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/fewshot_n5/draw3/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/fewshot_n5/draw3/manifest.json +504 -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/draw3/rbo.csv +51 -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/draw3/repro.json +53 -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/draw3/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/fewshot_n5/draw3/manifest.json
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_contrast_extra.v1",
|
| 3 |
+
"dataset": "ji2025_chili",
|
| 4 |
+
"design": "fewshot",
|
| 5 |
+
"unit": "fewshot_n5/draw3",
|
| 6 |
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"written_utc": "2026-10-02T06:31:30.743778+00:00",
|
| 7 |
+
"command": [
|
| 8 |
+
"tools/contrast_extra.py",
|
| 9 |
+
"--design",
|
| 10 |
+
"fewshot",
|
| 11 |
+
"--dataset",
|
| 12 |
+
"ji2025_chili",
|
| 13 |
+
"--draws",
|
| 14 |
+
"0,1,2,3,4",
|
| 15 |
+
"--threads",
|
| 16 |
+
"4"
|
| 17 |
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],
|
| 18 |
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"threads": 4,
|
| 19 |
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"donors": [
|
| 20 |
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"N064_TOL",
|
| 21 |
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"N064_FU1",
|
| 22 |
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"N032_AC",
|
| 23 |
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"N055_AC",
|
| 24 |
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"N136_TOL",
|
| 25 |
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"N136_FU1",
|
| 26 |
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"N138_TOL",
|
| 27 |
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"N138_FU1",
|
| 28 |
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"N128_BC",
|
| 29 |
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"N128_AC",
|
| 30 |
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"N129_BC",
|
| 31 |
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"N129_AC",
|
| 32 |
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"N158_AC",
|
| 33 |
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"N159_BC",
|
| 34 |
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"N002_TOL",
|
| 35 |
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"N002_FU1",
|
| 36 |
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"N005_BC",
|
| 37 |
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"N005_AC",
|
| 38 |
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"N012_TOL",
|
| 39 |
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"N012_FU1",
|
| 40 |
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"N022_TOL",
|
| 41 |
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"N022_FU1",
|
| 42 |
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"N035_TOL",
|
| 43 |
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"N043_TOL",
|
| 44 |
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"N043_FU1"
|
| 45 |
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],
|
| 46 |
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"n_samples": 25,
|
| 47 |
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"contrast": {
|
| 48 |
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"case_groups": [
|
| 49 |
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"TOL",
|
| 50 |
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"FU1"
|
| 51 |
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],
|
| 52 |
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"control_groups": [
|
| 53 |
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"BC",
|
| 54 |
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"AC"
|
| 55 |
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],
|
| 56 |
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"n_case_donors": 15,
|
| 57 |
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"n_control_donors": 10
|
| 58 |
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},
|
| 59 |
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"calls": {
|
| 60 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw3": {
|
| 61 |
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"arms": [
|
| 62 |
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"zs_raw",
|
| 63 |
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"zs_pseudo",
|
| 64 |
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"zs_cal",
|
| 65 |
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"lora5"
|
| 66 |
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],
|
| 67 |
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"summary_sha256": "1dfcde686ee38e143529c2f3f0f20201c09cbe0504729783b199a841cceddb1f",
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| 68 |
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"contrast_csv_sha256": "404a1a8bfd012cbaf39a09086c7b7d22f4d7f8f25869c0d0f807f9bce8ca25d5"
|
| 69 |
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},
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| 70 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw3_scsemi5": {
|
| 71 |
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"arms": [
|
| 72 |
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"scsemi5"
|
| 73 |
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],
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| 74 |
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"summary_sha256": "fdc4bae0393fe2e178d37dc1af2e23836ebda4c4f1de305c24c22a5f40d3d88e",
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"contrast_csv_sha256": "ca049abc219ca4d4a053199d4a72e3e6cf8f32bd8863125407c7508003f1586f"
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| 76 |
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}
|
| 77 |
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},
|
| 78 |
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"notes": {
|
| 79 |
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"source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores"
|
| 80 |
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},
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| 81 |
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"reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
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| 82 |
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"deg_reference": {
|
| 83 |
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"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",
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| 84 |
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"sha256": "4f5eb8c8389ef1308ce3ec44be8be024cedb97de37351d109d9070c818df5a9e"
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| 85 |
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},
|
| 86 |
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"gene_exclusion": null,
|
| 87 |
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"n_genes_disease_scores": 5752,
|
| 88 |
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"genes_per_type": {
|
| 89 |
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"T cell": 3028,
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| 90 |
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"B cell": 3238,
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| 91 |
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"Monocyte": 3132,
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| 92 |
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"NK cell": 3064
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| 93 |
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},
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| 94 |
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"arms": {
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| 95 |
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"zs_raw": {
|
| 96 |
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"call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw3",
|
| 97 |
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"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/fewshot_n5/zs__raw_all.npz",
|
| 98 |
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"npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/fewshot_n5/zs__raw_all.npz",
|
| 99 |
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"npz_sha256": "0d37cb4c8f0f60d75cefb35c8ec7c79c0d1cac6c891bda9205cfb1e195dd7da0",
|
| 100 |
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"receipt_verified": true,
|
| 101 |
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"condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/fewshot_n5/all_usable_raw.npz",
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| 102 |
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"condition_sha256": "78d8ac589dee9315807163c174fafde76bd890710e96c512773dfaf9151e5b86",
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| 103 |
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"condition_label": "all_usable_raw.npz@78d8ac58",
|
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"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881"
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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/fewshot_n5/draw3/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,fewshot,fewshot_n5/draw3,zs_raw,generated:zs_raw,T cell,0.98,0.034625091726958414,0.06920338015826635,0.05191423594261238,True,5667,4221
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| 3 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,broadcast:all_usable_raw.npz@78d8ac58,T cell,0.98,0.08215822116745816,0.01540040304762208,0.04877931210754012,True,5667,5524
|
| 4 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,generated:zs_raw,B cell,0.98,0.002246850483662763,0.01863918404434564,0.010443017264004203,True,5377,3084
|
| 5 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,broadcast:all_usable_raw.npz@78d8ac58,B cell,0.98,0.015209370360784548,0.032111701218171744,0.023660535789478146,True,5377,5524
|
| 6 |
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|
| 7 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,broadcast:all_usable_raw.npz@78d8ac58,Monocyte,0.98,0.06002634447604125,0.07310505283330183,0.06656569865467155,True,5684,5524
|
| 8 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,generated:zs_raw,NK cell,0.98,0.0019571512515471185,0.024275907775267596,0.013116529513407357,True,5460,2773
|
| 9 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,broadcast:all_usable_raw.npz@78d8ac58,NK cell,0.98,0.013064542098512587,0.016615237517941535,0.01483988980822706,True,5460,5524
|
| 10 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,generated:zs_raw,DC,0.98,0.0021001789806970347,0.030324139995112052,0.016212159487904543,True,4970,2145
|
| 11 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_raw,broadcast:all_usable_raw.npz@78d8ac58,DC,0.98,0.042140518273297206,0.05015713754614617,0.04614882790972169,True,4970,5524
|
| 12 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,generated:zs_pseudo,T cell,0.98,0.003890263679968365,0.03139507914788303,0.017642671413925698,True,5667,4196
|
| 13 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,broadcast:all_usable_pseudo.npz@49033eab,T cell,0.98,0.12667491311345705,0.29770391244937744,0.21218941278141723,True,5667,5744
|
| 14 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,generated:zs_pseudo,B cell,0.98,0.024958905689389046,0.007080865522305596,0.01601988560584732,True,5377,3364
|
| 15 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,broadcast:all_usable_pseudo.npz@49033eab,B cell,0.98,0.06791812887565694,0.0752052314770899,0.07156168017637343,True,5377,5744
|
| 16 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,generated:zs_pseudo,Monocyte,0.98,0.039806371204643226,0.019879948535038626,0.029843159869840926,True,5684,3856
|
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,broadcast:all_usable_pseudo.npz@49033eab,Monocyte,0.98,0.23662060040072613,0.12113106453182375,0.17887583246627495,True,5684,5744
|
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|
| 19 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,broadcast:all_usable_pseudo.npz@49033eab,NK cell,0.98,0.10338027226211577,0.2111732955277099,0.15727678389491284,True,5460,5744
|
| 20 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,generated:zs_pseudo,DC,0.98,0.0002383488792309091,0.0027100752314969836,0.0014742120553639464,True,4970,3299
|
| 21 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_pseudo,broadcast:all_usable_pseudo.npz@49033eab,DC,0.98,0.03902614508820257,0.3400480093368192,0.1895370772125109,True,4970,5744
|
| 22 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,generated:zs_cal,T cell,0.98,0.04046454152525825,0.024828941074024898,0.032646741299641575,True,5667,4183
|
| 23 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,broadcast:test_cal.npz@82faaec7,T cell,0.98,0.0802130697075954,0.013150355059663676,0.04668171238362954,True,5667,5524
|
| 24 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,generated:zs_cal,B cell,0.98,0.008510897432554312,0.02483300578863661,0.01667195161059546,True,5377,3081
|
| 25 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,broadcast:test_cal.npz@82faaec7,B cell,0.98,0.012255377442944426,0.02851641301408613,0.020385895228515277,True,5377,5524
|
| 26 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,generated:zs_cal,Monocyte,0.98,0.029890183153187568,0.01234485040326117,0.02111751677822437,True,5684,3717
|
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,broadcast:test_cal.npz@82faaec7,Monocyte,0.98,0.059316282758144295,0.054813940993922575,0.057065111876033435,True,5684,5524
|
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,generated:zs_cal,NK cell,0.98,0.006104026214025097,0.11424884692155468,0.06017643656778989,True,5460,2719
|
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,broadcast:test_cal.npz@82faaec7,NK cell,0.98,0.021869453987304395,0.01888131140950214,0.020375382698403267,True,5460,5524
|
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|
| 31 |
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ji2025_chili,fewshot,fewshot_n5/draw3,zs_cal,broadcast:test_cal.npz@82faaec7,DC,0.98,0.043248054462530765,0.0497650342290233,0.04650654434577703,True,4970,5524
|
| 32 |
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ji2025_chili,fewshot,fewshot_n5/draw3,lora5,generated:lora5,T cell,0.98,0.04720848855613766,0.17001855656758622,0.10861352256186194,True,5667,4110
|
| 33 |
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ji2025_chili,fewshot,fewshot_n5/draw3,lora5,broadcast:test_raw.npz@3d69ce8b,T cell,0.98,0.08215822116745816,0.01540040304762208,0.04877931210754012,True,5667,5524
|
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ji2025_chili,fewshot,fewshot_n5/draw3,lora5,generated:lora5,B cell,0.98,0.021842146505448114,0.037890775251302064,0.02986646087837509,True,5377,2810
|
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|
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ji2025_chili,fewshot,fewshot_n5/draw3,lora5,generated:lora5,Monocyte,0.98,0.0927552189001025,0.07682969192386946,0.08479245541198599,True,5684,3829
|
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|
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ji2025_chili,fewshot,fewshot_n5/draw3,lora5,generated:lora5,NK cell,0.98,0.021168405910014287,0.15973956097294328,0.09045398344147879,True,5460,3332
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|
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ji2025_chili,fewshot,fewshot_n5/draw3,lora5,generated:lora5,DC,0.98,0.008242892545352341,0.22571677408746016,0.11697983331640625,True,4970,2953
|
| 41 |
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ji2025_chili,fewshot,fewshot_n5/draw3,lora5,broadcast:test_raw.npz@3d69ce8b,DC,0.98,0.042140518273297206,0.05015713754614617,0.04614882790972169,True,4970,5524
|
| 42 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,T cell,0.98,0.019093848662374513,0.033739862036356726,0.02641685534936562,True,5667,1396
|
| 43 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@3d69ce8b,T cell,0.98,0.08215822116745816,0.01540040304762208,0.04877931210754012,True,5667,5524
|
| 44 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,B cell,0.98,0.007438142824576422,0.03130374464845428,0.01937094373651535,True,5377,647
|
| 45 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@3d69ce8b,B cell,0.98,0.015209370360784548,0.032111701218171744,0.023660535789478146,True,5377,5524
|
| 46 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,Monocyte,0.98,0.049368770599614316,0.03847858073013174,0.04392367566487303,True,5684,811
|
| 47 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@3d69ce8b,Monocyte,0.98,0.06002634447604125,0.07310505283330183,0.06656569865467155,True,5684,5524
|
| 48 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,NK cell,0.98,0.022012639185255263,0.16331435875029038,0.09266349896777282,True,5460,1195
|
| 49 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@3d69ce8b,NK cell,0.98,0.013064542098512587,0.016615237517941535,0.01483988980822706,True,5460,5524
|
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,DC,0.98,0.0035866033688221723,0.19345354420844815,0.09852007378863516,True,4970,457
|
| 51 |
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ji2025_chili,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@3d69ce8b,DC,0.98,0.042140518273297206,0.05015713754614617,0.04614882790972169,True,4970,5524
|
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/draw3/repro.json
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| 1 |
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{
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"arms": {
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| 3 |
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"zs_raw": {
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| 4 |
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"contrast_max_abs_diff": 8.326672684688674e-17,
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| 5 |
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"contrast_all_equal": true,
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| 6 |
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"n_genes_equal": true,
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| 7 |
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"welch_lists_equal": true,
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"welch_counts_equal": true,
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"pass": true
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},
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| 11 |
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"zs_pseudo": {
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"contrast_max_abs_diff": 6.938893903907228e-17,
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| 13 |
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"contrast_all_equal": true,
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| 14 |
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"n_genes_equal": true,
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| 15 |
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"welch_lists_equal": true,
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| 16 |
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"welch_counts_equal": true,
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| 17 |
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"pass": true
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| 18 |
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},
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| 19 |
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"zs_cal": {
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| 20 |
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"contrast_max_abs_diff": 9.71445146547012e-17,
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| 21 |
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"contrast_all_equal": true,
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| 22 |
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"n_genes_equal": true,
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| 23 |
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"welch_lists_equal": true,
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| 24 |
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"welch_counts_equal": true,
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| 25 |
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"pass": true
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| 26 |
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},
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| 27 |
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"lora5": {
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| 28 |
+
"contrast_max_abs_diff": 8.326672684688674e-17,
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| 29 |
+
"contrast_all_equal": true,
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| 30 |
+
"n_genes_equal": true,
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| 31 |
+
"welch_lists_equal": true,
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| 32 |
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"welch_counts_equal": true,
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| 33 |
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"pass": true
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| 34 |
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},
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| 35 |
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"scsemi5": {
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| 36 |
+
"contrast_max_abs_diff": 8.326672684688674e-17,
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| 37 |
+
"contrast_all_equal": true,
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| 38 |
+
"n_genes_equal": true,
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| 39 |
+
"welch_lists_equal": true,
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| 40 |
+
"welch_counts_equal": true,
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| 41 |
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"pass": true
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| 42 |
+
}
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| 43 |
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},
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| 44 |
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"observed_split_half_full_aggregates": {
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| 45 |
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"n_equal": true,
|
| 46 |
+
"det_equal": true,
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| 47 |
+
"sum_equal_float32": true,
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| 48 |
+
"cp10k_max_abs_diff_float32": 0.0,
|
| 49 |
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"cp10k_equal_float32": true
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| 50 |
+
},
|
| 51 |
+
"comparable_with_scorer": true,
|
| 52 |
+
"all_pass": true
|
| 53 |
+
}
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