junidude14 commited on
Commit
c3cb27e
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1 Parent(s): f642adb

Archive 4 checkpoints (1-4)

Browse files
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/pooled/headline.csv ADDED
@@ -0,0 +1,7 @@
 
 
 
 
 
 
 
 
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,pooled,pooled,pseudo_full__cal,sc-only fine-tune (+ calibration),other,conditions_pooled_cal.npz@7ad270e1,0.3441273714068387,0.20432479390870267,0.17515529453855735,0.5643395657145305,0.4710110292358014,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.33827076939519085,0.5496662519642362,0,101,0.0,2,0.09755311535340801,337,0,5,5,2,157,0.05861244019138756,16,0.4583768053300474,1123,4,15,5,1,155,0.13026979333299857,12,0.6226895399028884,620,2,12,5,0.05600000000000001,0.007222715529187905,0.062,0.01444543105837581,0.05820538760567712,0.059948030559418906,5,0.12,0.004897943725432538,0.12799999999999997,0.009795887450865076,0.16800414521732945,0.1398341507325511,5,True
3
+ giroux2022,pooled,pooled,pseudo_full__raw,"sc-only fine-tune, real bulk",other,conditions_pooled_raw.npz@1370617c,0.398147551245955,0.3547944561891905,0.3194546947956906,0.5752659929360795,0.4958964592770665,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.39037524076970687,0.5605251826360979,0,101,0.0,5,0.15608498456545283,337,0,8,5,0,157,0.012470611748988834,16,0.3361429905753681,1123,2,11,5,0,155,0.02610966057441253,12,0.46703603072378436,620,1,9,5,0.036,0.006581005279131111,0.039999999999999994,0.013162010558262221,0.05939438145089043,0.056308149319016496,5,0.128,0.004897943725432538,0.13399999999999998,0.009795887450865076,0.16975308975867145,0.14127058542196963,5,True
4
+ giroux2022,pooled,pooled,real_lora__raw,"LoRA, all training pairs",lora,conditions_pooled_raw.npz@1370617c,0.46094848304079133,0.37861361939512955,0.3230347269696575,0.5752659929360795,0.4958964592770665,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.45091776143261264,0.5605251826360979,5,101,0.6546216286986122,5,0.15608498456545283,337,77,8,5,4,157,1.455390366687081,16,0.3361429905753681,1123,977,11,5,7,155,1.6972165648336728,12,0.46703603072378436,620,119,9,5,0.052000000000000005,0.0077162250260124675,0.05800000000000001,0.015432450052024935,0.08606966945889905,0.07671637155618719,5,0.128,0.004897943725432538,0.13399999999999998,0.009795887450865076,0.16975308975867145,0.14127058542196963,5,True
5
+ giroux2022,pooled,pooled,zs__cal,Zero-shot + calibration,zs_cal,conditions_pooled_cal.npz@7ad270e1,0.26862025176520443,0.16882835772931584,0.13339193412452294,0.5643395657145305,0.4710110292358014,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.2654828565096056,0.5496662519642362,0,101,0.012903225806451613,2,0.09755311535340801,337,1,5,5,0,157,0.10023336438456146,16,0.4583768053300474,1123,7,15,5,0,155,0.21168501270110077,12,0.6226895399028884,620,5,12,5,0.008,0.007798695693819401,0.022,0.015597391387638802,0.020084192992015935,0.025333955783953765,5,0.12,0.004897943725432538,0.12799999999999997,0.009795887450865076,0.16800414521732945,0.1398341507325511,5,True
6
+ giroux2022,pooled,pooled,zs__pseudo,"Zero-shot, sc pseudobulk input (reference)",other,conditions_pooled_pseudo.npz@e35caf80,0.40995286106415924,0.32888473065692236,0.14426653827662855,0.7202428536715684,0.6744101540595969,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.40131859838315426,0.7026482550909734,3,101,0.763280879476918,27,0.971595235018782,337,77,220,5,2,157,1.3276813877618736,36,1.5219153050385095,1123,180,391,5,8,155,4.6459845776282815,28,2.6835482168110505,620,260,346,5,0.032,0.008427023125330689,0.05,0.016854046250661378,0.04740755642802233,0.05535355058373574,5,0.164,0.004878882064456874,0.192,0.009757764128913748,0.2698858281302703,0.21619106669662855,5,True
7
+ giroux2022,pooled,pooled,zs__raw,"Zero-shot, real bulk",zs_raw,conditions_pooled_raw.npz@1370617c,0.33402890838128363,0.2232208443948936,0.19038234933406017,0.5752659929360795,0.4958964592770665,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.32858721008573893,0.5605251826360979,1,101,0.05946717411988582,5,0.15608498456545283,337,5,8,5,0,157,0.023786869647954328,16,0.3361429905753681,1123,2,11,5,1,155,1.0732617825478301,12,0.46703603072378436,620,46,9,5,0.02,0.006627976180322459,0.026000000000000002,0.013255952360644918,0.027743383947820676,0.026290107718369614,5,0.128,0.004897943725432538,0.13399999999999998,0.009795887450865076,0.16975308975867145,0.14127058542196963,5,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/pooled/limma/R.log ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ limma jobs: 76 (76 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/pooled/limma/jobs.csv ADDED
@@ -0,0 +1,77 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ job,offset,n_samples,is_case,filter
2
+ obs|T cell|nonzero,0,24,000000000011111111000111,nonzero
3
+ obs|T cell|filterByExpr,0,24,000000000011111111000111,filterByExpr
4
+ obs|B cell|nonzero,131952,24,000000000011111111000111,nonzero
5
+ obs|B cell|filterByExpr,131952,24,000000000011111111000111,filterByExpr
6
+ obs|Monocyte|nonzero,263904,24,000000000011111111000111,nonzero
7
+ obs|Monocyte|filterByExpr,263904,24,000000000011111111000111,filterByExpr
8
+ obs|NK cell|nonzero,395856,24,000000000011111111000111,nonzero
9
+ obs|NK cell|filterByExpr,395856,24,000000000011111111000111,filterByExpr
10
+ obs|DC|nonzero,527808,24,000000000011111111000111,nonzero
11
+ obs|DC|filterByExpr,527808,24,000000000011111111000111,filterByExpr
12
+ gen:pseudo_full__cal|T cell|nonzero,659760,24,000000000011111111000111,nonzero
13
+ gen:pseudo_full__cal|T cell|filterByExpr,659760,24,000000000011111111000111,filterByExpr
14
+ gen:pseudo_full__cal|B cell|nonzero,791712,24,000000000011111111000111,nonzero
15
+ gen:pseudo_full__cal|B cell|filterByExpr,791712,24,000000000011111111000111,filterByExpr
16
+ gen:pseudo_full__cal|Monocyte|nonzero,923664,24,000000000011111111000111,nonzero
17
+ gen:pseudo_full__cal|Monocyte|filterByExpr,923664,24,000000000011111111000111,filterByExpr
18
+ gen:pseudo_full__cal|NK cell|nonzero,1055616,24,000000000011111111000111,nonzero
19
+ gen:pseudo_full__cal|NK cell|filterByExpr,1055616,24,000000000011111111000111,filterByExpr
20
+ gen:pseudo_full__cal|DC|nonzero,1187568,24,000000000011111111000111,nonzero
21
+ gen:pseudo_full__cal|DC|filterByExpr,1187568,24,000000000011111111000111,filterByExpr
22
+ bcast:7ad270e1b7bd1b5b|nonzero,1319520,24,000000000011111111000111,nonzero
23
+ bcast:7ad270e1b7bd1b5b|filterByExpr,1319520,24,000000000011111111000111,filterByExpr
24
+ gen:pseudo_full__raw|T cell|nonzero,1451472,24,000000000011111111000111,nonzero
25
+ gen:pseudo_full__raw|T cell|filterByExpr,1451472,24,000000000011111111000111,filterByExpr
26
+ gen:pseudo_full__raw|B cell|nonzero,1583424,24,000000000011111111000111,nonzero
27
+ gen:pseudo_full__raw|B cell|filterByExpr,1583424,24,000000000011111111000111,filterByExpr
28
+ gen:pseudo_full__raw|Monocyte|nonzero,1715376,24,000000000011111111000111,nonzero
29
+ gen:pseudo_full__raw|Monocyte|filterByExpr,1715376,24,000000000011111111000111,filterByExpr
30
+ gen:pseudo_full__raw|NK cell|nonzero,1847328,24,000000000011111111000111,nonzero
31
+ gen:pseudo_full__raw|NK cell|filterByExpr,1847328,24,000000000011111111000111,filterByExpr
32
+ gen:pseudo_full__raw|DC|nonzero,1979280,24,000000000011111111000111,nonzero
33
+ gen:pseudo_full__raw|DC|filterByExpr,1979280,24,000000000011111111000111,filterByExpr
34
+ bcast:1370617c5149f307|nonzero,2111232,24,000000000011111111000111,nonzero
35
+ bcast:1370617c5149f307|filterByExpr,2111232,24,000000000011111111000111,filterByExpr
36
+ gen:real_lora__raw|T cell|nonzero,2243184,24,000000000011111111000111,nonzero
37
+ gen:real_lora__raw|T cell|filterByExpr,2243184,24,000000000011111111000111,filterByExpr
38
+ gen:real_lora__raw|B cell|nonzero,2375136,24,000000000011111111000111,nonzero
39
+ gen:real_lora__raw|B cell|filterByExpr,2375136,24,000000000011111111000111,filterByExpr
40
+ gen:real_lora__raw|Monocyte|nonzero,2507088,24,000000000011111111000111,nonzero
41
+ gen:real_lora__raw|Monocyte|filterByExpr,2507088,24,000000000011111111000111,filterByExpr
42
+ gen:real_lora__raw|NK cell|nonzero,2639040,24,000000000011111111000111,nonzero
43
+ gen:real_lora__raw|NK cell|filterByExpr,2639040,24,000000000011111111000111,filterByExpr
44
+ gen:real_lora__raw|DC|nonzero,2770992,24,000000000011111111000111,nonzero
45
+ gen:real_lora__raw|DC|filterByExpr,2770992,24,000000000011111111000111,filterByExpr
46
+ gen:zs__cal|T cell|nonzero,2902944,24,000000000011111111000111,nonzero
47
+ gen:zs__cal|T cell|filterByExpr,2902944,24,000000000011111111000111,filterByExpr
48
+ gen:zs__cal|B cell|nonzero,3034896,24,000000000011111111000111,nonzero
49
+ gen:zs__cal|B cell|filterByExpr,3034896,24,000000000011111111000111,filterByExpr
50
+ gen:zs__cal|Monocyte|nonzero,3166848,24,000000000011111111000111,nonzero
51
+ gen:zs__cal|Monocyte|filterByExpr,3166848,24,000000000011111111000111,filterByExpr
52
+ gen:zs__cal|NK cell|nonzero,3298800,24,000000000011111111000111,nonzero
53
+ gen:zs__cal|NK cell|filterByExpr,3298800,24,000000000011111111000111,filterByExpr
54
+ gen:zs__cal|DC|nonzero,3430752,24,000000000011111111000111,nonzero
55
+ gen:zs__cal|DC|filterByExpr,3430752,24,000000000011111111000111,filterByExpr
56
+ gen:zs__pseudo|T cell|nonzero,3562704,24,000000000011111111000111,nonzero
57
+ gen:zs__pseudo|T cell|filterByExpr,3562704,24,000000000011111111000111,filterByExpr
58
+ gen:zs__pseudo|B cell|nonzero,3694656,24,000000000011111111000111,nonzero
59
+ gen:zs__pseudo|B cell|filterByExpr,3694656,24,000000000011111111000111,filterByExpr
60
+ gen:zs__pseudo|Monocyte|nonzero,3826608,24,000000000011111111000111,nonzero
61
+ gen:zs__pseudo|Monocyte|filterByExpr,3826608,24,000000000011111111000111,filterByExpr
62
+ gen:zs__pseudo|NK cell|nonzero,3958560,24,000000000011111111000111,nonzero
63
+ gen:zs__pseudo|NK cell|filterByExpr,3958560,24,000000000011111111000111,filterByExpr
64
+ gen:zs__pseudo|DC|nonzero,4090512,24,000000000011111111000111,nonzero
65
+ gen:zs__pseudo|DC|filterByExpr,4090512,24,000000000011111111000111,filterByExpr
66
+ bcast:e35caf80738a4e67|nonzero,4222464,24,000000000011111111000111,nonzero
67
+ bcast:e35caf80738a4e67|filterByExpr,4222464,24,000000000011111111000111,filterByExpr
68
+ gen:zs__raw|T cell|nonzero,4354416,24,000000000011111111000111,nonzero
69
+ gen:zs__raw|T cell|filterByExpr,4354416,24,000000000011111111000111,filterByExpr
70
+ gen:zs__raw|B cell|nonzero,4486368,24,000000000011111111000111,nonzero
71
+ gen:zs__raw|B cell|filterByExpr,4486368,24,000000000011111111000111,filterByExpr
72
+ gen:zs__raw|Monocyte|nonzero,4618320,24,000000000011111111000111,nonzero
73
+ gen:zs__raw|Monocyte|filterByExpr,4618320,24,000000000011111111000111,filterByExpr
74
+ gen:zs__raw|NK cell|nonzero,4750272,24,000000000011111111000111,nonzero
75
+ gen:zs__raw|NK cell|filterByExpr,4750272,24,000000000011111111000111,filterByExpr
76
+ gen:zs__raw|DC|nonzero,4882224,24,000000000011111111000111,nonzero
77
+ gen:zs__raw|DC|filterByExpr,4882224,24,000000000011111111000111,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/pooled/limma/limma_status.csv ADDED
@@ -0,0 +1,77 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ "job","status","n_tested","n_sig_fdr05","seconds"
2
+ "obs|T cell|nonzero","ok",5295,290,0.245
3
+ "obs|T cell|filterByExpr","ok",3799,383,0.162
4
+ "obs|B cell|nonzero","ok",5087,49,0.212
5
+ "obs|B cell|filterByExpr","ok",2795,62,0.106
6
+ "obs|Monocyte|nonzero","ok",5239,5,0.218
7
+ "obs|Monocyte|filterByExpr","ok",3307,2,0.126
8
+ "obs|NK cell|nonzero","ok",5103,776,0.202
9
+ "obs|NK cell|filterByExpr","ok",2957,170,0.139
10
+ "obs|DC|nonzero","ok",4914,3,0.19
11
+ "obs|DC|filterByExpr","ok",2111,3,0.087
12
+ "gen:pseudo_full__cal|T cell|nonzero","ok",3952,0,0.151
13
+ "gen:pseudo_full__cal|T cell|filterByExpr","ok",1358,0,0.058
14
+ "gen:pseudo_full__cal|B cell|nonzero","ok",3345,4,0.126
15
+ "gen:pseudo_full__cal|B cell|filterByExpr","ok",551,1,0.028
16
+ "gen:pseudo_full__cal|Monocyte|nonzero","ok",3651,0,0.141
17
+ "gen:pseudo_full__cal|Monocyte|filterByExpr","ok",1230,0,0.051
18
+ "gen:pseudo_full__cal|NK cell|nonzero","ok",3688,0,0.141
19
+ "gen:pseudo_full__cal|NK cell|filterByExpr","ok",1266,1,0.052
20
+ "gen:pseudo_full__cal|DC|nonzero","ok",2880,0,0.114
21
+ "gen:pseudo_full__cal|DC|filterByExpr","ok",189,0,0.014
22
+ "bcast:7ad270e1b7bd1b5b|nonzero","ok",5471,15,0.225
23
+ "bcast:7ad270e1b7bd1b5b|filterByExpr","ok",3784,12,0.143
24
+ "gen:pseudo_full__raw|T cell|nonzero","ok",4327,1,0.171
25
+ "gen:pseudo_full__raw|T cell|filterByExpr","ok",1915,1,0.077
26
+ "gen:pseudo_full__raw|B cell|nonzero","ok",3805,0,0.153
27
+ "gen:pseudo_full__raw|B cell|filterByExpr","ok",1302,0,0.054
28
+ "gen:pseudo_full__raw|Monocyte|nonzero","ok",3899,0,0.154
29
+ "gen:pseudo_full__raw|Monocyte|filterByExpr","ok",1527,0,0.086
30
+ "gen:pseudo_full__raw|NK cell|nonzero","ok",3817,0,0.144
31
+ "gen:pseudo_full__raw|NK cell|filterByExpr","ok",1287,0,0.052
32
+ "gen:pseudo_full__raw|DC|nonzero","ok",3300,1,0.124
33
+ "gen:pseudo_full__raw|DC|filterByExpr","ok",340,0,0.02
34
+ "bcast:1370617c5149f307|nonzero","ok",5471,11,0.229
35
+ "bcast:1370617c5149f307|filterByExpr","ok",3771,9,0.139
36
+ "gen:real_lora__raw|T cell|nonzero","ok",3821,82,0.149
37
+ "gen:real_lora__raw|T cell|filterByExpr","ok",1474,119,0.061
38
+ "gen:real_lora__raw|B cell|nonzero","ok",2983,0,0.113
39
+ "gen:real_lora__raw|B cell|filterByExpr","ok",733,0,0.034
40
+ "gen:real_lora__raw|Monocyte|nonzero","ok",3508,0,0.14
41
+ "gen:real_lora__raw|Monocyte|filterByExpr","ok",1245,0,0.051
42
+ "gen:real_lora__raw|NK cell|nonzero","ok",3123,895,0.123
43
+ "gen:real_lora__raw|NK cell|filterByExpr","ok",853,0,0.036
44
+ "gen:real_lora__raw|DC|nonzero","ok",2937,0,0.141
45
+ "gen:real_lora__raw|DC|filterByExpr","ok",393,0,0.021
46
+ "gen:zs__cal|T cell|nonzero","ok",3880,2,0.152
47
+ "gen:zs__cal|T cell|filterByExpr","ok",1536,0,0.064
48
+ "gen:zs__cal|B cell|nonzero","ok",3041,0,0.117
49
+ "gen:zs__cal|B cell|filterByExpr","ok",770,0,0.036
50
+ "gen:zs__cal|Monocyte|nonzero","ok",3487,0,0.14
51
+ "gen:zs__cal|Monocyte|filterByExpr","ok",1386,0,0.057
52
+ "gen:zs__cal|NK cell|nonzero","ok",3362,5,0.151
53
+ "gen:zs__cal|NK cell|filterByExpr","ok",1183,5,0.052
54
+ "gen:zs__cal|DC|nonzero","ok",2584,0,0.098
55
+ "gen:zs__cal|DC|filterByExpr","ok",146,0,0.013
56
+ "gen:zs__pseudo|T cell|nonzero","ok",3775,126,0.15
57
+ "gen:zs__pseudo|T cell|filterByExpr","ok",1469,206,0.059
58
+ "gen:zs__pseudo|B cell|nonzero","ok",2837,6,0.111
59
+ "gen:zs__pseudo|B cell|filterByExpr","ok",741,2,0.034
60
+ "gen:zs__pseudo|Monocyte|nonzero","ok",3185,16,0.128
61
+ "gen:zs__pseudo|Monocyte|filterByExpr","ok",982,6,0.044
62
+ "gen:zs__pseudo|NK cell|nonzero","ok",2988,32,0.119
63
+ "gen:zs__pseudo|NK cell|filterByExpr","ok",823,46,0.037
64
+ "gen:zs__pseudo|DC|nonzero","ok",2394,0,0.092
65
+ "gen:zs__pseudo|DC|filterByExpr","ok",166,0,0.016
66
+ "bcast:e35caf80738a4e67|nonzero","ok",5384,391,0.223
67
+ "bcast:e35caf80738a4e67|filterByExpr","ok",3240,346,0.126
68
+ "gen:zs__raw|T cell|nonzero","ok",4216,2,0.169
69
+ "gen:zs__raw|T cell|filterByExpr","ok",2147,46,0.09
70
+ "gen:zs__raw|B cell|nonzero","ok",3733,0,0.149
71
+ "gen:zs__raw|B cell|filterByExpr","ok",1480,0,0.063
72
+ "gen:zs__raw|Monocyte|nonzero","ok",3967,0,0.158
73
+ "gen:zs__raw|Monocyte|filterByExpr","ok",1888,0,0.102
74
+ "gen:zs__raw|NK cell|nonzero","ok",3630,0,0.144
75
+ "gen:zs__raw|NK cell|filterByExpr","ok",1372,0,0.056
76
+ "gen:zs__raw|DC|nonzero","ok",3453,0,0.137
77
+ "gen:zs__raw|DC|filterByExpr","ok",968,0,0.045