Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/76634c5d1c885724/score.json +71 -0
- paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/80709b5b3573469b/donor_deg_summary.csv +26 -0
- paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/c7d0f90e9cb99cf7/immicro-healthy-fold0-n5.json +168 -0
- paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/fab609446ff715bf/summary.json +755 -0
paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/76634c5d1c885724/score.json
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{
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"state": "completed",
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"stage": "score",
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"at": "2026-10-15T11:42:10.600455+00:00",
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"outputs": [
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{
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| 7 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw2/lora/score/arms/lora/deg_top50_lists.csv",
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw2/lora/score/arms/lora/labels/labels.parquet",
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| 23 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw2/lora/score/contrast.csv",
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw2/lora/scoring_support.json",
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| 43 |
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"support_sha256": "fa20d986ff3869bc9b0a15ab6f16bae3a01a5f09a515f0a961146219c92595b4",
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| 48 |
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"binding": {
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| 49 |
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"arm": "lora",
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| 50 |
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"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/disease/draw2/lora.npz",
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| 51 |
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"npz_sha256": "2406835f4d0e1a90a644e0340d1bc346a2dfbd90fc12874fd8d34d0f4e600d09",
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"receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/disease/draw2/lora.log",
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"receipt_sha256": "5abd988cc3e1303cb7393b78a9a0ff61f0dd481aa2d0dde0b458be9dcef41a22",
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"source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/ji2025_chili/disease/draw2/lora/RUN.json",
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"source_binding_sha256": "599e93e9eddd3575f9ab22d8ff2b794182502f9a2c5c18f0cb66c92daa40f99b",
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"condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw2/test_raw.npz",
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"condition_sha256": "70953ef3c751fa832f2c8bf184fa1cd9fc6ef2e04329101441f0fce90b64ddc0",
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"checkpoint_sha256": "2f29a930b31c4e7b8c02c7654fbd0d6f3c5d3b607587eab42c3fbf0709becfa9",
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| 59 |
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"support_sha256": "fa20d986ff3869bc9b0a15ab6f16bae3a01a5f09a515f0a961146219c92595b4"
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| 60 |
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},
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| 61 |
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"reuse": {
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| 62 |
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"source_summary": {
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| 63 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw2/score/summary.json",
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| 64 |
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"sha256": "046d8926e86d70983dbddcf74141c48878a593e297517d6f75296a6d3422bdfc",
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| 65 |
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"bytes": 15886
|
| 66 |
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},
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| 67 |
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"source_arm": "lora",
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| 68 |
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"validated_support_sha256": "fa20d986ff3869bc9b0a15ab6f16bae3a01a5f09a515f0a961146219c92595b4",
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"annotation_reexecuted": false
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}
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paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/80709b5b3573469b/donor_deg_summary.csv
ADDED
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@@ -0,0 +1,26 @@
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| 1 |
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arm,celltype,status,observed_status,generated_status,n_case_donors_observed,n_control_donors_observed,n_case_donors_generated,n_control_donors_generated,method_observed,method_generated,reason_observed,reason_generated,reason_fit,reason_population,top50_overlap_count,observed_top50_size,generated_top50_size
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| 2 |
+
lora,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,7,50,50
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| 3 |
+
lora,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,7,50,50
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| 4 |
+
lora,Monocyte,ok,ok,ok,57,20,53,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
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| 5 |
+
lora,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
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| 6 |
+
lora,DC,ok,ok,ok,54,20,34,16,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
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| 7 |
+
pairedcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
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| 8 |
+
pairedcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,28
|
| 9 |
+
pairedcal,Monocyte,ok,ok,ok,57,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,18
|
| 10 |
+
pairedcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,26
|
| 11 |
+
pairedcal,DC,ok,ok,ok,54,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
|
| 12 |
+
scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
|
| 13 |
+
scsemi,B cell,ok,ok,ok,57,20,52,19,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
|
| 14 |
+
scsemi,Monocyte,ok,ok,ok,57,20,47,19,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,2
|
| 15 |
+
scsemi,NK cell,ok,ok,ok,57,20,42,15,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
|
| 16 |
+
scsemi,DC,ok,ok,ok,54,20,51,17,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
|
| 17 |
+
raw,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
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| 18 |
+
raw,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,21
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| 19 |
+
raw,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
|
| 20 |
+
raw,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
|
| 21 |
+
raw,DC,ok,ok,ok,54,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
|
| 22 |
+
refcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
|
| 23 |
+
refcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
|
| 24 |
+
refcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
|
| 25 |
+
refcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
|
| 26 |
+
refcal,DC,ok,ok,ok,54,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,15
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paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/c7d0f90e9cb99cf7/immicro-healthy-fold0-n5.json
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| 1 |
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{
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| 2 |
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"state": "completed",
|
| 3 |
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"at": "2026-10-15T11:30:48.242366+00:00",
|
| 4 |
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"kind": "canonical_full_adoption",
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| 5 |
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"canonical_receipt": {
|
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paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/fab609446ff715bf/summary.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "giroux2022",
|
| 4 |
+
"written_utc": "2026-10-15T06:52:45.770874+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"giroux2022",
|
| 9 |
+
"--out",
|
| 10 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw3/score",
|
| 11 |
+
"--arm",
|
| 12 |
+
"lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw3/lora.npz",
|
| 13 |
+
"--condition",
|
| 14 |
+
"lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw3/test_raw.npz",
|
| 15 |
+
"--donors",
|
| 16 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw3/test_samples.txt",
|
| 17 |
+
"--threads",
|
| 18 |
+
"2",
|
| 19 |
+
"--case-groups",
|
| 20 |
+
"severe",
|
| 21 |
+
"--control-groups",
|
| 22 |
+
"mild",
|
| 23 |
+
"--exclude-genes",
|
| 24 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv"
|
| 25 |
+
],
|
| 26 |
+
"arms": [
|
| 27 |
+
"lora"
|
| 28 |
+
],
|
| 29 |
+
"donors": [
|
| 30 |
+
"0B943B_d0",
|
| 31 |
+
"0B943B_d14",
|
| 32 |
+
"2AD75E_d0",
|
| 33 |
+
"2AD75E_d7",
|
| 34 |
+
"2AD75E_d14",
|
| 35 |
+
"82CCF5_d0",
|
| 36 |
+
"82CCF5_d7",
|
| 37 |
+
"82CCF5_d14",
|
| 38 |
+
"0BF51C_d0",
|
| 39 |
+
"0BF51C_d7",
|
| 40 |
+
"0BF51C_d14"
|
| 41 |
+
],
|
| 42 |
+
"n_donors": 11,
|
| 43 |
+
"reference": {
|
| 44 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
|
| 45 |
+
"reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
|
| 46 |
+
"features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
|
| 47 |
+
"n_r1_cells": 1650,
|
| 48 |
+
"pca": {
|
| 49 |
+
"n_components": 50,
|
| 50 |
+
"explained_variance_ratio_sum": 0.2550526559352875,
|
| 51 |
+
"n_fit_cells": 1650
|
| 52 |
+
},
|
| 53 |
+
"r2_control": {
|
| 54 |
+
"precision": 0.9987878787878788,
|
| 55 |
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"coverage": 1.0,
|
| 56 |
+
"density": 5.482666666666667,
|
| 57 |
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"n_query": 1650,
|
| 58 |
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"depth_matched": {
|
| 59 |
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"precision": 0.9993939393939394,
|
| 60 |
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"coverage": 1.0,
|
| 61 |
+
"density": 5.389454545454546
|
| 62 |
+
}
|
| 63 |
+
},
|
| 64 |
+
"observed_l1_loo_null_mean": 0.213264334322415
|
| 65 |
+
},
|
| 66 |
+
"contrast_definition": {
|
| 67 |
+
"enabled": true,
|
| 68 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 69 |
+
"group_source": "features groups",
|
| 70 |
+
"case_groups": [
|
| 71 |
+
"severe"
|
| 72 |
+
],
|
| 73 |
+
"control_groups": [
|
| 74 |
+
"mild"
|
| 75 |
+
],
|
| 76 |
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"n_case_donors": 6,
|
| 77 |
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"n_control_donors": 5,
|
| 78 |
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"n_donors_in_neither": 0,
|
| 79 |
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"case": [
|
| 80 |
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false,
|
| 81 |
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false,
|
| 82 |
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false,
|
| 83 |
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false,
|
| 84 |
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false,
|
| 85 |
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true,
|
| 86 |
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true,
|
| 87 |
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true,
|
| 88 |
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true,
|
| 89 |
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true,
|
| 90 |
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true
|
| 91 |
+
],
|
| 92 |
+
"ctrl": [
|
| 93 |
+
true,
|
| 94 |
+
true,
|
| 95 |
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true,
|
| 96 |
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true,
|
| 97 |
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true,
|
| 98 |
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false,
|
| 99 |
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false,
|
| 100 |
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false,
|
| 101 |
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false,
|
| 102 |
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false,
|
| 103 |
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false
|
| 104 |
+
],
|
| 105 |
+
"groups": [
|
| 106 |
+
"mild",
|
| 107 |
+
"mild",
|
| 108 |
+
"mild",
|
| 109 |
+
"mild",
|
| 110 |
+
"mild",
|
| 111 |
+
"severe",
|
| 112 |
+
"severe",
|
| 113 |
+
"severe",
|
| 114 |
+
"severe",
|
| 115 |
+
"severe",
|
| 116 |
+
"severe"
|
| 117 |
+
]
|
| 118 |
+
},
|
| 119 |
+
"deg_definition": {
|
| 120 |
+
"enabled": true,
|
| 121 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
| 122 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
|
| 123 |
+
"functions": [
|
| 124 |
+
"welch_bh_deg",
|
| 125 |
+
"top_deg_genes",
|
| 126 |
+
"jaccard"
|
| 127 |
+
],
|
| 128 |
+
"reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
|
| 129 |
+
"top_n": 50,
|
| 130 |
+
"fdr": 0.05,
|
| 131 |
+
"n_genes": 5498,
|
| 132 |
+
"types": [
|
| 133 |
+
"T cell",
|
| 134 |
+
"B cell",
|
| 135 |
+
"Monocyte",
|
| 136 |
+
"NK cell",
|
| 137 |
+
"DC"
|
| 138 |
+
],
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