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/ji2025_chili/disease/draw1/lora/score/per_donor.csv

@@ -0,0 +1,27 @@
+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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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/ji2025_chili/disease/draw1/lora/score/summary.json

@@ -0,0 +1,544 @@
+{
+  "schema": "paired_ft_scores.v1",
+  "dataset": "ji2025_chili",
+  "written_utc": "2026-10-15T07:26:22.584689+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",
+    "ji2025_chili",
+    "--out",
+    "/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/draw1/score",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/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/ji2025_chili/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/disease_width_comparison_20261015/ji2025_chili/draw1/test_samples.txt",
+    "--threads",
+    "2",
+    "--case-groups",
+    "TOL,FU1",
+    "--control-groups",
+    "BC,AC"
+  ],
+  "arms": [
+    "lora"
+  ],
+  "donors": [
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+    "N064_FU1",
+    "N032_AC",
+    "N038_BC",
+    "N038_AC",
+    "N055_AC",
+    "N138_TOL",
+    "N138_FU1",
+    "N129_BC",
+    "N129_AC",
+    "N147_TOL",
+    "N158_AC",
+    "N001_TOL",
+    "N001_FU1",
+    "N002_TOL",
+    "N002_FU1",
+    "N005_BC",
+    "N005_AC",
+    "N012_TOL",
+    "N012_FU1",
+    "N018_BC",
+    "N018_AC",
+    "N022_TOL",
+    "N022_FU1",
+    "N043_TOL",
+    "N043_FU1"
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+  "n_donors": 26,
+  "reference": {
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+    "reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
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+    "control_groups": [
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+    "n_case_donors": 15,
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+    "n_donors_in_neither": 0,
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+      "AC",
+      "BC",
+      "AC",
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+      "BC",
+      "AC",
+      "TOL",
+      "AC",
+      "TOL",
+      "FU1",
+      "TOL",
+      "FU1",
+      "BC",
+      "AC",
+      "TOL",
+      "FU1",
+      "BC",
+      "AC",
+      "TOL",
+      "FU1",
+      "TOL",
+      "FU1"
+    ]
+  },
+  "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": 5752,
+    "types": [
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+      "B cell",
+      "Monocyte",
+      "NK cell",
+      "DC"
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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/ji2025_chili/disease/draw1/lora/scoring_support.json

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