Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_snapshot/ye2026_sepsis/draw4/scores/ye2026_sepsis/disease/draw4/score/summary.json

@@ -0,0 +1,1887 @@
+{
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+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-12T17:41:38.799629+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "ye2026_sepsis",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/score",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/test_sample_ids.txt",
+  "--threads",
+  "4",
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+  "--arm",
+  "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw4/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/draw4/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",
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+refcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_B cell,ok
+scsemi,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_B cell,ok
+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_DC,ok
+raw,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_DC,ok
+refcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_DC,ok
+scsemi,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_DC,ok
+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Monocyte,ok
+raw,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Monocyte,ok
+refcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Monocyte,ok
+scsemi,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Monocyte,ok
+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_NK cell,ok
+raw,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_NK cell,ok
+refcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_NK cell,ok
+scsemi,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_NK cell,ok
+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Other,ok
+raw,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Other,ok
+refcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Other,ok
+scsemi,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_Other,ok
+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_T cell,ok
+raw,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_T cell,ok
+refcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_T cell,ok
+scsemi,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,obs_T cell,ok
+pairedcal,lora,0.16883116883116883,-3.623701298701299,3.831818181818178,77,77,0,2000,20261012,donor_all_draws_and_visits,pb_own_rank,ok
+raw,lora,7.038961038961039,1.6487012987012988,12.610714285714284,77,77,0,2000,20261012,donor_all_draws_and_visits,pb_own_rank,ok
+refcal,lora,3.8701298701298703,-0.8444805194805194,8.7275974025974,77,77,0,2000,20261012,donor_all_draws_and_visits,pb_own_rank,ok
+scsemi,lora,12.64935064935065,5.80487012987013,18.923051948051942,77,77,0,2000,20261012,donor_all_draws_and_visits,pb_own_rank,ok
+pairedcal,lora,-0.02601606959374156,-0.028905607469765036,-0.022572937615228342,77,77,0,2000,20261012,donor_all_draws_and_visits,pb_r,ok
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+scsemi,lora,-0.29517469228527,-0.30693076259021784,-0.28254056024799323,77,77,0,2000,20261012,donor_all_draws_and_visits,pb_r,ok
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+raw,lora,-0.29160173160173153,-0.32277056277056276,-0.26103246753246756,77,77,0,2000,20261012,donor_all_draws_and_visits,precision_depth_matched,ok
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+scsemi,lora,-0.46640692640692644,-0.4982727272727272,-0.4351515151515152,77,77,0,2000,20261012,donor_all_draws_and_visits,precision_depth_matched,ok

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_snapshot/ye2026_sepsis/draw4/scores/ye2026_sepsis/disease/draw4/statistics/status.json

@@ -0,0 +1,18 @@
+{
+  "schema": "pbisc.paper.strict-statistics.v1",
+  "support_sha256": "e72d06f5f4f5c10cf7fff8edaee1493e18c67dc4bbf65793eae6c984120cc4d2",
+  "bootstrap_unit": "unique_donor_all_visits_and_draws",
+  "bootstrap_replicates": 2000,
+  "draws": [
+    "draw4_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/draw4/statistics/donor_deg/donor_deg_summary.csv"
+  }
+}

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_snapshot_tables/scores/imperial_eskd/disease/draw0/statistics/donor_deg/donor_deg_summary.csv

@@ -0,0 +1,26 @@
+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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+lora,B cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,1,50,50
+lora,Monocyte,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,18,50,50
+lora,NK cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,16,50,50
+lora,DC,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,19,50,50
+pairedcal,T cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,15,50,50
+pairedcal,B cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,1,50,50
+pairedcal,Monocyte,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,17,50,50
+pairedcal,NK cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,16,50,50
+pairedcal,DC,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,14,50,50
+scsemi,T cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,8,50,50
+scsemi,B cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,1,50,50
+scsemi,Monocyte,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,9,50,50
+scsemi,NK cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,4,50,50
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+raw,T cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,19,50,50
+raw,B cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,1,50,50
+raw,Monocyte,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,16,50,50
+raw,NK cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,15,50,50
+raw,DC,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,14,50,50
+refcal,T cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,12,50,50
+refcal,B cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,0,50,50
+refcal,Monocyte,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,8,50,50
+refcal,NK cell,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,7,50,50
+refcal,DC,ok,ok,ok,32,31,32,31,edgeR_TMM_limma_voom_duplicateCorrelation,edgeR_TMM_limma_voom_duplicateCorrelation,,,,,7,50,50