Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/status.json

@@ -0,0 +1,18 @@
+{
+  "schema": "pbisc.paper.strict-statistics.v1",
+  "support_sha256": "ea331f967a3a212b91cd144bd8ba62cea3cbfe3bdcc9e77268e190757327b0e2",
+  "bootstrap_unit": "unique_donor_all_visits_and_draws",
+  "bootstrap_replicates": 2000,
+  "draws": [
+    "draw2_n5"
+  ],
+  "disease_deg": {
+    "status": "ok",
+    "method": "donor_condition_pseudobulk_limma_duplicateCorrelation_if_repeated_condition",
+    "n_genes_kept": 5975,
+    "rows": 25,
+    "n_pending": 0,
+    "n_not_estimable": 0,
+    "summary_csv": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/donor_deg/donor_deg_summary.csv"
+  }
+}

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/contrast/ye2026_sepsis/strict/headline.csv

@@ -0,0 +1,6 @@
+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
+ye2026_sepsis,scored,strict,lora,lora,other,test_raw.npz@3278dc67,0.4117403746586899,0.3051414301824399,0.3620194401436488,0.3264466405549955,0.3383113176560135,0.9576200238786292,0.0015850845651131918,0.8347393836254738,0.978197437299057,0.9890183716634495,0.41009257225681567,0.3263627044282643,15,250,3.1350140255155523,19,2.246447283685753,7459,1588,1139,5,16,250,2.5718925171559808,37,2.246447283685753,5383,2478,633,5,15,242,8.648995704868604,30,5.677931797865433,3087,730,381,5,0.088,0.006270028051031104,0.094,0.012540056102062208,0.15561804740880672,0.10856063238859148,5,0.044,0.004492894567371506,0.05600000000000001,0.008985789134743013,0.06543513288031592,0.07061944160903703,5,True
+ye2026_sepsis,scored,strict,pairedcal,pairedcal,other,test_cal.npz@d5aff6eb,0.10070723305211987,0.12767486573511705,0.010413028422096186,0.3275506478456903,0.4039845192468114,0.9576200238786292,0.0015850845651131918,0.8347393836254738,0.978197437299057,0.9890183716634495,0.10317508492906557,0.32802255086402077,6,250,2.4226339320181065,33,2.246447283685753,7459,1204,2979,5,10,250,2.1964018414561837,37,2.246447283685753,5383,533,684,5,14,242,7.4219523183179135,29,5.710312716004443,3087,661,289,5,0.036,0.006247137022914718,0.05,0.012494274045829435,0.07517574518968832,0.06102312199034178,5,0.052000000000000005,0.004492894567371506,0.064,0.008985789134743013,0.06839148124225249,0.07232903336777015,5,True
+ye2026_sepsis,scored,strict,scsemi,scsemi,other,test_raw.npz@3278dc67,0.5062400256266513,0.23849990327851542,0.43364809135299587,0.3264466405549955,0.3383113176560135,0.9576200238786292,0.0015850845651131918,0.8347393836254738,0.978197437299057,0.9890183716634495,0.5034614893405126,0.3263627044282643,16,250,7.4446376132614365,19,2.246447283685753,7459,407,1139,5,23,250,7.4446376132614365,37,2.246447283685753,5383,3877,633,5,16,242,45.805003672970074,30,5.677931797865433,3087,530,381,5,0.016,0.014889275226522872,0.046,0.029778550453045744,0.06080828022015461,0.04796434263789197,5,0.044,0.004492894567371506,0.05600000000000001,0.008985789134743013,0.06543513288031592,0.07061944160903703,5,True
+ye2026_sepsis,scored,strict,raw,raw,other,conditions_raw.npz@36add186,-0.019690319843561142,-0.03981889593634906,-0.10443007913089528,0.3264466405549955,0.3383113176560135,0.9576200238786292,0.0015850845651131918,0.8347393836254738,0.978197437299057,0.9890183716634495,-0.01642808074117548,0.3263627044282643,12,250,2.5562600752800297,19,2.246447283685753,7459,2246,1139,5,12,250,1.9915229944879869,37,2.246447283685753,5383,3012,633,5,9,242,6.102906319765347,30,5.677931797865433,3087,2030,381,5,0.008,0.0059310355330043155,0.022,0.011862071066008631,0.03261231601182658,0.02592336606992853,5,0.044,0.004492894567371506,0.05600000000000001,0.008985789134743013,0.06543513288031592,0.07061944160903703,5,True
+ye2026_sepsis,scored,strict,refcal,refcal,other,conditions_refcal.npz@3886924b,0.1482193477827793,0.11061706122053544,0.07686374943320823,0.24774401774939386,0.19665611389540016,0.9576200238786292,0.0015850845651131918,0.8347393836254738,0.978197437299057,0.9890183716634495,0.14896980550075684,0.24844044139601137,6,250,2.577910620407454,9,2.246447283685753,7459,872,808,5,9,250,2.116834378339727,35,2.246447283685753,5383,2429,502,5,9,242,9.527305743218612,26,5.770278577104309,3087,366,345,5,0.024,0.0063487220263837175,0.046,0.012697444052767435,0.06683054745206232,0.05292713331942328,5,0.04,0.004492894567371506,0.06,0.008985789134743013,0.06875313925627537,0.06815222185111651,5,True

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/contrast/ye2026_sepsis/strict/manifest.json

@@ -0,0 +1,562 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "ye2026_sepsis",
+ "design": "scored",
+ "unit": "strict",
+ "written_utc": "2026-10-12T17:24:41.447504+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/tools/score_strict.py",
+  "--support-manifest",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/protocol/splits/ye2026_sepsis/disease/draw3/support.json",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3",
+  "--action",
+  "all",
+  "--threads",
+  "4",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/lora.npz",
+  "--arm",
+  "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/pairedcal.npz",
+  "--arm",
+  "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/scsemi.npz",
+  "--arm",
+  "raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+  "--arm",
+  "refcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz"
+ ],
+ "threads": 4,
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PIC01",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S136",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S77",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Skin-S74",
+  "Uri-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_samples": 77,
+ "contrast": {
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 57,
+  "n_control_donors": 20
+ },
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/score": {
+   "arms": [
+    "lora",
+    "pairedcal",
+    "scsemi",
+    "raw",
+    "refcal"
+   ],
+   "summary_sha256": "13c703fbb5995463861e38c95aed4d47ec9751b47704ec7be6a93d38c134a1d9",
+   "contrast_csv_sha256": "3fa6e82cebce68f01c9ae876b96d4d43f8ccc1de58651c44ddfb209fce9ddf62"
+  }
+ },
+ "notes": {
+  "source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores"
+ },
+ "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+ "deg_reference": {
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz",
+  "sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0"
+ },
+ "gene_exclusion": null,
+ "n_genes_disease_scores": 5975,
+ "genes_per_type": {
+  "T cell": 3267,
+  "B cell": 3307,
+  "Monocyte": 3299,
+  "NK cell": 3251
+ },
+ "arms": {
+  "lora": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/score",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/lora.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/lora.npz",
+   "npz_sha256": "43d9ca69044b5117508a08fd231db774d636c517eef8b00da38b06e822bddc0d",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw3/test_raw.npz",
+   "condition_sha256": "3278dc672b740fbb8ac68faf9fd17229672a8dd5a8d3902bf282a949b7edb1ef",
+   "condition_label": "test_raw.npz@3278dc67",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw3/test_raw.npz",
+   "condition_key": "bcast:3278dc672b740fbb",
+   "n_generated_cells": 115500,
+   "label": "lora",
+   "seconds": 11.6
+  },
+  "pairedcal": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/score",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/pairedcal.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/pairedcal.npz",
+   "npz_sha256": "052f9fc95351b199a9fbec9395b8d53310fd9d2bb16f0d57917d472a826e37a0",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw3/test_cal.npz",
+   "condition_sha256": "d5aff6ebf925776293cb87efd446b95fef6d584fe8a9408ceff16ca8beebea72",
+   "condition_label": "test_cal.npz@d5aff6eb",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw3/test_cal.npz",
+   "condition_key": "bcast:d5aff6ebf9257762",
+   "n_generated_cells": 115500,
+   "label": "pairedcal",
+   "seconds": 11.7
+  },
+  "scsemi": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/score",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/scsemi.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw3/scsemi.npz",
+   "npz_sha256": "e0432092ee6cab197a7b078545fd9bb66e73299dad07ac08f977687b9935e512",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/draw3/test_raw.npz",
+   "condition_sha256": "3278dc672b740fbb8ac68faf9fd17229672a8dd5a8d3902bf282a949b7edb1ef",
+   "condition_label": "test_raw.npz@3278dc67",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/draw3/test_raw.npz",
+   "condition_key": "bcast:3278dc672b740fbb",
+   "n_generated_cells": 115500,
+   "label": "scsemi",
+   "seconds": 8.9
+  },
+  "raw": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/score",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+   "npz_sha256": "665afa80f7749e56ee7a1c60d8452bff22a53e7bfcf87254c8e92d4d79c62b2a",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/ye2026_sepsis/conditions_raw.npz",
+   "condition_sha256": "36add186da47d10c067d7a1f0641fabf3ddba64d5e65168c5975e1e3a448c9cd",
+   "condition_label": "conditions_raw.npz@36add186",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/ye2026_sepsis/conditions_raw.npz",
+   "condition_key": "bcast:36add186da47d10c",
+   "n_generated_cells": 115500,
+   "label": "raw",
+   "seconds": 13.6
+  },
+  "refcal": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/score",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz",
+   "npz_sha256": "64784052e0289e347e2799523b4aa4ab07b16ddba6a54353a6011d9e77852891",
+   "receipt_verified": true,
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