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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/ji2025_chili/fewshot_n5/draw4/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/ji2025_chili/fewshot_n5/draw4/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/ji2025_chili/fewshot_n5/draw4/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/ji2025_chili/fewshot_n5/draw4/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/ji2025_chili/fewshot_n5/draw4/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
+ ji2025_chili,fewshot,fewshot_n5/draw4,zs_raw,"Zero-shot, real bulk",zs_raw,all_usable_raw.npz@78d8ac58,0.05018496145172948,0.0453975310630556,0.006177299120893313,0.2254541110690231,0.1095310112143923,0.8857487763591154,0.00318160740285981,0.7552598949026994,0.9377248423279909,0.9681125450185777,0.05011971751501566,0.21870111288318786,0,189,0.0237310143439046,0,0.07220996859687495,789,2,2,5,0,250,0.9743304140535765,14,1.386348692918018,2969,577,29,5,0,250,0.6791588692997144,20,7.037680792456886,846,19,42,5,0.004,0.008185724964374922,0.016,0.016371449928749844,0.011265762840569484,0.01587128479268567,5,0.044000000000000004,0.0047805127342000625,0.044000000000000004,0.009561025468400125,0.05954707981561893,0.05804750577241387,5,True
3
+ ji2025_chili,fewshot,fewshot_n5/draw4,zs_pseudo,"Zero-shot, sc pseudobulk input (reference)",other,all_usable_pseudo.npz@49033eab,0.21609467450510275,0.17724165363448724,0.11175764241973737,0.570851787297695,0.47665567666711645,0.8857487763591154,0.00318160740285981,0.7552598949026994,0.9377248423279909,0.9681125450185777,0.21296717036002438,0.5523724064537678,4,189,1.3461123159366484,35,1.7442245564682426,789,370,498,5,7,250,2.361213026342255,39,2.309839259872052,2969,1550,338,5,16,250,11.282302508079756,55,7.850936090554099,846,882,290,5,0.027999999999999997,0.006890418334514844,0.04,0.013780836669029689,0.056708106235805064,0.055286361755563874,5,0.092,0.004619678519744105,0.12200000000000003,0.00923935703948821,0.15266172756341903,0.13250741277660918,5,True
4
+ ji2025_chili,fewshot,fewshot_n5/draw4,zs_cal,Zero-shot + calibration,zs_cal,test_cal.npz@cdfdac00,0.07003406425395778,0.046670341946576946,0.04392739364503714,0.19118899631693526,0.08483818791555625,0.8857487763591154,0.00318160740285981,0.7552598949026994,0.9377248423279909,0.9681125450185777,0.07093697641165739,0.18675943713403872,0,189,0.0,1,0.25273489008906236,789,0,7,5,0,250,0.031065364715902863,12,1.2429333108920164,2969,2,26,5,0,250,0.0,15,3.872834103265513,846,0,24,5,0.008,0.008296405652813324,0.013999999999999999,0.016592811305626648,0.015956294201325084,0.019270870948218555,5,0.04,0.0047805127342000625,0.05,0.009561025468400125,0.058589933114239726,0.05613543391942703,5,True
5
+ ji2025_chili,fewshot,fewshot_n5/draw4,lora5,"LoRA, 5 donors",lora,test_raw.npz@cc4771e4,0.2725492074488929,0.2586071842237595,0.2467295164617603,0.2254541110690231,0.1095310112143923,0.8857487763591154,0.00318160740285981,0.7552598949026994,0.9377248423279909,0.9681125450185777,0.2686176010316517,0.21870111288318786,0,189,0.01473187978786093,0,0.07220996859687495,789,1,2,5,3,250,1.4361994443842774,14,1.386348692918018,2969,531,29,5,5,250,1.6292887556033144,20,7.037680792456886,846,47,42,5,0.06,0.007698267203687779,0.052000000000000005,0.015396534407375559,0.07085677743009866,0.0649124810466585,5,0.044000000000000004,0.0047805127342000625,0.044000000000000004,0.009561025468400125,0.05954707981561893,0.05804750577241387,5,True
6
+ ji2025_chili,fewshot,fewshot_n5/draw4,scsemi5,"scSemiProfiler, 5 donors",scsemi,test_raw.npz@cc4771e4,0.1056088500897695,0.02687364529423705,0.020120948384399442,0.2254541110690231,0.1095310112143923,0.8857487763591154,0.00318160740285981,0.7552598949026994,0.9377248423279909,0.9681125450185777,0.1040982625210457,0.21870111288318786,0,189,0.14749262536873156,0,0.07220996859687495,789,2,2,5,3,250,2.5833479516259734,14,1.386348692918018,2969,425,29,5,0,250,2.2162485065710875,20,7.037680792456886,846,12,42,5,0.032,0.021685522048563804,0.044000000000000004,0.04337104409712761,0.06375536472977064,0.04650236586851703,5,0.044000000000000004,0.0047805127342000625,0.044000000000000004,0.009561025468400125,0.05954707981561893,0.05804750577241387,5,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/ji2025_chili/fewshot_n5/draw4/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/ji2025_chili/fewshot_n5/draw4/limma/jobs.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ job,offset,n_samples,is_case,filter
2
+ obs|T cell|nonzero,0,24,000011110010011110011111,nonzero
3
+ obs|T cell|filterByExpr,0,24,000011110010011110011111,filterByExpr
4
+ obs|B cell|nonzero,138048,24,000011110010011110011111,nonzero
5
+ obs|B cell|filterByExpr,138048,24,000011110010011110011111,filterByExpr
6
+ obs|Monocyte|nonzero,276096,24,000011110010011110011111,nonzero
7
+ obs|Monocyte|filterByExpr,276096,24,000011110010011110011111,filterByExpr
8
+ obs|NK cell|nonzero,414144,24,000011110010011110011111,nonzero
9
+ obs|NK cell|filterByExpr,414144,24,000011110010011110011111,filterByExpr
10
+ obs|DC|nonzero,552192,22,0000111100100111100111,nonzero
11
+ obs|DC|filterByExpr,552192,22,0000111100100111100111,filterByExpr
12
+ gen:zs_raw|T cell|nonzero,678736,24,000011110010011110011111,nonzero
13
+ gen:zs_raw|T cell|filterByExpr,678736,24,000011110010011110011111,filterByExpr
14
+ gen:zs_raw|B cell|nonzero,816784,24,000011110010011110011111,nonzero
15
+ gen:zs_raw|B cell|filterByExpr,816784,24,000011110010011110011111,filterByExpr
16
+ gen:zs_raw|Monocyte|nonzero,954832,24,000011110010011110011111,nonzero
17
+ gen:zs_raw|Monocyte|filterByExpr,954832,24,000011110010011110011111,filterByExpr
18
+ gen:zs_raw|NK cell|nonzero,1092880,24,000011110010011110011111,nonzero
19
+ gen:zs_raw|NK cell|filterByExpr,1092880,24,000011110010011110011111,filterByExpr
20
+ gen:zs_raw|DC|nonzero,1230928,24,000011110010011110011111,nonzero
21
+ gen:zs_raw|DC|filterByExpr,1230928,24,000011110010011110011111,filterByExpr
22
+ bcast:78d8ac589dee9315|nonzero,1368976,24,000011110010011110011111,nonzero
23
+ bcast:78d8ac589dee9315|filterByExpr,1368976,24,000011110010011110011111,filterByExpr
24
+ gen:zs_pseudo|T cell|nonzero,1507024,24,000011110010011110011111,nonzero
25
+ gen:zs_pseudo|T cell|filterByExpr,1507024,24,000011110010011110011111,filterByExpr
26
+ gen:zs_pseudo|B cell|nonzero,1645072,24,000011110010011110011111,nonzero
27
+ gen:zs_pseudo|B cell|filterByExpr,1645072,24,000011110010011110011111,filterByExpr
28
+ gen:zs_pseudo|Monocyte|nonzero,1783120,24,000011110010011110011111,nonzero
29
+ gen:zs_pseudo|Monocyte|filterByExpr,1783120,24,000011110010011110011111,filterByExpr
30
+ gen:zs_pseudo|NK cell|nonzero,1921168,24,000011110010011110011111,nonzero
31
+ gen:zs_pseudo|NK cell|filterByExpr,1921168,24,000011110010011110011111,filterByExpr
32
+ gen:zs_pseudo|DC|nonzero,2059216,24,000011110010011110011111,nonzero
33
+ gen:zs_pseudo|DC|filterByExpr,2059216,24,000011110010011110011111,filterByExpr
34
+ bcast:49033eab3e3c50d0|nonzero,2197264,24,000011110010011110011111,nonzero
35
+ bcast:49033eab3e3c50d0|filterByExpr,2197264,24,000011110010011110011111,filterByExpr
36
+ gen:zs_cal|T cell|nonzero,2335312,24,000011110010011110011111,nonzero
37
+ gen:zs_cal|T cell|filterByExpr,2335312,24,000011110010011110011111,filterByExpr
38
+ gen:zs_cal|B cell|nonzero,2473360,24,000011110010011110011111,nonzero
39
+ gen:zs_cal|B cell|filterByExpr,2473360,24,000011110010011110011111,filterByExpr
40
+ gen:zs_cal|Monocyte|nonzero,2611408,24,000011110010011110011111,nonzero
41
+ gen:zs_cal|Monocyte|filterByExpr,2611408,24,000011110010011110011111,filterByExpr
42
+ gen:zs_cal|NK cell|nonzero,2749456,24,000011110010011110011111,nonzero
43
+ gen:zs_cal|NK cell|filterByExpr,2749456,24,000011110010011110011111,filterByExpr
44
+ gen:zs_cal|DC|nonzero,2887504,24,000011110010011110011111,nonzero
45
+ gen:zs_cal|DC|filterByExpr,2887504,24,000011110010011110011111,filterByExpr
46
+ bcast:cdfdac0013eb4d3a|nonzero,3025552,24,000011110010011110011111,nonzero
47
+ bcast:cdfdac0013eb4d3a|filterByExpr,3025552,24,000011110010011110011111,filterByExpr
48
+ gen:lora5|T cell|nonzero,3163600,24,000011110010011110011111,nonzero
49
+ gen:lora5|T cell|filterByExpr,3163600,24,000011110010011110011111,filterByExpr
50
+ gen:lora5|B cell|nonzero,3301648,24,000011110010011110011111,nonzero
51
+ gen:lora5|B cell|filterByExpr,3301648,24,000011110010011110011111,filterByExpr
52
+ gen:lora5|Monocyte|nonzero,3439696,24,000011110010011110011111,nonzero
53
+ gen:lora5|Monocyte|filterByExpr,3439696,24,000011110010011110011111,filterByExpr
54
+ gen:lora5|NK cell|nonzero,3577744,24,000011110010011110011111,nonzero
55
+ gen:lora5|NK cell|filterByExpr,3577744,24,000011110010011110011111,filterByExpr
56
+ gen:lora5|DC|nonzero,3715792,24,000011110010011110011111,nonzero
57
+ gen:lora5|DC|filterByExpr,3715792,24,000011110010011110011111,filterByExpr
58
+ bcast:cc4771e4a9c4ec2a|nonzero,3853840,24,000011110010011110011111,nonzero
59
+ bcast:cc4771e4a9c4ec2a|filterByExpr,3853840,24,000011110010011110011111,filterByExpr
60
+ gen:scsemi5|T cell|nonzero,3991888,24,000011110010011110011111,nonzero
61
+ gen:scsemi5|T cell|filterByExpr,3991888,24,000011110010011110011111,filterByExpr
62
+ gen:scsemi5|B cell|nonzero,4129936,23,00001111001011110011111,nonzero
63
+ gen:scsemi5|B cell|filterByExpr,4129936,23,00001111001011110011111,filterByExpr
64
+ gen:scsemi5|Monocyte|nonzero,4262232,24,000011110010011110011111,nonzero
65
+ gen:scsemi5|Monocyte|filterByExpr,4262232,24,000011110010011110011111,filterByExpr
66
+ gen:scsemi5|NK cell|nonzero,4400280,23,00001111001011110011111,nonzero
67
+ gen:scsemi5|NK cell|filterByExpr,4400280,23,00001111001011110011111,filterByExpr
68
+ gen:scsemi5|DC|nonzero,4532576,23,00001111001011110011111,nonzero
69
+ gen:scsemi5|DC|filterByExpr,4532576,23,00001111001011110011111,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/ji2025_chili/fewshot_n5/draw4/limma/limma_status.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ "job","status","n_tested","n_sig_fdr05","seconds"
2
+ "obs|T cell|nonzero","ok",5662,73,0.292
3
+ "obs|T cell|filterByExpr","ok",3449,87,0.137
4
+ "obs|B cell|nonzero","ok",5327,311,0.214
5
+ "obs|B cell|filterByExpr","ok",1567,240,0.066
6
+ "obs|Monocyte|nonzero","ok",5675,308,0.229
7
+ "obs|Monocyte|filterByExpr","ok",3059,363,0.119
8
+ "obs|NK cell|nonzero","ok",5453,54,0.22
9
+ "obs|NK cell|filterByExpr","ok",2705,73,0.106
10
+ "obs|DC|nonzero","ok",5000,2223,0.183
11
+ "obs|DC|filterByExpr","ok",668,83,0.035
12
+ "gen:zs_raw|T cell|nonzero","ok",4178,4,0.16
13
+ "gen:zs_raw|T cell|filterByExpr","ok",1307,11,0.058
14
+ "gen:zs_raw|B cell|nonzero","ok",3066,0,0.119
15
+ "gen:zs_raw|B cell|filterByExpr","ok",687,0,0.03
16
+ "gen:zs_raw|Monocyte|nonzero","ok",4275,2,0.168
17
+ "gen:zs_raw|Monocyte|filterByExpr","ok",1568,8,0.065
18
+ "gen:zs_raw|NK cell|nonzero","ok",2772,571,0.13
19
+ "gen:zs_raw|NK cell|filterByExpr","ok",277,0,0.017
20
+ "gen:zs_raw|DC|nonzero","ok",2109,0,0.079
21
+ "gen:zs_raw|DC|filterByExpr","ok",119,0,0.013
22
+ "bcast:78d8ac589dee9315|nonzero","ok",5493,29,0.228
23
+ "bcast:78d8ac589dee9315|filterByExpr","ok",3765,42,0.141
24
+ "gen:zs_pseudo|T cell|nonzero","ok",4185,1325,0.166
25
+ "gen:zs_pseudo|T cell|filterByExpr","ok",1649,513,0.067
26
+ "gen:zs_pseudo|B cell|nonzero","ok",3306,71,0.128
27
+ "gen:zs_pseudo|B cell|filterByExpr","ok",794,76,0.061
28
+ "gen:zs_pseudo|Monocyte|nonzero","ok",3837,129,0.15
29
+ "gen:zs_pseudo|Monocyte|filterByExpr","ok",1618,203,0.067
30
+ "gen:zs_pseudo|NK cell|nonzero","ok",3720,15,0.146
31
+ "gen:zs_pseudo|NK cell|filterByExpr","ok",1405,55,0.06
32
+ "gen:zs_pseudo|DC|nonzero","ok",3269,10,0.123
33
+ "gen:zs_pseudo|DC|filterByExpr","ok",695,35,0.034
34
+ "bcast:49033eab3e3c50d0|nonzero","ok",5745,338,0.246
35
+ "bcast:49033eab3e3c50d0|filterByExpr","ok",3821,290,0.151
36
+ "gen:zs_cal|T cell|nonzero","ok",4161,1,0.16
37
+ "gen:zs_cal|T cell|filterByExpr","ok",1359,0,0.059
38
+ "gen:zs_cal|B cell|nonzero","ok",3051,0,0.118
39
+ "gen:zs_cal|B cell|filterByExpr","ok",774,0,0.036
40
+ "gen:zs_cal|Monocyte|nonzero","ok",3627,0,0.142
41
+ "gen:zs_cal|Monocyte|filterByExpr","ok",1244,0,0.052
42
+ "gen:zs_cal|NK cell|nonzero","ok",2630,1,0.099
43
+ "gen:zs_cal|NK cell|filterByExpr","ok",366,0,0.025
44
+ "gen:zs_cal|DC|nonzero","ok",2305,0,0.091
45
+ "gen:zs_cal|DC|filterByExpr","ok",195,0,0.018
46
+ "bcast:cdfdac0013eb4d3a|nonzero","ok",5493,26,0.243
47
+ "bcast:cdfdac0013eb4d3a|filterByExpr","ok",3872,24,0.144
48
+ "gen:lora5|T cell|nonzero","ok",4166,24,0.161
49
+ "gen:lora5|T cell|filterByExpr","ok",1577,36,0.066
50
+ "gen:lora5|B cell|nonzero","ok",2992,487,0.114
51
+ "gen:lora5|B cell|filterByExpr","ok",788,0,0.04
52
+ "gen:lora5|Monocyte|nonzero","ok",3394,6,0.132
53
+ "gen:lora5|Monocyte|filterByExpr","ok",1129,11,0.049
54
+ "gen:lora5|NK cell|nonzero","ok",3132,14,0.122
55
+ "gen:lora5|NK cell|filterByExpr","ok",1011,0,0.045
56
+ "gen:lora5|DC|nonzero","ok",2853,0,0.114
57
+ "gen:lora5|DC|filterByExpr","ok",381,0,0.025
58
+ "bcast:cc4771e4a9c4ec2a|nonzero","ok",5493,29,0.225
59
+ "bcast:cc4771e4a9c4ec2a|filterByExpr","ok",3765,42,0.147
60
+ "gen:scsemi5|T cell|nonzero","ok",2518,1,0.092
61
+ "gen:scsemi5|T cell|filterByExpr","ok",355,0,0.023
62
+ "gen:scsemi5|B cell|nonzero","ok",1006,422,0.04
63
+ "gen:scsemi5|B cell|filterByExpr","ok",161,0,0.013
64
+ "gen:scsemi5|Monocyte|nonzero","ok",1146,1,0.046
65
+ "gen:scsemi5|Monocyte|filterByExpr","ok",270,11,0.02
66
+ "gen:scsemi5|NK cell|nonzero","ok",1680,1,0.063
67
+ "gen:scsemi5|NK cell|filterByExpr","ok",279,1,0.017
68
+ "gen:scsemi5|DC|nonzero","ok",679,0,0.033
69
+ "gen:scsemi5|DC|filterByExpr","ok",165,0,0.015