Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw1/lora/receipts/score.json

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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/giroux2022/disease/draw1/test_raw.npz",
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+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw1/lora/score/contrast.csv

@@ -0,0 +1,14 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+lora,T cell,mean_cp10k,2916,0.5661891183203449,0.6571144835533105,0.3734775041012176,0.4875816477079288,6,4,6,4,58362,9153,,,,,,,,,,,
+lora,T cell,pseudobulk_log1p_cpm,2916,0.3580964430012459,0.6872156600560435,0.1900400326010505,0.3315556047121546,6,4,6,4,58362,9153,,,,,,,,,,,
+lora,B cell,mean_cp10k,3099,0.1261830377098587,0.3825835491576257,0.0838738993804189,0.1289581094343801,6,4,6,4,6177,596,,,,,,,,,,,
+lora,B cell,pseudobulk_log1p_cpm,3099,0.0599827494870239,0.3771207985959151,0.046529676614197,0.0448983247961429,6,4,6,4,6177,596,,,,,,,,,,,
+lora,Monocyte,mean_cp10k,3045,0.2322052641132174,0.4614533190457718,0.1875678172124402,0.1464867862193682,6,4,6,4,18467,3225,,,,,,,,,,,
+lora,Monocyte,pseudobulk_log1p_cpm,3045,0.1588870713707421,0.5171610414843097,0.1103802098160208,0.1260091036829418,6,4,6,4,18467,3225,,,,,,,,,,,
+lora,NK cell,mean_cp10k,2993,0.2110533214384482,0.5038596937916778,0.1155658253047733,0.225874484093407,6,4,6,4,9050,969,,,,,,,,,,,
+lora,NK cell,pseudobulk_log1p_cpm,2993,0.1349091122703371,0.5135427805432597,0.081093390324696,0.128326426953764,6,4,6,4,9050,969,,,,,,,,,,,
+lora,T cell,welch_top50_deg,5498,,,,,6,4,6,4,58362,9153,True,0.0,0.0,50.0,3.0,84.0,3.0,0.0,0.0,3.0,3.0
+lora,B cell,welch_top50_deg,5498,,,,,6,4,6,4,6177,596,True,0.0,,0.0,0.0,0.0,0.0,0.0,0.0,3.0,3.0
+lora,Monocyte,welch_top50_deg,5498,,,,,6,4,6,4,18467,3225,True,0.0,,0.0,0.0,0.0,0.0,0.0,0.0,3.0,3.0
+lora,NK cell,welch_top50_deg,5498,,,,,6,4,6,4,9050,969,True,0.0,,0.0,0.0,0.0,0.0,0.0,0.0,3.0,3.0
+lora,DC,welch_top50_deg,5498,,,,,6,4,6,4,1271,368,True,0.0,,0.0,0.0,0.0,0.0,0.0,0.0,3.0,3.0

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw1/lora/score/per_donor.csv

@@ -0,0 +1,11 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
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+lora,450905_d14,mild,1500,7407,150,0.5253333333333333,0.4422843256379101,0.0293333333333333,0.0292966113136222,0.2693333333333333,0.2742000810044552,0.0953333333333333,0.1578236803024166,0.0266666666666666,0.0298366410152558,0.054,0.0665586607263399,0.1661714594302687,0.4172767195297901,0.8683588070494046,1,True,1.0,0.9533333333333334,1.0,0.98,26.93333333333333,27.420008100445525,482.5,558.0
+lora,0B943B_d0,mild,1500,11344,150,0.5486666666666666,0.6220028208744711,0.028,0.0831276445698166,0.2726666666666666,0.1258815232722143,0.0666666666666666,0.1186530324400564,0.0406666666666666,0.0239774330042313,0.0433333333333333,0.0263575458392101,0.3609003291020217,0.2728815283194795,0.8533928930687678,7,False,1.0,0.96,0.9866666666666668,0.9933333333333332,27.266666666666666,12.588152327221438,474.5,539.0
+lora,0B943B_d14,mild,1500,15650,150,0.488,0.5652396166134185,0.102,0.1117571884984025,0.216,0.1708626198083067,0.11,0.0978913738019169,0.0246666666666666,0.0099680511182108,0.0593333333333333,0.0442811501597444,0.1739936102236421,0.1514797576931834,0.8703283904454833,1,True,1.0,0.98,0.9933333333333332,1.0,21.6,17.08626198083067,499.0,461.0
+lora,180E1A_d0,severe,1500,7157,150,0.7326666666666667,0.7019700992035769,0.034,0.0413581109403381,0.12,0.131759116948442,0.052,0.0655302501047925,0.0213333333333333,0.0132737180382841,0.04,0.0461087047645661,0.0775123655162778,0.379474858924216,0.8567296619077492,1,True,1.0,1.0,1.0,1.0,12.0,13.175911694844208,403.0,433.0
+lora,180E1A_d7,severe,1500,10591,150,0.7606666666666667,0.7348692285903126,0.0393333333333333,0.0490982910017939,0.0866666666666666,0.0906429987725427,0.056,0.0828061561703333,0.0226666666666666,0.0104805967330752,0.0346666666666666,0.0321027287319422,0.08109489188934,0.4452731176976873,0.8557970744308521,5,False,1.0,1.0,1.0,1.0,8.666666666666668,9.064299877254273,403.0,408.0
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+lora,0BF51C_d7,severe,1500,10105,150,0.7173333333333334,0.612370113805047,0.0406666666666666,0.0570014844136566,0.1293333333333333,0.1607125185551707,0.0326666666666666,0.0529440870856011,0.0166666666666666,0.0073231073725878,0.0633333333333333,0.1096486887679366,0.2286135576447303,0.1808073735664534,0.8500915173892076,6,False,1.0,0.9066666666666666,1.0,0.98,12.933333333333334,16.071251855517072,342.0,509.0
+lora,0BF51C_d14,severe,1500,11419,150,0.7186666666666667,0.6330676941938874,0.0413333333333333,0.0796041684911113,0.126,0.151589456169542,0.0386666666666666,0.0790787284350643,0.0193333333333333,0.0105088011209387,0.056,0.0461511515894561,0.2085447061914352,0.1513608508189656,0.8545213598922642,3,False,1.0,0.92,1.0,0.9666666666666668,12.6,15.1589456169542,354.0,541.0

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw1/lora/score/summary.json

@@ -0,0 +1,751 @@
+{
+  "schema": "paired_ft_scores.v1",
+  "dataset": "giroux2022",
+  "written_utc": "2026-10-15T06:52:31.675476+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",
+    "giroux2022",
+    "--out",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw1/score",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw1/lora.npz",
+    "--condition",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw1/test_raw.npz",
+    "--donors",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw1/test_samples.txt",
+    "--threads",
+    "2",
+    "--case-groups",
+    "severe",
+    "--control-groups",
+    "mild",
+    "--exclude-genes",
+    "/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"
+  ],
+  "arms": [
+    "lora"
+  ],
+  "donors": [
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+    "450905_d14",
+    "0B943B_d0",
+    "0B943B_d14",
+    "180E1A_d0",
+    "180E1A_d7",
+    "180E1A_d14",
+    "0BF51C_d0",
+    "0BF51C_d7",
+    "0BF51C_d14"
+  ],
+  "n_donors": 10,
+  "reference": {
+    "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
+    "reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
+    "features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
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+        "density": 6.024133333333333
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+    "observed_l1_loo_null_mean": 0.3545447454778543
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+  "contrast_definition": {
+    "enabled": true,
+    "rule": "explicit --case-groups / --control-groups",
+    "group_source": "features groups",
+    "case_groups": [
+      "severe"
+    ],
+    "control_groups": [
+      "mild"
+    ],
+    "n_case_donors": 6,
+    "n_control_donors": 4,
+    "n_donors_in_neither": 0,
+    "case": [
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+      false,
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+      true,
+      true,
+      true,
+      true,
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+      true
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+    "ctrl": [
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+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ],
+    "groups": [
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+      "mild",
+      "mild",
+      "mild",
+      "severe",
+      "severe",
+      "severe",
+      "severe",
+      "severe",
+      "severe"
+    ]
+  },
+  "deg_definition": {
+    "enabled": true,
+    "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
+    "functions": [
+      "welch_bh_deg",
+      "top_deg_genes",
+      "jaccard"
+    ],
+    "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",
+    "top_n": 50,
+    "fdr": 0.05,
+    "n_genes": 5498,
+    "types": [
+      "T cell",
+      "B cell",
+      "Monocyte",
+      "NK cell",
+      "DC"
+    ],
+    "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022/deg_reference.npz",
+    "aggregates_sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e",
+    "aggregates_note": null,
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+      {
+        "gene_id": "ENSG00000114374",
+        "symbol": "USP9Y"
+      },
+      {
+        "gene_id": "ENSG00000067048",
+        "symbol": "DDX3Y"
+      },
+      {
+        "gene_id": "ENSG00000183878",
+        "symbol": "UTY"
+      },
+      {
+        "gene_id": "ENSG00000165246",
+        "symbol": "NLGN4Y"
+      },
+      {
+        "gene_id": "ENSG00000012817",
+        "symbol": "KDM5D"
+      }
+    ],
+    "applies_to": "group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene"
+  },
+  "core_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw1/score"
+}