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junidude14 commited on
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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/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/ji2025_chili/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/ji2025_chili/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/ji2025_chili/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/ji2025_chili/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
+ ji2025_chili,fewshot,fewshot_n5/draw0,zs_raw,"Zero-shot, real bulk",zs_raw,all_usable_raw.npz@78d8ac58,0.10251919469370015,0.09058263406125786,0.06069608987631346,0.21311861411338662,0.12839857231119842,0.8637970625882474,0.002573154905189082,0.7464905934101889,0.9229385610082795,0.960042843221488,0.10221299646298583,0.2091147779670266,0,125,0.008662175168431183,0,0.0939035567098322,2214,3,4,5,0,204,0.4082557036718402,1,0.2715198959152765,655,31,7,5,0,233,1.851765408351675,1,0.9332834681074509,778,51,7,5,0.004,0.008074621995404561,0.012,0.016149243990809123,0.015480544882812263,0.017214197074113986,5,0.004,0.004777468666286105,0.038,0.00955493733257221,0.055958678853070244,0.035273625547994146,5,True
3
+ ji2025_chili,fewshot,fewshot_n5/draw0,zs_pseudo,"Zero-shot, sc pseudobulk input (reference)",other,all_usable_pseudo.npz@49033eab,0.1840352599240339,0.18219709668082743,0.03990019370988619,0.6482949200986768,0.5641620959602385,0.8637970625882474,0.002573154905189082,0.7464905934101889,0.9229385610082795,0.960042843221488,0.18101818463783767,0.6269338222690107,0,125,0.05911045050441538,18,1.1330037347526778,2214,12,858,5,0,204,0.4285156752120458,25,1.8766795674303016,655,35,171,5,0,233,2.6329756160284483,73,6.283597380491289,778,87,186,5,0.004,0.006878325813465903,0.01,0.013756651626931807,0.015480872633170616,0.012039579983749363,5,0.372,0.004626058812341157,0.384,0.009252117624682313,0.1313097229972201,0.24721611852030234,5,True
4
+ ji2025_chili,fewshot,fewshot_n5/draw0,zs_cal,Zero-shot + calibration,zs_cal,test_cal.npz@7141bb69,0.11356580338558689,0.1033091793219145,0.10582109050331304,0.11641070898187766,0.05097332646136788,0.8637970625882474,0.002573154905189082,0.7464905934101889,0.9229385610082795,0.960042843221488,0.11227560100789438,0.11549119641328769,0,125,0.0,0,0.02347588917745805,2214,0,1,5,0,204,0.0,1,0.15515422623730085,655,0,4,5,0,233,0.0,1,0.39127873715142303,778,0,3,5,0.0,0.007884491820584975,0.014000000000000002,0.01576898364116995,0.02540977662304844,0.018153744459510877,5,0.0,0.004777468666286105,0.027999999999999997,0.00955493733257221,0.05309741969990996,0.03351015698516206,5,True
5
+ ji2025_chili,fewshot,fewshot_n5/draw0,lora5,"LoRA, 5 donors",lora,test_raw.npz@ca5da7eb,0.38697985726899736,0.358689213530799,0.36588903106531123,0.21311861411338662,0.12839857231119842,0.8637970625882474,0.002573154905189082,0.7464905934101889,0.9229385610082795,0.960042843221488,0.37828525709076277,0.2091147779670266,0,125,0.051171559385941284,0,0.0939035567098322,2214,19,4,5,6,204,1.7537108721954067,1,0.2715198959152765,655,1242,7,5,6,233,3.5899195845833596,1,0.9332834681074509,778,113,7,5,0.044000000000000004,0.007205763218435269,0.06999999999999999,0.014411526436870537,0.025866060195225544,0.058117507796358006,5,0.004,0.004777468666286105,0.038,0.00955493733257221,0.055958678853070244,0.035273625547994146,5,True
6
+ ji2025_chili,fewshot,fewshot_n5/draw0,scsemi5,"scSemiProfiler, 5 donors",scsemi,test_raw.npz@ca5da7eb,0.04315298104902922,0.03340024728136994,-0.02209705474122556,0.21311861411338662,0.12839857231119842,0.8637970625882474,0.002573154905189082,0.7464905934101889,0.9229385610082795,0.960042843221488,0.04370919793256445,0.2091147779670266,0,125,0.0,0,0.0939035567098322,2214,0,4,5,0,204,0.0,1,0.2715198959152765,655,0,7,5,0,233,2.366863905325444,1,0.9332834681074509,778,8,7,5,0.028000000000000004,0.022877589925094338,0.04,0.045755179850188676,0.011291208125821173,0.05013115124202405,5,0.004,0.004777468666286105,0.038,0.00955493733257221,0.055958678853070244,0.035273625547994146,5,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/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/ji2025_chili/fewshot_n5/draw0/limma/jobs.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ job,offset,n_samples,is_case,filter
2
+ obs|T cell|nonzero,0,25,1100011000010011110011111,nonzero
3
+ obs|T cell|filterByExpr,0,25,1100011000010011110011111,filterByExpr
4
+ obs|B cell|nonzero,143800,25,1100011000010011110011111,nonzero
5
+ obs|B cell|filterByExpr,143800,25,1100011000010011110011111,filterByExpr
6
+ obs|Monocyte|nonzero,287600,25,1100011000010011110011111,nonzero
7
+ obs|Monocyte|filterByExpr,287600,25,1100011000010011110011111,filterByExpr
8
+ obs|NK cell|nonzero,431400,25,1100011000010011110011111,nonzero
9
+ obs|NK cell|filterByExpr,431400,25,1100011000010011110011111,filterByExpr
10
+ obs|DC|nonzero,575200,23,11000110000100111100111,nonzero
11
+ obs|DC|filterByExpr,575200,23,11000110000100111100111,filterByExpr
12
+ gen:zs_raw|T cell|nonzero,707496,25,1100011000010011110011111,nonzero
13
+ gen:zs_raw|T cell|filterByExpr,707496,25,1100011000010011110011111,filterByExpr
14
+ gen:zs_raw|B cell|nonzero,851296,25,1100011000010011110011111,nonzero
15
+ gen:zs_raw|B cell|filterByExpr,851296,25,1100011000010011110011111,filterByExpr
16
+ gen:zs_raw|Monocyte|nonzero,995096,25,1100011000010011110011111,nonzero
17
+ gen:zs_raw|Monocyte|filterByExpr,995096,25,1100011000010011110011111,filterByExpr
18
+ gen:zs_raw|NK cell|nonzero,1138896,25,1100011000010011110011111,nonzero
19
+ gen:zs_raw|NK cell|filterByExpr,1138896,25,1100011000010011110011111,filterByExpr
20
+ gen:zs_raw|DC|nonzero,1282696,25,1100011000010011110011111,nonzero
21
+ gen:zs_raw|DC|filterByExpr,1282696,25,1100011000010011110011111,filterByExpr
22
+ bcast:78d8ac589dee9315|nonzero,1426496,25,1100011000010011110011111,nonzero
23
+ bcast:78d8ac589dee9315|filterByExpr,1426496,25,1100011000010011110011111,filterByExpr
24
+ gen:zs_pseudo|T cell|nonzero,1570296,25,1100011000010011110011111,nonzero
25
+ gen:zs_pseudo|T cell|filterByExpr,1570296,25,1100011000010011110011111,filterByExpr
26
+ gen:zs_pseudo|B cell|nonzero,1714096,25,1100011000010011110011111,nonzero
27
+ gen:zs_pseudo|B cell|filterByExpr,1714096,25,1100011000010011110011111,filterByExpr
28
+ gen:zs_pseudo|Monocyte|nonzero,1857896,25,1100011000010011110011111,nonzero
29
+ gen:zs_pseudo|Monocyte|filterByExpr,1857896,25,1100011000010011110011111,filterByExpr
30
+ gen:zs_pseudo|NK cell|nonzero,2001696,25,1100011000010011110011111,nonzero
31
+ gen:zs_pseudo|NK cell|filterByExpr,2001696,25,1100011000010011110011111,filterByExpr
32
+ gen:zs_pseudo|DC|nonzero,2145496,25,1100011000010011110011111,nonzero
33
+ gen:zs_pseudo|DC|filterByExpr,2145496,25,1100011000010011110011111,filterByExpr
34
+ bcast:49033eab3e3c50d0|nonzero,2289296,25,1100011000010011110011111,nonzero
35
+ bcast:49033eab3e3c50d0|filterByExpr,2289296,25,1100011000010011110011111,filterByExpr
36
+ gen:zs_cal|T cell|nonzero,2433096,25,1100011000010011110011111,nonzero
37
+ gen:zs_cal|T cell|filterByExpr,2433096,25,1100011000010011110011111,filterByExpr
38
+ gen:zs_cal|B cell|nonzero,2576896,25,1100011000010011110011111,nonzero
39
+ gen:zs_cal|B cell|filterByExpr,2576896,25,1100011000010011110011111,filterByExpr
40
+ gen:zs_cal|Monocyte|nonzero,2720696,25,1100011000010011110011111,nonzero
41
+ gen:zs_cal|Monocyte|filterByExpr,2720696,25,1100011000010011110011111,filterByExpr
42
+ gen:zs_cal|NK cell|nonzero,2864496,25,1100011000010011110011111,nonzero
43
+ gen:zs_cal|NK cell|filterByExpr,2864496,25,1100011000010011110011111,filterByExpr
44
+ gen:zs_cal|DC|nonzero,3008296,25,1100011000010011110011111,nonzero
45
+ gen:zs_cal|DC|filterByExpr,3008296,25,1100011000010011110011111,filterByExpr
46
+ bcast:7141bb69609b7484|nonzero,3152096,25,1100011000010011110011111,nonzero
47
+ bcast:7141bb69609b7484|filterByExpr,3152096,25,1100011000010011110011111,filterByExpr
48
+ gen:lora5|T cell|nonzero,3295896,25,1100011000010011110011111,nonzero
49
+ gen:lora5|T cell|filterByExpr,3295896,25,1100011000010011110011111,filterByExpr
50
+ gen:lora5|B cell|nonzero,3439696,25,1100011000010011110011111,nonzero
51
+ gen:lora5|B cell|filterByExpr,3439696,25,1100011000010011110011111,filterByExpr
52
+ gen:lora5|Monocyte|nonzero,3583496,25,1100011000010011110011111,nonzero
53
+ gen:lora5|Monocyte|filterByExpr,3583496,25,1100011000010011110011111,filterByExpr
54
+ gen:lora5|NK cell|nonzero,3727296,25,1100011000010011110011111,nonzero
55
+ gen:lora5|NK cell|filterByExpr,3727296,25,1100011000010011110011111,filterByExpr
56
+ gen:lora5|DC|nonzero,3871096,25,1100011000010011110011111,nonzero
57
+ gen:lora5|DC|filterByExpr,3871096,25,1100011000010011110011111,filterByExpr
58
+ bcast:ca5da7eba08208ca|nonzero,4014896,25,1100011000010011110011111,nonzero
59
+ bcast:ca5da7eba08208ca|filterByExpr,4014896,25,1100011000010011110011111,filterByExpr
60
+ gen:scsemi5|T cell|nonzero,4158696,25,1100011000010011110011111,nonzero
61
+ gen:scsemi5|T cell|filterByExpr,4158696,25,1100011000010011110011111,filterByExpr
62
+ gen:scsemi5|B cell|nonzero,4302496,21,110000000101111001111,nonzero
63
+ gen:scsemi5|B cell|filterByExpr,4302496,21,110000000101111001111,filterByExpr
64
+ gen:scsemi5|Monocyte|nonzero,4423288,24,110001100001011110011111,nonzero
65
+ gen:scsemi5|Monocyte|filterByExpr,4423288,24,110001100001011110011111,filterByExpr
66
+ gen:scsemi5|NK cell|nonzero,4561336,22,1100000001011110011111,nonzero
67
+ gen:scsemi5|NK cell|filterByExpr,4561336,22,1100000001011110011111,filterByExpr
68
+ gen:scsemi5|DC|nonzero,4687880,21,110000000101111001111,nonzero
69
+ gen:scsemi5|DC|filterByExpr,4687880,21,110000000101111001111,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/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",5660,287,0.281
3
+ "obs|T cell|filterByExpr","ok",3453,331,0.138
4
+ "obs|B cell|nonzero","ok",5271,4,0.204
5
+ "obs|B cell|filterByExpr","ok",1616,33,0.068
6
+ "obs|Monocyte|nonzero","ok",5668,78,0.222
7
+ "obs|Monocyte|filterByExpr","ok",2909,145,0.118
8
+ "obs|NK cell|nonzero","ok",5459,113,0.217
9
+ "obs|NK cell|filterByExpr","ok",2614,141,0.102
10
+ "obs|DC|nonzero","ok",5020,173,0.187
11
+ "obs|DC|filterByExpr","ok",936,128,0.044
12
+ "gen:zs_raw|T cell|nonzero","ok",4226,1,0.184
13
+ "gen:zs_raw|T cell|filterByExpr","ok",1311,9,0.054
14
+ "gen:zs_raw|B cell|nonzero","ok",3134,2,0.118
15
+ "gen:zs_raw|B cell|filterByExpr","ok",662,1,0.032
16
+ "gen:zs_raw|Monocyte|nonzero","ok",4261,17,0.168
17
+ "gen:zs_raw|Monocyte|filterByExpr","ok",1563,40,0.063
18
+ "gen:zs_raw|NK cell|nonzero","ok",2837,11,0.107
19
+ "gen:zs_raw|NK cell|filterByExpr","ok",299,1,0.018
20
+ "gen:zs_raw|DC|nonzero","ok",2134,0,0.08
21
+ "gen:zs_raw|DC|filterByExpr","ok",118,0,0.012
22
+ "bcast:78d8ac589dee9315|nonzero","ok",5512,7,0.229
23
+ "bcast:78d8ac589dee9315|filterByExpr","ok",3799,7,0.141
24
+ "gen:zs_pseudo|T cell|nonzero","ok",4217,25,0.173
25
+ "gen:zs_pseudo|T cell|filterByExpr","ok",1740,52,0.069
26
+ "gen:zs_pseudo|B cell|nonzero","ok",3283,0,0.128
27
+ "gen:zs_pseudo|B cell|filterByExpr","ok",710,3,0.034
28
+ "gen:zs_pseudo|Monocyte|nonzero","ok",3826,5,0.156
29
+ "gen:zs_pseudo|Monocyte|filterByExpr","ok",1531,29,0.086
30
+ "gen:zs_pseudo|NK cell|nonzero","ok",3755,5,0.142
31
+ "gen:zs_pseudo|NK cell|filterByExpr","ok",1422,3,0.06
32
+ "gen:zs_pseudo|DC|nonzero","ok",3280,0,0.122
33
+ "gen:zs_pseudo|DC|filterByExpr","ok",611,0,0.031
34
+ "bcast:49033eab3e3c50d0|nonzero","ok",5746,171,0.243
35
+ "bcast:49033eab3e3c50d0|filterByExpr","ok",3778,186,0.144
36
+ "gen:zs_cal|T cell|nonzero","ok",4225,0,0.162
37
+ "gen:zs_cal|T cell|filterByExpr","ok",1371,0,0.058
38
+ "gen:zs_cal|B cell|nonzero","ok",3118,0,0.118
39
+ "gen:zs_cal|B cell|filterByExpr","ok",782,0,0.04
40
+ "gen:zs_cal|Monocyte|nonzero","ok",3715,0,0.144
41
+ "gen:zs_cal|Monocyte|filterByExpr","ok",1382,0,0.06
42
+ "gen:zs_cal|NK cell|nonzero","ok",2782,0,0.105
43
+ "gen:zs_cal|NK cell|filterByExpr","ok",497,0,0.027
44
+ "gen:zs_cal|DC|nonzero","ok",2580,0,0.098
45
+ "gen:zs_cal|DC|filterByExpr","ok",278,0,0.019
46
+ "bcast:7141bb69609b7484|nonzero","ok",5512,4,0.231
47
+ "bcast:7141bb69609b7484|filterByExpr","ok",3666,3,0.164
48
+ "gen:lora5|T cell|nonzero","ok",4156,12,0.162
49
+ "gen:lora5|T cell|filterByExpr","ok",1486,28,0.061
50
+ "gen:lora5|B cell|nonzero","ok",3284,0,0.126
51
+ "gen:lora5|B cell|filterByExpr","ok",1025,3,0.045
52
+ "gen:lora5|Monocyte|nonzero","ok",3714,47,0.146
53
+ "gen:lora5|Monocyte|filterByExpr","ok",1523,65,0.065
54
+ "gen:lora5|NK cell|nonzero","ok",3403,10,0.13
55
+ "gen:lora5|NK cell|filterByExpr","ok",1231,13,0.052
56
+ "gen:lora5|DC|nonzero","ok",3022,1173,0.122
57
+ "gen:lora5|DC|filterByExpr","ok",569,4,0.03
58
+ "bcast:ca5da7eba08208ca|nonzero","ok",5512,7,0.224
59
+ "bcast:ca5da7eba08208ca|filterByExpr","ok",3799,7,0.144
60
+ "gen:scsemi5|T cell|nonzero","ok",2148,0,0.102
61
+ "gen:scsemi5|T cell|filterByExpr","ok",215,0,0.018
62
+ "gen:scsemi5|B cell|nonzero","ok",1007,0,0.036
63
+ "gen:scsemi5|B cell|filterByExpr","ok",134,0,0.014
64
+ "gen:scsemi5|Monocyte|nonzero","ok",1243,0,0.049
65
+ "gen:scsemi5|Monocyte|filterByExpr","ok",248,0,0.015
66
+ "gen:scsemi5|NK cell|nonzero","ok",1296,0,0.049
67
+ "gen:scsemi5|NK cell|filterByExpr","ok",205,0,0.013
68
+ "gen:scsemi5|DC|nonzero","ok",654,0,0.032
69
+ "gen:scsemi5|DC|filterByExpr","ok",169,8,0.012