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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/draw3/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/draw3/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/draw3/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/draw3/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/draw3/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/draw3,zs_raw,"Zero-shot, real bulk",zs_raw,all_usable_raw.npz@ac755a41,0.20868988692878626,0.08991039998067686,0.055390494801996606,0.4657480400911531,0.3682998803763819,0.9157828180905879,0.0016241434498649979,0.8188912532619861,0.9556708168304803,0.9775340633995764,0.2073250504374558,0.45599371337680533,0,27,0.0,0,0.0,27,0,0,5,0,145,0.0,9,0.20213971989487223,332,0,7,5,0,153,0.0,8,0.24257575497685616,415,0,5,5,0.024,0.007066905310372682,0.028000000000000004,0.014133810620745363,0.0356153838822774,0.02585721245256143,5,0.188,0.005057997946483127,0.18,0.010115995892966254,0.1823339587689489,0.16755365624967317,5,True
3
+ giroux2022,fewshot,fewshot_n5/draw3,zs_pseudo,"Zero-shot, sc pseudobulk input (reference)",other,all_usable_pseudo.npz@6400d82f,0.3903722846107435,0.3331490915932292,0.23027691197059708,0.6834646008550196,0.6776416946600692,0.9157828180905879,0.0016241434498649979,0.8188912532619861,0.9556708168304803,0.9775340633995764,0.3826865585706537,0.6698843799481754,0,27,0.012397858551704706,3,0.02607372015094978,27,11,5,5,1,145,0.33937060396885954,45,1.437525565794222,332,21,108,5,0,153,0.30131346635242556,35,2.516090096114514,415,6,101,5,0.024,0.00942113115773197,0.044,0.01884226231546394,0.04321391673954057,0.047880866083658005,5,0.22400000000000003,0.005035734535716498,0.26,0.010071469071432996,0.27389766796455156,0.26730462529061405,5,True
4
+ giroux2022,fewshot,fewshot_n5/draw3,zs_cal,Zero-shot + calibration,zs_cal,test_cal.npz@2d7f83dd,0.13512758815407414,0.06160496650968852,0.05318371579560868,0.4873794301776414,0.36745249695936993,0.9157828180905879,0.0016241434498649979,0.8188912532619861,0.9556708168304803,0.9775340633995764,0.13281664376943877,0.47776200726000956,0,27,0.0,0,0.00523924038849412,27,14,1,5,2,145,0.1838312211547619,0,0.028877102842124604,332,237,1,5,0,153,0.0,0,0.0,415,0,0,5,0.016,0.008441353816709084,0.030000000000000006,0.01688270763341817,0.03938497208664431,0.029532276689254074,5,0.168,0.005057997946483127,0.182,0.010115995892966254,0.1727778039382558,0.15717317763037297,5,True
5
+ giroux2022,fewshot,fewshot_n5/draw3,lora5,"LoRA, 5 donors",lora,test_raw.npz@4efbb07e,0.24186295766157903,0.17532820299739277,0.14697551642627654,0.4657480400911531,0.3682998803763819,0.9157828180905879,0.0016241434498649979,0.8188912532619861,0.9556708168304803,0.9775340633995764,0.23760141856005212,0.45599371337680533,0,27,0.0,0,0.0,27,0,0,5,0,145,0.013931457230426303,9,0.20213971989487223,332,1,7,5,0,153,0.05549389567147614,8,0.24257575497685616,415,1,5,5,0.05600000000000001,0.008525886430650682,0.046,0.017051772861301363,0.025732639452940874,0.04755289179346063,5,0.188,0.005057997946483127,0.18,0.010115995892966254,0.1823339587689489,0.16755365624967317,5,True
6
+ giroux2022,fewshot,fewshot_n5/draw3,scsemi5,"scSemiProfiler, 5 donors",scsemi,test_raw.npz@4efbb07e,0.3613647484944552,0.26273683620043203,0.21528092263936202,0.4657480400911531,0.3682998803763819,0.9157828180905879,0.0016241434498649979,0.8188912532619861,0.9556708168304803,0.9775340633995764,0.352323750631146,0.45599371337680533,0,27,0.0057273768613974796,0,0.0,27,1,0,5,0,145,0.361933605612811,9,0.20213971989487223,332,24,7,5,0,153,0.0,8,0.24257575497685616,415,6,5,5,0.048,0.03388100830410497,0.06999999999999999,0.06776201660820994,0.048884004371936234,0.06175441270796137,5,0.188,0.005057997946483127,0.18,0.010115995892966254,0.1823339587689489,0.16755365624967317,5,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/draw3/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/draw3/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:2d7f83dd66505753|nonzero,1330516,11,00000111111,nonzero
47
+ bcast:2d7f83dd66505753|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:4efbb07e4fe68471|nonzero,1693384,11,00000111111,nonzero
59
+ bcast:4efbb07e4fe68471|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,1995774,11,00000111111,nonzero
69
+ gen:scsemi5|DC|filterByExpr,1995774,11,00000111111,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/draw3/limma/limma_status.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ "job","status","n_tested","n_sig_fdr05","seconds"
2
+ "obs|T cell|nonzero","ok",5225,154,0.335
3
+ "obs|T cell|filterByExpr","ok",3848,208,0.165
4
+ "obs|B cell|nonzero","ok",4979,133,0.238
5
+ "obs|B cell|filterByExpr","ok",3102,145,0.122
6
+ "obs|Monocyte|nonzero","ok",5105,4,0.221
7
+ "obs|Monocyte|filterByExpr","ok",3332,3,0.151
8
+ "obs|NK cell|nonzero","ok",4907,41,0.221
9
+ "obs|NK cell|filterByExpr","ok",3024,59,0.141
10
+ "obs|DC|nonzero","ok",4646,0,0.204
11
+ "obs|DC|filterByExpr","ok",2078,0,0.094
12
+ "gen:zs_raw|T cell|nonzero","ok",3968,0,0.174
13
+ "gen:zs_raw|T cell|filterByExpr","ok",2114,0,0.097
14
+ "gen:zs_raw|B cell|nonzero","ok",3529,0,0.153
15
+ "gen:zs_raw|B cell|filterByExpr","ok",1560,0,0.056
16
+ "gen:zs_raw|Monocyte|nonzero","ok",3733,0,0.178
17
+ "gen:zs_raw|Monocyte|filterByExpr","ok",1918,0,0.089
18
+ "gen:zs_raw|NK cell|nonzero","ok",3368,0,0.125
19
+ "gen:zs_raw|NK cell|filterByExpr","ok",1372,0,0.068
20
+ "gen:zs_raw|DC|nonzero","ok",3251,0,0.146
21
+ "gen:zs_raw|DC|filterByExpr","ok",991,0,0.038
22
+ "bcast:ac755a41a900fac6|nonzero","ok",5466,7,0.316
23
+ "bcast:ac755a41a900fac6|filterByExpr","ok",3814,5,0.16
24
+ "gen:zs_pseudo|T cell|nonzero","ok",3553,1,0.149
25
+ "gen:zs_pseudo|T cell|filterByExpr","ok",1471,3,0.067
26
+ "gen:zs_pseudo|B cell|nonzero","ok",2751,4,0.121
27
+ "gen:zs_pseudo|B cell|filterByExpr","ok",1002,0,0.056
28
+ "gen:zs_pseudo|Monocyte|nonzero","ok",2808,0,0.114
29
+ "gen:zs_pseudo|Monocyte|filterByExpr","ok",946,0,0.052
30
+ "gen:zs_pseudo|NK cell|nonzero","ok",2600,16,0.114
31
+ "gen:zs_pseudo|NK cell|filterByExpr","ok",753,3,0.04
32
+ "gen:zs_pseudo|DC|nonzero","ok",2012,0,0.078
33
+ "gen:zs_pseudo|DC|filterByExpr","ok",111,0,0.015
34
+ "bcast:6400d82fe1115aed|nonzero","ok",5337,108,0.257
35
+ "bcast:6400d82fe1115aed|filterByExpr","ok",3285,101,0.139
36
+ "gen:zs_cal|T cell|nonzero","ok",3604,5,0.158
37
+ "gen:zs_cal|T cell|filterByExpr","ok",1468,0,0.049
38
+ "gen:zs_cal|B cell|nonzero","ok",2853,5,0.094
39
+ "gen:zs_cal|B cell|filterByExpr","ok",1074,0,0.036
40
+ "gen:zs_cal|Monocyte|nonzero","ok",3248,0,0.107
41
+ "gen:zs_cal|Monocyte|filterByExpr","ok",1457,0,0.05
42
+ "gen:zs_cal|NK cell|nonzero","ok",3096,2,0.1
43
+ "gen:zs_cal|NK cell|filterByExpr","ok",1202,0,0.041
44
+ "gen:zs_cal|DC|nonzero","ok",2346,225,0.076
45
+ "gen:zs_cal|DC|filterByExpr","ok",168,0,0.011
46
+ "bcast:2d7f83dd66505753|nonzero","ok",5466,1,0.181
47
+ "bcast:2d7f83dd66505753|filterByExpr","ok",3824,0,0.116
48
+ "gen:lora5|T cell|nonzero","ok",3590,1,0.12
49
+ "gen:lora5|T cell|filterByExpr","ok",1489,0,0.05
50
+ "gen:lora5|B cell|nonzero","ok",2725,0,0.088
51
+ "gen:lora5|B cell|filterByExpr","ok",919,0,0.032
52
+ "gen:lora5|Monocyte|nonzero","ok",3166,0,0.108
53
+ "gen:lora5|Monocyte|filterByExpr","ok",1335,0,0.046
54
+ "gen:lora5|NK cell|nonzero","ok",2743,0,0.09
55
+ "gen:lora5|NK cell|filterByExpr","ok",901,1,0.034
56
+ "gen:lora5|DC|nonzero","ok",2642,0,0.086
57
+ "gen:lora5|DC|filterByExpr","ok",421,0,0.02
58
+ "bcast:4efbb07e4fe68471|nonzero","ok",5466,7,0.183
59
+ "bcast:4efbb07e4fe68471|filterByExpr","ok",3814,5,0.117
60
+ "gen:scsemi5|T cell|nonzero","ok",2022,9,0.066
61
+ "gen:scsemi5|T cell|filterByExpr","ok",525,0,0.022
62
+ "gen:scsemi5|B cell|nonzero","ok",875,1,0.032
63
+ "gen:scsemi5|B cell|filterByExpr","ok",173,0,0.013
64
+ "gen:scsemi5|Monocyte|nonzero","ok",1281,2,0.044
65
+ "gen:scsemi5|Monocyte|filterByExpr","ok",268,0,0.013
66
+ "gen:scsemi5|NK cell|nonzero","ok",1094,2,0.039
67
+ "gen:scsemi5|NK cell|filterByExpr","ok",271,0,0.017
68
+ "gen:scsemi5|DC|nonzero","ok",291,10,0.014
69
+ "gen:scsemi5|DC|filterByExpr","ok",62,6,0.009