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junidude14 commited on
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Archive 4 checkpoints (1-4)

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Files changed (4) hide show
  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/draw1/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/draw1/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/draw1/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/draw1/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/draw1/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/draw1,zs_raw,"Zero-shot, real bulk",zs_raw,all_usable_raw.npz@78d8ac58,0.03695897416331737,0.028532668097033722,-0.002459888071068273,0.20791984755382747,0.100049126968919,0.8839875692912933,0.002874667672659483,0.7765443349108496,0.9362123886704333,0.9672438742086434,0.0370474557100814,0.20323960776215574,0,243,0.027564102564102563,0,0.0,2492,2,0,5,0,250,0.06789286094265348,3,0.28419491236768224,1912,4,6,5,1,250,0.7967079480708918,2,0.5826289859302354,928,12,4,5,0.004,0.008045625863447769,0.006,0.016091251726895538,0.011144658236783908,0.011187571295748665,5,0.032,0.004736581872794704,0.05,0.009473163745589408,0.05594136138504341,0.03915616730169732,5,True
3
+ ji2025_chili,fewshot,fewshot_n5/draw1,zs_pseudo,"Zero-shot, sc pseudobulk input (reference)",other,all_usable_pseudo.npz@49033eab,0.14598862881808508,0.1342115944154656,0.04262878630514758,0.5715523189410769,0.4826633241959282,0.8839875692912933,0.002874667672659483,0.7765443349108496,0.9362123886704333,0.9672438742086434,0.1420948121291085,0.5547941658857469,0,243,0.7857320750087755,28,2.2241321620153593,2492,103,983,5,0,250,0.8120257271026883,39,2.2892242207841895,1912,65,267,5,2,250,4.568814677570536,63,6.868845610762955,928,166,236,5,0.016,0.006832806883318247,0.026000000000000002,0.013665613766636494,0.02657010568158185,0.022406564444211907,5,0.264,0.00457844844156838,0.33799999999999997,0.00915689688313676,0.17178766697560305,0.2213186890153493,5,True
4
+ ji2025_chili,fewshot,fewshot_n5/draw1,zs_cal,Zero-shot + calibration,zs_cal,test_cal.npz@79890ab3,0.05364414433733922,0.017742447213698147,0.025958195511900886,0.18626952279703363,0.11051375894222132,0.8839875692912933,0.002874667672659483,0.7765443349108496,0.9362123886704333,0.9672438742086434,0.05361531992771158,0.1822769608113426,0,243,0.0,0,0.0920434654128833,2492,0,2,5,0,250,0.0,0,0.0,1912,0,0,5,0,250,0.0,0,0.0,928,0,0,5,0.012,0.007671382748374311,0.022000000000000002,0.015342765496748623,0.024264391756687844,0.02143718740087922,5,0.036000000000000004,0.004736581872794704,0.046000000000000006,0.009473163745589408,0.054242225980972766,0.038202555624287884,5,True
5
+ ji2025_chili,fewshot,fewshot_n5/draw1,lora5,"LoRA, 5 donors",lora,test_raw.npz@0c873c5d,0.27568480061697936,0.2088340644701692,0.2420147625491504,0.20791984755382747,0.100049126968919,0.8839875692912933,0.002874667672659483,0.7765443349108496,0.9362123886704333,0.9672438742086434,0.2709210291634057,0.20323960776215574,1,243,0.0514668039114771,0,0.0,2492,4,0,5,3,250,0.9600184089399814,3,0.28419491236768224,1912,496,6,5,6,250,0.5105105105105106,2,0.5826289859302354,928,17,4,5,0.06000000000000001,0.006889627224936935,0.078,0.01377925444987387,0.06257000440519897,0.07106831580797025,5,0.032,0.004736581872794704,0.05,0.009473163745589408,0.05594136138504341,0.03915616730169732,5,True
6
+ ji2025_chili,fewshot,fewshot_n5/draw1,scsemi5,"scSemiProfiler, 5 donors",scsemi,test_raw.npz@0c873c5d,0.1801656001049191,0.06519553975011483,0.14057873632576154,0.20791984755382747,0.100049126968919,0.8839875692912933,0.002874667672659483,0.7765443349108496,0.9362123886704333,0.9672438742086434,0.17573313019255762,0.20323960776215574,0,243,0.0,0,0.0,2492,0,0,5,0,250,0.0,3,0.28419491236768224,1912,0,6,5,1,250,4.891304347826087,2,0.5826289859302354,928,18,4,5,0.012,0.022190847744776834,0.014000000000000002,0.04438169548955367,0.020379814847448708,0.06022358098197665,5,0.032,0.004736581872794704,0.05,0.009473163745589408,0.05594136138504341,0.03915616730169732,5,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/draw1/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/draw1/limma/jobs.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ job,offset,n_samples,is_case,filter
2
+ obs|T cell|nonzero,0,26,11000011001011110011001111,nonzero
3
+ obs|T cell|filterByExpr,0,26,11000011001011110011001111,filterByExpr
4
+ obs|B cell|nonzero,149552,26,11000011001011110011001111,nonzero
5
+ obs|B cell|filterByExpr,149552,26,11000011001011110011001111,filterByExpr
6
+ obs|Monocyte|nonzero,299104,26,11000011001011110011001111,nonzero
7
+ obs|Monocyte|filterByExpr,299104,26,11000011001011110011001111,filterByExpr
8
+ obs|NK cell|nonzero,448656,26,11000011001011110011001111,nonzero
9
+ obs|NK cell|filterByExpr,448656,26,11000011001011110011001111,filterByExpr
10
+ obs|DC|nonzero,598208,24,110000110010111100110011,nonzero
11
+ obs|DC|filterByExpr,598208,24,110000110010111100110011,filterByExpr
12
+ gen:zs_raw|T cell|nonzero,736256,26,11000011001011110011001111,nonzero
13
+ gen:zs_raw|T cell|filterByExpr,736256,26,11000011001011110011001111,filterByExpr
14
+ gen:zs_raw|B cell|nonzero,885808,26,11000011001011110011001111,nonzero
15
+ gen:zs_raw|B cell|filterByExpr,885808,26,11000011001011110011001111,filterByExpr
16
+ gen:zs_raw|Monocyte|nonzero,1035360,26,11000011001011110011001111,nonzero
17
+ gen:zs_raw|Monocyte|filterByExpr,1035360,26,11000011001011110011001111,filterByExpr
18
+ gen:zs_raw|NK cell|nonzero,1184912,26,11000011001011110011001111,nonzero
19
+ gen:zs_raw|NK cell|filterByExpr,1184912,26,11000011001011110011001111,filterByExpr
20
+ gen:zs_raw|DC|nonzero,1334464,26,11000011001011110011001111,nonzero
21
+ gen:zs_raw|DC|filterByExpr,1334464,26,11000011001011110011001111,filterByExpr
22
+ bcast:78d8ac589dee9315|nonzero,1484016,26,11000011001011110011001111,nonzero
23
+ bcast:78d8ac589dee9315|filterByExpr,1484016,26,11000011001011110011001111,filterByExpr
24
+ gen:zs_pseudo|T cell|nonzero,1633568,26,11000011001011110011001111,nonzero
25
+ gen:zs_pseudo|T cell|filterByExpr,1633568,26,11000011001011110011001111,filterByExpr
26
+ gen:zs_pseudo|B cell|nonzero,1783120,26,11000011001011110011001111,nonzero
27
+ gen:zs_pseudo|B cell|filterByExpr,1783120,26,11000011001011110011001111,filterByExpr
28
+ gen:zs_pseudo|Monocyte|nonzero,1932672,26,11000011001011110011001111,nonzero
29
+ gen:zs_pseudo|Monocyte|filterByExpr,1932672,26,11000011001011110011001111,filterByExpr
30
+ gen:zs_pseudo|NK cell|nonzero,2082224,26,11000011001011110011001111,nonzero
31
+ gen:zs_pseudo|NK cell|filterByExpr,2082224,26,11000011001011110011001111,filterByExpr
32
+ gen:zs_pseudo|DC|nonzero,2231776,26,11000011001011110011001111,nonzero
33
+ gen:zs_pseudo|DC|filterByExpr,2231776,26,11000011001011110011001111,filterByExpr
34
+ bcast:49033eab3e3c50d0|nonzero,2381328,26,11000011001011110011001111,nonzero
35
+ bcast:49033eab3e3c50d0|filterByExpr,2381328,26,11000011001011110011001111,filterByExpr
36
+ gen:zs_cal|T cell|nonzero,2530880,26,11000011001011110011001111,nonzero
37
+ gen:zs_cal|T cell|filterByExpr,2530880,26,11000011001011110011001111,filterByExpr
38
+ gen:zs_cal|B cell|nonzero,2680432,26,11000011001011110011001111,nonzero
39
+ gen:zs_cal|B cell|filterByExpr,2680432,26,11000011001011110011001111,filterByExpr
40
+ gen:zs_cal|Monocyte|nonzero,2829984,26,11000011001011110011001111,nonzero
41
+ gen:zs_cal|Monocyte|filterByExpr,2829984,26,11000011001011110011001111,filterByExpr
42
+ gen:zs_cal|NK cell|nonzero,2979536,26,11000011001011110011001111,nonzero
43
+ gen:zs_cal|NK cell|filterByExpr,2979536,26,11000011001011110011001111,filterByExpr
44
+ gen:zs_cal|DC|nonzero,3129088,26,11000011001011110011001111,nonzero
45
+ gen:zs_cal|DC|filterByExpr,3129088,26,11000011001011110011001111,filterByExpr
46
+ bcast:79890ab3b6471434|nonzero,3278640,26,11000011001011110011001111,nonzero
47
+ bcast:79890ab3b6471434|filterByExpr,3278640,26,11000011001011110011001111,filterByExpr
48
+ gen:lora5|T cell|nonzero,3428192,26,11000011001011110011001111,nonzero
49
+ gen:lora5|T cell|filterByExpr,3428192,26,11000011001011110011001111,filterByExpr
50
+ gen:lora5|B cell|nonzero,3577744,26,11000011001011110011001111,nonzero
51
+ gen:lora5|B cell|filterByExpr,3577744,26,11000011001011110011001111,filterByExpr
52
+ gen:lora5|Monocyte|nonzero,3727296,26,11000011001011110011001111,nonzero
53
+ gen:lora5|Monocyte|filterByExpr,3727296,26,11000011001011110011001111,filterByExpr
54
+ gen:lora5|NK cell|nonzero,3876848,26,11000011001011110011001111,nonzero
55
+ gen:lora5|NK cell|filterByExpr,3876848,26,11000011001011110011001111,filterByExpr
56
+ gen:lora5|DC|nonzero,4026400,26,11000011001011110011001111,nonzero
57
+ gen:lora5|DC|filterByExpr,4026400,26,11000011001011110011001111,filterByExpr
58
+ bcast:0c873c5de82a9be4|nonzero,4175952,26,11000011001011110011001111,nonzero
59
+ bcast:0c873c5de82a9be4|filterByExpr,4175952,26,11000011001011110011001111,filterByExpr
60
+ gen:scsemi5|T cell|nonzero,4325504,26,11000011001011110011001111,nonzero
61
+ gen:scsemi5|T cell|filterByExpr,4325504,26,11000011001011110011001111,filterByExpr
62
+ gen:scsemi5|B cell|nonzero,4475056,26,11000011001011110011001111,nonzero
63
+ gen:scsemi5|B cell|filterByExpr,4475056,26,11000011001011110011001111,filterByExpr
64
+ gen:scsemi5|Monocyte|nonzero,4624608,26,11000011001011110011001111,nonzero
65
+ gen:scsemi5|Monocyte|filterByExpr,4624608,26,11000011001011110011001111,filterByExpr
66
+ gen:scsemi5|NK cell|nonzero,4774160,25,1100001100111110011001111,nonzero
67
+ gen:scsemi5|NK cell|filterByExpr,4774160,25,1100001100111110011001111,filterByExpr
68
+ gen:scsemi5|DC|nonzero,4917960,26,11000011001011110011001111,nonzero
69
+ gen:scsemi5|DC|filterByExpr,4917960,26,11000011001011110011001111,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/draw1/limma/limma_status.csv ADDED
@@ -0,0 +1,69 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ "job","status","n_tested","n_sig_fdr05","seconds"
2
+ "obs|T cell|nonzero","ok",5685,218,0.284
3
+ "obs|T cell|filterByExpr","ok",3478,259,0.141
4
+ "obs|B cell|nonzero","ok",5377,100,0.213
5
+ "obs|B cell|filterByExpr","ok",1658,168,0.069
6
+ "obs|Monocyte|nonzero","ok",5696,160,0.236
7
+ "obs|Monocyte|filterByExpr","ok",3023,201,0.119
8
+ "obs|NK cell|nonzero","ok",5494,165,0.221
9
+ "obs|NK cell|filterByExpr","ok",2737,167,0.114
10
+ "obs|DC|nonzero","ok",5096,1269,0.216
11
+ "obs|DC|filterByExpr","ok",876,133,0.037
12
+ "gen:zs_raw|T cell|nonzero","ok",4217,0,0.162
13
+ "gen:zs_raw|T cell|filterByExpr","ok",1322,8,0.057
14
+ "gen:zs_raw|B cell|nonzero","ok",3129,1,0.123
15
+ "gen:zs_raw|B cell|filterByExpr","ok",694,2,0.035
16
+ "gen:zs_raw|Monocyte|nonzero","ok",4298,0,0.176
17
+ "gen:zs_raw|Monocyte|filterByExpr","ok",1573,0,0.067
18
+ "gen:zs_raw|NK cell|nonzero","ok",2894,3,0.113
19
+ "gen:zs_raw|NK cell|filterByExpr","ok",292,2,0.02
20
+ "gen:zs_raw|DC|nonzero","ok",2119,0,0.104
21
+ "gen:zs_raw|DC|filterByExpr","ok",113,0,0.013
22
+ "bcast:78d8ac589dee9315|nonzero","ok",5501,6,0.231
23
+ "bcast:78d8ac589dee9315|filterByExpr","ok",3799,4,0.145
24
+ "gen:zs_pseudo|T cell|nonzero","ok",4208,31,0.178
25
+ "gen:zs_pseudo|T cell|filterByExpr","ok",1698,49,0.072
26
+ "gen:zs_pseudo|B cell|nonzero","ok",3298,1,0.131
27
+ "gen:zs_pseudo|B cell|filterByExpr","ok",794,3,0.039
28
+ "gen:zs_pseudo|Monocyte|nonzero","ok",3860,31,0.16
29
+ "gen:zs_pseudo|Monocyte|filterByExpr","ok",1548,85,0.068
30
+ "gen:zs_pseudo|NK cell|nonzero","ok",3749,2,0.15
31
+ "gen:zs_pseudo|NK cell|filterByExpr","ok",1407,22,0.067
32
+ "gen:zs_pseudo|DC|nonzero","ok",3343,0,0.134
33
+ "gen:zs_pseudo|DC|filterByExpr","ok",756,7,0.038
34
+ "bcast:49033eab3e3c50d0|nonzero","ok",5748,267,0.252
35
+ "bcast:49033eab3e3c50d0|filterByExpr","ok",3815,236,0.154
36
+ "gen:zs_cal|T cell|nonzero","ok",4250,0,0.198
37
+ "gen:zs_cal|T cell|filterByExpr","ok",1417,0,0.06
38
+ "gen:zs_cal|B cell|nonzero","ok",3373,0,0.133
39
+ "gen:zs_cal|B cell|filterByExpr","ok",966,0,0.045
40
+ "gen:zs_cal|Monocyte|nonzero","ok",3796,0,0.154
41
+ "gen:zs_cal|Monocyte|filterByExpr","ok",1417,0,0.063
42
+ "gen:zs_cal|NK cell|nonzero","ok",3141,0,0.124
43
+ "gen:zs_cal|NK cell|filterByExpr","ok",754,0,0.037
44
+ "gen:zs_cal|DC|nonzero","ok",2390,0,0.094
45
+ "gen:zs_cal|DC|filterByExpr","ok",206,0,0.021
46
+ "bcast:79890ab3b6471434|nonzero","ok",5501,0,0.233
47
+ "bcast:79890ab3b6471434|filterByExpr","ok",3870,0,0.155
48
+ "gen:lora5|T cell|nonzero","ok",4260,1,0.174
49
+ "gen:lora5|T cell|filterByExpr","ok",1598,0,0.068
50
+ "gen:lora5|B cell|nonzero","ok",3301,0,0.138
51
+ "gen:lora5|B cell|filterByExpr","ok",1017,0,0.046
52
+ "gen:lora5|Monocyte|nonzero","ok",3886,13,0.16
53
+ "gen:lora5|Monocyte|filterByExpr","ok",1666,17,0.094
54
+ "gen:lora5|NK cell|nonzero","ok",3702,0,0.147
55
+ "gen:lora5|NK cell|filterByExpr","ok",1354,0,0.061
56
+ "gen:lora5|DC|nonzero","ok",3207,482,0.125
57
+ "gen:lora5|DC|filterByExpr","ok",633,0,0.033
58
+ "bcast:0c873c5de82a9be4|nonzero","ok",5501,6,0.238
59
+ "bcast:0c873c5de82a9be4|filterByExpr","ok",3799,4,0.145
60
+ "gen:scsemi5|T cell|nonzero","ok",2092,0,0.082
61
+ "gen:scsemi5|T cell|filterByExpr","ok",267,0,0.02
62
+ "gen:scsemi5|B cell|nonzero","ok",966,0,0.041
63
+ "gen:scsemi5|B cell|filterByExpr","ok",146,0,0.016
64
+ "gen:scsemi5|Monocyte|nonzero","ok",1355,0,0.077
65
+ "gen:scsemi5|Monocyte|filterByExpr","ok",277,0,0.02
66
+ "gen:scsemi5|NK cell|nonzero","ok",1279,0,0.052
67
+ "gen:scsemi5|NK cell|filterByExpr","ok",204,0,0.015
68
+ "gen:scsemi5|DC|nonzero","ok",716,0,0.033
69
+ "gen:scsemi5|DC|filterByExpr","ok",185,18,0.015