+
"top50_overlap": 1,
|
| 516 |
+
"top50_jaccard": 0.010101010101010102,
|
| 517 |
+
"obs_top_list_size": 50,
|
| 518 |
+
"gen_top_list_size": 50,
|
| 519 |
+
"top50_overlap_broadcast": 2,
|
| 520 |
+
"top50_jaccard_broadcast": 0.031746031746031744,
|
| 521 |
+
"n_cells_obs": 34457,
|
| 522 |
+
"n_cells_gen": 12692
|
| 523 |
+
},
|
| 524 |
+
"NK cell": {
|
| 525 |
+
"deg_scored": true,
|
| 526 |
+
"top50_overlap": 0,
|
| 527 |
+
"top50_jaccard": 0.0,
|
| 528 |
+
"obs_top_list_size": 50,
|
| 529 |
+
"gen_top_list_size": 4,
|
| 530 |
+
"top50_overlap_broadcast": 1,
|
| 531 |
+
"top50_jaccard_broadcast": 0.015625,
|
| 532 |
+
"n_cells_obs": 18147,
|
| 533 |
+
"n_cells_gen": 2645
|
| 534 |
+
},
|
| 535 |
+
"DC": {
|
| 536 |
+
"deg_scored": true,
|
| 537 |
+
"top50_overlap": 0,
|
| 538 |
+
"top50_jaccard": 0.0,
|
| 539 |
+
"obs_top_list_size": 50,
|
| 540 |
+
"gen_top_list_size": 0,
|
| 541 |
+
"top50_overlap_broadcast": 0,
|
| 542 |
+
"top50_jaccard_broadcast": 0.0,
|
| 543 |
+
"n_cells_obs": 1755,
|
| 544 |
+
"n_cells_gen": 726
|
| 545 |
+
}
|
| 546 |
+
},
|
| 547 |
+
"sum": 9,
|
| 548 |
+
"sum_4type": 9,
|
| 549 |
+
"max": 250,
|
| 550 |
+
"mean": 1.8,
|
| 551 |
+
"sum_broadcast": 4,
|
| 552 |
+
"sum_broadcast_4type": 4,
|
| 553 |
+
"broadcast_n_significant": 15,
|
| 554 |
+
"seconds": 0.11
|
| 555 |
+
},
|
| 556 |
+
"seconds": 13.1
|
| 557 |
+
}
|
| 558 |
+
},
|
| 559 |
+
"code_sha256": {
|
| 560 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 561 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
|
| 562 |
+
"/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",
|
| 563 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
|
| 564 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
|
| 565 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
|
| 566 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
|
| 567 |
+
},
|
| 568 |
+
"seconds": 15.7
|
| 569 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ji2025_chili/zs_K1000/summary.json
ADDED
|
@@ -0,0 +1,569 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "ji2025_chili",
|
| 4 |
+
"written_utc": "2026-10-02T11:42:35.917176+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 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ji2025_chili/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"zs_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/fewshot_n5/zs__raw_all.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"TOL,FU1",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"BC,AC",
|
| 19 |
+
"--out",
|
| 20 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/ji2025_chili/zs_K1000"
|
| 21 |
+
],
|
| 22 |
+
"arms": [
|
| 23 |
+
"zs_K1000"
|
| 24 |
+
],
|
| 25 |
+
"donors": [
|
| 26 |
+
"N064_TOL",
|
| 27 |
+
"N064_FU1",
|
| 28 |
+
"N032_AC",
|
| 29 |
+
"N038_BC",
|
| 30 |
+
"N038_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 |
+
"N147_TOL",
|
| 41 |
+
"N150_BC",
|
| 42 |
+
"N158_AC",
|
| 43 |
+
"N159_BC",
|
| 44 |
+
"N001_TOL",
|
| 45 |
+
"N001_FU1",
|
| 46 |
+
"N002_TOL",
|
| 47 |
+
"N002_FU1",
|
| 48 |
+
"N005_BC",
|
| 49 |
+
"N005_AC",
|
| 50 |
+
"N012_TOL",
|
| 51 |
+
"N012_FU1",
|
| 52 |
+
"N018_BC",
|
| 53 |
+
"N018_AC",
|
| 54 |
+
"N022_TOL",
|
| 55 |
+
"N022_FU1",
|
| 56 |
+
"N035_TOL",
|
| 57 |
+
"N043_TOL",
|
| 58 |
+
"N043_FU1"
|
| 59 |
+
],
|
| 60 |
+
"n_donors": 33,
|
| 61 |
+
"reference": {
|
| 62 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili",
|
| 63 |
+
"reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
|
| 64 |
+
"features_sha256": "049795e3a2470a223347015c0c965f56ca90c21143aad6f72d12e39f3e95e58b",
|
| 65 |
+
"n_r1_cells": 4950,
|
| 66 |
+
"pca": {
|
| 67 |
+
"n_components": 50,
|
| 68 |
+
"explained_variance_ratio_sum": 0.2840818762779236,
|
| 69 |
+
"n_fit_cells": 4950
|
| 70 |
+
},
|
| 71 |
+
"r2_control": {
|
| 72 |
+
"precision": 0.9961616161616161,
|
| 73 |
+
"coverage": 1.0,
|
| 74 |
+
"density": 2.2093535353535354,
|
| 75 |
+
"n_query": 4950,
|
| 76 |
+
"depth_matched": {
|
| 77 |
+
"precision": 0.9967676767676767,
|
| 78 |
+
"coverage": 1.0,
|
| 79 |
+
"density": 2.1805656565656566
|
| 80 |
+
}
|
| 81 |
+
},
|
| 82 |
+
"observed_l1_loo_null_mean": 0.45223248248542647
|
| 83 |
+
},
|
| 84 |
+
"contrast_definition": {
|
| 85 |
+
"enabled": true,
|
| 86 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 87 |
+
"group_source": "features groups",
|
| 88 |
+
"case_groups": [
|
| 89 |
+
"TOL",
|
| 90 |
+
"FU1"
|
| 91 |
+
],
|
| 92 |
+
"control_groups": [
|
| 93 |
+
"BC",
|
| 94 |
+
"AC"
|
| 95 |
+
],
|
| 96 |
+
"n_case_donors": 18,
|
| 97 |
+
"n_control_donors": 15,
|
| 98 |
+
"n_donors_in_neither": 0,
|
| 99 |
+
"case": [
|
| 100 |
+
true,
|
| 101 |
+
true,
|
| 102 |
+
false,
|
| 103 |
+
false,
|
| 104 |
+
false,
|
| 105 |
+
false,
|
| 106 |
+
true,
|
| 107 |
+
true,
|
| 108 |
+
true,
|
| 109 |
+
true,
|
| 110 |
+
false,
|
| 111 |
+
false,
|
| 112 |
+
false,
|
| 113 |
+
false,
|
| 114 |
+
true,
|
| 115 |
+
false,
|
| 116 |
+
false,
|
| 117 |
+
false,
|
| 118 |
+
true,
|
| 119 |
+
true,
|
| 120 |
+
true,
|
| 121 |
+
true,
|
| 122 |
+
false,
|
| 123 |
+
false,
|
| 124 |
+
true,
|
| 125 |
+
true,
|
| 126 |
+
false,
|
| 127 |
+
false,
|
| 128 |
+
true,
|
| 129 |
+
true,
|
| 130 |
+
true,
|
| 131 |
+
true,
|
| 132 |
+
true
|
| 133 |
+
],
|
| 134 |
+
"ctrl": [
|
| 135 |
+
false,
|
| 136 |
+
false,
|
| 137 |
+
true,
|
| 138 |
+
true,
|
| 139 |
+
true,
|
| 140 |
+
true,
|
| 141 |
+
false,
|
| 142 |
+
false,
|
| 143 |
+
false,
|
| 144 |
+
false,
|
| 145 |
+
true,
|
| 146 |
+
true,
|
| 147 |
+
true,
|
| 148 |
+
true,
|
| 149 |
+
false,
|
| 150 |
+
true,
|
| 151 |
+
true,
|
| 152 |
+
true,
|
| 153 |
+
false,
|
| 154 |
+
false,
|
| 155 |
+
false,
|
| 156 |
+
false,
|
| 157 |
+
true,
|
| 158 |
+
true,
|
| 159 |
+
false,
|
| 160 |
+
false,
|
| 161 |
+
true,
|
| 162 |
+
true,
|
| 163 |
+
false,
|
| 164 |
+
false,
|
| 165 |
+
false,
|
| 166 |
+
false,
|
| 167 |
+
false
|
| 168 |
+
],
|
| 169 |
+
"groups": [
|
| 170 |
+
"TOL",
|
| 171 |
+
"FU1",
|
| 172 |
+
"AC",
|
| 173 |
+
"BC",
|
| 174 |
+
"AC",
|
| 175 |
+
"AC",
|
| 176 |
+
"TOL",
|
| 177 |
+
"FU1",
|
| 178 |
+
"TOL",
|
| 179 |
+
"FU1",
|
| 180 |
+
"BC",
|
| 181 |
+
"AC",
|
| 182 |
+
"BC",
|
| 183 |
+
"AC",
|
| 184 |
+
"TOL",
|
| 185 |
+
"BC",
|
| 186 |
+
"AC",
|
| 187 |
+
"BC",
|
| 188 |
+
"TOL",
|
| 189 |
+
"FU1",
|
| 190 |
+
"TOL",
|
| 191 |
+
"FU1",
|
| 192 |
+
"BC",
|
| 193 |
+
"AC",
|
| 194 |
+
"TOL",
|
| 195 |
+
"FU1",
|
| 196 |
+
"BC",
|
| 197 |
+
"AC",
|
| 198 |
+
"TOL",
|
| 199 |
+
"FU1",
|
| 200 |
+
"TOL",
|
| 201 |
+
"TOL",
|
| 202 |
+
"FU1"
|
| 203 |
+
]
|
| 204 |
+
},
|
| 205 |
+
"deg_definition": {
|
| 206 |
+
"enabled": true,
|
| 207 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
| 208 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
|
| 209 |
+
"functions": [
|
| 210 |
+
"welch_bh_deg",
|
| 211 |
+
"top_deg_genes",
|
| 212 |
+
"jaccard"
|
| 213 |
+
],
|
| 214 |
+
"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",
|
| 215 |
+
"top_n": 50,
|
| 216 |
+
"fdr": 0.05,
|
| 217 |
+
"n_genes": 5752,
|
| 218 |
+
"types": [
|
| 219 |
+
"T cell",
|
| 220 |
+
"B cell",
|
| 221 |
+
"Monocyte",
|
| 222 |
+
"NK cell",
|
| 223 |
+
"DC"
|
| 224 |
+
],
|
| 225 |
+
"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",
|
| 226 |
+
"aggregates_sha256": "4f5eb8c8389ef1308ce3ec44be8be024cedb97de37351d109d9070c818df5a9e",
|
| 227 |
+
"aggregates_note": null,
|
| 228 |
+
"types_not_scored_observed": [],
|
| 229 |
+
"observed": {
|
| 230 |
+
"T cell": {
|
| 231 |
+
"n_significant": 1897,
|
| 232 |
+
"n_tested": 5696,
|
| 233 |
+
"n_case_donors": 18,
|
| 234 |
+
"n_control_donors": 15,
|
| 235 |
+
"n_cells": 59396,
|
| 236 |
+
"top_list_size": 50
|
| 237 |
+
},
|
| 238 |
+
"B cell": {
|
| 239 |
+
"n_significant": 73,
|
| 240 |
+
"n_tested": 5418,
|
| 241 |
+
"n_case_donors": 18,
|
| 242 |
+
"n_control_donors": 15,
|
| 243 |
+
"n_cells": 7162,
|
| 244 |
+
"top_list_size": 50
|
| 245 |
+
},
|
| 246 |
+
"Monocyte": {
|
| 247 |
+
"n_significant": 346,
|
| 248 |
+
"n_tested": 5699,
|
| 249 |
+
"n_case_donors": 18,
|
| 250 |
+
"n_control_donors": 15,
|
| 251 |
+
"n_cells": 34457,
|
| 252 |
+
"top_list_size": 50
|
| 253 |
+
},
|
| 254 |
+
"NK cell": {
|
| 255 |
+
"n_significant": 396,
|
| 256 |
+
"n_tested": 5516,
|
| 257 |
+
"n_case_donors": 18,
|
| 258 |
+
"n_control_donors": 15,
|
| 259 |
+
"n_cells": 18147,
|
| 260 |
+
"top_list_size": 50
|
| 261 |
+
},
|
| 262 |
+
"DC": {
|
| 263 |
+
"n_significant": 138,
|
| 264 |
+
"n_tested": 5168,
|
| 265 |
+
"n_case_donors": 16,
|
| 266 |
+
"n_control_donors": 15,
|
| 267 |
+
"n_cells": 1755,
|
| 268 |
+
"top_list_size": 50
|
| 269 |
+
}
|
| 270 |
+
},
|
| 271 |
+
"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"
|
| 272 |
+
},
|
| 273 |
+
"headline": {
|
| 274 |
+
"zs_K1000": {
|
| 275 |
+
"comp_l1": 0.7246556382795132,
|
| 276 |
+
"comp_l1_obs_loo_null": 0.45223248248542647,
|
| 277 |
+
"precision": 0.7212121212121212,
|
| 278 |
+
"coverage": 0.05898989898989899,
|
| 279 |
+
"precision_dm": 0.4991919191919192,
|
| 280 |
+
"coverage_dm": 0.19474747474747475,
|
| 281 |
+
"pb_r_median": 0.8343238300989376,
|
| 282 |
+
"pb_top1": 0.06060606060606061,
|
| 283 |
+
"mono_pct_gen": 52.93333333333332,
|
| 284 |
+
"mono_pct_obs": 26.35512163470612,
|
| 285 |
+
"median_umi_gen": 405.0,
|
| 286 |
+
"median_umi_obs": 1056.0,
|
| 287 |
+
"contrast_mean_cp10k_r_gen": 0.07494970415326974,
|
| 288 |
+
"contrast_pseudobulk_log1p_cpm_r_gen": 0.044007895209439055,
|
| 289 |
+
"contrast_mean_cp10k_r_broadcast": 0.2398746224459366,
|
| 290 |
+
"contrast_pseudobulk_log1p_cpm_r_broadcast": 0.18795071850481,
|
| 291 |
+
"deg_top50_T": 0,
|
| 292 |
+
"deg_top50_B": 0,
|
| 293 |
+
"deg_top50_Mono": 0,
|
| 294 |
+
"deg_top50_NK": 0,
|
| 295 |
+
"deg_top50_DC": 0,
|
| 296 |
+
"deg_top50_sum": 0,
|
| 297 |
+
"deg_top50_max": 250,
|
| 298 |
+
"deg_top50_sum_4type": 0,
|
| 299 |
+
"deg_top50_sum_broadcast": 4,
|
| 300 |
+
"seconds": 13.2
|
| 301 |
+
}
|
| 302 |
+
},
|
| 303 |
+
"per_arm": {
|
| 304 |
+
"zs_K1000": {
|
| 305 |
+
"arm": "zs_K1000",
|
| 306 |
+
"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/fewshot_n5/zs__raw_all.npz",
|
| 307 |
+
"npz_sha256": "0d37cb4c8f0f60d75cefb35c8ec7c79c0d1cac6c891bda9205cfb1e195dd7da0",
|
| 308 |
+
"receipt_verified": true,
|
| 309 |
+
"generation": {
|
| 310 |
+
"checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
|
| 311 |
+
"checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
|
| 312 |
+
"input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/fewshot_n5/all_usable_raw.npz",
|
| 313 |
+
"input_condition_sha256": "78d8ac589dee9315807163c174fafde76bd890710e96c512773dfaf9151e5b86",
|
| 314 |
+
"seed": 20260927,
|
| 315 |
+
"steps": 50,
|
| 316 |
+
"support_readout": "bernoulli",
|
| 317 |
+
"weights": "ema"
|
| 318 |
+
},
|
| 319 |
+
"condition_for_broadcast": {
|
| 320 |
+
"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/fewshot_n5/all_usable_raw.npz",
|
| 321 |
+
"sha256": "78d8ac589dee9315807163c174fafde76bd890710e96c512773dfaf9151e5b86"
|
| 322 |
+
},
|
| 323 |
+
"poisson": {
|
| 324 |
+
"seed": 20260916,
|
| 325 |
+
"rule": "whole NPZ, rows in NPZ order",
|
| 326 |
+
"nnz_whole_npz": 7953355,
|
| 327 |
+
"median_library_whole_npz_panel": 405.0,
|
| 328 |
+
"n_rows_whole_npz": 49500
|
| 329 |
+
},
|
| 330 |
+
"annotation": {
|
| 331 |
+
"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 332 |
+
"zero_padded_model_genes": 1,
|
| 333 |
+
"label_counts": {
|
| 334 |
+
"Monocyte": 26202,
|
| 335 |
+
"T cell": 14510,
|
| 336 |
+
"Other": 4857,
|
| 337 |
+
"B cell": 2617,
|
| 338 |
+
"NK cell": 1074,
|
| 339 |
+
"DC": 240
|
| 340 |
+
},
|
| 341 |
+
"mean_l2_max_prob": 0.884570407278008,
|
| 342 |
+
"predict_seconds": 5.8
|
| 343 |
+
},
|
| 344 |
+
"n_donors": 33,
|
| 345 |
+
"n_generated_cells": 49500,
|
| 346 |
+
"composition": {
|
| 347 |
+
"l1_mean": 0.7246556382795132,
|
| 348 |
+
"l1_median": 0.7046166007905139,
|
| 349 |
+
"l1_obs_loo_null_mean": 0.45223248248542647,
|
| 350 |
+
"l1_generated_loo_mean_vs_observed_mean": 0.7333294806163062,
|
| 351 |
+
"composition_top1": 0.030303030303030304,
|
| 352 |
+
"mean_fraction_generated": {
|
| 353 |
+
"T cell": 0.293131,
|
| 354 |
+
"B cell": 0.052869,
|
| 355 |
+
"Monocyte": 0.529333,
|
| 356 |
+
"NK cell": 0.021697,
|
| 357 |
+
"DC": 0.004848,
|
| 358 |
+
"Other": 0.098121
|
| 359 |
+
},
|
| 360 |
+
"mean_fraction_observed": {
|
| 361 |
+
"T cell": 0.479517,
|
| 362 |
+
"B cell": 0.055487,
|
| 363 |
+
"Monocyte": 0.263551,
|
| 364 |
+
"NK cell": 0.155783,
|
| 365 |
+
"DC": 0.014105,
|
| 366 |
+
"Other": 0.031557
|
| 367 |
+
}
|
| 368 |
+
},
|
| 369 |
+
"pseudobulk": {
|
| 370 |
+
"n_genes": 5752,
|
| 371 |
+
"r_median": 0.8343238300989376,
|
| 372 |
+
"r_mean": 0.8329340244525818,
|
| 373 |
+
"top1": 0.06060606060606061,
|
| 374 |
+
"n_top1": 2,
|
| 375 |
+
"own_rank_median": 13.0,
|
| 376 |
+
"chance_top1": 0.030303030303030304
|
| 377 |
+
},
|
| 378 |
+
"precision_coverage": {
|
| 379 |
+
"precision": 0.7212121212121212,
|
| 380 |
+
"coverage": 0.05898989898989899,
|
| 381 |
+
"density": 0.478989898989899,
|
| 382 |
+
"n_query": 4950,
|
| 383 |
+
"n_reference": 4950
|
| 384 |
+
},
|
| 385 |
+
"precision_coverage_depth_matched": {
|
| 386 |
+
"precision": 0.4991919191919192,
|
| 387 |
+
"coverage": 0.19474747474747475,
|
| 388 |
+
"density": 0.14894949494949494,
|
| 389 |
+
"detected_median_before": {
|
| 390 |
+
"R1": 358.5,
|
| 391 |
+
"Q": 154.0
|
| 392 |
+
},
|
| 393 |
+
"detected_median_after": {
|
| 394 |
+
"R1": 154.0,
|
| 395 |
+
"Q": 154.0
|
| 396 |
+
}
|
| 397 |
+
},
|
| 398 |
+
"monocyte_pct": {
|
| 399 |
+
"generated_mean_over_donors": 52.93333333333332,
|
| 400 |
+
"observed_mean_over_donors": 26.35512163470612,
|
| 401 |
+
"generated_pooled_cells": 52.93333333333333
|
| 402 |
+
},
|
| 403 |
+
"median_umi_per_cell_scoring_genes": {
|
| 404 |
+
"generated_pooled": 405.0,
|
| 405 |
+
"observed_pooled": 1056.0,
|
| 406 |
+
"generated_mean_of_donor_medians": 409.7727355957031,
|
| 407 |
+
"observed_mean_of_donor_medians": 1155.8030303030303
|
| 408 |
+
},
|
| 409 |
+
"contrast": {
|
| 410 |
+
"mean_cp10k": {
|
| 411 |
+
"per_type": {
|
| 412 |
+
"T cell": {
|
| 413 |
+
"r_generated": 0.19571663549808774,
|
| 414 |
+
"r_broadcast": 0.22039608693345034,
|
| 415 |
+
"partial_r_generated_given_broadcast": 0.1482708208152166,
|
| 416 |
+
"r_generated_vs_broadcast": 0.2532010443016586,
|
| 417 |
+
"n_genes": 3021
|
| 418 |
+
},
|
| 419 |
+
"B cell": {
|
| 420 |
+
"r_generated": -0.08908110897621051,
|
| 421 |
+
"r_broadcast": 0.13326750229861392,
|
| 422 |
+
"partial_r_generated_given_broadcast": -0.1077651779992899,
|
| 423 |
+
"r_generated_vs_broadcast": 0.1265441007184561,
|
| 424 |
+
"n_genes": 3245
|
| 425 |
+
},
|
| 426 |
+
"Monocyte": {
|
| 427 |
+
"r_generated": 0.2036215726172367,
|
| 428 |
+
"r_broadcast": 0.3983317004681723,
|
| 429 |
+
"partial_r_generated_given_broadcast": 0.09809050580716451,
|
| 430 |
+
"r_generated_vs_broadcast": 0.295391531877229,
|
| 431 |
+
"n_genes": 3154
|
| 432 |
+
},
|
| 433 |
+
"NK cell": {
|
| 434 |
+
"r_generated": -0.010458282526034986,
|
| 435 |
+
"r_broadcast": 0.20750320008350984,
|
| 436 |
+
"partial_r_generated_given_broadcast": -0.04661204907651572,
|
| 437 |
+
"r_generated_vs_broadcast": 0.1662837651651097,
|
| 438 |
+
"n_genes": 3051
|
| 439 |
+
}
|
| 440 |
+
},
|
| 441 |
+
"mean_r_generated": 0.07494970415326974,
|
| 442 |
+
"mean_r_broadcast": 0.2398746224459366,
|
| 443 |
+
"mean_partial_r": 0.022996024886643866
|
| 444 |
+
},
|
| 445 |
+
"pseudobulk_log1p_cpm": {
|
| 446 |
+
"per_type": {
|
| 447 |
+
"T cell": {
|
| 448 |
+
"r_generated": 0.10954524145016434,
|
| 449 |
+
"r_broadcast": 0.27145331834905573,
|
| 450 |
+
"partial_r_generated_given_broadcast": 0.0776578066867918,
|
| 451 |
+
"r_generated_vs_broadcast": 0.13056831473567765,
|
| 452 |
+
"n_genes": 3021
|
| 453 |
+
},
|
| 454 |
+
"B cell": {
|
| 455 |
+
"r_generated": -0.09982618477043084,
|
| 456 |
+
"r_broadcast": 0.01993963216355321,
|
| 457 |
+
"partial_r_generated_given_broadcast": -0.10131847867152856,
|
| 458 |
+
"r_generated_vs_broadcast": 0.06355863652163926,
|
| 459 |
+
"n_genes": 3245
|
| 460 |
+
},
|
| 461 |
+
"Monocyte": {
|
| 462 |
+
"r_generated": 0.13168819603510043,
|
| 463 |
+
"r_broadcast": 0.35676796217145185,
|
| 464 |
+
"partial_r_generated_given_broadcast": 0.08453324573079685,
|
| 465 |
+
"r_generated_vs_broadcast": 0.15027874254241963,
|
| 466 |
+
"n_genes": 3154
|
| 467 |
+
},
|
| 468 |
+
"NK cell": {
|
| 469 |
+
"r_generated": 0.034624328122922286,
|
| 470 |
+
"r_broadcast": 0.10364196133517908,
|
| 471 |
+
"partial_r_generated_given_broadcast": 0.022351771627865346,
|
| 472 |
+
"r_generated_vs_broadcast": 0.12115452118158426,
|
| 473 |
+
"n_genes": 3051
|
| 474 |
+
}
|
| 475 |
+
},
|
| 476 |
+
"mean_r_generated": 0.044007895209439055,
|
| 477 |
+
"mean_r_broadcast": 0.18795071850481,
|
| 478 |
+
"mean_partial_r": 0.02080608634348136
|
| 479 |
+
}
|
| 480 |
+
},
|
| 481 |
+
"deg_top50": {
|
| 482 |
+
"types_scored": [
|
| 483 |
+
"T cell",
|
| 484 |
+
"B cell",
|
| 485 |
+
"Monocyte",
|
| 486 |
+
"NK cell",
|
| 487 |
+
"DC"
|
| 488 |
+
],
|
| 489 |
+
"types_not_scored": {},
|
| 490 |
+
"per_type": {
|
| 491 |
+
"T cell": {
|
| 492 |
+
"deg_scored": true,
|
| 493 |
+
"top50_overlap": 0,
|
| 494 |
+
"top50_jaccard": 0.0,
|
| 495 |
+
"obs_top_list_size": 50,
|
| 496 |
+
"gen_top_list_size": 1,
|
| 497 |
+
"top50_overlap_broadcast": 0,
|
| 498 |
+
"top50_jaccard_broadcast": 0.0,
|
| 499 |
+
"n_cells_obs": 59396,
|
| 500 |
+
"n_cells_gen": 14510
|
| 501 |
+
},
|
| 502 |
+
"B cell": {
|
| 503 |
+
"deg_scored": true,
|
| 504 |
+
"top50_overlap": 0,
|
| 505 |
+
"top50_jaccard": 0.0,
|
| 506 |
+
"obs_top_list_size": 50,
|
| 507 |
+
"gen_top_list_size": 2,
|
| 508 |
+
"top50_overlap_broadcast": 1,
|
| 509 |
+
"top50_jaccard_broadcast": 0.015625,
|
| 510 |
+
"n_cells_obs": 7162,
|
| 511 |
+
"n_cells_gen": 2617
|
| 512 |
+
},
|
| 513 |
+
"Monocyte": {
|
| 514 |
+
"deg_scored": true,
|
| 515 |
+
"top50_overlap": 0,
|
| 516 |
+
"top50_jaccard": 0.0,
|
| 517 |
+
"obs_top_list_size": 50,
|
| 518 |
+
"gen_top_list_size": 5,
|
| 519 |
+
"top50_overlap_broadcast": 2,
|
| 520 |
+
"top50_jaccard_broadcast": 0.031746031746031744,
|
| 521 |
+
"n_cells_obs": 34457,
|
| 522 |
+
"n_cells_gen": 26202
|
| 523 |
+
},
|
| 524 |
+
"NK cell": {
|
| 525 |
+
"deg_scored": true,
|
| 526 |
+
"top50_overlap": 0,
|
| 527 |
+
"top50_jaccard": 0.0,
|
| 528 |
+
"obs_top_list_size": 50,
|
| 529 |
+
"gen_top_list_size": 1,
|
| 530 |
+
"top50_overlap_broadcast": 1,
|
| 531 |
+
"top50_jaccard_broadcast": 0.015625,
|
| 532 |
+
"n_cells_obs": 18147,
|
| 533 |
+
"n_cells_gen": 1074
|
| 534 |
+
},
|
| 535 |
+
"DC": {
|
| 536 |
+
"deg_scored": true,
|
| 537 |
+
"top50_overlap": 0,
|
| 538 |
+
"top50_jaccard": 0.0,
|
| 539 |
+
"obs_top_list_size": 50,
|
| 540 |
+
"gen_top_list_size": 0,
|
| 541 |
+
"top50_overlap_broadcast": 0,
|
| 542 |
+
"top50_jaccard_broadcast": 0.0,
|
| 543 |
+
"n_cells_obs": 1755,
|
| 544 |
+
"n_cells_gen": 240
|
| 545 |
+
}
|
| 546 |
+
},
|
| 547 |
+
"sum": 0,
|
| 548 |
+
"sum_4type": 0,
|
| 549 |
+
"max": 250,
|
| 550 |
+
"mean": 0.0,
|
| 551 |
+
"sum_broadcast": 4,
|
| 552 |
+
"sum_broadcast_4type": 4,
|
| 553 |
+
"broadcast_n_significant": 15,
|
| 554 |
+
"seconds": 0.1
|
| 555 |
+
},
|
| 556 |
+
"seconds": 13.2
|
| 557 |
+
}
|
| 558 |
+
},
|
| 559 |
+
"code_sha256": {
|
| 560 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 561 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
|
| 562 |
+
"/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",
|
| 563 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
|
| 564 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
|
| 565 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
|
| 566 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
|
| 567 |
+
},
|
| 568 |
+
"seconds": 16.2
|
| 569 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/loco_lora16_K1000/summary.json
ADDED
|
@@ -0,0 +1,767 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "ye2026_sepsis",
|
| 4 |
+
"written_utc": "2026-10-02T12:33:44.003037+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 |
+
"ye2026_sepsis",
|
| 9 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"loco_lora16_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/ho_ye2026_sepsis/K1000_lora16.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"adult_sepsis,ped_sepsis",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl",
|
| 19 |
+
"--out",
|
| 20 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/loco_lora16_K1000"
|
| 21 |
+
],
|
| 22 |
+
"arms": [
|
| 23 |
+
"loco_lora16_K1000"
|
| 24 |
+
],
|
| 25 |
+
"donors": [
|
| 26 |
+
"Abd-PS04",
|
| 27 |
+
"Abd-PS05",
|
| 28 |
+
"Abd-PS07",
|
| 29 |
+
"Abd-PS19",
|
| 30 |
+
"Abd-PS20",
|
| 31 |
+
"Abd-PS23",
|
| 32 |
+
"Abd-PS27",
|
| 33 |
+
"Abd-S102",
|
| 34 |
+
"Abd-S103",
|
| 35 |
+
"Abd-S120",
|
| 36 |
+
"Abd-S123",
|
| 37 |
+
"Abd-S156",
|
| 38 |
+
"Abd-S39",
|
| 39 |
+
"Abd-S42",
|
| 40 |
+
"Abd-S47",
|
| 41 |
+
"Abd-S51",
|
| 42 |
+
"Abd-S54",
|
| 43 |
+
"Abd-S57",
|
| 44 |
+
"Abd-S66",
|
| 45 |
+
"Abd-S79",
|
| 46 |
+
"Abd-S83",
|
| 47 |
+
"Abd-S98",
|
| 48 |
+
"HC01",
|
| 49 |
+
"HC05",
|
| 50 |
+
"HC07",
|
| 51 |
+
"HC09",
|
| 52 |
+
"HC12",
|
| 53 |
+
"HC13",
|
| 54 |
+
"HC16",
|
| 55 |
+
"IC10",
|
| 56 |
+
"IC15",
|
| 57 |
+
"IC16",
|
| 58 |
+
"IC19",
|
| 59 |
+
"IC22",
|
| 60 |
+
"IC23",
|
| 61 |
+
"PHC01",
|
| 62 |
+
"PHC02",
|
| 63 |
+
"PHC03",
|
| 64 |
+
"PHC05",
|
| 65 |
+
"PIC01",
|
| 66 |
+
"PIC02",
|
| 67 |
+
"PIC04",
|
| 68 |
+
"PIC05",
|
| 69 |
+
"Res-PS02",
|
| 70 |
+
"Res-PS03",
|
| 71 |
+
"Res-PS12",
|
| 72 |
+
"Res-PS16",
|
| 73 |
+
"Res-PS21",
|
| 74 |
+
"Res-PS22",
|
| 75 |
+
"Res-PS25",
|
| 76 |
+
"Res-PS26",
|
| 77 |
+
"Res-S10",
|
| 78 |
+
"Res-S125",
|
| 79 |
+
"Res-S127",
|
| 80 |
+
"Res-S136",
|
| 81 |
+
"Res-S139",
|
| 82 |
+
"Res-S146",
|
| 83 |
+
"Res-S149",
|
| 84 |
+
"Res-S150",
|
| 85 |
+
"Res-S164",
|
| 86 |
+
"Res-S166",
|
| 87 |
+
"Res-S174",
|
| 88 |
+
"Res-S177",
|
| 89 |
+
"Res-S184",
|
| 90 |
+
"Res-S19",
|
| 91 |
+
"Res-S26",
|
| 92 |
+
"Res-S40",
|
| 93 |
+
"Res-S77",
|
| 94 |
+
"Res-S87",
|
| 95 |
+
"Skin-S140",
|
| 96 |
+
"Skin-S142",
|
| 97 |
+
"Skin-S152",
|
| 98 |
+
"Skin-S38",
|
| 99 |
+
"Skin-S43",
|
| 100 |
+
"Skin-S46",
|
| 101 |
+
"Skin-S52",
|
| 102 |
+
"Skin-S74",
|
| 103 |
+
"Uri-S134",
|
| 104 |
+
"Uri-S147",
|
| 105 |
+
"Uri-S157",
|
| 106 |
+
"Uri-S20",
|
| 107 |
+
"Uri-S93"
|
| 108 |
+
],
|
| 109 |
+
"n_donors": 82,
|
| 110 |
+
"reference": {
|
| 111 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis",
|
| 112 |
+
"reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
|
| 113 |
+
"features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
|
| 114 |
+
"n_r1_cells": 12300,
|
| 115 |
+
"pca": {
|
| 116 |
+
"n_components": 50,
|
| 117 |
+
"explained_variance_ratio_sum": 0.33549821376800537,
|
| 118 |
+
"n_fit_cells": 12300
|
| 119 |
+
},
|
| 120 |
+
"r2_control": {
|
| 121 |
+
"precision": 0.9804878048780488,
|
| 122 |
+
"coverage": 0.9996747967479674,
|
| 123 |
+
"density": 1.2890731707317074,
|
| 124 |
+
"n_query": 12300,
|
| 125 |
+
"depth_matched": {
|
| 126 |
+
"precision": 0.9795934959349594,
|
| 127 |
+
"coverage": 0.9998373983739838,
|
| 128 |
+
"density": 1.2835853658536585
|
| 129 |
+
}
|
| 130 |
+
},
|
| 131 |
+
"observed_l1_loo_null_mean": 0.515468004498372
|
| 132 |
+
},
|
| 133 |
+
"contrast_definition": {
|
| 134 |
+
"enabled": true,
|
| 135 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 136 |
+
"group_source": "features groups",
|
| 137 |
+
"case_groups": [
|
| 138 |
+
"adult_sepsis",
|
| 139 |
+
"ped_sepsis"
|
| 140 |
+
],
|
| 141 |
+
"control_groups": [
|
| 142 |
+
"adult_HC",
|
| 143 |
+
"adult_ICU_ctrl",
|
| 144 |
+
"ped_HC",
|
| 145 |
+
"ped_ICU_ctrl"
|
| 146 |
+
],
|
| 147 |
+
"n_case_donors": 61,
|
| 148 |
+
"n_control_donors": 21,
|
| 149 |
+
"n_donors_in_neither": 0,
|
| 150 |
+
"case": [
|
| 151 |
+
true,
|
| 152 |
+
true,
|
| 153 |
+
true,
|
| 154 |
+
true,
|
| 155 |
+
true,
|
| 156 |
+
true,
|
| 157 |
+
true,
|
| 158 |
+
true,
|
| 159 |
+
true,
|
| 160 |
+
true,
|
| 161 |
+
true,
|
| 162 |
+
true,
|
| 163 |
+
true,
|
| 164 |
+
true,
|
| 165 |
+
true,
|
| 166 |
+
true,
|
| 167 |
+
true,
|
| 168 |
+
true,
|
| 169 |
+
true,
|
| 170 |
+
true,
|
| 171 |
+
true,
|
| 172 |
+
true,
|
| 173 |
+
false,
|
| 174 |
+
false,
|
| 175 |
+
false,
|
| 176 |
+
false,
|
| 177 |
+
false,
|
| 178 |
+
false,
|
| 179 |
+
false,
|
| 180 |
+
false,
|
| 181 |
+
false,
|
| 182 |
+
false,
|
| 183 |
+
false,
|
| 184 |
+
false,
|
| 185 |
+
false,
|
| 186 |
+
false,
|
| 187 |
+
false,
|
| 188 |
+
false,
|
| 189 |
+
false,
|
| 190 |
+
false,
|
| 191 |
+
false,
|
| 192 |
+
false,
|
| 193 |
+
false,
|
| 194 |
+
true,
|
| 195 |
+
true,
|
| 196 |
+
true,
|
| 197 |
+
true,
|
| 198 |
+
true,
|
| 199 |
+
true,
|
| 200 |
+
true,
|
| 201 |
+
true,
|
| 202 |
+
true,
|
| 203 |
+
true,
|
| 204 |
+
true,
|
| 205 |
+
true,
|
| 206 |
+
true,
|
| 207 |
+
true,
|
| 208 |
+
true,
|
| 209 |
+
true,
|
| 210 |
+
true,
|
| 211 |
+
true,
|
| 212 |
+
true,
|
| 213 |
+
true,
|
| 214 |
+
true,
|
| 215 |
+
true,
|
| 216 |
+
true,
|
| 217 |
+
true,
|
| 218 |
+
true,
|
| 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 |
+
],
|
| 234 |
+
"ctrl": [
|
| 235 |
+
false,
|
| 236 |
+
false,
|
| 237 |
+
false,
|
| 238 |
+
false,
|
| 239 |
+
false,
|
| 240 |
+
false,
|
| 241 |
+
false,
|
| 242 |
+
false,
|
| 243 |
+
false,
|
| 244 |
+
false,
|
| 245 |
+
false,
|
| 246 |
+
false,
|
| 247 |
+
false,
|
| 248 |
+
false,
|
| 249 |
+
false,
|
| 250 |
+
false,
|
| 251 |
+
false,
|
| 252 |
+
false,
|
| 253 |
+
false,
|
| 254 |
+
false,
|
| 255 |
+
false,
|
| 256 |
+
false,
|
| 257 |
+
true,
|
| 258 |
+
true,
|
| 259 |
+
true,
|
| 260 |
+
true,
|
| 261 |
+
true,
|
| 262 |
+
true,
|
| 263 |
+
true,
|
| 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 |
+
false,
|
| 279 |
+
false,
|
| 280 |
+
false,
|
| 281 |
+
false,
|
| 282 |
+
false,
|
| 283 |
+
false,
|
| 284 |
+
false,
|
| 285 |
+
false,
|
| 286 |
+
false,
|
| 287 |
+
false,
|
| 288 |
+
false,
|
| 289 |
+
false,
|
| 290 |
+
false,
|
| 291 |
+
false,
|
| 292 |
+
false,
|
| 293 |
+
false,
|
| 294 |
+
false,
|
| 295 |
+
false,
|
| 296 |
+
false,
|
| 297 |
+
false,
|
| 298 |
+
false,
|
| 299 |
+
false,
|
| 300 |
+
false,
|
| 301 |
+
false,
|
| 302 |
+
false,
|
| 303 |
+
false,
|
| 304 |
+
false,
|
| 305 |
+
false,
|
| 306 |
+
false,
|
| 307 |
+
false,
|
| 308 |
+
false,
|
| 309 |
+
false,
|
| 310 |
+
false,
|
| 311 |
+
false,
|
| 312 |
+
false,
|
| 313 |
+
false,
|
| 314 |
+
false,
|
| 315 |
+
false,
|
| 316 |
+
false
|
| 317 |
+
],
|
| 318 |
+
"groups": [
|
| 319 |
+
"ped_sepsis",
|
| 320 |
+
"ped_sepsis",
|
| 321 |
+
"ped_sepsis",
|
| 322 |
+
"ped_sepsis",
|
| 323 |
+
"ped_sepsis",
|
| 324 |
+
"ped_sepsis",
|
| 325 |
+
"ped_sepsis",
|
| 326 |
+
"adult_sepsis",
|
| 327 |
+
"adult_sepsis",
|
| 328 |
+
"adult_sepsis",
|
| 329 |
+
"adult_sepsis",
|
| 330 |
+
"adult_sepsis",
|
| 331 |
+
"adult_sepsis",
|
| 332 |
+
"adult_sepsis",
|
| 333 |
+
"adult_sepsis",
|
| 334 |
+
"adult_sepsis",
|
| 335 |
+
"adult_sepsis",
|
| 336 |
+
"adult_sepsis",
|
| 337 |
+
"adult_sepsis",
|
| 338 |
+
"adult_sepsis",
|
| 339 |
+
"adult_sepsis",
|
| 340 |
+
"adult_sepsis",
|
| 341 |
+
"adult_HC",
|
| 342 |
+
"adult_HC",
|
| 343 |
+
"adult_HC",
|
| 344 |
+
"adult_HC",
|
| 345 |
+
"adult_HC",
|
| 346 |
+
"adult_HC",
|
| 347 |
+
"adult_HC",
|
| 348 |
+
"adult_ICU_ctrl",
|
| 349 |
+
"adult_ICU_ctrl",
|
| 350 |
+
"adult_ICU_ctrl",
|
| 351 |
+
"adult_ICU_ctrl",
|
| 352 |
+
"adult_ICU_ctrl",
|
| 353 |
+
"adult_ICU_ctrl",
|
| 354 |
+
"ped_HC",
|
| 355 |
+
"ped_HC",
|
| 356 |
+
"ped_HC",
|
| 357 |
+
"ped_HC",
|
| 358 |
+
"ped_ICU_ctrl",
|
| 359 |
+
"ped_ICU_ctrl",
|
| 360 |
+
"ped_ICU_ctrl",
|
| 361 |
+
"ped_ICU_ctrl",
|
| 362 |
+
"ped_sepsis",
|
| 363 |
+
"ped_sepsis",
|
| 364 |
+
"ped_sepsis",
|
| 365 |
+
"ped_sepsis",
|
| 366 |
+
"ped_sepsis",
|
| 367 |
+
"ped_sepsis",
|
| 368 |
+
"ped_sepsis",
|
| 369 |
+
"ped_sepsis",
|
| 370 |
+
"adult_sepsis",
|
| 371 |
+
"adult_sepsis",
|
| 372 |
+
"adult_sepsis",
|
| 373 |
+
"adult_sepsis",
|
| 374 |
+
"adult_sepsis",
|
| 375 |
+
"adult_sepsis",
|
| 376 |
+
"adult_sepsis",
|
| 377 |
+
"adult_sepsis",
|
| 378 |
+
"adult_sepsis",
|
| 379 |
+
"adult_sepsis",
|
| 380 |
+
"adult_sepsis",
|
| 381 |
+
"adult_sepsis",
|
| 382 |
+
"adult_sepsis",
|
| 383 |
+
"adult_sepsis",
|
| 384 |
+
"adult_sepsis",
|
| 385 |
+
"adult_sepsis",
|
| 386 |
+
"adult_sepsis",
|
| 387 |
+
"adult_sepsis",
|
| 388 |
+
"adult_sepsis",
|
| 389 |
+
"adult_sepsis",
|
| 390 |
+
"adult_sepsis",
|
| 391 |
+
"adult_sepsis",
|
| 392 |
+
"adult_sepsis",
|
| 393 |
+
"adult_sepsis",
|
| 394 |
+
"adult_sepsis",
|
| 395 |
+
"adult_sepsis",
|
| 396 |
+
"adult_sepsis",
|
| 397 |
+
"adult_sepsis",
|
| 398 |
+
"adult_sepsis",
|
| 399 |
+
"adult_sepsis",
|
| 400 |
+
"adult_sepsis"
|
| 401 |
+
]
|
| 402 |
+
},
|
| 403 |
+
"deg_definition": {
|
| 404 |
+
"enabled": true,
|
| 405 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
| 406 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
|
| 407 |
+
"functions": [
|
| 408 |
+
"welch_bh_deg",
|
| 409 |
+
"top_deg_genes",
|
| 410 |
+
"jaccard"
|
| 411 |
+
],
|
| 412 |
+
"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",
|
| 413 |
+
"top_n": 50,
|
| 414 |
+
"fdr": 0.05,
|
| 415 |
+
"n_genes": 5975,
|
| 416 |
+
"types": [
|
| 417 |
+
"T cell",
|
| 418 |
+
"B cell",
|
| 419 |
+
"Monocyte",
|
| 420 |
+
"NK cell",
|
| 421 |
+
"DC"
|
| 422 |
+
],
|
| 423 |
+
"aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz",
|
| 424 |
+
"aggregates_sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0",
|
| 425 |
+
"aggregates_note": null,
|
| 426 |
+
"types_not_scored_observed": [],
|
| 427 |
+
"observed": {
|
| 428 |
+
"T cell": {
|
| 429 |
+
"n_significant": 1578,
|
| 430 |
+
"n_tested": 5810,
|
| 431 |
+
"n_case_donors": 61,
|
| 432 |
+
"n_control_donors": 21,
|
| 433 |
+
"n_cells": 298117,
|
| 434 |
+
"top_list_size": 50
|
| 435 |
+
},
|
| 436 |
+
"B cell": {
|
| 437 |
+
"n_significant": 1102,
|
| 438 |
+
"n_tested": 5752,
|
| 439 |
+
"n_case_donors": 61,
|
| 440 |
+
"n_control_donors": 21,
|
| 441 |
+
"n_cells": 99729,
|
| 442 |
+
"top_list_size": 50
|
| 443 |
+
},
|
| 444 |
+
"Monocyte": {
|
| 445 |
+
"n_significant": 2459,
|
| 446 |
+
"n_tested": 5754,
|
| 447 |
+
"n_case_donors": 61,
|
| 448 |
+
"n_control_donors": 21,
|
| 449 |
+
"n_cells": 111269,
|
| 450 |
+
"top_list_size": 50
|
| 451 |
+
},
|
| 452 |
+
"NK cell": {
|
| 453 |
+
"n_significant": 1235,
|
| 454 |
+
"n_tested": 5623,
|
| 455 |
+
"n_case_donors": 61,
|
| 456 |
+
"n_control_donors": 21,
|
| 457 |
+
"n_cells": 47832,
|
| 458 |
+
"top_list_size": 50
|
| 459 |
+
},
|
| 460 |
+
"DC": {
|
| 461 |
+
"n_significant": 1572,
|
| 462 |
+
"n_tested": 5330,
|
| 463 |
+
"n_case_donors": 57,
|
| 464 |
+
"n_control_donors": 21,
|
| 465 |
+
"n_cells": 3300,
|
| 466 |
+
"top_list_size": 50
|
| 467 |
+
}
|
| 468 |
+
},
|
| 469 |
+
"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"
|
| 470 |
+
},
|
| 471 |
+
"headline": {
|
| 472 |
+
"loco_lora16_K1000": {
|
| 473 |
+
"comp_l1": 0.537784206603567,
|
| 474 |
+
"comp_l1_obs_loo_null": 0.515468004498372,
|
| 475 |
+
"precision": 0.8506504065040651,
|
| 476 |
+
"coverage": 0.28804878048780486,
|
| 477 |
+
"precision_dm": 0.7960162601626016,
|
| 478 |
+
"coverage_dm": 0.5129268292682927,
|
| 479 |
+
"pb_r_median": 0.8657510412987999,
|
| 480 |
+
"pb_top1": 0.12195121951219512,
|
| 481 |
+
"mono_pct_gen": 20.058536585365854,
|
| 482 |
+
"mono_pct_obs": 20.817070783198325,
|
| 483 |
+
"median_umi_gen": 1045.0,
|
| 484 |
+
"median_umi_obs": 1967.0,
|
| 485 |
+
"contrast_mean_cp10k_r_gen": 0.09162100245097674,
|
| 486 |
+
"contrast_pseudobulk_log1p_cpm_r_gen": 0.12771676049617198,
|
| 487 |
+
"contrast_mean_cp10k_r_broadcast": 0.31594581626202867,
|
| 488 |
+
"contrast_pseudobulk_log1p_cpm_r_broadcast": 0.29096860411544245,
|
| 489 |
+
"deg_top50_T": 1,
|
| 490 |
+
"deg_top50_B": 1,
|
| 491 |
+
"deg_top50_Mono": 5,
|
| 492 |
+
"deg_top50_NK": 0,
|
| 493 |
+
"deg_top50_DC": 0,
|
| 494 |
+
"deg_top50_sum": 7,
|
| 495 |
+
"deg_top50_max": 250,
|
| 496 |
+
"deg_top50_sum_4type": 7,
|
| 497 |
+
"deg_top50_sum_broadcast": 21,
|
| 498 |
+
"seconds": 21.7
|
| 499 |
+
}
|
| 500 |
+
},
|
| 501 |
+
"per_arm": {
|
| 502 |
+
"loco_lora16_K1000": {
|
| 503 |
+
"arm": "loco_lora16_K1000",
|
| 504 |
+
"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/ho_ye2026_sepsis/K1000_lora16.npz",
|
| 505 |
+
"npz_sha256": "43b9aa5b6003bf792c2d9b39ef7910ac27a2a85e6e72c0b27b6eb5ca8239b830",
|
| 506 |
+
"receipt_verified": true,
|
| 507 |
+
"generation": {
|
| 508 |
+
"checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/runs/ho_ye2026_sepsis/K1000/lora16/checkpoint_ft.pt",
|
| 509 |
+
"checkpoint_sha256": "a3fa8d6376524218a1d0c70a40373eee23098619c5ac019f8b6430d14db9e618",
|
| 510 |
+
"input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/test_raw_K1000.npz",
|
| 511 |
+
"input_condition_sha256": "ffcc1562915493d43b6970aec5791ec01193f7ed72a0f8ab8103bb45ce46c641",
|
| 512 |
+
"seed": 20260927,
|
| 513 |
+
"steps": 50,
|
| 514 |
+
"support_readout": "bernoulli",
|
| 515 |
+
"weights": "ema"
|
| 516 |
+
},
|
| 517 |
+
"condition_for_broadcast": {
|
| 518 |
+
"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/test_raw_K1000.npz",
|
| 519 |
+
"sha256": "ffcc1562915493d43b6970aec5791ec01193f7ed72a0f8ab8103bb45ce46c641"
|
| 520 |
+
},
|
| 521 |
+
"poisson": {
|
| 522 |
+
"seed": 20260916,
|
| 523 |
+
"rule": "whole NPZ, rows in NPZ order",
|
| 524 |
+
"nnz_whole_npz": 30301754,
|
| 525 |
+
"median_library_whole_npz_panel": 1045.0,
|
| 526 |
+
"n_rows_whole_npz": 123000
|
| 527 |
+
},
|
| 528 |
+
"annotation": {
|
| 529 |
+
"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 530 |
+
"zero_padded_model_genes": 0,
|
| 531 |
+
"label_counts": {
|
| 532 |
+
"T cell": 43422,
|
| 533 |
+
"B cell": 29702,
|
| 534 |
+
"Monocyte": 24672,
|
| 535 |
+
"NK cell": 18981,
|
| 536 |
+
"DC": 3737,
|
| 537 |
+
"Other": 2486
|
| 538 |
+
},
|
| 539 |
+
"mean_l2_max_prob": 0.915221229400092,
|
| 540 |
+
"predict_seconds": 5.1
|
| 541 |
+
},
|
| 542 |
+
"n_donors": 82,
|
| 543 |
+
"n_generated_cells": 123000,
|
| 544 |
+
"composition": {
|
| 545 |
+
"l1_mean": 0.537784206603567,
|
| 546 |
+
"l1_median": 0.5106736217235832,
|
| 547 |
+
"l1_obs_loo_null_mean": 0.515468004498372,
|
| 548 |
+
"l1_generated_loo_mean_vs_observed_mean": 0.6381611741541935,
|
| 549 |
+
"composition_top1": 0.04878048780487805,
|
| 550 |
+
"mean_fraction_generated": {
|
| 551 |
+
"T cell": 0.353024,
|
| 552 |
+
"B cell": 0.24148,
|
| 553 |
+
"Monocyte": 0.200585,
|
| 554 |
+
"NK cell": 0.154317,
|
| 555 |
+
"DC": 0.030382,
|
| 556 |
+
"Other": 0.020211
|
| 557 |
+
},
|
| 558 |
+
"mean_fraction_observed": {
|
| 559 |
+
"T cell": 0.484547,
|
| 560 |
+
"B cell": 0.172757,
|
| 561 |
+
"Monocyte": 0.208171,
|
| 562 |
+
"NK cell": 0.080723,
|
| 563 |
+
"DC": 0.005542,
|
| 564 |
+
"Other": 0.04826
|
| 565 |
+
}
|
| 566 |
+
},
|
| 567 |
+
"pseudobulk": {
|
| 568 |
+
"n_genes": 5975,
|
| 569 |
+
"r_median": 0.8657510412987999,
|
| 570 |
+
"r_mean": 0.8618747570191742,
|
| 571 |
+
"top1": 0.12195121951219512,
|
| 572 |
+
"n_top1": 10,
|
| 573 |
+
"own_rank_median": 16.5,
|
| 574 |
+
"chance_top1": 0.012195121951219513
|
| 575 |
+
},
|
| 576 |
+
"precision_coverage": {
|
| 577 |
+
"precision": 0.8506504065040651,
|
| 578 |
+
"coverage": 0.28804878048780486,
|
| 579 |
+
"density": 0.3859430894308943,
|
| 580 |
+
"n_query": 12300,
|
| 581 |
+
"n_reference": 12300
|
| 582 |
+
},
|
| 583 |
+
"precision_coverage_depth_matched": {
|
| 584 |
+
"precision": 0.7960162601626016,
|
| 585 |
+
"coverage": 0.5129268292682927,
|
| 586 |
+
"density": 0.3879186991869919,
|
| 587 |
+
"detected_median_before": {
|
| 588 |
+
"R1": 411.0,
|
| 589 |
+
"Q": 239.0
|
| 590 |
+
},
|
| 591 |
+
"detected_median_after": {
|
| 592 |
+
"R1": 239.0,
|
| 593 |
+
"Q": 239.0
|
| 594 |
+
}
|
| 595 |
+
},
|
| 596 |
+
"monocyte_pct": {
|
| 597 |
+
"generated_mean_over_donors": 20.058536585365854,
|
| 598 |
+
"observed_mean_over_donors": 20.817070783198325,
|
| 599 |
+
"generated_pooled_cells": 20.058536585365854
|
| 600 |
+
},
|
| 601 |
+
"median_umi_per_cell_scoring_genes": {
|
| 602 |
+
"generated_pooled": 1045.0,
|
| 603 |
+
"observed_pooled": 1967.0,
|
| 604 |
+
"generated_mean_of_donor_medians": 1081.93896484375,
|
| 605 |
+
"observed_mean_of_donor_medians": 2112.9146341463415
|
| 606 |
+
},
|
| 607 |
+
"contrast": {
|
| 608 |
+
"mean_cp10k": {
|
| 609 |
+
"per_type": {
|
| 610 |
+
"T cell": {
|
| 611 |
+
"r_generated": -0.011975171459846714,
|
| 612 |
+
"r_broadcast": 0.2548893770824626,
|
| 613 |
+
"partial_r_generated_given_broadcast": -0.05122236503031578,
|
| 614 |
+
"r_generated_vs_broadcast": 0.1452781368297155,
|
| 615 |
+
"n_genes": 3258
|
| 616 |
+
},
|
| 617 |
+
"B cell": {
|
| 618 |
+
"r_generated": 0.16157610893841604,
|
| 619 |
+
"r_broadcast": 0.27458639801653467,
|
| 620 |
+
"partial_r_generated_given_broadcast": 0.10525937099016786,
|
| 621 |
+
"r_generated_vs_broadcast": 0.22968585775784886,
|
| 622 |
+
"n_genes": 3310
|
| 623 |
+
},
|
| 624 |
+
"Monocyte": {
|
| 625 |
+
"r_generated": 0.21645254552397006,
|
| 626 |
+
"r_broadcast": 0.5481103923782986,
|
| 627 |
+
"partial_r_generated_given_broadcast": 0.10304899373389625,
|
| 628 |
+
"r_generated_vs_broadcast": 0.2423436168446589,
|
| 629 |
+
"n_genes": 3289
|
| 630 |
+
},
|
| 631 |
+
"NK cell": {
|
| 632 |
+
"r_generated": 0.0004305268013675477,
|
| 633 |
+
"r_broadcast": 0.1861970975708186,
|
| 634 |
+
"partial_r_generated_given_broadcast": -0.02278747175940871,
|
| 635 |
+
"r_generated_vs_broadcast": 0.12166239617831853,
|
| 636 |
+
"n_genes": 3240
|
| 637 |
+
}
|
| 638 |
+
},
|
| 639 |
+
"mean_r_generated": 0.09162100245097674,
|
| 640 |
+
"mean_r_broadcast": 0.31594581626202867,
|
| 641 |
+
"mean_partial_r": 0.03357463198358491
|
| 642 |
+
},
|
| 643 |
+
"pseudobulk_log1p_cpm": {
|
| 644 |
+
"per_type": {
|
| 645 |
+
"T cell": {
|
| 646 |
+
"r_generated": 0.04800011269924342,
|
| 647 |
+
"r_broadcast": 0.2164745523777111,
|
| 648 |
+
"partial_r_generated_given_broadcast": 0.0015655672204354047,
|
| 649 |
+
"r_generated_vs_broadcast": 0.21483983940437876,
|
| 650 |
+
"n_genes": 3258
|
| 651 |
+
},
|
| 652 |
+
"B cell": {
|
| 653 |
+
"r_generated": 0.2821712145687276,
|
| 654 |
+
"r_broadcast": 0.2711145517540278,
|
| 655 |
+
"partial_r_generated_given_broadcast": 0.22054611458977494,
|
| 656 |
+
"r_generated_vs_broadcast": 0.2918619927416837,
|
| 657 |
+
"n_genes": 3310
|
| 658 |
+
},
|
| 659 |
+
"Monocyte": {
|
| 660 |
+
"r_generated": 0.1512310645029765,
|
| 661 |
+
"r_broadcast": 0.6203629305570988,
|
| 662 |
+
"partial_r_generated_given_broadcast": -0.03342966230326073,
|
| 663 |
+
"r_generated_vs_broadcast": 0.2842989364079799,
|
| 664 |
+
"n_genes": 3289
|
| 665 |
+
},
|
| 666 |
+
"NK cell": {
|
| 667 |
+
"r_generated": 0.029464650213740368,
|
| 668 |
+
"r_broadcast": 0.05592238177293225,
|
| 669 |
+
"partial_r_generated_given_broadcast": 0.0221225534008507,
|
| 670 |
+
"r_generated_vs_broadcast": 0.13555562487052558,
|
| 671 |
+
"n_genes": 3240
|
| 672 |
+
}
|
| 673 |
+
},
|
| 674 |
+
"mean_r_generated": 0.12771676049617198,
|
| 675 |
+
"mean_r_broadcast": 0.29096860411544245,
|
| 676 |
+
"mean_partial_r": 0.05270114322695008
|
| 677 |
+
}
|
| 678 |
+
},
|
| 679 |
+
"deg_top50": {
|
| 680 |
+
"types_scored": [
|
| 681 |
+
"T cell",
|
| 682 |
+
"B cell",
|
| 683 |
+
"Monocyte",
|
| 684 |
+
"NK cell",
|
| 685 |
+
"DC"
|
| 686 |
+
],
|
| 687 |
+
"types_not_scored": {},
|
| 688 |
+
"per_type": {
|
| 689 |
+
"T cell": {
|
| 690 |
+
"deg_scored": true,
|
| 691 |
+
"top50_overlap": 1,
|
| 692 |
+
"top50_jaccard": 0.019230769230769232,
|
| 693 |
+
"obs_top_list_size": 50,
|
| 694 |
+
"gen_top_list_size": 3,
|
| 695 |
+
"top50_overlap_broadcast": 3,
|
| 696 |
+
"top50_jaccard_broadcast": 0.030927835051546393,
|
| 697 |
+
"n_cells_obs": 298117,
|
| 698 |
+
"n_cells_gen": 43422
|
| 699 |
+
},
|
| 700 |
+
"B cell": {
|
| 701 |
+
"deg_scored": true,
|
| 702 |
+
"top50_overlap": 1,
|
| 703 |
+
"top50_jaccard": 0.010101010101010102,
|
| 704 |
+
"obs_top_list_size": 50,
|
| 705 |
+
"gen_top_list_size": 50,
|
| 706 |
+
"top50_overlap_broadcast": 2,
|
| 707 |
+
"top50_jaccard_broadcast": 0.02040816326530612,
|
| 708 |
+
"n_cells_obs": 99729,
|
| 709 |
+
"n_cells_gen": 29702
|
| 710 |
+
},
|
| 711 |
+
"Monocyte": {
|
| 712 |
+
"deg_scored": true,
|
| 713 |
+
"top50_overlap": 5,
|
| 714 |
+
"top50_jaccard": 0.05263157894736842,
|
| 715 |
+
"obs_top_list_size": 50,
|
| 716 |
+
"gen_top_list_size": 50,
|
| 717 |
+
"top50_overlap_broadcast": 13,
|
| 718 |
+
"top50_jaccard_broadcast": 0.14942528735632185,
|
| 719 |
+
"n_cells_obs": 111269,
|
| 720 |
+
"n_cells_gen": 24672
|
| 721 |
+
},
|
| 722 |
+
"NK cell": {
|
| 723 |
+
"deg_scored": true,
|
| 724 |
+
"top50_overlap": 0,
|
| 725 |
+
"top50_jaccard": 0.0,
|
| 726 |
+
"obs_top_list_size": 50,
|
| 727 |
+
"gen_top_list_size": 1,
|
| 728 |
+
"top50_overlap_broadcast": 2,
|
| 729 |
+
"top50_jaccard_broadcast": 0.02040816326530612,
|
| 730 |
+
"n_cells_obs": 47832,
|
| 731 |
+
"n_cells_gen": 18981
|
| 732 |
+
},
|
| 733 |
+
"DC": {
|
| 734 |
+
"deg_scored": true,
|
| 735 |
+
"top50_overlap": 0,
|
| 736 |
+
"top50_jaccard": 0.0,
|
| 737 |
+
"obs_top_list_size": 50,
|
| 738 |
+
"gen_top_list_size": 3,
|
| 739 |
+
"top50_overlap_broadcast": 1,
|
| 740 |
+
"top50_jaccard_broadcast": 0.010101010101010102,
|
| 741 |
+
"n_cells_obs": 3300,
|
| 742 |
+
"n_cells_gen": 3737
|
| 743 |
+
}
|
| 744 |
+
},
|
| 745 |
+
"sum": 7,
|
| 746 |
+
"sum_4type": 7,
|
| 747 |
+
"max": 250,
|
| 748 |
+
"mean": 1.4,
|
| 749 |
+
"sum_broadcast": 21,
|
| 750 |
+
"sum_broadcast_4type": 20,
|
| 751 |
+
"broadcast_n_significant": 1378,
|
| 752 |
+
"seconds": 0.27
|
| 753 |
+
},
|
| 754 |
+
"seconds": 21.7
|
| 755 |
+
}
|
| 756 |
+
},
|
| 757 |
+
"code_sha256": {
|
| 758 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 759 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
|
| 760 |
+
"/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",
|
| 761 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
|
| 762 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
|
| 763 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
|
| 764 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
|
| 765 |
+
},
|
| 766 |
+
"seconds": 28.1
|
| 767 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/zs_K1000/summary.json
ADDED
|
@@ -0,0 +1,767 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "ye2026_sepsis",
|
| 4 |
+
"written_utc": "2026-10-02T11:40:10.289161+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 |
+
"ye2026_sepsis",
|
| 9 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"zs_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/zs__raw_all.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"adult_sepsis,ped_sepsis",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl",
|
| 19 |
+
"--out",
|
| 20 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/zs_K1000"
|
| 21 |
+
],
|
| 22 |
+
"arms": [
|
| 23 |
+
"zs_K1000"
|
| 24 |
+
],
|
| 25 |
+
"donors": [
|
| 26 |
+
"Abd-PS04",
|
| 27 |
+
"Abd-PS05",
|
| 28 |
+
"Abd-PS07",
|
| 29 |
+
"Abd-PS19",
|
| 30 |
+
"Abd-PS20",
|
| 31 |
+
"Abd-PS23",
|
| 32 |
+
"Abd-PS27",
|
| 33 |
+
"Abd-S102",
|
| 34 |
+
"Abd-S103",
|
| 35 |
+
"Abd-S120",
|
| 36 |
+
"Abd-S123",
|
| 37 |
+
"Abd-S156",
|
| 38 |
+
"Abd-S39",
|
| 39 |
+
"Abd-S42",
|
| 40 |
+
"Abd-S47",
|
| 41 |
+
"Abd-S51",
|
| 42 |
+
"Abd-S54",
|
| 43 |
+
"Abd-S57",
|
| 44 |
+
"Abd-S66",
|
| 45 |
+
"Abd-S79",
|
| 46 |
+
"Abd-S83",
|
| 47 |
+
"Abd-S98",
|
| 48 |
+
"HC01",
|
| 49 |
+
"HC05",
|
| 50 |
+
"HC07",
|
| 51 |
+
"HC09",
|
| 52 |
+
"HC12",
|
| 53 |
+
"HC13",
|
| 54 |
+
"HC16",
|
| 55 |
+
"IC10",
|
| 56 |
+
"IC15",
|
| 57 |
+
"IC16",
|
| 58 |
+
"IC19",
|
| 59 |
+
"IC22",
|
| 60 |
+
"IC23",
|
| 61 |
+
"PHC01",
|
| 62 |
+
"PHC02",
|
| 63 |
+
"PHC03",
|
| 64 |
+
"PHC05",
|
| 65 |
+
"PIC01",
|
| 66 |
+
"PIC02",
|
| 67 |
+
"PIC04",
|
| 68 |
+
"PIC05",
|
| 69 |
+
"Res-PS02",
|
| 70 |
+
"Res-PS03",
|
| 71 |
+
"Res-PS12",
|
| 72 |
+
"Res-PS16",
|
| 73 |
+
"Res-PS21",
|
| 74 |
+
"Res-PS22",
|
| 75 |
+
"Res-PS25",
|
| 76 |
+
"Res-PS26",
|
| 77 |
+
"Res-S10",
|
| 78 |
+
"Res-S125",
|
| 79 |
+
"Res-S127",
|
| 80 |
+
"Res-S136",
|
| 81 |
+
"Res-S139",
|
| 82 |
+
"Res-S146",
|
| 83 |
+
"Res-S149",
|
| 84 |
+
"Res-S150",
|
| 85 |
+
"Res-S164",
|
| 86 |
+
"Res-S166",
|
| 87 |
+
"Res-S174",
|
| 88 |
+
"Res-S177",
|
| 89 |
+
"Res-S184",
|
| 90 |
+
"Res-S19",
|
| 91 |
+
"Res-S26",
|
| 92 |
+
"Res-S40",
|
| 93 |
+
"Res-S77",
|
| 94 |
+
"Res-S87",
|
| 95 |
+
"Skin-S140",
|
| 96 |
+
"Skin-S142",
|
| 97 |
+
"Skin-S152",
|
| 98 |
+
"Skin-S38",
|
| 99 |
+
"Skin-S43",
|
| 100 |
+
"Skin-S46",
|
| 101 |
+
"Skin-S52",
|
| 102 |
+
"Skin-S74",
|
| 103 |
+
"Uri-S134",
|
| 104 |
+
"Uri-S147",
|
| 105 |
+
"Uri-S157",
|
| 106 |
+
"Uri-S20",
|
| 107 |
+
"Uri-S93"
|
| 108 |
+
],
|
| 109 |
+
"n_donors": 82,
|
| 110 |
+
"reference": {
|
| 111 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis",
|
| 112 |
+
"reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
|
| 113 |
+
"features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
|
| 114 |
+
"n_r1_cells": 12300,
|
| 115 |
+
"pca": {
|
| 116 |
+
"n_components": 50,
|
| 117 |
+
"explained_variance_ratio_sum": 0.33549821376800537,
|
| 118 |
+
"n_fit_cells": 12300
|
| 119 |
+
},
|
| 120 |
+
"r2_control": {
|
| 121 |
+
"precision": 0.9804878048780488,
|
| 122 |
+
"coverage": 0.9996747967479674,
|
| 123 |
+
"density": 1.2890731707317074,
|
| 124 |
+
"n_query": 12300,
|
| 125 |
+
"depth_matched": {
|
| 126 |
+
"precision": 0.9795934959349594,
|
| 127 |
+
"coverage": 0.9998373983739838,
|
| 128 |
+
"density": 1.2835853658536585
|
| 129 |
+
}
|
| 130 |
+
},
|
| 131 |
+
"observed_l1_loo_null_mean": 0.515468004498372
|
| 132 |
+
},
|
| 133 |
+
"contrast_definition": {
|
| 134 |
+
"enabled": true,
|
| 135 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 136 |
+
"group_source": "features groups",
|
| 137 |
+
"case_groups": [
|
| 138 |
+
"adult_sepsis",
|
| 139 |
+
"ped_sepsis"
|
| 140 |
+
],
|
| 141 |
+
"control_groups": [
|
| 142 |
+
"adult_HC",
|
| 143 |
+
"adult_ICU_ctrl",
|
| 144 |
+
"ped_HC",
|
| 145 |
+
"ped_ICU_ctrl"
|
| 146 |
+
],
|
| 147 |
+
"n_case_donors": 61,
|
| 148 |
+
"n_control_donors": 21,
|
| 149 |
+
"n_donors_in_neither": 0,
|
| 150 |
+
"case": [
|
| 151 |
+
true,
|
| 152 |
+
true,
|
| 153 |
+
true,
|
| 154 |
+
true,
|
| 155 |
+
true,
|
| 156 |
+
true,
|
| 157 |
+
true,
|
| 158 |
+
true,
|
| 159 |
+
true,
|
| 160 |
+
true,
|
| 161 |
+
true,
|
| 162 |
+
true,
|
| 163 |
+
true,
|
| 164 |
+
true,
|
| 165 |
+
true,
|
| 166 |
+
true,
|
| 167 |
+
true,
|
| 168 |
+
true,
|
| 169 |
+
true,
|
| 170 |
+
true,
|
| 171 |
+
true,
|
| 172 |
+
true,
|
| 173 |
+
false,
|
| 174 |
+
false,
|
| 175 |
+
false,
|
| 176 |
+
false,
|
| 177 |
+
false,
|
| 178 |
+
false,
|
| 179 |
+
false,
|
| 180 |
+
false,
|
| 181 |
+
false,
|
| 182 |
+
false,
|
| 183 |
+
false,
|
| 184 |
+
false,
|
| 185 |
+
false,
|
| 186 |
+
false,
|
| 187 |
+
false,
|
| 188 |
+
false,
|
| 189 |
+
false,
|
| 190 |
+
false,
|
| 191 |
+
false,
|
| 192 |
+
false,
|
| 193 |
+
false,
|
| 194 |
+
true,
|
| 195 |
+
true,
|
| 196 |
+
true,
|
| 197 |
+
true,
|
| 198 |
+
true,
|
| 199 |
+
true,
|
| 200 |
+
true,
|
| 201 |
+
true,
|
| 202 |
+
true,
|
| 203 |
+
true,
|
| 204 |
+
true,
|
| 205 |
+
true,
|
| 206 |
+
true,
|
| 207 |
+
true,
|
| 208 |
+
true,
|
| 209 |
+
true,
|
| 210 |
+
true,
|
| 211 |
+
true,
|
| 212 |
+
true,
|
| 213 |
+
true,
|
| 214 |
+
true,
|
| 215 |
+
true,
|
| 216 |
+
true,
|
| 217 |
+
true,
|
| 218 |
+
true,
|
| 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 |
+
],
|
| 234 |
+
"ctrl": [
|
| 235 |
+
false,
|
| 236 |
+
false,
|
| 237 |
+
false,
|
| 238 |
+
false,
|
| 239 |
+
false,
|
| 240 |
+
false,
|
| 241 |
+
false,
|
| 242 |
+
false,
|
| 243 |
+
false,
|
| 244 |
+
false,
|
| 245 |
+
false,
|
| 246 |
+
false,
|
| 247 |
+
false,
|
| 248 |
+
false,
|
| 249 |
+
false,
|
| 250 |
+
false,
|
| 251 |
+
false,
|
| 252 |
+
false,
|
| 253 |
+
false,
|
| 254 |
+
false,
|
| 255 |
+
false,
|
| 256 |
+
false,
|
| 257 |
+
true,
|
| 258 |
+
true,
|
| 259 |
+
true,
|
| 260 |
+
true,
|
| 261 |
+
true,
|
| 262 |
+
true,
|
| 263 |
+
true,
|
| 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 |
+
false,
|
| 279 |
+
false,
|
| 280 |
+
false,
|
| 281 |
+
false,
|
| 282 |
+
false,
|
| 283 |
+
false,
|
| 284 |
+
false,
|
| 285 |
+
false,
|
| 286 |
+
false,
|
| 287 |
+
false,
|
| 288 |
+
false,
|
| 289 |
+
false,
|
| 290 |
+
false,
|
| 291 |
+
false,
|
| 292 |
+
false,
|
| 293 |
+
false,
|
| 294 |
+
false,
|
| 295 |
+
false,
|
| 296 |
+
false,
|
| 297 |
+
false,
|
| 298 |
+
false,
|
| 299 |
+
false,
|
| 300 |
+
false,
|
| 301 |
+
false,
|
| 302 |
+
false,
|
| 303 |
+
false,
|
| 304 |
+
false,
|
| 305 |
+
false,
|
| 306 |
+
false,
|
| 307 |
+
false,
|
| 308 |
+
false,
|
| 309 |
+
false,
|
| 310 |
+
false,
|
| 311 |
+
false,
|
| 312 |
+
false,
|
| 313 |
+
false,
|
| 314 |
+
false,
|
| 315 |
+
false,
|
| 316 |
+
false
|
| 317 |
+
],
|
| 318 |
+
"groups": [
|
| 319 |
+
"ped_sepsis",
|
| 320 |
+
"ped_sepsis",
|
| 321 |
+
"ped_sepsis",
|
| 322 |
+
"ped_sepsis",
|
| 323 |
+
"ped_sepsis",
|
| 324 |
+
"ped_sepsis",
|
| 325 |
+
"ped_sepsis",
|
| 326 |
+
"adult_sepsis",
|
| 327 |
+
"adult_sepsis",
|
| 328 |
+
"adult_sepsis",
|
| 329 |
+
"adult_sepsis",
|
| 330 |
+
"adult_sepsis",
|
| 331 |
+
"adult_sepsis",
|
| 332 |
+
"adult_sepsis",
|
| 333 |
+
"adult_sepsis",
|
| 334 |
+
"adult_sepsis",
|
| 335 |
+
"adult_sepsis",
|
| 336 |
+
"adult_sepsis",
|
| 337 |
+
"adult_sepsis",
|
| 338 |
+
"adult_sepsis",
|
| 339 |
+
"adult_sepsis",
|
| 340 |
+
"adult_sepsis",
|
| 341 |
+
"adult_HC",
|
| 342 |
+
"adult_HC",
|
| 343 |
+
"adult_HC",
|
| 344 |
+
"adult_HC",
|
| 345 |
+
"adult_HC",
|
| 346 |
+
"adult_HC",
|
| 347 |
+
"adult_HC",
|
| 348 |
+
"adult_ICU_ctrl",
|
| 349 |
+
"adult_ICU_ctrl",
|
| 350 |
+
"adult_ICU_ctrl",
|
| 351 |
+
"adult_ICU_ctrl",
|
| 352 |
+
"adult_ICU_ctrl",
|
| 353 |
+
"adult_ICU_ctrl",
|
| 354 |
+
"ped_HC",
|
| 355 |
+
"ped_HC",
|
| 356 |
+
"ped_HC",
|
| 357 |
+
"ped_HC",
|
| 358 |
+
"ped_ICU_ctrl",
|
| 359 |
+
"ped_ICU_ctrl",
|
| 360 |
+
"ped_ICU_ctrl",
|
| 361 |
+
"ped_ICU_ctrl",
|
| 362 |
+
"ped_sepsis",
|
| 363 |
+
"ped_sepsis",
|
| 364 |
+
"ped_sepsis",
|
| 365 |
+
"ped_sepsis",
|
| 366 |
+
"ped_sepsis",
|
| 367 |
+
"ped_sepsis",
|
| 368 |
+
"ped_sepsis",
|
| 369 |
+
"ped_sepsis",
|
| 370 |
+
"adult_sepsis",
|
| 371 |
+
"adult_sepsis",
|
| 372 |
+
"adult_sepsis",
|
| 373 |
+
"adult_sepsis",
|
| 374 |
+
"adult_sepsis",
|
| 375 |
+
"adult_sepsis",
|
| 376 |
+
"adult_sepsis",
|
| 377 |
+
"adult_sepsis",
|
| 378 |
+
"adult_sepsis",
|
| 379 |
+
"adult_sepsis",
|
| 380 |
+
"adult_sepsis",
|
| 381 |
+
"adult_sepsis",
|
| 382 |
+
"adult_sepsis",
|
| 383 |
+
"adult_sepsis",
|
| 384 |
+
"adult_sepsis",
|
| 385 |
+
"adult_sepsis",
|
| 386 |
+
"adult_sepsis",
|
| 387 |
+
"adult_sepsis",
|
| 388 |
+
"adult_sepsis",
|
| 389 |
+
"adult_sepsis",
|
| 390 |
+
"adult_sepsis",
|
| 391 |
+
"adult_sepsis",
|
| 392 |
+
"adult_sepsis",
|
| 393 |
+
"adult_sepsis",
|
| 394 |
+
"adult_sepsis",
|
| 395 |
+
"adult_sepsis",
|
| 396 |
+
"adult_sepsis",
|
| 397 |
+
"adult_sepsis",
|
| 398 |
+
"adult_sepsis",
|
| 399 |
+
"adult_sepsis",
|
| 400 |
+
"adult_sepsis"
|
| 401 |
+
]
|
| 402 |
+
},
|
| 403 |
+
"deg_definition": {
|
| 404 |
+
"enabled": true,
|
| 405 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
| 406 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
|
| 407 |
+
"functions": [
|
| 408 |
+
"welch_bh_deg",
|
| 409 |
+
"top_deg_genes",
|
| 410 |
+
"jaccard"
|
| 411 |
+
],
|
| 412 |
+
"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",
|
| 413 |
+
"top_n": 50,
|
| 414 |
+
"fdr": 0.05,
|
| 415 |
+
"n_genes": 5975,
|
| 416 |
+
"types": [
|
| 417 |
+
"T cell",
|
| 418 |
+
"B cell",
|
| 419 |
+
"Monocyte",
|
| 420 |
+
"NK cell",
|
| 421 |
+
"DC"
|
| 422 |
+
],
|
| 423 |
+
"aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz",
|
| 424 |
+
"aggregates_sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0",
|
| 425 |
+
"aggregates_note": null,
|
| 426 |
+
"types_not_scored_observed": [],
|
| 427 |
+
"observed": {
|
| 428 |
+
"T cell": {
|
| 429 |
+
"n_significant": 1578,
|
| 430 |
+
"n_tested": 5810,
|
| 431 |
+
"n_case_donors": 61,
|
| 432 |
+
"n_control_donors": 21,
|
| 433 |
+
"n_cells": 298117,
|
| 434 |
+
"top_list_size": 50
|
| 435 |
+
},
|
| 436 |
+
"B cell": {
|
| 437 |
+
"n_significant": 1102,
|
| 438 |
+
"n_tested": 5752,
|
| 439 |
+
"n_case_donors": 61,
|
| 440 |
+
"n_control_donors": 21,
|
| 441 |
+
"n_cells": 99729,
|
| 442 |
+
"top_list_size": 50
|
| 443 |
+
},
|
| 444 |
+
"Monocyte": {
|
| 445 |
+
"n_significant": 2459,
|
| 446 |
+
"n_tested": 5754,
|
| 447 |
+
"n_case_donors": 61,
|
| 448 |
+
"n_control_donors": 21,
|
| 449 |
+
"n_cells": 111269,
|
| 450 |
+
"top_list_size": 50
|
| 451 |
+
},
|
| 452 |
+
"NK cell": {
|
| 453 |
+
"n_significant": 1235,
|
| 454 |
+
"n_tested": 5623,
|
| 455 |
+
"n_case_donors": 61,
|
| 456 |
+
"n_control_donors": 21,
|
| 457 |
+
"n_cells": 47832,
|
| 458 |
+
"top_list_size": 50
|
| 459 |
+
},
|
| 460 |
+
"DC": {
|
| 461 |
+
"n_significant": 1572,
|
| 462 |
+
"n_tested": 5330,
|
| 463 |
+
"n_case_donors": 57,
|
| 464 |
+
"n_control_donors": 21,
|
| 465 |
+
"n_cells": 3300,
|
| 466 |
+
"top_list_size": 50
|
| 467 |
+
}
|
| 468 |
+
},
|
| 469 |
+
"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"
|
| 470 |
+
},
|
| 471 |
+
"headline": {
|
| 472 |
+
"zs_K1000": {
|
| 473 |
+
"comp_l1": 0.5094583598384997,
|
| 474 |
+
"comp_l1_obs_loo_null": 0.515468004498372,
|
| 475 |
+
"precision": 0.6169918699186991,
|
| 476 |
+
"coverage": 0.07398373983739838,
|
| 477 |
+
"precision_dm": 0.5752032520325203,
|
| 478 |
+
"coverage_dm": 0.07121951219512195,
|
| 479 |
+
"pb_r_median": 0.8786516011139656,
|
| 480 |
+
"pb_top1": 0.0975609756097561,
|
| 481 |
+
"mono_pct_gen": 36.77317073170731,
|
| 482 |
+
"mono_pct_obs": 20.817070783198325,
|
| 483 |
+
"median_umi_gen": 979.0,
|
| 484 |
+
"median_umi_obs": 1967.0,
|
| 485 |
+
"contrast_mean_cp10k_r_gen": -0.021848803748335324,
|
| 486 |
+
"contrast_pseudobulk_log1p_cpm_r_gen": 0.04940533892641523,
|
| 487 |
+
"contrast_mean_cp10k_r_broadcast": 0.31594581626202867,
|
| 488 |
+
"contrast_pseudobulk_log1p_cpm_r_broadcast": 0.29096860411544245,
|
| 489 |
+
"deg_top50_T": 3,
|
| 490 |
+
"deg_top50_B": 0,
|
| 491 |
+
"deg_top50_Mono": 4,
|
| 492 |
+
"deg_top50_NK": 1,
|
| 493 |
+
"deg_top50_DC": 1,
|
| 494 |
+
"deg_top50_sum": 9,
|
| 495 |
+
"deg_top50_max": 250,
|
| 496 |
+
"deg_top50_sum_4type": 8,
|
| 497 |
+
"deg_top50_sum_broadcast": 21,
|
| 498 |
+
"seconds": 29.7
|
| 499 |
+
}
|
| 500 |
+
},
|
| 501 |
+
"per_arm": {
|
| 502 |
+
"zs_K1000": {
|
| 503 |
+
"arm": "zs_K1000",
|
| 504 |
+
"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/zs__raw_all.npz",
|
| 505 |
+
"npz_sha256": "bcb34be0a83ca4d5934dbfa37022a46088c39b15029b2064cbe50efca9f74a9f",
|
| 506 |
+
"receipt_verified": true,
|
| 507 |
+
"generation": {
|
| 508 |
+
"checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
|
| 509 |
+
"checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
|
| 510 |
+
"input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/all_usable_raw.npz",
|
| 511 |
+
"input_condition_sha256": "ffcc1562915493d43b6970aec5791ec01193f7ed72a0f8ab8103bb45ce46c641",
|
| 512 |
+
"seed": 20260927,
|
| 513 |
+
"steps": 50,
|
| 514 |
+
"support_readout": "bernoulli",
|
| 515 |
+
"weights": "ema"
|
| 516 |
+
},
|
| 517 |
+
"condition_for_broadcast": {
|
| 518 |
+
"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/all_usable_raw.npz",
|
| 519 |
+
"sha256": "ffcc1562915493d43b6970aec5791ec01193f7ed72a0f8ab8103bb45ce46c641"
|
| 520 |
+
},
|
| 521 |
+
"poisson": {
|
| 522 |
+
"seed": 20260916,
|
| 523 |
+
"rule": "whole NPZ, rows in NPZ order",
|
| 524 |
+
"nnz_whole_npz": 41806783,
|
| 525 |
+
"median_library_whole_npz_panel": 979.0,
|
| 526 |
+
"n_rows_whole_npz": 123000
|
| 527 |
+
},
|
| 528 |
+
"annotation": {
|
| 529 |
+
"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 530 |
+
"zero_padded_model_genes": 0,
|
| 531 |
+
"label_counts": {
|
| 532 |
+
"Monocyte": 45231,
|
| 533 |
+
"T cell": 43713,
|
| 534 |
+
"B cell": 18529,
|
| 535 |
+
"NK cell": 11319,
|
| 536 |
+
"Other": 3049,
|
| 537 |
+
"DC": 1159
|
| 538 |
+
},
|
| 539 |
+
"mean_l2_max_prob": 0.9337576795042288,
|
| 540 |
+
"predict_seconds": 6.9
|
| 541 |
+
},
|
| 542 |
+
"n_donors": 82,
|
| 543 |
+
"n_generated_cells": 123000,
|
| 544 |
+
"composition": {
|
| 545 |
+
"l1_mean": 0.5094583598384997,
|
| 546 |
+
"l1_median": 0.43554859946210034,
|
| 547 |
+
"l1_obs_loo_null_mean": 0.515468004498372,
|
| 548 |
+
"l1_generated_loo_mean_vs_observed_mean": 0.5986166826642287,
|
| 549 |
+
"composition_top1": 0.06097560975609756,
|
| 550 |
+
"mean_fraction_generated": {
|
| 551 |
+
"T cell": 0.35539,
|
| 552 |
+
"B cell": 0.150642,
|
| 553 |
+
"Monocyte": 0.367732,
|
| 554 |
+
"NK cell": 0.092024,
|
| 555 |
+
"DC": 0.009423,
|
| 556 |
+
"Other": 0.024789
|
| 557 |
+
},
|
| 558 |
+
"mean_fraction_observed": {
|
| 559 |
+
"T cell": 0.484547,
|
| 560 |
+
"B cell": 0.172757,
|
| 561 |
+
"Monocyte": 0.208171,
|
| 562 |
+
"NK cell": 0.080723,
|
| 563 |
+
"DC": 0.005542,
|
| 564 |
+
"Other": 0.04826
|
| 565 |
+
}
|
| 566 |
+
},
|
| 567 |
+
"pseudobulk": {
|
| 568 |
+
"n_genes": 5975,
|
| 569 |
+
"r_median": 0.8786516011139656,
|
| 570 |
+
"r_mean": 0.8701814218205658,
|
| 571 |
+
"top1": 0.0975609756097561,
|
| 572 |
+
"n_top1": 8,
|
| 573 |
+
"own_rank_median": 17.0,
|
| 574 |
+
"chance_top1": 0.012195121951219513
|
| 575 |
+
},
|
| 576 |
+
"precision_coverage": {
|
| 577 |
+
"precision": 0.6169918699186991,
|
| 578 |
+
"coverage": 0.07398373983739838,
|
| 579 |
+
"density": 0.2257073170731707,
|
| 580 |
+
"n_query": 12300,
|
| 581 |
+
"n_reference": 12300
|
| 582 |
+
},
|
| 583 |
+
"precision_coverage_depth_matched": {
|
| 584 |
+
"precision": 0.5752032520325203,
|
| 585 |
+
"coverage": 0.07121951219512195,
|
| 586 |
+
"density": 0.1904959349593496,
|
| 587 |
+
"detected_median_before": {
|
| 588 |
+
"R1": 411.0,
|
| 589 |
+
"Q": 340.0
|
| 590 |
+
},
|
| 591 |
+
"detected_median_after": {
|
| 592 |
+
"R1": 333.0,
|
| 593 |
+
"Q": 333.0
|
| 594 |
+
}
|
| 595 |
+
},
|
| 596 |
+
"monocyte_pct": {
|
| 597 |
+
"generated_mean_over_donors": 36.77317073170731,
|
| 598 |
+
"observed_mean_over_donors": 20.817070783198325,
|
| 599 |
+
"generated_pooled_cells": 36.77317073170732
|
| 600 |
+
},
|
| 601 |
+
"median_umi_per_cell_scoring_genes": {
|
| 602 |
+
"generated_pooled": 979.0,
|
| 603 |
+
"observed_pooled": 1967.0,
|
| 604 |
+
"generated_mean_of_donor_medians": 1041.28662109375,
|
| 605 |
+
"observed_mean_of_donor_medians": 2112.9146341463415
|
| 606 |
+
},
|
| 607 |
+
"contrast": {
|
| 608 |
+
"mean_cp10k": {
|
| 609 |
+
"per_type": {
|
| 610 |
+
"T cell": {
|
| 611 |
+
"r_generated": -0.10432230143312773,
|
| 612 |
+
"r_broadcast": 0.2548893770824626,
|
| 613 |
+
"partial_r_generated_given_broadcast": -0.17298372266935502,
|
| 614 |
+
"r_generated_vs_broadcast": 0.2294525413871452,
|
| 615 |
+
"n_genes": 3258
|
| 616 |
+
},
|
| 617 |
+
"B cell": {
|
| 618 |
+
"r_generated": 0.047437779482892545,
|
| 619 |
+
"r_broadcast": 0.27458639801653467,
|
| 620 |
+
"partial_r_generated_given_broadcast": -0.015553323632773097,
|
| 621 |
+
"r_generated_vs_broadcast": 0.2258194826100485,
|
| 622 |
+
"n_genes": 3310
|
| 623 |
+
},
|
| 624 |
+
"Monocyte": {
|
| 625 |
+
"r_generated": 0.049849833404431006,
|
| 626 |
+
"r_broadcast": 0.5481103923782986,
|
| 627 |
+
"partial_r_generated_given_broadcast": -0.0829739879467094,
|
| 628 |
+
"r_generated_vs_broadcast": 0.21461492174973537,
|
| 629 |
+
"n_genes": 3289
|
| 630 |
+
},
|
| 631 |
+
"NK cell": {
|
| 632 |
+
"r_generated": -0.08036052644753712,
|
| 633 |
+
"r_broadcast": 0.1861970975708186,
|
| 634 |
+
"partial_r_generated_given_broadcast": -0.14059337337126476,
|
| 635 |
+
"r_generated_vs_broadcast": 0.2805016269078411,
|
| 636 |
+
"n_genes": 3240
|
| 637 |
+
}
|
| 638 |
+
},
|
| 639 |
+
"mean_r_generated": -0.021848803748335324,
|
| 640 |
+
"mean_r_broadcast": 0.31594581626202867,
|
| 641 |
+
"mean_partial_r": -0.10302610190502556
|
| 642 |
+
},
|
| 643 |
+
"pseudobulk_log1p_cpm": {
|
| 644 |
+
"per_type": {
|
| 645 |
+
"T cell": {
|
| 646 |
+
"r_generated": -0.026301310225745313,
|
| 647 |
+
"r_broadcast": 0.2164745523777111,
|
| 648 |
+
"partial_r_generated_given_broadcast": -0.0886971581714242,
|
| 649 |
+
"r_generated_vs_broadcast": 0.2642967617857989,
|
| 650 |
+
"n_genes": 3258
|
| 651 |
+
},
|
| 652 |
+
"B cell": {
|
| 653 |
+
"r_generated": 0.09858083558441715,
|
| 654 |
+
"r_broadcast": 0.2711145517540278,
|
| 655 |
+
"partial_r_generated_given_broadcast": 0.03901229562465431,
|
| 656 |
+
"r_generated_vs_broadcast": 0.22878001258534544,
|
| 657 |
+
"n_genes": 3310
|
| 658 |
+
},
|
| 659 |
+
"Monocyte": {
|
| 660 |
+
"r_generated": 0.18929013682344356,
|
| 661 |
+
"r_broadcast": 0.6203629305570988,
|
| 662 |
+
"partial_r_generated_given_broadcast": -0.05740162287711388,
|
| 663 |
+
"r_generated_vs_broadcast": 0.3724778103826463,
|
| 664 |
+
"n_genes": 3289
|
| 665 |
+
},
|
| 666 |
+
"NK cell": {
|
| 667 |
+
"r_generated": -0.06394830647645451,
|
| 668 |
+
"r_broadcast": 0.05592238177293225,
|
| 669 |
+
"partial_r_generated_given_broadcast": -0.08252801674133732,
|
| 670 |
+
"r_generated_vs_broadcast": 0.27367752588949024,
|
| 671 |
+
"n_genes": 3240
|
| 672 |
+
}
|
| 673 |
+
},
|
| 674 |
+
"mean_r_generated": 0.04940533892641523,
|
| 675 |
+
"mean_r_broadcast": 0.29096860411544245,
|
| 676 |
+
"mean_partial_r": -0.04740362554130527
|
| 677 |
+
}
|
| 678 |
+
},
|
| 679 |
+
"deg_top50": {
|
| 680 |
+
"types_scored": [
|
| 681 |
+
"T cell",
|
| 682 |
+
"B cell",
|
| 683 |
+
"Monocyte",
|
| 684 |
+
"NK cell",
|
| 685 |
+
"DC"
|
| 686 |
+
],
|
| 687 |
+
"types_not_scored": {},
|
| 688 |
+
"per_type": {
|
| 689 |
+
"T cell": {
|
| 690 |
+
"deg_scored": true,
|
| 691 |
+
"top50_overlap": 3,
|
| 692 |
+
"top50_jaccard": 0.030927835051546393,
|
| 693 |
+
"obs_top_list_size": 50,
|
| 694 |
+
"gen_top_list_size": 50,
|
| 695 |
+
"top50_overlap_broadcast": 3,
|
| 696 |
+
"top50_jaccard_broadcast": 0.030927835051546393,
|
| 697 |
+
"n_cells_obs": 298117,
|
| 698 |
+
"n_cells_gen": 43713
|
| 699 |
+
},
|
| 700 |
+
"B cell": {
|
| 701 |
+
"deg_scored": true,
|
| 702 |
+
"top50_overlap": 0,
|
| 703 |
+
"top50_jaccard": 0.0,
|
| 704 |
+
"obs_top_list_size": 50,
|
| 705 |
+
"gen_top_list_size": 50,
|
| 706 |
+
"top50_overlap_broadcast": 2,
|
| 707 |
+
"top50_jaccard_broadcast": 0.02040816326530612,
|
| 708 |
+
"n_cells_obs": 99729,
|
| 709 |
+
"n_cells_gen": 18529
|
| 710 |
+
},
|
| 711 |
+
"Monocyte": {
|
| 712 |
+
"deg_scored": true,
|
| 713 |
+
"top50_overlap": 4,
|
| 714 |
+
"top50_jaccard": 0.041666666666666664,
|
| 715 |
+
"obs_top_list_size": 50,
|
| 716 |
+
"gen_top_list_size": 50,
|
| 717 |
+
"top50_overlap_broadcast": 13,
|
| 718 |
+
"top50_jaccard_broadcast": 0.14942528735632185,
|
| 719 |
+
"n_cells_obs": 111269,
|
| 720 |
+
"n_cells_gen": 45231
|
| 721 |
+
},
|
| 722 |
+
"NK cell": {
|
| 723 |
+
"deg_scored": true,
|
| 724 |
+
"top50_overlap": 1,
|
| 725 |
+
"top50_jaccard": 0.010101010101010102,
|
| 726 |
+
"obs_top_list_size": 50,
|
| 727 |
+
"gen_top_list_size": 50,
|
| 728 |
+
"top50_overlap_broadcast": 2,
|
| 729 |
+
"top50_jaccard_broadcast": 0.02040816326530612,
|
| 730 |
+
"n_cells_obs": 47832,
|
| 731 |
+
"n_cells_gen": 11319
|
| 732 |
+
},
|
| 733 |
+
"DC": {
|
| 734 |
+
"deg_scored": true,
|
| 735 |
+
"top50_overlap": 1,
|
| 736 |
+
"top50_jaccard": 0.010416666666666666,
|
| 737 |
+
"obs_top_list_size": 50,
|
| 738 |
+
"gen_top_list_size": 47,
|
| 739 |
+
"top50_overlap_broadcast": 1,
|
| 740 |
+
"top50_jaccard_broadcast": 0.010101010101010102,
|
| 741 |
+
"n_cells_obs": 3300,
|
| 742 |
+
"n_cells_gen": 1159
|
| 743 |
+
}
|
| 744 |
+
},
|
| 745 |
+
"sum": 9,
|
| 746 |
+
"sum_4type": 8,
|
| 747 |
+
"max": 250,
|
| 748 |
+
"mean": 1.8,
|
| 749 |
+
"sum_broadcast": 21,
|
| 750 |
+
"sum_broadcast_4type": 20,
|
| 751 |
+
"broadcast_n_significant": 1378,
|
| 752 |
+
"seconds": 0.52
|
| 753 |
+
},
|
| 754 |
+
"seconds": 29.7
|
| 755 |
+
}
|
| 756 |
+
},
|
| 757 |
+
"code_sha256": {
|
| 758 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 759 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
|
| 760 |
+
"/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",
|
| 761 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
|
| 762 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
|
| 763 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
|
| 764 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
|
| 765 |
+
},
|
| 766 |
+
"seconds": 41.8
|
| 767 |
+
}
|