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  1. paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/headline.csv +6 -0
  2. paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/limma/R.log +3 -0
  3. paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/limma/jobs.csv +69 -0
  4. paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/limma/limma_status.csv +69 -0
paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/headline.csv ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ dataset,design,unit,arm,label,role,condition,pearson_r,spearman_r,partial_r,broadcast_pearson_r,broadcast_spearman_r,splithalf_r_AB,splithalf_r_AB_sd,splithalf_spearman_AB,sb_reliability,noise_free_ceiling,r_generated_vs_halfB,r_broadcast_vs_halfB,welch_top50,welch_top50_max,welch_top50_chance,welch_top50_broadcast,welch_top50_broadcast_chance,welch_n_sig_obs,welch_n_sig_gen,welch_n_sig_broadcast_per_type,welch_types_scored,limma_top50,limma_top50_max,limma_top50_chance,limma_top50_broadcast,limma_top50_broadcast_chance,limma_n_sig_obs,limma_n_sig_gen,limma_n_sig_broadcast_per_type,limma_types_scored,limma_fbe_top50,limma_fbe_top50_max,limma_fbe_top50_chance,limma_fbe_top50_broadcast,limma_fbe_top50_broadcast_chance,limma_fbe_n_sig_obs,limma_fbe_n_sig_gen,limma_fbe_n_sig_broadcast_per_type,limma_fbe_types_scored,cat50,cat50_chance,cat100,cat100_chance,rbo,rbo_up_down,cat_types,broadcast_cat50,broadcast_cat50_chance,broadcast_cat100,broadcast_cat100_chance,broadcast_rbo,broadcast_rbo_up_down,broadcast_cat_types,repro_pass
2
+ giroux2022,fewshot,fewshot_n5/draw2,zs_raw,"Zero-shot, real bulk",zs_raw,all_usable_raw.npz@ac755a41,0.13187725460083927,0.0479696906777865,-0.015048970829610778,0.39643909018360535,0.28957885738959505,0.9104124563197754,0.0015633021491813326,0.8127871688310353,0.9526629414859596,0.9759830070639475,0.13015142999533336,0.3866090394252903,0,63,0.0,0,0.0,63,0,0,5,0,161,0.0029411764705882353,17,0.32020040144308415,407,1,10,5,0,142,0.0,12,0.3649442474081072,404,0,8,5,0.012,0.0070218609636721625,0.016,0.014043721927344325,0.014357975669403989,0.014194429646700086,5,0.18,0.005032739915099746,0.16,0.010065479830199491,0.18991708023833048,0.1786452018716356,5,True
3
+ giroux2022,fewshot,fewshot_n5/draw2,zs_pseudo,"Zero-shot, sc pseudobulk input (reference)",other,all_usable_pseudo.npz@6400d82f,0.33617447099026354,0.29080581698518204,0.15916932694846841,0.6900599750313551,0.6768295934178677,0.9104124563197754,0.0015633021491813326,0.8127871688310353,0.9526629414859596,0.9759830070639475,0.3289924805831215,0.6742906105457502,0,63,0.007415647015202077,2,0.0373399034912725,63,3,3,5,1,161,0.41122064616440673,53,1.5941244231366665,407,33,154,5,0,142,0.17513784435707463,36,2.379232480182067,404,4,80,5,0.048,0.00917955058598061,0.068,0.01835910117196122,0.038879816208100326,0.057787626190680806,5,0.284,0.0050112541997134885,0.26599999999999996,0.010022508399426977,0.3264401451404372,0.292445806854585,5,True
4
+ giroux2022,fewshot,fewshot_n5/draw2,zs_cal,Zero-shot + calibration,zs_cal,test_cal.npz@8ac9ec21,0.12294495954442436,0.046907350729964395,0.02884327654231229,0.4135379923236512,0.28098912706766427,0.9104124563197754,0.0015633021491813326,0.8127871688310353,0.9526629414859596,0.9759830070639475,0.12121579536405473,0.4040239235047601,0,63,0.0,0,0.0,63,0,0,5,0,161,0.0,9,0.12808016057723368,407,0,4,5,0,142,0.0,8,0.1830826760685598,404,0,4,5,0.008,0.008245708198757102,0.028000000000000004,0.016491416397514204,0.028672539186293942,0.024554962796297118,5,0.176,0.005032739915099746,0.15,0.010065479830199491,0.19256239411650994,0.17165773637766116,5,True
5
+ giroux2022,fewshot,fewshot_n5/draw2,lora5,"LoRA, 5 donors",lora,test_raw.npz@fedb8e80,0.230513969445487,0.1559240583685004,0.15040912208962715,0.39643909018360535,0.28957885738959505,0.9104124563197754,0.0015633021491813326,0.8127871688310353,0.9526629414859596,0.9759830070639475,0.22682396314633807,0.3866090394252903,0,63,0.00355998576005696,0,0.0,63,1,0,5,2,161,0.9314214607267502,17,0.32020040144308415,407,284,10,5,0,142,0.0,12,0.3649442474081072,404,0,8,5,0.032,0.008446019316537986,0.019999999999999997,0.01689203863307597,0.012834424423892371,0.03794956946220568,5,0.18,0.005032739915099746,0.16,0.010065479830199491,0.18991708023833048,0.1786452018716356,5,True
6
+ giroux2022,fewshot,fewshot_n5/draw2,scsemi5,"scSemiProfiler, 5 donors",scsemi,test_raw.npz@fedb8e80,0.36978188721088606,0.26662730577954064,0.260430342889284,0.39643909018360535,0.28957885738959505,0.9104124563197754,0.0015633021491813326,0.8127871688310353,0.9526629414859596,0.9759830070639475,0.3606682995958165,0.3866090394252903,0,63,0.03942659210922517,0,0.0,63,2,0,5,4,161,1.9230578868007087,17,0.32020040144308415,407,53,10,5,4,142,6.149683867439874,12,0.3649442474081072,404,41,8,5,0.048,0.027777259450448132,0.06999999999999999,0.055554518900896264,0.029643770759668786,0.06511823166061989,5,0.18,0.005032739915099746,0.16,0.010065479830199491,0.18991708023833048,0.1786452018716356,5,True
paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/limma/R.log ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ limma jobs: 68 (68 ok)
2
+
3
+ --- stderr ---
paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/limma/jobs.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ job,offset,n_samples,is_case,filter
2
+ obs|T cell|nonzero,0,12,000000111111,nonzero
3
+ obs|T cell|filterByExpr,0,12,000000111111,filterByExpr
4
+ obs|B cell|nonzero,65976,12,000000111111,nonzero
5
+ obs|B cell|filterByExpr,65976,12,000000111111,filterByExpr
6
+ obs|Monocyte|nonzero,131952,12,000000111111,nonzero
7
+ obs|Monocyte|filterByExpr,131952,12,000000111111,filterByExpr
8
+ obs|NK cell|nonzero,197928,12,000000111111,nonzero
9
+ obs|NK cell|filterByExpr,197928,12,000000111111,filterByExpr
10
+ obs|DC|nonzero,263904,12,000000111111,nonzero
11
+ obs|DC|filterByExpr,263904,12,000000111111,filterByExpr
12
+ gen:zs_raw|T cell|nonzero,329880,12,000000111111,nonzero
13
+ gen:zs_raw|T cell|filterByExpr,329880,12,000000111111,filterByExpr
14
+ gen:zs_raw|B cell|nonzero,395856,12,000000111111,nonzero
15
+ gen:zs_raw|B cell|filterByExpr,395856,12,000000111111,filterByExpr
16
+ gen:zs_raw|Monocyte|nonzero,461832,12,000000111111,nonzero
17
+ gen:zs_raw|Monocyte|filterByExpr,461832,12,000000111111,filterByExpr
18
+ gen:zs_raw|NK cell|nonzero,527808,12,000000111111,nonzero
19
+ gen:zs_raw|NK cell|filterByExpr,527808,12,000000111111,filterByExpr
20
+ gen:zs_raw|DC|nonzero,593784,12,000000111111,nonzero
21
+ gen:zs_raw|DC|filterByExpr,593784,12,000000111111,filterByExpr
22
+ bcast:ac755a41a900fac6|nonzero,659760,12,000000111111,nonzero
23
+ bcast:ac755a41a900fac6|filterByExpr,659760,12,000000111111,filterByExpr
24
+ gen:zs_pseudo|T cell|nonzero,725736,12,000000111111,nonzero
25
+ gen:zs_pseudo|T cell|filterByExpr,725736,12,000000111111,filterByExpr
26
+ gen:zs_pseudo|B cell|nonzero,791712,12,000000111111,nonzero
27
+ gen:zs_pseudo|B cell|filterByExpr,791712,12,000000111111,filterByExpr
28
+ gen:zs_pseudo|Monocyte|nonzero,857688,12,000000111111,nonzero
29
+ gen:zs_pseudo|Monocyte|filterByExpr,857688,12,000000111111,filterByExpr
30
+ gen:zs_pseudo|NK cell|nonzero,923664,12,000000111111,nonzero
31
+ gen:zs_pseudo|NK cell|filterByExpr,923664,12,000000111111,filterByExpr
32
+ gen:zs_pseudo|DC|nonzero,989640,12,000000111111,nonzero
33
+ gen:zs_pseudo|DC|filterByExpr,989640,12,000000111111,filterByExpr
34
+ bcast:6400d82fe1115aed|nonzero,1055616,12,000000111111,nonzero
35
+ bcast:6400d82fe1115aed|filterByExpr,1055616,12,000000111111,filterByExpr
36
+ gen:zs_cal|T cell|nonzero,1121592,12,000000111111,nonzero
37
+ gen:zs_cal|T cell|filterByExpr,1121592,12,000000111111,filterByExpr
38
+ gen:zs_cal|B cell|nonzero,1187568,12,000000111111,nonzero
39
+ gen:zs_cal|B cell|filterByExpr,1187568,12,000000111111,filterByExpr
40
+ gen:zs_cal|Monocyte|nonzero,1253544,12,000000111111,nonzero
41
+ gen:zs_cal|Monocyte|filterByExpr,1253544,12,000000111111,filterByExpr
42
+ gen:zs_cal|NK cell|nonzero,1319520,12,000000111111,nonzero
43
+ gen:zs_cal|NK cell|filterByExpr,1319520,12,000000111111,filterByExpr
44
+ gen:zs_cal|DC|nonzero,1385496,12,000000111111,nonzero
45
+ gen:zs_cal|DC|filterByExpr,1385496,12,000000111111,filterByExpr
46
+ bcast:8ac9ec213fd4ef60|nonzero,1451472,12,000000111111,nonzero
47
+ bcast:8ac9ec213fd4ef60|filterByExpr,1451472,12,000000111111,filterByExpr
48
+ gen:lora5|T cell|nonzero,1517448,12,000000111111,nonzero
49
+ gen:lora5|T cell|filterByExpr,1517448,12,000000111111,filterByExpr
50
+ gen:lora5|B cell|nonzero,1583424,12,000000111111,nonzero
51
+ gen:lora5|B cell|filterByExpr,1583424,12,000000111111,filterByExpr
52
+ gen:lora5|Monocyte|nonzero,1649400,12,000000111111,nonzero
53
+ gen:lora5|Monocyte|filterByExpr,1649400,12,000000111111,filterByExpr
54
+ gen:lora5|NK cell|nonzero,1715376,12,000000111111,nonzero
55
+ gen:lora5|NK cell|filterByExpr,1715376,12,000000111111,filterByExpr
56
+ gen:lora5|DC|nonzero,1781352,12,000000111111,nonzero
57
+ gen:lora5|DC|filterByExpr,1781352,12,000000111111,filterByExpr
58
+ bcast:fedb8e8039576499|nonzero,1847328,12,000000111111,nonzero
59
+ bcast:fedb8e8039576499|filterByExpr,1847328,12,000000111111,filterByExpr
60
+ gen:scsemi5|T cell|nonzero,1913304,12,000000111111,nonzero
61
+ gen:scsemi5|T cell|filterByExpr,1913304,12,000000111111,filterByExpr
62
+ gen:scsemi5|B cell|nonzero,1979280,12,000000111111,nonzero
63
+ gen:scsemi5|B cell|filterByExpr,1979280,12,000000111111,filterByExpr
64
+ gen:scsemi5|Monocyte|nonzero,2045256,12,000000111111,nonzero
65
+ gen:scsemi5|Monocyte|filterByExpr,2045256,12,000000111111,filterByExpr
66
+ gen:scsemi5|NK cell|nonzero,2111232,12,000000111111,nonzero
67
+ gen:scsemi5|NK cell|filterByExpr,2111232,12,000000111111,filterByExpr
68
+ gen:scsemi5|DC|nonzero,2177208,12,000000111111,nonzero
69
+ gen:scsemi5|DC|filterByExpr,2177208,12,000000111111,filterByExpr
paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw2/limma/limma_status.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ "job","status","n_tested","n_sig_fdr05","seconds"
2
+ "obs|T cell|nonzero","ok",5225,152,0.313
3
+ "obs|T cell|filterByExpr","ok",3743,161,0.154
4
+ "obs|B cell|nonzero","ok",4949,185,0.23
5
+ "obs|B cell|filterByExpr","ok",2981,201,0.1
6
+ "obs|Monocyte|nonzero","ok",5151,11,0.231
7
+ "obs|Monocyte|filterByExpr","ok",3307,4,0.116
8
+ "obs|NK cell|nonzero","ok",4963,59,0.218
9
+ "obs|NK cell|filterByExpr","ok",3066,38,0.122
10
+ "obs|DC|nonzero","ok",4691,0,0.21
11
+ "obs|DC|filterByExpr","ok",2166,0,0.094
12
+ "gen:zs_raw|T cell|nonzero","ok",3981,0,0.172
13
+ "gen:zs_raw|T cell|filterByExpr","ok",2072,0,0.084
14
+ "gen:zs_raw|B cell|nonzero","ok",3550,0,0.153
15
+ "gen:zs_raw|B cell|filterByExpr","ok",1471,0,0.066
16
+ "gen:zs_raw|Monocyte|nonzero","ok",3757,1,0.152
17
+ "gen:zs_raw|Monocyte|filterByExpr","ok",1872,0,0.085
18
+ "gen:zs_raw|NK cell|nonzero","ok",3413,0,0.151
19
+ "gen:zs_raw|NK cell|filterByExpr","ok",1375,0,0.061
20
+ "gen:zs_raw|DC|nonzero","ok",3260,0,0.147
21
+ "gen:zs_raw|DC|filterByExpr","ok",957,0,0.044
22
+ "bcast:ac755a41a900fac6|nonzero","ok",5468,10,0.248
23
+ "bcast:ac755a41a900fac6|filterByExpr","ok",3763,8,0.147
24
+ "gen:zs_pseudo|T cell|nonzero","ok",3564,1,0.162
25
+ "gen:zs_pseudo|T cell|filterByExpr","ok",1463,1,0.066
26
+ "gen:zs_pseudo|B cell|nonzero","ok",2749,0,0.11
27
+ "gen:zs_pseudo|B cell|filterByExpr","ok",975,0,0.048
28
+ "gen:zs_pseudo|Monocyte|nonzero","ok",2942,12,0.133
29
+ "gen:zs_pseudo|Monocyte|filterByExpr","ok",894,0,0.04
30
+ "gen:zs_pseudo|NK cell|nonzero","ok",2701,19,0.102
31
+ "gen:zs_pseudo|NK cell|filterByExpr","ok",809,3,0.04
32
+ "gen:zs_pseudo|DC|nonzero","ok",2086,1,0.089
33
+ "gen:zs_pseudo|DC|filterByExpr","ok",129,0,0.013
34
+ "bcast:6400d82fe1115aed|nonzero","ok",5345,154,0.217
35
+ "bcast:6400d82fe1115aed|filterByExpr","ok",3225,80,0.138
36
+ "gen:zs_cal|T cell|nonzero","ok",3670,0,0.134
37
+ "gen:zs_cal|T cell|filterByExpr","ok",1532,0,0.064
38
+ "gen:zs_cal|B cell|nonzero","ok",2923,0,0.168
39
+ "gen:zs_cal|B cell|filterByExpr","ok",1002,0,0.046
40
+ "gen:zs_cal|Monocyte|nonzero","ok",3286,0,0.129
41
+ "gen:zs_cal|Monocyte|filterByExpr","ok",1417,0,0.062
42
+ "gen:zs_cal|NK cell|nonzero","ok",3156,0,0.133
43
+ "gen:zs_cal|NK cell|filterByExpr","ok",1200,0,0.045
44
+ "gen:zs_cal|DC|nonzero","ok",2435,0,0.1
45
+ "gen:zs_cal|DC|filterByExpr","ok",153,0,0.013
46
+ "bcast:8ac9ec213fd4ef60|nonzero","ok",5468,4,0.223
47
+ "bcast:8ac9ec213fd4ef60|filterByExpr","ok",3747,4,0.144
48
+ "gen:lora5|T cell|nonzero","ok",3623,3,0.152
49
+ "gen:lora5|T cell|filterByExpr","ok",1481,0,0.068
50
+ "gen:lora5|B cell|nonzero","ok",2759,0,0.121
51
+ "gen:lora5|B cell|filterByExpr","ok",850,0,0.043
52
+ "gen:lora5|Monocyte|nonzero","ok",3166,0,0.142
53
+ "gen:lora5|Monocyte|filterByExpr","ok",1284,0,0.061
54
+ "gen:lora5|NK cell|nonzero","ok",2811,281,0.12
55
+ "gen:lora5|NK cell|filterByExpr","ok",839,0,0.04
56
+ "gen:lora5|DC|nonzero","ok",2643,0,0.117
57
+ "gen:lora5|DC|filterByExpr","ok",427,0,0.022
58
+ "bcast:fedb8e8039576499|nonzero","ok",5468,10,0.235
59
+ "bcast:fedb8e8039576499|filterByExpr","ok",3763,8,0.163
60
+ "gen:scsemi5|T cell|nonzero","ok",2020,9,0.079
61
+ "gen:scsemi5|T cell|filterByExpr","ok",513,7,0.027
62
+ "gen:scsemi5|B cell|nonzero","ok",887,7,0.044
63
+ "gen:scsemi5|B cell|filterByExpr","ok",161,7,0.015
64
+ "gen:scsemi5|Monocyte|nonzero","ok",1505,7,0.068
65
+ "gen:scsemi5|Monocyte|filterByExpr","ok",256,5,0.017
66
+ "gen:scsemi5|NK cell|nonzero","ok",1121,28,0.056
67
+ "gen:scsemi5|NK cell|filterByExpr","ok",260,22,0.018
68
+ "gen:scsemi5|DC|nonzero","ok",422,2,0.019
69
+ "gen:scsemi5|DC|filterByExpr","ok",47,0,0.009