Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold2/per_donor.csv +7 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold2/summary.json +457 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/arms/scsemi__raw/deg_top50_lists.csv +24 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/arms/scsemi__raw/generated_cells.parquet +3 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold2/per_donor.csv
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
|
| 2 |
+
scsemi__raw,2AD75E_d0,mild,1500,7693,150,0.6686666666666666,0.6034056934875861,0.036,0.06408423241908229,0.16266666666666665,0.14064734173924348,0.11533333333333333,0.15949564539191471,0.002,0.025347718705316522,0.015333333333333332,0.007019368256856883,0.19118852636596034,0.27979198209841943,0.5917595856033825,3,False,1.0,0.8066666666666666,0.84,0.29333333333333333,16.266666666666666,14.064734173924348,487.0,532.0
|
| 3 |
+
scsemi__raw,2AD75E_d7,mild,1500,10499,150,0.6926666666666667,0.5808172206876845,0.04133333333333333,0.14372797409277074,0.14066666666666666,0.10277169254214687,0.10666666666666667,0.14715687208305553,0.005333333333333333,0.013715591961139155,0.013333333333333334,0.011810648633203162,0.30253420960726424,0.33995903279163037,0.6062670315494059,1,True,1.0,0.8933333333333333,0.8933333333333333,0.3933333333333333,14.066666666666666,10.277169254214687,487.0,443.0
|
| 4 |
+
scsemi__raw,2AD75E_d14,mild,1500,13692,150,0.694,0.5811422728600643,0.043333333333333335,0.12503651767455448,0.15,0.14198071866783524,0.08733333333333333,0.12496348232544552,0.008,0.016579024247735902,0.017333333333333333,0.010297984224364592,0.2558247151621384,0.3177615914184477,0.591443566405085,2,False,1.0,0.9133333333333333,0.86,0.3933333333333333,15.0,14.198071866783524,487.0,428.0
|
| 5 |
+
scsemi__raw,180E1A_d0,severe,1500,7157,150,0.6286666666666667,0.7019700992035769,0.094,0.04135811094033813,0.16066666666666668,0.13175911694844208,0.09866666666666667,0.0655302501047925,0.004666666666666667,0.013273718038284197,0.013333333333333334,0.04610870476456616,0.22937171067952117,0.3064138811005136,0.6142210890148238,6,False,1.0,0.84,0.68,0.36,16.066666666666666,13.175911694844208,486.0,433.0
|
| 6 |
+
scsemi__raw,180E1A_d7,severe,1500,10591,150,0.5446666666666666,0.7348692285903126,0.035333333333333335,0.04909829100179398,0.212,0.09064299877254273,0.178,0.08280615617033331,0.009333333333333334,0.010480596733075253,0.020666666666666667,0.03210272873194221,0.433101690114248,0.33761512254466985,0.6136145963010454,3,False,1.0,0.8933333333333333,0.74,0.24666666666666667,21.2,9.064299877254273,487.0,408.0
|
| 7 |
+
scsemi__raw,180E1A_d14,severe,1500,12511,150,0.6633333333333333,0.680840860043162,0.10066666666666667,0.05147470226200943,0.12,0.12277196067460634,0.07866666666666666,0.0800095915594277,0.007333333333333333,0.009831348413396212,0.03,0.05507153704739829,0.09838392880931449,0.275496002081281,0.6596975131129077,1,True,1.0,0.88,0.74,0.4266666666666667,12.0,12.277196067460634,488.0,342.0
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold2/summary.json
ADDED
|
@@ -0,0 +1,457 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "giroux2022",
|
| 4 |
+
"written_utc": "2026-10-08T01:56:10.152081+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"giroux2022",
|
| 9 |
+
"--out",
|
| 10 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold2",
|
| 11 |
+
"--threads",
|
| 12 |
+
"8",
|
| 13 |
+
"--arm",
|
| 14 |
+
"scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fold2/scsemi__raw.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"severe",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"mild"
|
| 19 |
+
],
|
| 20 |
+
"arms": [
|
| 21 |
+
"scsemi__raw"
|
| 22 |
+
],
|
| 23 |
+
"donors": [
|
| 24 |
+
"2AD75E_d0",
|
| 25 |
+
"2AD75E_d7",
|
| 26 |
+
"2AD75E_d14",
|
| 27 |
+
"180E1A_d0",
|
| 28 |
+
"180E1A_d7",
|
| 29 |
+
"180E1A_d14"
|
| 30 |
+
],
|
| 31 |
+
"n_donors": 6,
|
| 32 |
+
"reference": {
|
| 33 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
|
| 34 |
+
"reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
|
| 35 |
+
"features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
|
| 36 |
+
"n_r1_cells": 900,
|
| 37 |
+
"pca": {
|
| 38 |
+
"n_components": 50,
|
| 39 |
+
"explained_variance_ratio_sum": 0.27353203296661377,
|
| 40 |
+
"n_fit_cells": 900
|
| 41 |
+
},
|
| 42 |
+
"r2_control": {
|
| 43 |
+
"precision": 1.0,
|
| 44 |
+
"coverage": 1.0,
|
| 45 |
+
"density": 8.636888888888889,
|
| 46 |
+
"n_query": 900,
|
| 47 |
+
"depth_matched": {
|
| 48 |
+
"precision": 1.0,
|
| 49 |
+
"coverage": 1.0,
|
| 50 |
+
"density": 8.635111111111112
|
| 51 |
+
}
|
| 52 |
+
},
|
| 53 |
+
"observed_l1_loo_null_mean": 0.30950626867249365
|
| 54 |
+
},
|
| 55 |
+
"contrast_definition": {
|
| 56 |
+
"enabled": true,
|
| 57 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 58 |
+
"group_source": "features groups",
|
| 59 |
+
"case_groups": [
|
| 60 |
+
"severe"
|
| 61 |
+
],
|
| 62 |
+
"control_groups": [
|
| 63 |
+
"mild"
|
| 64 |
+
],
|
| 65 |
+
"n_case_donors": 3,
|
| 66 |
+
"n_control_donors": 3,
|
| 67 |
+
"n_donors_in_neither": 0,
|
| 68 |
+
"case": [
|
| 69 |
+
false,
|
| 70 |
+
false,
|
| 71 |
+
false,
|
| 72 |
+
true,
|
| 73 |
+
true,
|
| 74 |
+
true
|
| 75 |
+
],
|
| 76 |
+
"ctrl": [
|
| 77 |
+
true,
|
| 78 |
+
true,
|
| 79 |
+
true,
|
| 80 |
+
false,
|
| 81 |
+
false,
|
| 82 |
+
false
|
| 83 |
+
],
|
| 84 |
+
"groups": [
|
| 85 |
+
"mild",
|
| 86 |
+
"mild",
|
| 87 |
+
"mild",
|
| 88 |
+
"severe",
|
| 89 |
+
"severe",
|
| 90 |
+
"severe"
|
| 91 |
+
]
|
| 92 |
+
},
|
| 93 |
+
"deg_definition": {
|
| 94 |
+
"enabled": true,
|
| 95 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
| 96 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
|
| 97 |
+
"functions": [
|
| 98 |
+
"welch_bh_deg",
|
| 99 |
+
"top_deg_genes",
|
| 100 |
+
"jaccard"
|
| 101 |
+
],
|
| 102 |
+
"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",
|
| 103 |
+
"top_n": 50,
|
| 104 |
+
"fdr": 0.05,
|
| 105 |
+
"n_genes": 5563,
|
| 106 |
+
"types": [
|
| 107 |
+
"T cell",
|
| 108 |
+
"B cell",
|
| 109 |
+
"Monocyte",
|
| 110 |
+
"NK cell",
|
| 111 |
+
"DC"
|
| 112 |
+
],
|
| 113 |
+
"aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022/deg_reference.npz",
|
| 114 |
+
"aggregates_sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e",
|
| 115 |
+
"aggregates_note": null,
|
| 116 |
+
"types_not_scored_observed": [],
|
| 117 |
+
"observed": {
|
| 118 |
+
"T cell": {
|
| 119 |
+
"n_significant": 824,
|
| 120 |
+
"n_tested": 5175,
|
| 121 |
+
"n_case_donors": 3,
|
| 122 |
+
"n_control_donors": 3,
|
| 123 |
+
"n_cells": 40022,
|
| 124 |
+
"top_list_size": 50
|
| 125 |
+
},
|
| 126 |
+
"B cell": {
|
| 127 |
+
"n_significant": 0,
|
| 128 |
+
"n_tested": 4751,
|
| 129 |
+
"n_case_donors": 3,
|
| 130 |
+
"n_control_donors": 3,
|
| 131 |
+
"n_cells": 5174,
|
| 132 |
+
"top_list_size": 0
|
| 133 |
+
},
|
| 134 |
+
"Monocyte": {
|
| 135 |
+
"n_significant": 5,
|
| 136 |
+
"n_tested": 4888,
|
| 137 |
+
"n_case_donors": 3,
|
| 138 |
+
"n_control_donors": 3,
|
| 139 |
+
"n_cells": 7544,
|
| 140 |
+
"top_list_size": 5
|
| 141 |
+
},
|
| 142 |
+
"NK cell": {
|
| 143 |
+
"n_significant": 3,
|
| 144 |
+
"n_tested": 4794,
|
| 145 |
+
"n_case_donors": 3,
|
| 146 |
+
"n_control_donors": 3,
|
| 147 |
+
"n_cells": 6830,
|
| 148 |
+
"top_list_size": 3
|
| 149 |
+
},
|
| 150 |
+
"DC": {
|
| 151 |
+
"n_significant": 0,
|
| 152 |
+
"n_tested": 4427,
|
| 153 |
+
"n_case_donors": 3,
|
| 154 |
+
"n_control_donors": 3,
|
| 155 |
+
"n_cells": 895,
|
| 156 |
+
"top_list_size": 0
|
| 157 |
+
}
|
| 158 |
+
},
|
| 159 |
+
"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"
|
| 160 |
+
},
|
| 161 |
+
"headline": {
|
| 162 |
+
"scsemi__raw": {
|
| 163 |
+
"comp_l1": 0.25173413012307444,
|
| 164 |
+
"comp_l1_obs_loo_null": 0.30950626867249365,
|
| 165 |
+
"precision": 1.0,
|
| 166 |
+
"coverage": 0.8711111111111111,
|
| 167 |
+
"precision_dm": 0.7922222222222223,
|
| 168 |
+
"coverage_dm": 0.3522222222222222,
|
| 169 |
+
"pb_r_median": 0.6099408139252256,
|
| 170 |
+
"pb_top1": 0.3333333333333333,
|
| 171 |
+
"mono_pct_gen": 15.766666666666667,
|
| 172 |
+
"mono_pct_obs": 12.17623048908028,
|
| 173 |
+
"median_umi_gen": 487.0,
|
| 174 |
+
"median_umi_obs": 428.0,
|
| 175 |
+
"contrast_mean_cp10k_r_gen": 0.31242290903775627,
|
| 176 |
+
"contrast_pseudobulk_log1p_cpm_r_gen": 0.18298919596276164,
|
| 177 |
+
"contrast_mean_cp10k_r_broadcast": 0.32683278426853035,
|
| 178 |
+
"contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5526476790228007,
|
| 179 |
+
"deg_top50_T": 0,
|
| 180 |
+
"deg_top50_B": 0,
|
| 181 |
+
"deg_top50_Mono": 0,
|
| 182 |
+
"deg_top50_NK": 0,
|
| 183 |
+
"deg_top50_DC": 0,
|
| 184 |
+
"deg_top50_sum": 0,
|
| 185 |
+
"deg_top50_max": 58,
|
| 186 |
+
"deg_top50_sum_4type": 0,
|
| 187 |
+
"deg_top50_sum_broadcast": 2,
|
| 188 |
+
"seconds": 3.8
|
| 189 |
+
}
|
| 190 |
+
},
|
| 191 |
+
"per_arm": {
|
| 192 |
+
"scsemi__raw": {
|
| 193 |
+
"arm": "scsemi__raw",
|
| 194 |
+
"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fold2/scsemi__raw.npz",
|
| 195 |
+
"npz_sha256": "219d7e8499c90e2478d4d58cc803e167860ed8e10599450a9ea29939e8347d51",
|
| 196 |
+
"receipt_verified": true,
|
| 197 |
+
"generation": {
|
| 198 |
+
"checkpoint": null,
|
| 199 |
+
"checkpoint_sha256": null,
|
| 200 |
+
"input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fold2/test_raw.npz",
|
| 201 |
+
"input_condition_sha256": "90810fa9b6fef46663327f6486e61d7aafeacd5fc0c95513e6fdd7f46023bcb5",
|
| 202 |
+
"seed": 20260927,
|
| 203 |
+
"steps": null,
|
| 204 |
+
"support_readout": "upstream (values <= 10 normalized units zeroed by fast_semi)",
|
| 205 |
+
"weights": null
|
| 206 |
+
},
|
| 207 |
+
"condition_for_broadcast": {
|
| 208 |
+
"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fold2/test_raw.npz",
|
| 209 |
+
"sha256": "90810fa9b6fef46663327f6486e61d7aafeacd5fc0c95513e6fdd7f46023bcb5"
|
| 210 |
+
},
|
| 211 |
+
"poisson": {
|
| 212 |
+
"seed": 20260916,
|
| 213 |
+
"rule": "whole NPZ, rows in NPZ order",
|
| 214 |
+
"nnz_whole_npz": 999949,
|
| 215 |
+
"median_library_whole_npz_panel": 487.0,
|
| 216 |
+
"n_rows_whole_npz": 9000
|
| 217 |
+
},
|
| 218 |
+
"annotation": {
|
| 219 |
+
"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 220 |
+
"zero_padded_model_genes": 0,
|
| 221 |
+
"label_counts": {
|
| 222 |
+
"T cell": 5838,
|
| 223 |
+
"Monocyte": 1419,
|
| 224 |
+
"NK cell": 997,
|
| 225 |
+
"B cell": 526,
|
| 226 |
+
"Other": 165,
|
| 227 |
+
"DC": 55
|
| 228 |
+
},
|
| 229 |
+
"mean_l2_max_prob": 0.8373674499011702,
|
| 230 |
+
"predict_seconds": 2.9
|
| 231 |
+
},
|
| 232 |
+
"n_donors": 6,
|
| 233 |
+
"n_generated_cells": 9000,
|
| 234 |
+
"composition": {
|
| 235 |
+
"l1_mean": 0.25173413012307444,
|
| 236 |
+
"l1_median": 0.24259821292082978,
|
| 237 |
+
"l1_obs_loo_null_mean": 0.30950626867249365,
|
| 238 |
+
"l1_generated_loo_mean_vs_observed_mean": 0.13981322332880128,
|
| 239 |
+
"composition_top1": 0.16666666666666666,
|
| 240 |
+
"mean_fraction_generated": {
|
| 241 |
+
"T cell": 0.648667,
|
| 242 |
+
"B cell": 0.058444,
|
| 243 |
+
"Monocyte": 0.157667,
|
| 244 |
+
"NK cell": 0.110778,
|
| 245 |
+
"DC": 0.006111,
|
| 246 |
+
"Other": 0.018333
|
| 247 |
+
},
|
| 248 |
+
"mean_fraction_observed": {
|
| 249 |
+
"T cell": 0.647174,
|
| 250 |
+
"B cell": 0.07913,
|
| 251 |
+
"Monocyte": 0.121762,
|
| 252 |
+
"NK cell": 0.109994,
|
| 253 |
+
"DC": 0.014871,
|
| 254 |
+
"Other": 0.027068
|
| 255 |
+
}
|
| 256 |
+
},
|
| 257 |
+
"pseudobulk": {
|
| 258 |
+
"n_genes": 5563,
|
| 259 |
+
"r_median": 0.6099408139252256,
|
| 260 |
+
"r_mean": 0.612833896997775,
|
| 261 |
+
"top1": 0.3333333333333333,
|
| 262 |
+
"n_top1": 2,
|
| 263 |
+
"own_rank_median": 2.5,
|
| 264 |
+
"chance_top1": 0.16666666666666666
|
| 265 |
+
},
|
| 266 |
+
"precision_coverage": {
|
| 267 |
+
"precision": 1.0,
|
| 268 |
+
"coverage": 0.8711111111111111,
|
| 269 |
+
"density": 3.8004444444444445,
|
| 270 |
+
"n_query": 900,
|
| 271 |
+
"n_reference": 900
|
| 272 |
+
},
|
| 273 |
+
"precision_coverage_depth_matched": {
|
| 274 |
+
"precision": 0.7922222222222223,
|
| 275 |
+
"coverage": 0.3522222222222222,
|
| 276 |
+
"density": 0.3967777777777778,
|
| 277 |
+
"detected_median_before": {
|
| 278 |
+
"R1": 230.0,
|
| 279 |
+
"Q": 107.0
|
| 280 |
+
},
|
| 281 |
+
"detected_median_after": {
|
| 282 |
+
"R1": 107.0,
|
| 283 |
+
"Q": 107.0
|
| 284 |
+
}
|
| 285 |
+
},
|
| 286 |
+
"monocyte_pct": {
|
| 287 |
+
"generated_mean_over_donors": 15.766666666666667,
|
| 288 |
+
"observed_mean_over_donors": 12.17623048908028,
|
| 289 |
+
"generated_pooled_cells": 15.766666666666667
|
| 290 |
+
},
|
| 291 |
+
"median_umi_per_cell_scoring_genes": {
|
| 292 |
+
"generated_pooled": 487.0,
|
| 293 |
+
"observed_pooled": 428.0,
|
| 294 |
+
"generated_mean_of_donor_medians": 487.0,
|
| 295 |
+
"observed_mean_of_donor_medians": 431.0
|
| 296 |
+
},
|
| 297 |
+
"contrast": {
|
| 298 |
+
"mean_cp10k": {
|
| 299 |
+
"per_type": {
|
| 300 |
+
"T cell": {
|
| 301 |
+
"r_generated": 0.4008055026519221,
|
| 302 |
+
"r_broadcast": 0.30966577451220284,
|
| 303 |
+
"partial_r_generated_given_broadcast": 0.34550805510905336,
|
| 304 |
+
"r_generated_vs_broadcast": 0.27402339827414474,
|
| 305 |
+
"n_genes": 2784
|
| 306 |
+
},
|
| 307 |
+
"B cell": {
|
| 308 |
+
"r_generated": 0.24433725091042072,
|
| 309 |
+
"r_broadcast": 0.3058342551145908,
|
| 310 |
+
"partial_r_generated_given_broadcast": 0.20132417412071743,
|
| 311 |
+
"r_generated_vs_broadcast": 0.1827363989732401,
|
| 312 |
+
"n_genes": 2943
|
| 313 |
+
},
|
| 314 |
+
"Monocyte": {
|
| 315 |
+
"r_generated": 0.3155988171210716,
|
| 316 |
+
"r_broadcast": 0.3574346964728684,
|
| 317 |
+
"partial_r_generated_given_broadcast": 0.2837136473450366,
|
| 318 |
+
"r_generated_vs_broadcast": 0.15003310229403524,
|
| 319 |
+
"n_genes": 3019
|
| 320 |
+
},
|
| 321 |
+
"NK cell": {
|
| 322 |
+
"r_generated": 0.2889500654676106,
|
| 323 |
+
"r_broadcast": 0.33439641097445927,
|
| 324 |
+
"partial_r_generated_given_broadcast": 0.2535462264867015,
|
| 325 |
+
"r_generated_vs_broadcast": 0.15856283855560205,
|
| 326 |
+
"n_genes": 2879
|
| 327 |
+
}
|
| 328 |
+
},
|
| 329 |
+
"mean_r_generated": 0.31242290903775627,
|
| 330 |
+
"mean_r_broadcast": 0.32683278426853035,
|
| 331 |
+
"mean_partial_r": 0.27102302576537723
|
| 332 |
+
},
|
| 333 |
+
"pseudobulk_log1p_cpm": {
|
| 334 |
+
"per_type": {
|
| 335 |
+
"T cell": {
|
| 336 |
+
"r_generated": 0.30569707714977723,
|
| 337 |
+
"r_broadcast": 0.5497627805837346,
|
| 338 |
+
"partial_r_generated_given_broadcast": 0.18709570650031132,
|
| 339 |
+
"r_generated_vs_broadcast": 0.28343329589227595,
|
| 340 |
+
"n_genes": 2784
|
| 341 |
+
},
|
| 342 |
+
"B cell": {
|
| 343 |
+
"r_generated": 0.12672962810244418,
|
| 344 |
+
"r_broadcast": 0.5414361396943234,
|
| 345 |
+
"partial_r_generated_given_broadcast": 0.05119218380693279,
|
| 346 |
+
"r_generated_vs_broadcast": 0.1555382142596088,
|
| 347 |
+
"n_genes": 2943
|
| 348 |
+
},
|
| 349 |
+
"Monocyte": {
|
| 350 |
+
"r_generated": 0.1497047702789244,
|
| 351 |
+
"r_broadcast": 0.5691948795446303,
|
| 352 |
+
"partial_r_generated_given_broadcast": 0.12739021450068674,
|
| 353 |
+
"r_generated_vs_broadcast": 0.07957974508039928,
|
| 354 |
+
"n_genes": 3019
|
| 355 |
+
},
|
| 356 |
+
"NK cell": {
|
| 357 |
+
"r_generated": 0.14982530831990076,
|
| 358 |
+
"r_broadcast": 0.5501969162685141,
|
| 359 |
+
"partial_r_generated_given_broadcast": 0.09039892443570172,
|
| 360 |
+
"r_generated_vs_broadcast": 0.1363957293519263,
|
| 361 |
+
"n_genes": 2879
|
| 362 |
+
}
|
| 363 |
+
},
|
| 364 |
+
"mean_r_generated": 0.18298919596276164,
|
| 365 |
+
"mean_r_broadcast": 0.5526476790228007,
|
| 366 |
+
"mean_partial_r": 0.11401925731090815
|
| 367 |
+
}
|
| 368 |
+
},
|
| 369 |
+
"deg_top50": {
|
| 370 |
+
"types_scored": [
|
| 371 |
+
"T cell",
|
| 372 |
+
"B cell",
|
| 373 |
+
"Monocyte",
|
| 374 |
+
"NK cell",
|
| 375 |
+
"DC"
|
| 376 |
+
],
|
| 377 |
+
"types_not_scored": {},
|
| 378 |
+
"per_type": {
|
| 379 |
+
"T cell": {
|
| 380 |
+
"deg_scored": true,
|
| 381 |
+
"top50_overlap": 0,
|
| 382 |
+
"top50_jaccard": 0.0,
|
| 383 |
+
"obs_top_list_size": 50,
|
| 384 |
+
"gen_top_list_size": 0,
|
| 385 |
+
"top50_overlap_broadcast": 1,
|
| 386 |
+
"top50_jaccard_broadcast": 0.02,
|
| 387 |
+
"n_cells_obs": 40022,
|
| 388 |
+
"n_cells_gen": 5838
|
| 389 |
+
},
|
| 390 |
+
"B cell": {
|
| 391 |
+
"deg_scored": true,
|
| 392 |
+
"top50_overlap": 0,
|
| 393 |
+
"top50_jaccard": null,
|
| 394 |
+
"obs_top_list_size": 0,
|
| 395 |
+
"gen_top_list_size": 0,
|
| 396 |
+
"top50_overlap_broadcast": 0,
|
| 397 |
+
"top50_jaccard_broadcast": 0.0,
|
| 398 |
+
"n_cells_obs": 5174,
|
| 399 |
+
"n_cells_gen": 526
|
| 400 |
+
},
|
| 401 |
+
"Monocyte": {
|
| 402 |
+
"deg_scored": true,
|
| 403 |
+
"top50_overlap": 0,
|
| 404 |
+
"top50_jaccard": 0.0,
|
| 405 |
+
"obs_top_list_size": 5,
|
| 406 |
+
"gen_top_list_size": 0,
|
| 407 |
+
"top50_overlap_broadcast": 1,
|
| 408 |
+
"top50_jaccard_broadcast": 0.2,
|
| 409 |
+
"n_cells_obs": 7544,
|
| 410 |
+
"n_cells_gen": 1419
|
| 411 |
+
},
|
| 412 |
+
"NK cell": {
|
| 413 |
+
"deg_scored": true,
|
| 414 |
+
"top50_overlap": 0,
|
| 415 |
+
"top50_jaccard": 0.0,
|
| 416 |
+
"obs_top_list_size": 3,
|
| 417 |
+
"gen_top_list_size": 0,
|
| 418 |
+
"top50_overlap_broadcast": 0,
|
| 419 |
+
"top50_jaccard_broadcast": 0.0,
|
| 420 |
+
"n_cells_obs": 6830,
|
| 421 |
+
"n_cells_gen": 997
|
| 422 |
+
},
|
| 423 |
+
"DC": {
|
| 424 |
+
"deg_scored": true,
|
| 425 |
+
"top50_overlap": 0,
|
| 426 |
+
"top50_jaccard": null,
|
| 427 |
+
"obs_top_list_size": 0,
|
| 428 |
+
"gen_top_list_size": 0,
|
| 429 |
+
"top50_overlap_broadcast": 0,
|
| 430 |
+
"top50_jaccard_broadcast": 0.0,
|
| 431 |
+
"n_cells_obs": 895,
|
| 432 |
+
"n_cells_gen": 55
|
| 433 |
+
}
|
| 434 |
+
},
|
| 435 |
+
"sum": 0,
|
| 436 |
+
"sum_4type": 0,
|
| 437 |
+
"max": 58,
|
| 438 |
+
"mean": 0.0,
|
| 439 |
+
"sum_broadcast": 2,
|
| 440 |
+
"sum_broadcast_4type": 2,
|
| 441 |
+
"broadcast_n_significant": 1,
|
| 442 |
+
"seconds": 0.01
|
| 443 |
+
},
|
| 444 |
+
"seconds": 3.8
|
| 445 |
+
}
|
| 446 |
+
},
|
| 447 |
+
"code_sha256": {
|
| 448 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 449 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
|
| 450 |
+
"/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",
|
| 451 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
|
| 452 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
|
| 453 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
|
| 454 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
|
| 455 |
+
},
|
| 456 |
+
"seconds": 4.2
|
| 457 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/arms/scsemi__raw/deg_top50_lists.csv
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
celltype,source,rank,gene_id
|
| 2 |
+
T cell,observed,1,ENSG00000114374
|
| 3 |
+
T cell,observed,2,ENSG00000116983
|
| 4 |
+
T cell,generated,1,ENSG00000153283
|
| 5 |
+
B cell,observed,1,ENSG00000183878
|
| 6 |
+
B cell,observed,2,ENSG00000166444
|
| 7 |
+
B cell,observed,3,ENSG00000180611
|
| 8 |
+
B cell,observed,4,ENSG00000186187
|
| 9 |
+
B cell,observed,5,ENSG00000065923
|
| 10 |
+
B cell,observed,6,ENSG00000113810
|
| 11 |
+
B cell,observed,7,ENSG00000033122
|
| 12 |
+
B cell,observed,8,ENSG00000162747
|
| 13 |
+
B cell,observed,9,ENSG00000075391
|
| 14 |
+
B cell,observed,10,ENSG00000134317
|
| 15 |
+
B cell,observed,11,ENSG00000081148
|
| 16 |
+
B cell,observed,12,ENSG00000153162
|
| 17 |
+
B cell,observed,13,ENSG00000196569
|
| 18 |
+
B cell,observed,14,ENSG00000267368
|
| 19 |
+
B cell,observed,15,ENSG00000148346
|
| 20 |
+
B cell,observed,16,ENSG00000183230
|
| 21 |
+
B cell,observed,17,ENSG00000182326
|
| 22 |
+
B cell,observed,18,ENSG00000124343
|
| 23 |
+
Monocyte,observed,1,ENSG00000067048
|
| 24 |
+
Monocyte,observed,2,ENSG00000012817
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/arms/scsemi__raw/generated_cells.parquet
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:57a394b9b842d31aa9f164e44129fd9e0af67e5687b6194b6ec522e0d6e3ef79
|
| 3 |
+
size 69338
|