Archive 4 checkpoints (1-4)
Browse files- 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/pooled/limma/versions.txt +3 -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/pooled/manifest.json +552 -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/pooled/rbo.csv +61 -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/pooled/repro.json +61 -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/pooled/limma/versions.txt
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R version 4.5.2 (2025-10-31)
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limma 3.66.0
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edgeR 4.8.1
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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/pooled/manifest.json
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| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_contrast_extra.v1",
|
| 3 |
+
"dataset": "ji2025_chili",
|
| 4 |
+
"design": "pooled",
|
| 5 |
+
"unit": "pooled",
|
| 6 |
+
"written_utc": "2026-10-02T06:32:44.053385+00:00",
|
| 7 |
+
"command": [
|
| 8 |
+
"tools/contrast_extra.py",
|
| 9 |
+
"--design",
|
| 10 |
+
"pooled",
|
| 11 |
+
"--dataset",
|
| 12 |
+
"ji2025_chili",
|
| 13 |
+
"--threads",
|
| 14 |
+
"4"
|
| 15 |
+
],
|
| 16 |
+
"threads": 4,
|
| 17 |
+
"donors": [
|
| 18 |
+
"N064_TOL",
|
| 19 |
+
"N064_FU1",
|
| 20 |
+
"N032_AC",
|
| 21 |
+
"N038_BC",
|
| 22 |
+
"N038_AC",
|
| 23 |
+
"N055_AC",
|
| 24 |
+
"N136_TOL",
|
| 25 |
+
"N136_FU1",
|
| 26 |
+
"N138_TOL",
|
| 27 |
+
"N138_FU1",
|
| 28 |
+
"N128_BC",
|
| 29 |
+
"N128_AC",
|
| 30 |
+
"N129_BC",
|
| 31 |
+
"N129_AC",
|
| 32 |
+
"N147_TOL",
|
| 33 |
+
"N150_BC",
|
| 34 |
+
"N158_AC",
|
| 35 |
+
"N159_BC",
|
| 36 |
+
"N001_TOL",
|
| 37 |
+
"N001_FU1",
|
| 38 |
+
"N002_TOL",
|
| 39 |
+
"N002_FU1",
|
| 40 |
+
"N005_BC",
|
| 41 |
+
"N005_AC",
|
| 42 |
+
"N012_TOL",
|
| 43 |
+
"N012_FU1",
|
| 44 |
+
"N018_BC",
|
| 45 |
+
"N018_AC",
|
| 46 |
+
"N022_TOL",
|
| 47 |
+
"N022_FU1",
|
| 48 |
+
"N035_TOL",
|
| 49 |
+
"N043_TOL",
|
| 50 |
+
"N043_FU1"
|
| 51 |
+
],
|
| 52 |
+
"n_samples": 33,
|
| 53 |
+
"contrast": {
|
| 54 |
+
"case_groups": [
|
| 55 |
+
"TOL",
|
| 56 |
+
"FU1"
|
| 57 |
+
],
|
| 58 |
+
"control_groups": [
|
| 59 |
+
"BC",
|
| 60 |
+
"AC"
|
| 61 |
+
],
|
| 62 |
+
"n_case_donors": 18,
|
| 63 |
+
"n_control_donors": 15
|
| 64 |
+
},
|
| 65 |
+
"calls": {
|
| 66 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled": {
|
| 67 |
+
"arms": [
|
| 68 |
+
"pseudo_full__cal",
|
| 69 |
+
"pseudo_full__raw",
|
| 70 |
+
"real_lora__raw",
|
| 71 |
+
"zs__cal",
|
| 72 |
+
"zs__pseudo",
|
| 73 |
+
"zs__raw"
|
| 74 |
+
],
|
| 75 |
+
"summary_sha256": "c5affd46bccadfd4ca31a8a75f8b0047e691ca8f1ca3f56a04db53df53e743d9",
|
| 76 |
+
"contrast_csv_sha256": "210695ecacb2243c2cb2118373d96a5f7708e8b0150784d784dd658d1cbe4124"
|
| 77 |
+
}
|
| 78 |
+
},
|
| 79 |
+
"notes": {
|
| 80 |
+
"source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores"
|
| 81 |
+
},
|
| 82 |
+
"reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
|
| 83 |
+
"deg_reference": {
|
| 84 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili/deg_reference.npz",
|
| 85 |
+
"sha256": "4f5eb8c8389ef1308ce3ec44be8be024cedb97de37351d109d9070c818df5a9e"
|
| 86 |
+
},
|
| 87 |
+
"gene_exclusion": null,
|
| 88 |
+
"n_genes_disease_scores": 5752,
|
| 89 |
+
"genes_per_type": {
|
| 90 |
+
"T cell": 3021,
|
| 91 |
+
"B cell": 3245,
|
| 92 |
+
"Monocyte": 3154,
|
| 93 |
+
"NK cell": 3051
|
| 94 |
+
},
|
| 95 |
+
"arms": {
|
| 96 |
+
"pseudo_full__cal": {
|
| 97 |
+
"call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled",
|
| 98 |
+
"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/pseudo_full__cal.npz",
|
| 99 |
+
"npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/pseudo_full__cal.npz",
|
| 100 |
+
"npz_sha256": "f08492665ec5c89211a009a0aa0020217e974e045c456c8c794ded36a0996d79",
|
| 101 |
+
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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/pooled/rbo.csv
ADDED
|
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| 1 |
+
dataset,design,unit,arm,predictor,celltype,p,rbo_ext_t_desc,rbo_ext_t_asc,rbo_ext_mean_up_down,pred_defined,len_obs,len_pred
|
| 2 |
+
ji2025_chili,pooled,pooled,pseudo_full__cal,generated:pseudo_full__cal,T cell,0.98,0.06675838750882143,0.00532042904121526,0.03603940827501834,True,5696,4222
|
| 3 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,broadcast:conditions_pooled_cal.npz@b0274507,T cell,0.98,0.06766325513028809,0.026128668079776027,0.04689596160503206,True,5696,5541
|
| 4 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,generated:pseudo_full__cal,B cell,0.98,0.02331131017652769,0.012607220605343368,0.01795926539093553,True,5418,2935
|
| 5 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,broadcast:conditions_pooled_cal.npz@b0274507,B cell,0.98,0.018613652285234008,0.00940024141445994,0.014006946849846973,True,5418,5541
|
| 6 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,generated:pseudo_full__cal,Monocyte,0.98,0.06329694838257979,0.052066363056271034,0.05768165571942541,True,5699,3386
|
| 7 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,broadcast:conditions_pooled_cal.npz@b0274507,Monocyte,0.98,0.10119917265398101,0.029020279290778776,0.06510972597237989,True,5699,5541
|
| 8 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,generated:pseudo_full__cal,NK cell,0.98,0.017023298554118882,0.024437747386701528,0.020730522970410205,True,5516,2296
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| 9 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,broadcast:conditions_pooled_cal.npz@b0274507,NK cell,0.98,0.05143993531460399,0.022958824943778346,0.03719938012919117,True,5516,5541
|
| 10 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,generated:pseudo_full__cal,DC,0.98,0.0037337485375562875,0.06495211591033971,0.034342932223948,True,5168,2666
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| 11 |
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ji2025_chili,pooled,pooled,pseudo_full__cal,broadcast:conditions_pooled_cal.npz@b0274507,DC,0.98,0.08699015552665139,0.045437886717258964,0.06621402112195518,True,5168,5541
|
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ji2025_chili,pooled,pooled,pseudo_full__raw,generated:pseudo_full__raw,T cell,0.98,0.035950038502756285,0.05653044426487563,0.04624024138381595,True,5696,4417
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ji2025_chili,pooled,pooled,pseudo_full__raw,broadcast:conditions_pooled_raw.npz@a13338f5,T cell,0.98,0.06862133972224015,0.026907909519025466,0.04776462462063281,True,5696,5541
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| 14 |
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ji2025_chili,pooled,pooled,pseudo_full__raw,generated:pseudo_full__raw,B cell,0.98,0.01587318645689747,0.002818378749172629,0.00934578260303505,True,5418,3002
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| 15 |
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ji2025_chili,pooled,pooled,pseudo_full__raw,broadcast:conditions_pooled_raw.npz@a13338f5,B cell,0.98,0.02088705394053869,0.010974416557598995,0.015930735249068843,True,5418,5541
|
| 16 |
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ji2025_chili,pooled,pooled,pseudo_full__raw,generated:pseudo_full__raw,Monocyte,0.98,0.1344591981597528,0.029749864541576687,0.08210453135066474,True,5699,3931
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ji2025_chili,pooled,pooled,pseudo_full__raw,broadcast:conditions_pooled_raw.npz@a13338f5,Monocyte,0.98,0.1069044021836209,0.029628771308169273,0.06826658674589509,True,5699,5541
|
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ji2025_chili,pooled,pooled,pseudo_full__raw,generated:pseudo_full__raw,NK cell,0.98,0.023518068822657945,0.06718696336791526,0.0453525160952866,True,5516,2614
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| 19 |
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ji2025_chili,pooled,pooled,pseudo_full__raw,broadcast:conditions_pooled_raw.npz@a13338f5,NK cell,0.98,0.052019645865070636,0.020611336546570918,0.036315491205820775,True,5516,5541
|
| 20 |
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ji2025_chili,pooled,pooled,pseudo_full__raw,generated:pseudo_full__raw,DC,0.98,0.008596858426879996,0.03431367756361882,0.021455267995249407,True,5168,2535
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| 21 |
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ji2025_chili,pooled,pooled,pseudo_full__raw,broadcast:conditions_pooled_raw.npz@a13338f5,DC,0.98,0.07810266432508176,0.04437506040888489,0.061238862366983324,True,5168,5541
|
| 22 |
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ji2025_chili,pooled,pooled,real_lora__raw,generated:real_lora__raw,T cell,0.98,0.07323291048810274,0.05255480810778183,0.06289385929794228,True,5696,4291
|
| 23 |
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ji2025_chili,pooled,pooled,real_lora__raw,broadcast:conditions_pooled_raw.npz@a13338f5,T cell,0.98,0.06862133972224015,0.026907909519025466,0.04776462462063281,True,5696,5541
|
| 24 |
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ji2025_chili,pooled,pooled,real_lora__raw,generated:real_lora__raw,B cell,0.98,0.03063899217586974,0.045227082630528666,0.0379330374031992,True,5418,3234
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| 25 |
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ji2025_chili,pooled,pooled,real_lora__raw,broadcast:conditions_pooled_raw.npz@a13338f5,B cell,0.98,0.02088705394053869,0.010974416557598995,0.015930735249068843,True,5418,5541
|
| 26 |
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ji2025_chili,pooled,pooled,real_lora__raw,generated:real_lora__raw,Monocyte,0.98,0.2869061518101244,0.14647570311642052,0.21669092746327245,True,5699,3851
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ji2025_chili,pooled,pooled,real_lora__raw,broadcast:conditions_pooled_raw.npz@a13338f5,Monocyte,0.98,0.1069044021836209,0.029628771308169273,0.06826658674589509,True,5699,5541
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ji2025_chili,pooled,pooled,real_lora__raw,generated:real_lora__raw,NK cell,0.98,0.10794863359825409,0.18914103211070576,0.14854483285447992,True,5516,3649
|
| 29 |
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ji2025_chili,pooled,pooled,real_lora__raw,broadcast:conditions_pooled_raw.npz@a13338f5,NK cell,0.98,0.052019645865070636,0.020611336546570918,0.036315491205820775,True,5516,5541
|
| 30 |
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ji2025_chili,pooled,pooled,real_lora__raw,generated:real_lora__raw,DC,0.98,0.01016928066540375,0.11481966669729705,0.0624944736813504,True,5168,3147
|
| 31 |
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ji2025_chili,pooled,pooled,real_lora__raw,broadcast:conditions_pooled_raw.npz@a13338f5,DC,0.98,0.07810266432508176,0.04437506040888489,0.061238862366983324,True,5168,5541
|
| 32 |
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ji2025_chili,pooled,pooled,zs__cal,generated:zs__cal,T cell,0.98,0.03584274703130962,0.007927364820735127,0.021885055926022374,True,5696,4326
|
| 33 |
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ji2025_chili,pooled,pooled,zs__cal,broadcast:conditions_pooled_cal.npz@b0274507,T cell,0.98,0.06766325513028809,0.026128668079776027,0.04689596160503206,True,5696,5541
|
| 34 |
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ji2025_chili,pooled,pooled,zs__cal,generated:zs__cal,B cell,0.98,0.011067672236137107,0.007381018639709999,0.009224345437923553,True,5418,3313
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ji2025_chili,pooled,pooled,zs__cal,broadcast:conditions_pooled_cal.npz@b0274507,B cell,0.98,0.018613652285234008,0.00940024141445994,0.014006946849846973,True,5418,5541
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| 36 |
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ji2025_chili,pooled,pooled,zs__cal,generated:zs__cal,Monocyte,0.98,0.026922907298408526,0.04209690082193196,0.034509904060170245,True,5699,3825
|
| 37 |
+
ji2025_chili,pooled,pooled,zs__cal,broadcast:conditions_pooled_cal.npz@b0274507,Monocyte,0.98,0.10119917265398101,0.029020279290778776,0.06510972597237989,True,5699,5541
|
| 38 |
+
ji2025_chili,pooled,pooled,zs__cal,generated:zs__cal,NK cell,0.98,0.009444467717305371,0.009200160912657282,0.009322314314981327,True,5516,3102
|
| 39 |
+
ji2025_chili,pooled,pooled,zs__cal,broadcast:conditions_pooled_cal.npz@b0274507,NK cell,0.98,0.05143993531460399,0.022958824943778346,0.03719938012919117,True,5516,5541
|
| 40 |
+
ji2025_chili,pooled,pooled,zs__cal,generated:zs__cal,DC,0.98,0.0037887261567000484,0.11211792155323694,0.05795332385496849,True,5168,2485
|
| 41 |
+
ji2025_chili,pooled,pooled,zs__cal,broadcast:conditions_pooled_cal.npz@b0274507,DC,0.98,0.08699015552665139,0.045437886717258964,0.06621402112195518,True,5168,5541
|
| 42 |
+
ji2025_chili,pooled,pooled,zs__pseudo,generated:zs__pseudo,T cell,0.98,0.025023330920464562,0.018463302622753985,0.021743316771609275,True,5696,4318
|
| 43 |
+
ji2025_chili,pooled,pooled,zs__pseudo,broadcast:conditions_pooled_pseudo.npz@089c6d4f,T cell,0.98,0.17623424326919718,0.31963985173582343,0.2479370475025103,True,5696,5749
|
| 44 |
+
ji2025_chili,pooled,pooled,zs__pseudo,generated:zs__pseudo,B cell,0.98,0.00281513738173142,0.003168298121539406,0.0029917177516354133,True,5418,3404
|
| 45 |
+
ji2025_chili,pooled,pooled,zs__pseudo,broadcast:conditions_pooled_pseudo.npz@089c6d4f,B cell,0.98,0.060660665848369384,0.10959130053461298,0.08512598319149119,True,5418,5749
|
| 46 |
+
ji2025_chili,pooled,pooled,zs__pseudo,generated:zs__pseudo,Monocyte,0.98,0.06783056934896671,0.043221201518281856,0.055525885433624286,True,5699,3908
|
| 47 |
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ji2025_chili,pooled,pooled,zs__pseudo,broadcast:conditions_pooled_pseudo.npz@089c6d4f,Monocyte,0.98,0.21574500607786506,0.0987642115130627,0.15725460879546388,True,5699,5749
|
| 48 |
+
ji2025_chili,pooled,pooled,zs__pseudo,generated:zs__pseudo,NK cell,0.98,0.04847548257075313,0.006173399137902632,0.02732444085432788,True,5516,3827
|
| 49 |
+
ji2025_chili,pooled,pooled,zs__pseudo,broadcast:conditions_pooled_pseudo.npz@089c6d4f,NK cell,0.98,0.1873886193504566,0.2718494205037086,0.22961901992708258,True,5516,5749
|
| 50 |
+
ji2025_chili,pooled,pooled,zs__pseudo,generated:zs__pseudo,DC,0.98,0.00010233996703758881,0.011376639991614255,0.005739489979325922,True,5168,3396
|
| 51 |
+
ji2025_chili,pooled,pooled,zs__pseudo,broadcast:conditions_pooled_pseudo.npz@089c6d4f,DC,0.98,0.06338469456795506,0.34629748671300525,0.20484109064048017,True,5168,5749
|
| 52 |
+
ji2025_chili,pooled,pooled,zs__raw,generated:zs__raw,T cell,0.98,0.014412917116566162,0.02021208531521237,0.017312501215889266,True,5696,4321
|
| 53 |
+
ji2025_chili,pooled,pooled,zs__raw,broadcast:conditions_pooled_raw.npz@a13338f5,T cell,0.98,0.06862133972224015,0.026907909519025466,0.04776462462063281,True,5696,5541
|
| 54 |
+
ji2025_chili,pooled,pooled,zs__raw,generated:zs__raw,B cell,0.98,0.01539173767518902,0.009672091687894211,0.012531914681541616,True,5418,3189
|
| 55 |
+
ji2025_chili,pooled,pooled,zs__raw,broadcast:conditions_pooled_raw.npz@a13338f5,B cell,0.98,0.02088705394053869,0.010974416557598995,0.015930735249068843,True,5418,5541
|
| 56 |
+
ji2025_chili,pooled,pooled,zs__raw,generated:zs__raw,Monocyte,0.98,0.04330806310392906,0.03552268940795938,0.03941537625594422,True,5699,4367
|
| 57 |
+
ji2025_chili,pooled,pooled,zs__raw,broadcast:conditions_pooled_raw.npz@a13338f5,Monocyte,0.98,0.1069044021836209,0.029628771308169273,0.06826658674589509,True,5699,5541
|
| 58 |
+
ji2025_chili,pooled,pooled,zs__raw,generated:zs__raw,NK cell,0.98,0.0035746524220419303,0.03194287591500989,0.017758764168525912,True,5516,2979
|
| 59 |
+
ji2025_chili,pooled,pooled,zs__raw,broadcast:conditions_pooled_raw.npz@a13338f5,NK cell,0.98,0.052019645865070636,0.020611336546570918,0.036315491205820775,True,5516,5541
|
| 60 |
+
ji2025_chili,pooled,pooled,zs__raw,generated:zs__raw,DC,0.98,0.0011687244099097183,0.0421912161618743,0.02167997028589201,True,5168,2223
|
| 61 |
+
ji2025_chili,pooled,pooled,zs__raw,broadcast:conditions_pooled_raw.npz@a13338f5,DC,0.98,0.07810266432508176,0.04437506040888489,0.061238862366983324,True,5168,5541
|
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/pooled/repro.json
ADDED
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| 1 |
+
{
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| 2 |
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| 3 |
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| 4 |
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| 8 |
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| 9 |
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| 10 |
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},
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| 11 |
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|
| 12 |
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| 14 |
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| 15 |
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| 17 |
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| 18 |
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| 19 |
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"real_lora__raw": {
|
| 20 |
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| 21 |
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| 23 |
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| 24 |
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| 25 |
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| 26 |
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},
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| 27 |
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"zs__cal": {
|
| 28 |
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"contrast_max_abs_diff": 9.71445146547012e-17,
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| 29 |
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| 30 |
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| 31 |
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|
| 32 |
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|
| 33 |
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"pass": true
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| 34 |
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},
|
| 35 |
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"zs__pseudo": {
|
| 36 |
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"contrast_max_abs_diff": 9.71445146547012e-17,
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| 37 |
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"n_genes_equal": true,
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| 39 |
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| 40 |
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|
| 41 |
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|
| 42 |
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},
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| 43 |
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"zs__raw": {
|
| 44 |
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|
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| 50 |
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}
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| 51 |
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},
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| 55 |
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| 58 |
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},
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"comparable_with_scorer": true,
|
| 60 |
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|
| 61 |
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}
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