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junidude14 commited on
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96711b1
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Archive 4 checkpoints (1-4)

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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/draw0/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/draw0/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/draw0/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/draw0/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/draw0/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/draw0,zs_raw,"Zero-shot, real bulk",zs_raw,all_usable_raw.npz@ac755a41,0.14641874658292783,0.03796099026900451,-0.0010740288179362238,0.4709654147613206,0.35580101454568397,0.8779127648861704,0.0015242575785035046,0.7640912590762394,0.9337152499913626,0.9660956301191179,0.1438517679278641,0.45678029574592377,0,3,0.0,0,0.0,3,0,0,5,0,91,0.0,4,0.07369766757742145,91,0,4,5,0,92,0.0,4,0.09093538251237761,106,0,3,5,0.028000000000000004,0.007021534161167702,0.028000000000000004,0.014043068322335404,0.027618712545457384,0.021944752734766513,5,0.12800000000000003,0.005075658777947857,0.13200000000000003,0.010151317555895715,0.1529544670733114,0.1221131460927288,5,True
3
+ giroux2022,fewshot,fewshot_n5/draw0,zs_pseudo,"Zero-shot, sc pseudobulk input (reference)",other,all_usable_pseudo.npz@6400d82f,0.34770957181723616,0.28199419693625394,0.10364828313612912,0.7063018404234562,0.6790100653817397,0.8779127648861704,0.0015242575785035046,0.7640912590762394,0.9337152499913626,0.9660956301191179,0.3392873663116775,0.6886472967727262,0,3,0.0,1,0.0041921874063268125,3,1,7,5,0,91,0.00904295403165034,21,0.917638639110968,91,1,53,5,0,92,0.0,13,1.060437499395541,106,0,34,5,0.052000000000000005,0.009256716196842912,0.048,0.018513432393685823,0.04589746359249615,0.04702398197853156,5,0.192,0.00505543822111832,0.22600000000000003,0.01011087644223664,0.277423710951683,0.2257209708317081,5,True
4
+ giroux2022,fewshot,fewshot_n5/draw0,zs_cal,Zero-shot + calibration,zs_cal,test_cal.npz@a1c99db4,0.11201111078574608,0.01928806746106137,0.011550119248630872,0.4941527115486404,0.36022248060145995,0.8779127648861704,0.0015242575785035046,0.7640912590762394,0.9337152499913626,0.9660956301191179,0.11026346602069655,0.47945547746830375,0,3,0.0,0,0.0,3,5,0,5,1,91,0.1667233752977203,2,0.018424416894355363,91,10,1,5,0,92,0.0,1,0.030319153397779117,106,0,1,5,0.02,0.008355940410418868,0.030000000000000006,0.016711880820837736,0.030634389253959164,0.020484958794531327,5,0.11200000000000002,0.005075658777947857,0.10400000000000001,0.010151317555895715,0.14770661279662212,0.11338654518132148,5,True
5
+ giroux2022,fewshot,fewshot_n5/draw0,lora5,"LoRA, 5 donors",lora,test_raw.npz@f04c5725,0.243392212681724,0.1602044193859629,0.15035969319388034,0.4709654147613206,0.35580101454568397,0.8779127648861704,0.0015242575785035046,0.7640912590762394,0.9337152499913626,0.9660956301191179,0.23630519687783286,0.45678029574592377,0,3,0.00027839643652561246,0,0.0,3,4,0,5,0,91,0.017811704834605598,4,0.07369766757742145,91,1,4,5,0,92,0.0,4,0.09093538251237761,106,0,3,5,0.016,0.008441745063469536,0.027999999999999997,0.01688349012693907,0.01824978900008769,0.02696776133488723,5,0.12800000000000003,0.005075658777947857,0.13200000000000003,0.010151317555895715,0.1529544670733114,0.1221131460927288,5,True
6
+ giroux2022,fewshot,fewshot_n5/draw0,scsemi5,"scSemiProfiler, 5 donors",scsemi,test_raw.npz@f04c5725,0.37134845918992154,0.2631585912428766,0.23699629820059617,0.4709654147613206,0.35580101454568397,0.8779127648861704,0.0015242575785035046,0.7640912590762394,0.9337152499913626,0.9660956301191179,0.36145853526116933,0.45678029574592377,0,3,0.002325581395348837,0,0.0,3,1,0,5,1,91,0.24262456160056428,4,0.07369766757742145,91,16,4,5,0,92,0.22661870503597123,4,0.09093538251237761,106,3,3,5,0.028000000000000004,0.030337201515828506,0.068,0.06067440303165701,0.04350853633529385,0.06391490470299888,5,0.12800000000000003,0.005075658777947857,0.13200000000000003,0.010151317555895715,0.1529544670733114,0.1221131460927288,5,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/draw0/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/draw0/limma/jobs.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ job,offset,n_samples,is_case,filter
2
+ obs|T cell|nonzero,0,11,00000111111,nonzero
3
+ obs|T cell|filterByExpr,0,11,00000111111,filterByExpr
4
+ obs|B cell|nonzero,60478,11,00000111111,nonzero
5
+ obs|B cell|filterByExpr,60478,11,00000111111,filterByExpr
6
+ obs|Monocyte|nonzero,120956,11,00000111111,nonzero
7
+ obs|Monocyte|filterByExpr,120956,11,00000111111,filterByExpr
8
+ obs|NK cell|nonzero,181434,11,00000111111,nonzero
9
+ obs|NK cell|filterByExpr,181434,11,00000111111,filterByExpr
10
+ obs|DC|nonzero,241912,11,00000111111,nonzero
11
+ obs|DC|filterByExpr,241912,11,00000111111,filterByExpr
12
+ gen:zs_raw|T cell|nonzero,302390,11,00000111111,nonzero
13
+ gen:zs_raw|T cell|filterByExpr,302390,11,00000111111,filterByExpr
14
+ gen:zs_raw|B cell|nonzero,362868,11,00000111111,nonzero
15
+ gen:zs_raw|B cell|filterByExpr,362868,11,00000111111,filterByExpr
16
+ gen:zs_raw|Monocyte|nonzero,423346,11,00000111111,nonzero
17
+ gen:zs_raw|Monocyte|filterByExpr,423346,11,00000111111,filterByExpr
18
+ gen:zs_raw|NK cell|nonzero,483824,11,00000111111,nonzero
19
+ gen:zs_raw|NK cell|filterByExpr,483824,11,00000111111,filterByExpr
20
+ gen:zs_raw|DC|nonzero,544302,11,00000111111,nonzero
21
+ gen:zs_raw|DC|filterByExpr,544302,11,00000111111,filterByExpr
22
+ bcast:ac755a41a900fac6|nonzero,604780,11,00000111111,nonzero
23
+ bcast:ac755a41a900fac6|filterByExpr,604780,11,00000111111,filterByExpr
24
+ gen:zs_pseudo|T cell|nonzero,665258,11,00000111111,nonzero
25
+ gen:zs_pseudo|T cell|filterByExpr,665258,11,00000111111,filterByExpr
26
+ gen:zs_pseudo|B cell|nonzero,725736,11,00000111111,nonzero
27
+ gen:zs_pseudo|B cell|filterByExpr,725736,11,00000111111,filterByExpr
28
+ gen:zs_pseudo|Monocyte|nonzero,786214,11,00000111111,nonzero
29
+ gen:zs_pseudo|Monocyte|filterByExpr,786214,11,00000111111,filterByExpr
30
+ gen:zs_pseudo|NK cell|nonzero,846692,11,00000111111,nonzero
31
+ gen:zs_pseudo|NK cell|filterByExpr,846692,11,00000111111,filterByExpr
32
+ gen:zs_pseudo|DC|nonzero,907170,11,00000111111,nonzero
33
+ gen:zs_pseudo|DC|filterByExpr,907170,11,00000111111,filterByExpr
34
+ bcast:6400d82fe1115aed|nonzero,967648,11,00000111111,nonzero
35
+ bcast:6400d82fe1115aed|filterByExpr,967648,11,00000111111,filterByExpr
36
+ gen:zs_cal|T cell|nonzero,1028126,11,00000111111,nonzero
37
+ gen:zs_cal|T cell|filterByExpr,1028126,11,00000111111,filterByExpr
38
+ gen:zs_cal|B cell|nonzero,1088604,11,00000111111,nonzero
39
+ gen:zs_cal|B cell|filterByExpr,1088604,11,00000111111,filterByExpr
40
+ gen:zs_cal|Monocyte|nonzero,1149082,11,00000111111,nonzero
41
+ gen:zs_cal|Monocyte|filterByExpr,1149082,11,00000111111,filterByExpr
42
+ gen:zs_cal|NK cell|nonzero,1209560,11,00000111111,nonzero
43
+ gen:zs_cal|NK cell|filterByExpr,1209560,11,00000111111,filterByExpr
44
+ gen:zs_cal|DC|nonzero,1270038,11,00000111111,nonzero
45
+ gen:zs_cal|DC|filterByExpr,1270038,11,00000111111,filterByExpr
46
+ bcast:a1c99db4c3a3cf82|nonzero,1330516,11,00000111111,nonzero
47
+ bcast:a1c99db4c3a3cf82|filterByExpr,1330516,11,00000111111,filterByExpr
48
+ gen:lora5|T cell|nonzero,1390994,11,00000111111,nonzero
49
+ gen:lora5|T cell|filterByExpr,1390994,11,00000111111,filterByExpr
50
+ gen:lora5|B cell|nonzero,1451472,11,00000111111,nonzero
51
+ gen:lora5|B cell|filterByExpr,1451472,11,00000111111,filterByExpr
52
+ gen:lora5|Monocyte|nonzero,1511950,11,00000111111,nonzero
53
+ gen:lora5|Monocyte|filterByExpr,1511950,11,00000111111,filterByExpr
54
+ gen:lora5|NK cell|nonzero,1572428,11,00000111111,nonzero
55
+ gen:lora5|NK cell|filterByExpr,1572428,11,00000111111,filterByExpr
56
+ gen:lora5|DC|nonzero,1632906,11,00000111111,nonzero
57
+ gen:lora5|DC|filterByExpr,1632906,11,00000111111,filterByExpr
58
+ bcast:f04c5725cf7d20ca|nonzero,1693384,11,00000111111,nonzero
59
+ bcast:f04c5725cf7d20ca|filterByExpr,1693384,11,00000111111,filterByExpr
60
+ gen:scsemi5|T cell|nonzero,1753862,11,00000111111,nonzero
61
+ gen:scsemi5|T cell|filterByExpr,1753862,11,00000111111,filterByExpr
62
+ gen:scsemi5|B cell|nonzero,1814340,11,00000111111,nonzero
63
+ gen:scsemi5|B cell|filterByExpr,1814340,11,00000111111,filterByExpr
64
+ gen:scsemi5|Monocyte|nonzero,1874818,11,00000111111,nonzero
65
+ gen:scsemi5|Monocyte|filterByExpr,1874818,11,00000111111,filterByExpr
66
+ gen:scsemi5|NK cell|nonzero,1935296,11,00000111111,nonzero
67
+ gen:scsemi5|NK cell|filterByExpr,1935296,11,00000111111,filterByExpr
68
+ gen:scsemi5|DC|nonzero,1995774,10,0000011111,nonzero
69
+ gen:scsemi5|DC|filterByExpr,1995774,10,0000011111,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/draw0/limma/limma_status.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ "job","status","n_tested","n_sig_fdr05","seconds"
2
+ "obs|T cell|nonzero","ok",5216,13,0.296
3
+ "obs|T cell|filterByExpr","ok",3770,20,0.15
4
+ "obs|B cell|nonzero","ok",4912,49,0.186
5
+ "obs|B cell|filterByExpr","ok",3070,64,0.116
6
+ "obs|Monocyte|nonzero","ok",5113,5,0.193
7
+ "obs|Monocyte|filterByExpr","ok",3355,0,0.128
8
+ "obs|NK cell|nonzero","ok",4891,24,0.186
9
+ "obs|NK cell|filterByExpr","ok",2938,21,0.114
10
+ "obs|DC|nonzero","ok",4635,0,0.174
11
+ "obs|DC|filterByExpr","ok",2047,1,0.082
12
+ "gen:zs_raw|T cell|nonzero","ok",3980,0,0.159
13
+ "gen:zs_raw|T cell|filterByExpr","ok",2083,0,0.083
14
+ "gen:zs_raw|B cell|nonzero","ok",3525,0,0.141
15
+ "gen:zs_raw|B cell|filterByExpr","ok",1546,0,0.049
16
+ "gen:zs_raw|Monocyte|nonzero","ok",3798,0,0.15
17
+ "gen:zs_raw|Monocyte|filterByExpr","ok",1913,0,0.079
18
+ "gen:zs_raw|NK cell|nonzero","ok",3390,0,0.117
19
+ "gen:zs_raw|NK cell|filterByExpr","ok",1368,0,0.046
20
+ "gen:zs_raw|DC|nonzero","ok",3278,0,0.131
21
+ "gen:zs_raw|DC|filterByExpr","ok",958,0,0.046
22
+ "bcast:ac755a41a900fac6|nonzero","ok",5469,4,0.214
23
+ "bcast:ac755a41a900fac6|filterByExpr","ok",3797,3,0.145
24
+ "gen:zs_pseudo|T cell|nonzero","ok",3540,0,0.134
25
+ "gen:zs_pseudo|T cell|filterByExpr","ok",1462,0,0.062
26
+ "gen:zs_pseudo|B cell|nonzero","ok",2727,0,0.111
27
+ "gen:zs_pseudo|B cell|filterByExpr","ok",1013,0,0.036
28
+ "gen:zs_pseudo|Monocyte|nonzero","ok",2955,0,0.119
29
+ "gen:zs_pseudo|Monocyte|filterByExpr","ok",942,0,0.041
30
+ "gen:zs_pseudo|NK cell|nonzero","ok",2656,1,0.109
31
+ "gen:zs_pseudo|NK cell|filterByExpr","ok",768,0,0.032
32
+ "gen:zs_pseudo|DC|nonzero","ok",2061,0,0.082
33
+ "gen:zs_pseudo|DC|filterByExpr","ok",176,0,0.014
34
+ "bcast:6400d82fe1115aed|nonzero","ok",5335,53,0.212
35
+ "bcast:6400d82fe1115aed|filterByExpr","ok",3276,34,0.128
36
+ "gen:zs_cal|T cell|nonzero","ok",3607,0,0.138
37
+ "gen:zs_cal|T cell|filterByExpr","ok",1481,0,0.062
38
+ "gen:zs_cal|B cell|nonzero","ok",2946,10,0.118
39
+ "gen:zs_cal|B cell|filterByExpr","ok",1113,0,0.047
40
+ "gen:zs_cal|Monocyte|nonzero","ok",3316,0,0.169
41
+ "gen:zs_cal|Monocyte|filterByExpr","ok",1411,0,0.055
42
+ "gen:zs_cal|NK cell|nonzero","ok",3095,0,0.119
43
+ "gen:zs_cal|NK cell|filterByExpr","ok",1155,0,0.042
44
+ "gen:zs_cal|DC|nonzero","ok",2344,0,0.085
45
+ "gen:zs_cal|DC|filterByExpr","ok",146,0,0.015
46
+ "bcast:a1c99db4c3a3cf82|nonzero","ok",5469,1,0.2
47
+ "bcast:a1c99db4c3a3cf82|filterByExpr","ok",3799,1,0.132
48
+ "gen:lora5|T cell|nonzero","ok",3594,0,0.134
49
+ "gen:lora5|T cell|filterByExpr","ok",1490,0,0.055
50
+ "gen:lora5|B cell|nonzero","ok",2754,1,0.106
51
+ "gen:lora5|B cell|filterByExpr","ok",993,0,0.044
52
+ "gen:lora5|Monocyte|nonzero","ok",3210,0,0.127
53
+ "gen:lora5|Monocyte|filterByExpr","ok",1213,0,0.044
54
+ "gen:lora5|NK cell|nonzero","ok",2798,0,0.11
55
+ "gen:lora5|NK cell|filterByExpr","ok",913,0,0.042
56
+ "gen:lora5|DC|nonzero","ok",2656,0,0.106
57
+ "gen:lora5|DC|filterByExpr","ok",447,0,0.022
58
+ "bcast:f04c5725cf7d20ca|nonzero","ok",5469,4,0.221
59
+ "bcast:f04c5725cf7d20ca|filterByExpr","ok",3797,3,0.139
60
+ "gen:scsemi5|T cell|nonzero","ok",1871,7,0.077
61
+ "gen:scsemi5|T cell|filterByExpr","ok",510,0,0.027
62
+ "gen:scsemi5|B cell|nonzero","ok",864,3,0.04
63
+ "gen:scsemi5|B cell|filterByExpr","ok",170,0,0.013
64
+ "gen:scsemi5|Monocyte|nonzero","ok",1134,0,0.049
65
+ "gen:scsemi5|Monocyte|filterByExpr","ok",266,0,0.018
66
+ "gen:scsemi5|NK cell|nonzero","ok",1051,1,0.038
67
+ "gen:scsemi5|NK cell|filterByExpr","ok",278,3,0.017
68
+ "gen:scsemi5|DC|nonzero","ok",395,5,0.019
69
+ "gen:scsemi5|DC|filterByExpr","ok",62,0,0.012