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/draw2/lora/score/per_donor.csv

@@ -0,0 +1,13 @@
+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
+lora,7085CA_d0,mild,1500,12585,150,0.3813333333333333,0.2166070719110051,0.0433333333333333,0.0247914183551847,0.4106666666666667,0.5874453714739769,0.106,0.1319825188716726,0.0126666666666666,0.0177195073500198,0.046,0.0214541120381406,0.4156281287246722,0.8990236963821155,0.8857429836399208,1,True,1.0,0.9866666666666668,0.9866666666666668,1.0,41.06666666666667,58.74453714739769,528.5,640.0
+lora,7085CA_d7,mild,1500,9515,150,0.6666666666666666,0.521492380451918,0.0306666666666666,0.0722017866526537,0.1253333333333333,0.1011035207566999,0.116,0.2725170782974251,0.0206666666666666,0.019863373620599,0.0406666666666666,0.0128218602207041,0.3961043965668242,0.3579081617616235,0.8621034962980838,3,False,1.0,0.9466666666666668,1.0,0.9666666666666668,12.533333333333331,10.110352075669994,444.0,502.0
+lora,7085CA_d14,mild,1500,11887,150,0.6426666666666667,0.472533019264743,0.0426666666666666,0.0713384369479263,0.1446666666666666,0.162109867922941,0.1,0.2427021115504332,0.0266666666666666,0.0185917388744006,0.0433333333333333,0.0327248254395558,0.3776341661759345,0.2957349587752428,0.8593441428508096,1,True,1.0,0.9466666666666668,1.0,0.9933333333333332,14.466666666666669,16.2109867922941,443.5,536.0
+lora,2AD75E_d0,mild,1500,7693,150,0.708,0.6034056934875861,0.0593333333333333,0.0640842324190822,0.0913333333333333,0.1406473417392434,0.088,0.1594956453919147,0.01,0.0253477187053165,0.0433333333333333,0.0070193682568568,0.2818165431777806,0.2679231341021514,0.8559897593899317,10,False,1.0,0.9533333333333334,1.0,0.9133333333333332,9.133333333333333,14.064734173924348,425.5,532.0
+lora,2AD75E_d7,mild,1500,10499,150,0.7673333333333333,0.5808172206876845,0.068,0.1437279740927707,0.0633333333333333,0.1027716925421468,0.0546666666666666,0.1471568720830555,0.0133333333333333,0.0137155919611391,0.0333333333333333,0.0118106486332031,0.416077594691558,0.3201835922843184,0.8460067334532199,6,False,1.0,0.92,0.9933333333333332,0.86,6.333333333333334,10.277169254214687,359.0,443.0
+lora,2AD75E_d14,mild,1500,13692,150,0.7053333333333334,0.5811422728600643,0.0666666666666666,0.1250365176745544,0.118,0.1419807186678352,0.0626666666666666,0.1249634823254455,0.0206666666666666,0.0165790242477359,0.0266666666666666,0.0102979842243645,0.2892947706690039,0.2444370525746645,0.8606023072528465,5,False,0.9933333333333332,0.9266666666666666,0.9933333333333332,0.92,11.8,14.198071866783524,455.0,428.0
+lora,82CCF5_d0,severe,1500,10125,150,0.63,0.5422222222222223,0.092,0.1183209876543209,0.174,0.1539753086419753,0.056,0.093037037037037,0.0173333333333333,0.0166913580246913,0.0306666666666666,0.075753086419753,0.2168888888888888,0.23874194415185,0.8624872048857414,5,False,1.0,0.96,1.0,0.9866666666666668,17.4,15.397530864197533,497.5,390.0
+lora,82CCF5_d7,severe,1500,10860,150,0.712,0.619060773480663,0.0526666666666666,0.0997237569060773,0.1146666666666666,0.1415285451197053,0.06,0.0941068139963167,0.0266666666666666,0.0136279926335174,0.034,0.03195211786372,0.2160515653775321,0.2648593194536384,0.8765659034678561,1,True,1.0,0.9733333333333334,0.9866666666666668,0.9933333333333332,11.466666666666669,14.152854511970531,506.0,497.0
+lora,82CCF5_d14,severe,1500,11056,150,0.7133333333333334,0.6330499276410999,0.0513333333333333,0.101212011577424,0.1393333333333333,0.1136939218523878,0.0446666666666666,0.0682887120115774,0.0286666666666666,0.0145622286541244,0.0226666666666666,0.0691931982633864,0.2400545103714423,0.369853189694563,0.8674824684211488,2,False,1.0,0.9866666666666668,1.0,0.9933333333333332,13.933333333333334,11.369392185238784,509.0,394.0
+lora,0BF51C_d0,severe,1500,6510,150,0.5613333333333334,0.4012288786482335,0.014,0.0167434715821812,0.2686666666666666,0.4609831029185868,0.0153333333333333,0.0772657450076804,0.004,0.0061443932411674,0.1366666666666666,0.0376344086021505,0.5182734254992319,0.5709498030244532,0.865819781401572,1,True,0.9866666666666668,0.8133333333333334,0.98,0.8666666666666667,26.866666666666667,46.09831029185868,320.0,628.0
+lora,0BF51C_d7,severe,1500,10105,150,0.7466666666666667,0.612370113805047,0.0346666666666666,0.0570014844136566,0.126,0.1607125185551707,0.0346666666666666,0.0529440870856011,0.014,0.0073231073725878,0.044,0.1096486887679366,0.2819468909780637,0.3232914310644849,0.8601670475845816,4,False,1.0,0.94,0.9933333333333332,0.98,12.6,16.071251855517072,409.0,509.0
+lora,0BF51C_d14,severe,1500,11419,150,0.7533333333333333,0.6330676941938874,0.038,0.0796041684911113,0.11,0.151589456169542,0.0433333333333333,0.0790787284350643,0.01,0.0105088011209387,0.0453333333333333,0.0461511515894561,0.2405312782788918,0.2376915174852046,0.8576870519879147,3,False,1.0,0.9333333333333332,0.9933333333333332,0.98,11.0,15.1589456169542,395.0,541.0

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/draw2/lora/score/summary.json

@@ -0,0 +1,759 @@
+{
+  "schema": "paired_ft_scores.v1",
+  "dataset": "giroux2022",
+  "written_utc": "2026-10-15T06:52:38.744721+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/draw2/score",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw2/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/draw2/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/draw2/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": [
+    "7085CA_d0",
+    "7085CA_d7",
+    "7085CA_d14",
+    "2AD75E_d0",
+    "2AD75E_d7",
+    "2AD75E_d14",
+    "82CCF5_d0",
+    "82CCF5_d7",
+    "82CCF5_d14",
+    "0BF51C_d0",
+    "0BF51C_d7",
+    "0BF51C_d14"
+  ],
+  "n_donors": 12,
+  "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",
+    "n_r1_cells": 1800,
+    "pca": {
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+      "explained_variance_ratio_sum": 0.26048365235328674,
+      "n_fit_cells": 1800
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+    "r2_control": {
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+      "coverage": 1.0,
+      "density": 4.929388888888889,
+      "n_query": 1800,
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+        "coverage": 1.0,
+        "density": 4.851277777777778
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+    },
+    "observed_l1_loo_null_mean": 0.36588315006285926
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+  "contrast_definition": {
+    "enabled": true,
+    "rule": "explicit --case-groups / --control-groups",
+    "group_source": "features groups",
+    "case_groups": [
+      "severe"
+    ],
+    "control_groups": [
+      "mild"
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+    "n_case_donors": 6,
+    "n_control_donors": 6,
+    "n_donors_in_neither": 0,
+    "case": [
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+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
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+      true,
+      true,
+      true,
+      true
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+    "ctrl": [
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+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ],
+    "groups": [
+      "mild",
+      "mild",
+      "mild",
+      "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,
+    "types_not_scored_observed": [],
+    "observed": {
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+      "B cell": {
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+      "Monocyte": {
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+      "DC": {
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+    "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
+  },
+  "headline": {
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+      "seconds": 4.8
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+  "per_arm": {
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+      "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw2/lora.npz",
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+        "checkpoint_sha256": "0a84ab6c8c78762ba3cca12894bd394d946d48b130e984793f0f01ad6ef6971d",
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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/draw2/lora/scoring_support.json

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