Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/4d7a08e639641156/support.json

@@ -0,0 +1,170 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "ji2025_chili",
+  "design": "disease_existing_draw",
+  "unit": "draw2_n5",
+  "n_pairs": 5,
+  "train_sample_ids": [
+    "N032_AC",
+    "N005_BC",
+    "N018_BC",
+    "N035_TOL",
+    "N147_TOL"
+  ],
+  "train_donor_ids": [
+    "N032",
+    "N005",
+    "N018",
+    "N035",
+    "N147"
+  ],
+  "test_sample_ids": [
+    "N064_TOL",
+    "N064_FU1",
+    "N038_BC",
+    "N038_AC",
+    "N055_AC",
+    "N136_TOL",
+    "N136_FU1",
+    "N138_TOL",
+    "N138_FU1",
+    "N128_BC",
+    "N128_AC",
+    "N129_BC",
+    "N129_AC",
+    "N150_BC",
+    "N158_AC",
+    "N159_BC",
+    "N001_TOL",
+    "N001_FU1",
+    "N002_TOL",
+    "N002_FU1",
+    "N012_TOL",
+    "N012_FU1",
+    "N022_TOL",
+    "N022_FU1",
+    "N043_TOL",
+    "N043_FU1"
+  ],
+  "test_donor_ids": [
+    "N064",
+    "N064",
+    "N038",
+    "N038",
+    "N055",
+    "N136",
+    "N136",
+    "N138",
+    "N138",
+    "N128",
+    "N128",
+    "N129",
+    "N129",
+    "N150",
+    "N158",
+    "N159",
+    "N001",
+    "N001",
+    "N002",
+    "N002",
+    "N012",
+    "N012",
+    "N022",
+    "N022",
+    "N043",
+    "N043"
+  ],
+  "excluded_sample_ids": [
+    "N005_AC",
+    "N018_AC",
+    "N032_BC"
+  ],
+  "seed": null,
+  "selection_audit": [
+    {
+      "donor_id": "N032",
+      "assigned_stratum": false,
+      "selected_sample_id": "N032_AC",
+      "candidates": [
+        {
+          "sample_id": "N032_AC",
+          "time_value": 1.0,
+          "time_raw": "AC",
+          "time_field": "timepoint",
+          "group": "AC"
+        }
+      ]
+    },
+    {
+      "donor_id": "N005",
+      "assigned_stratum": false,
+      "selected_sample_id": "N005_BC",
+      "candidates": [
+        {
+          "sample_id": "N005_BC",
+          "time_value": 0.0,
+          "time_raw": "BC",
+          "time_field": "timepoint",
+          "group": "BC"
+        },
+        {
+          "sample_id": "N005_AC",
+          "time_value": 1.0,
+          "time_raw": "AC",
+          "time_field": "timepoint",
+          "group": "AC"
+        }
+      ]
+    },
+    {
+      "donor_id": "N018",
+      "assigned_stratum": false,
+      "selected_sample_id": "N018_BC",
+      "candidates": [
+        {
+          "sample_id": "N018_BC",
+          "time_value": 0.0,
+          "time_raw": "BC",
+          "time_field": "timepoint",
+          "group": "BC"
+        },
+        {
+          "sample_id": "N018_AC",
+          "time_value": 1.0,
+          "time_raw": "AC",
+          "time_field": "timepoint",
+          "group": "AC"
+        }
+      ]
+    },
+    {
+      "donor_id": "N035",
+      "assigned_stratum": true,
+      "selected_sample_id": "N035_TOL",
+      "candidates": [
+        {
+          "sample_id": "N035_TOL",
+          "time_value": 0.0,
+          "time_raw": "TOL",
+          "time_field": "timepoint",
+          "group": "TOL"
+        }
+      ]
+    },
+    {
+      "donor_id": "N147",
+      "assigned_stratum": true,
+      "selected_sample_id": "N147_TOL",
+      "candidates": [
+        {
+          "sample_id": "N147_TOL",
+          "time_value": 0.0,
+          "time_raw": "TOL",
+          "time_field": "timepoint",
+          "group": "TOL"
+        }
+      ]
+    }
+  ],
+  "sha256": "fa20d986ff3869bc9b0a15ab6f16bae3a01a5f09a515f0a961146219c92595b4"
+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/531111f34626b580/metrics.csv

@@ -0,0 +1,25 @@
+dataset,design,unit,label,set,real_side,mode,n_real,n_gen,precision_k3,coverage_k3,density_k3,expected_coverage_identical_k3,precision_k5,coverage_k5,density_k5,expected_coverage_identical_k5,precision_k10,coverage_k10,density_k10,expected_coverage_identical_k10,c2st_knn_auc,c2st_knn_auc_sd,c2st_rf_auc,c2st_rf_auc_sd,nn1_acc,nn1_acc_real,nn1_acc_gen,mmd2_bw0.5,mmd2_bw1,mmd2_bw2,mmd2_sum,mmd_bandwidth_m,seconds
+imperial_eskd,scored,strict,Real vs real control (held-out real cells),real_R2,R1,raw,21250,21250,0.8417882352941176,0.9170352941176471,1.3199215686274508,0.8750176472664262,0.9142117647058824,0.9840941176470588,1.310164705882353,0.9687610288926725,0.9688470588235294,0.9998117647058824,1.290729411764706,0.9990247007812885,0.5026381397923876,0.006627819371826972,0.5604882491349481,0.004842499677312456,0.5032470588235294,0.42451764705882356,0.5819764705882353,5.25696996987457e-05,-1.5129454440376833e-06,-3.737897549038749e-06,4.7318856705669265e-05,25.87528764310995,91.8
+imperial_eskd,scored,strict,Real vs real control (held-out real cells),real_R2,R1,dm,21250,21250,0.8390588235294117,0.9164705882352941,1.310729411764706,0.8750176472664262,0.9133176470588236,0.9840470588235294,1.303124705882353,0.9687610288926725,0.969835294117647,0.9997176470588235,1.287590588235294,0.9990247007812885,0.5018989785467128,0.006308277747021118,0.5584554519031142,0.004630410453182378,0.5037647058823529,0.42710588235294117,0.5804235294117647,4.6335199650082703e-05,-3.419423888484374e-06,-4.100354209057855e-06,3.8815421552540474e-05,25.87528764310995,91.5
+imperial_eskd,scored,strict,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,20649,20649,,,,,,,,,,,,,0.4961569048063071,0.0029785077635676874,0.49711296852909087,0.003661000217832483,0.4980870744345973,0.5011380696401763,0.4950360792290184,-2.1951926343966033e-05,-1.830535417379764e-05,-6.660259249668954e-06,-4.6917539767432626e-05,25.87528764310995,79.7
+imperial_eskd,scored,strict,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,20649,20649,,,,,,,,,,,,,0.4992387683379086,0.005206892476655908,0.49691748568548577,0.004940857589397424,0.4978691462056274,0.4993462153130902,0.4963920770981646,-2.2746662518113858e-05,-1.8789147550046792e-05,-6.826709684881749e-06,-4.83625197530424e-05,25.87528764310995,78.8
+imperial_eskd,scored,strict,,lora,R1,raw,21250,21250,0.5079058823529412,0.3459764705882353,0.41956078431372545,0.8750176472664262,0.6292235294117647,0.4563764705882353,0.42810352941176466,0.9687610288926725,0.7797176470588235,0.6124705882352941,0.4406258823529412,0.9990247007812885,0.9472783612456748,0.002764736680915113,0.9468885979238755,0.0037333364673279227,0.8496,0.8340235294117647,0.8651764705882353,0.030779098850540643,0.02463421096679852,0.008919527845599573,0.06433283766293874,25.87528764310995,62.3
+imperial_eskd,scored,strict,,lora,R1,dm,21250,21250,0.5824941176470588,0.5212705882352942,0.5971607843137255,0.8750176472664262,0.7013647058823529,0.6635294117647059,0.6108611764705882,0.9687610288926725,0.8398117647058824,0.8260235294117647,0.6332658823529412,0.9990247007812885,0.9063540373702421,0.0036033575739927233,0.9182118311418686,0.0020387514199609715,0.7872941176470588,0.7468705882352941,0.8277176470588236,0.02069215317887685,0.016511509658920787,0.005888979324693677,0.04309264216249131,25.87528764310995,63.2
+imperial_eskd,scored,strict,,lora,R2,raw,21250,21250,,,,,,,,,,,,,0.9497997121107267,0.003451631785708644,0.9465186657439446,0.0022426466052494973,0.8522352941176471,0.8678588235294118,0.8366117647058824,0.030892267492815872,0.024419175432218942,0.008823521728575479,0.0641349646536103,25.87528764310995,57.7
+imperial_eskd,scored,strict,,lora,R2,dm,21250,21250,,,,,,,,,,,,,0.9069501010380623,0.0021892080754564347,0.9166867211072663,0.0037980190467663015,0.7906823529411765,0.7755294117647059,0.8058352941176471,0.020870441218776847,0.01639533119355474,0.005811722462357949,0.04307749487468954,25.87528764310995,57.2
+imperial_eskd,scored,strict,,pairedcal,R1,raw,21250,21250,0.598964705882353,0.35816470588235294,0.6319372549019607,0.8750176472664262,0.7128,0.46743529411764706,0.6524988235294118,0.9687610288926725,0.8378823529411765,0.619764705882353,0.6806776470588235,0.9990247007812885,0.9619489051903114,0.0029278210200982015,0.9707058491349481,0.0007332993412713264,0.8796705882352941,0.8261176470588235,0.9332235294117647,0.03959130488543877,0.023697527031829813,0.0077147593782034285,0.07100359129547201,25.87528764310995,64.2
+imperial_eskd,scored,strict,,pairedcal,R1,dm,21250,21250,0.6468705882352941,0.4112470588235294,0.8010509803921568,0.8750176472664262,0.7527058823529412,0.5228235294117647,0.8246776470588235,0.9687610288926725,0.8648470588235294,0.6810352941176471,0.8520658823529411,0.9990247007812885,0.949395659515571,0.0027380059115619947,0.9682970186851211,0.0016517667487663038,0.862,0.7949647058823529,0.9290352941176471,0.040347572807772014,0.02465320557022599,0.00803116870549725,0.07303194708349525,25.87528764310995,66.1
+imperial_eskd,scored,strict,,pairedcal,R2,raw,21250,21250,,,,,,,,,,,,,0.9640597259515571,0.0019407422854211822,0.9715850851211073,0.00019601026321382684,0.8855294117647059,0.8528941176470588,0.918164705882353,0.03885032534360916,0.023329357302040776,0.007612628760762297,0.06979231140641223,25.87528764310995,58.6
+imperial_eskd,scored,strict,,pairedcal,R2,dm,21250,21250,,,,,,,,,,,,,0.9538678975778547,0.001557483221140233,0.9689430145328719,0.001159472929339577,0.8671529411764706,0.8172235294117647,0.9170823529411765,0.03995902846251698,0.02443854723214356,0.007957674038284068,0.0723552497329446,25.87528764310995,60.1
+imperial_eskd,scored,strict,,scsemi,R1,raw,21250,21250,0.10649411764705882,0.014494117647058824,0.04064313725490196,0.8750176472664262,0.1684235294117647,0.022070588235294116,0.04188235294117647,0.9687610288926725,0.3111529411764706,0.03515294117647059,0.046338823529411766,0.9990247007812885,0.9993314214532873,0.00017915895844373386,0.9999339570934256,2.046653478212373e-05,0.9968941176470588,0.9940235294117648,0.9997647058823529,0.17814331688689972,0.14094730920153475,0.050220698929774876,0.36931132501820935,25.87528764310995,66.8
+imperial_eskd,scored,strict,,scsemi,R1,dm,21250,21250,0.19167058823529412,0.04809411764705882,0.0987764705882353,0.8750176472664262,0.2807058823529412,0.0715764705882353,0.1052329411764706,0.9687610288926725,0.4319529411764706,0.11609411764705882,0.12636235294117648,0.9990247007812885,0.9973439667820069,0.0006958133748992241,0.9997189148788926,7.680116406965817e-05,0.9898117647058824,0.9805647058823529,0.9990588235294118,0.1558957480991333,0.10956572456444635,0.036486745131886655,0.3019482177954663,25.87528764310995,71.0
+imperial_eskd,scored,strict,,scsemi,R2,raw,21250,21250,,,,,,,,,,,,,0.9994470532871972,0.0003149733906796602,0.9999261896193772,1.5851535185266836e-05,0.996964705882353,0.9944941176470589,0.9994352941176471,0.17992813065478147,0.14074015685895103,0.04999907759781386,0.37066736511154635,25.87528764310995,61.5
+imperial_eskd,scored,strict,,scsemi,R2,dm,21250,21250,,,,,,,,,,,,,0.9978091072664359,0.0007932579479014099,0.9997491764705881,4.3350466431872675e-05,0.9905411764705883,0.9818823529411764,0.9992,0.15636397393519713,0.10935221001599804,0.03636129757793927,0.30207748152913444,25.87528764310995,65.6
+imperial_eskd,scored,strict,,raw,R1,raw,21250,21250,0.22329411764705884,0.047341176470588234,0.10663529411764705,0.8750176472664262,0.31585882352941175,0.06710588235294118,0.10908235294117648,0.9687610288926725,0.506164705882353,0.10649411764705882,0.12202823529411763,0.9990247007812885,0.9953843377162631,0.00046059502278275084,0.9976385162629757,0.00034704473463035033,0.9807764705882352,0.9797176470588236,0.981835294117647,0.16614952031644306,0.24853108136343338,0.11258752241666192,0.5272681240965383,25.87528764310995,67.4
+imperial_eskd,scored,strict,,raw,R1,dm,21250,21250,0.25021176470588236,0.06263529411764705,0.12023529411764707,0.8750176472664262,0.3808,0.09021176470588235,0.13184,0.9687610288926725,0.5699294117647059,0.14503529411764707,0.1415576470588235,0.9990247007812885,0.9947796096885814,0.0005632159833962009,0.9966671944636678,0.0003684562977244872,0.9739764705882353,0.9717176470588236,0.9762352941176471,0.15034465788067852,0.22993506374257144,0.10412869389543467,0.48440841551868463,25.87528764310995,66.3
+imperial_eskd,scored,strict,,raw,R2,raw,21250,21250,,,,,,,,,,,,,0.9953516179930796,0.0010287786896508346,0.9977792553633218,0.00035390709245262096,0.9805411764705882,0.9833411764705883,0.9777411764705882,0.17141170757514992,0.2504981576943426,0.11277081803228284,0.5346806833017753,25.87528764310995,62.0
+imperial_eskd,scored,strict,,raw,R2,dm,21250,21250,,,,,,,,,,,,,0.9943526311418684,0.0009659340204692012,0.9967804456747406,0.0004920333921918404,0.9752,0.9785411764705882,0.9718588235294118,0.15451447773751031,0.23136797936367037,0.10420530995004595,0.49008776705122664,25.87528764310995,60.5
+imperial_eskd,scored,strict,,refcal,R1,raw,21250,21250,0.5543529411764706,0.21110588235294117,0.4697254901960785,0.8750176472664262,0.6816470588235294,0.27496470588235294,0.4806023529411765,0.9687610288926725,0.8161882352941177,0.3748705882352941,0.4895482352941176,0.9990247007812885,0.9802691487889273,0.0016270658901613396,0.9858304387543253,0.0006171930420838758,0.9289882352941177,0.8938352941176471,0.9641411764705883,0.0878361467147813,0.06021232939064958,0.020313176274214806,0.16836165237964568,25.87528764310995,65.7
+imperial_eskd,scored,strict,,refcal,R1,dm,21250,21250,0.5944,0.28818823529411763,0.568643137254902,0.8750176472664262,0.7107294117647058,0.3769882352941176,0.58464,0.9687610288926725,0.8359529411764706,0.5111529411764706,0.6062164705882352,0.9990247007812885,0.9732875570934256,0.001549515861452235,0.9808009190311419,0.0013950014538769075,0.9069411764705883,0.8568941176470588,0.9569882352941177,0.06905654069633244,0.04586735434033473,0.015335019668581307,0.13025891470524847,25.87528764310995,67.9
+imperial_eskd,scored,strict,,refcal,R2,raw,21250,21250,,,,,,,,,,,,,0.9834273993079584,0.0013921740562085237,0.9857276899653978,0.0005056399377148222,0.9344235294117647,0.9149647058823529,0.9538823529411765,0.0877555643324851,0.059975750587974996,0.020241688919493184,0.16797300383995328,25.87528764310995,59.6
+imperial_eskd,scored,strict,,refcal,R2,dm,21250,21250,,,,,,,,,,,,,0.9745010878892734,0.002559563674891916,0.9810417550173012,0.0005883484421527207,0.9102823529411764,0.8712,0.9493647058823529,0.06913871391504894,0.04581634760556397,0.015306575607385797,0.1302616371279987,25.87528764310995,61.3

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/90da410b514cdb99/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": [
+    "450905_d0",
+    "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",
+    "n_r1_cells": 1500,
+    "pca": {
+      "n_components": 50,
+      "explained_variance_ratio_sum": 0.25688883662223816,
+      "n_fit_cells": 1500
+    },
+    "r2_control": {
+      "precision": 1.0,
+      "coverage": 1.0,
+      "density": 6.064666666666667,
+      "n_query": 1500,
+      "depth_matched": {
+        "precision": 0.9993333333333333,
+        "coverage": 1.0,
+        "density": 6.024133333333333
+      }
+    },
+    "observed_l1_loo_null_mean": 0.3545447454778543
+  },
+  "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": [
+      false,
+      false,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true
+    ],
+    "ctrl": [
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ],
+    "groups": [
+      "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": {
+      "T cell": {
+        "n_significant": 84,
+        "n_tested": 5224,
+        "n_case_donors": 6,
+        "n_control_donors": 4,
+        "n_cells": 58362,
+        "top_list_size": 50
+      },
+      "B cell": {
+        "n_significant": 0,
+        "n_tested": 4886,
+        "n_case_donors": 6,
+        "n_control_donors": 4,
+        "n_cells": 6177,
+        "top_list_size": 0
+      },
+      "Monocyte": {
+        "n_significant": 0,
+        "n_tested": 5098,
+        "n_case_donors": 6,
+        "n_control_donors": 4,
+        "n_cells": 18467,
+        "top_list_size": 0
+      },
+      "NK cell": {
+        "n_significant": 0,
+        "n_tested": 4876,
+        "n_case_donors": 6,
+        "n_control_donors": 4,
+        "n_cells": 9050,
+        "top_list_size": 0
+      },
+      "DC": {
+        "n_significant": 0,
+        "n_tested": 4578,
+        "n_case_donors": 6,
+        "n_control_donors": 4,
+        "n_cells": 1271,
+        "top_list_size": 0
+      }
+    },
+    "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": {
+    "lora": {
+      "comp_l1": 0.20476432986678444,
+      "comp_l1_obs_loo_null": 0.3545447454778543,
+      "precision": 1.0,
+      "coverage": 0.9346666666666666,
+      "precision_dm": 0.9973333333333333,
+      "coverage_dm": 0.9586666666666667,
+      "pb_r_median": 0.8578153598003033,
+      "pb_top1": 0.5,
+      "mono_pct_gen": 21.5,
+      "mono_pct_obs": 21.18723635141114,
+      "median_umi_gen": 427.0,
+      "median_umi_obs": 482.0,
+      "contrast_mean_cp10k_r_gen": 0.28390768539546735,
+      "contrast_pseudobulk_log1p_cpm_r_gen": 0.1779688440323373,
+      "contrast_mean_cp10k_r_broadcast": 0.5012527613870964,
+      "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.523760070169882,
+      "deg_top50_T": 0,
+      "deg_top50_B": 0,
+      "deg_top50_Mono": 0,
+      "deg_top50_NK": 0,
+      "deg_top50_DC": 0,
+      "deg_top50_sum": 0,
+      "deg_top50_max": 50,
+      "deg_top50_sum_4type": 0,
+      "deg_top50_sum_broadcast": 0,
+      "seconds": 4.5
+    }
+  },
+  "per_arm": {
+    "lora": {
+      "arm": "lora",
+      "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw1/lora.npz",
+      "npz_sha256": "23c22a3ecafc54d6a746016ef7c1c55ff6ec6fcb6df8f81d0cca50e86a2830c3",
+      "receipt_verified": true,
+      "generation": {
+        "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw1/lora/checkpoint_ft.pt",
+        "checkpoint_sha256": "0492c0d21a4a15193013661d303b3ffa49f744c69d62330ee4eec3f6bf012a78",
+        "input_condition_path": "/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",
+        "input_condition_sha256": "935e890f67fc789b9ecf47b5c90157bfe0a1983d6ffdb1ea2d198b6de9767f47",
+        "seed": 20260928,
+        "steps": 50,
+        "support_readout": "bernoulli",
+        "weights": "ema"
+      },
+      "condition_for_broadcast": {
+        "path": "/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",
+        "sha256": "935e890f67fc789b9ecf47b5c90157bfe0a1983d6ffdb1ea2d198b6de9767f47"
+      },
+      "poisson": {
+        "seed": 20260916,
+        "rule": "whole NPZ, rows in NPZ order",
+        "nnz_whole_npz": 3454153,
+        "median_library_whole_npz_panel": 1267.0,
+        "n_rows_whole_npz": 15000
+      },
+      "annotation": {
+        "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+        "zero_padded_model_genes": 0,
+        "label_counts": {
+          "T cell": 9153,
+          "Monocyte": 3225,
+          "NK cell": 969,
+          "Other": 689,
+          "B cell": 596,
+          "DC": 368
+        },
+        "mean_l2_max_prob": 0.8698659753213326,
+        "predict_seconds": 2.9
+      },
+      "n_donors": 10,
+      "n_generated_cells": 15000,
+      "composition": {
+        "l1_mean": 0.20476432986678444,
+        "l1_median": 0.1912691582075387,
+        "l1_obs_loo_null_mean": 0.3545447454778543,
+        "l1_generated_loo_mean_vs_observed_mean": 0.35258918402254064,
+        "composition_top1": 0.4,
+        "mean_fraction_generated": {
+          "T cell": 0.6102,
+          "B cell": 0.039733,
+          "Monocyte": 0.215,
+          "NK cell": 0.0646,
+          "DC": 0.024533,
+          "Other": 0.045933
+        },
+        "mean_fraction_observed": {
+          "T cell": 0.570331,
+          "B cell": 0.055565,
+          "Monocyte": 0.211872,
+          "NK cell": 0.09329,
+          "DC": 0.013132,
+          "Other": 0.05581
+        }
+      },
+      "pseudobulk": {
+        "n_genes": 5563,
+        "r_median": 0.8578153598003033,
+        "r_mean": 0.861645848561257,
+        "top1": 0.5,
+        "n_top1": 5,
+        "own_rank_median": 1.5,
+        "chance_top1": 0.1
+      },
+      "precision_coverage": {
+        "precision": 1.0,
+        "coverage": 0.9346666666666666,
+        "density": 5.292333333333334,
+        "n_query": 1500,
+        "n_reference": 1500
+      },
+      "precision_coverage_depth_matched": {
+        "precision": 0.9973333333333333,
+        "coverage": 0.9586666666666667,
+        "density": 2.8571999999999997,
+        "detected_median_before": {
+          "R1": 264.0,
+          "Q": 153.0
+        },
+        "detected_median_after": {
+          "R1": 153.0,
+          "Q": 153.0
+        }
+      },
+      "monocyte_pct": {
+        "generated_mean_over_donors": 21.5,
+        "observed_mean_over_donors": 21.18723635141114,
+        "generated_pooled_cells": 21.5
+      },
+      "median_umi_per_cell_scoring_genes": {
+        "generated_pooled": 427.0,
+        "observed_pooled": 482.0,
+        "generated_mean_of_donor_medians": 436.20001220703125,
+        "observed_mean_of_donor_medians": 499.35
+      },
+      "contrast": {
+        "mean_cp10k": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.5661891183203449,
+              "r_broadcast": 0.6571144835533105,
+              "partial_r_generated_given_broadcast": 0.37347750410121766,
+              "r_generated_vs_broadcast": 0.48758164770792883,
+              "n_genes": 2916
+            },
+            "B cell": {
+              "r_generated": 0.12618303770985873,
+              "r_broadcast": 0.3825835491576257,
+              "partial_r_generated_given_broadcast": 0.08387389938041898,
+              "r_generated_vs_broadcast": 0.12895810943438019,
+              "n_genes": 3099
+            },
+            "Monocyte": {
+              "r_generated": 0.23220526411321746,
+              "r_broadcast": 0.4614533190457718,
+              "partial_r_generated_given_broadcast": 0.18756781721244029,
+              "r_generated_vs_broadcast": 0.1464867862193682,
+              "n_genes": 3045
+            },
+            "NK cell": {
+              "r_generated": 0.21105332143844824,
+              "r_broadcast": 0.5038596937916778,
+              "partial_r_generated_given_broadcast": 0.11556582530477336,
+              "r_generated_vs_broadcast": 0.22587448409340705,
+              "n_genes": 2993
+            }
+          },
+          "mean_r_generated": 0.28390768539546735,
+          "mean_r_broadcast": 0.5012527613870964,
+          "mean_partial_r": 0.19012126149971256
+        },
+        "pseudobulk_log1p_cpm": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.35809644300124593,
+              "r_broadcast": 0.6872156600560435,
+              "partial_r_generated_given_broadcast": 0.19004003260105057,
+              "r_generated_vs_broadcast": 0.3315556047121546,
+              "n_genes": 2916
+            },
+            "B cell": {
+              "r_generated": 0.05998274948702396,
+              "r_broadcast": 0.3771207985959151,
+              "partial_r_generated_given_broadcast": 0.046529676614197,
+              "r_generated_vs_broadcast": 0.04489832479614293,
+              "n_genes": 3099
+            },
+            "Monocyte": {
+              "r_generated": 0.15888707137074218,
+              "r_broadcast": 0.5171610414843097,
+              "partial_r_generated_given_broadcast": 0.11038020981602084,
+              "r_generated_vs_broadcast": 0.12600910368294188,
+              "n_genes": 3045
+            },
+            "NK cell": {
+              "r_generated": 0.1349091122703371,
+              "r_broadcast": 0.5135427805432597,
+              "partial_r_generated_given_broadcast": 0.08109339032469605,
+              "r_generated_vs_broadcast": 0.128326426953764,
+              "n_genes": 2993
+            }
+          },
+          "mean_r_generated": 0.1779688440323373,
+          "mean_r_broadcast": 0.523760070169882,
+          "mean_partial_r": 0.1070108273389911
+        }
+      },
+      "deg_top50": {
+        "types_scored": [
+          "T cell",
+          "B cell",
+          "Monocyte",
+          "NK cell",
+          "DC"
+        ],
+        "types_not_scored": {},
+        "per_type": {
+          "T cell": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": 0.0,
+            "obs_top_list_size": 50,
+            "gen_top_list_size": 3,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 58362,
+            "n_cells_gen": 9153
+          },
+          "B cell": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": null,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 6177,
+            "n_cells_gen": 596
+          },
+          "Monocyte": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": null,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 18467,
+            "n_cells_gen": 3225
+          },
+          "NK cell": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": null,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 9050,
+            "n_cells_gen": 969
+          },
+          "DC": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": null,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 1271,
+            "n_cells_gen": 368
+          }
+        },
+        "sum": 0,
+        "sum_4type": 0,
+        "max": 50,
+        "mean": 0.0,
+        "sum_broadcast": 0,
+        "sum_broadcast_4type": 0,
+        "broadcast_n_significant": 3,
+        "seconds": 0.03
+      },
+      "seconds": 4.5
+    }
+  },
+  "code_sha256": {
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+  },
+  "seconds": 5.2,
+  "gene_exclusion": {
+    "file": "/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",
+    "sha256": "e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de",
+    "n_listed": 196,
+    "n_scoring_genes": 5563,
+    "n_dropped_from_scoring_genes": 65,
+    "n_scoring_genes_kept": 5498,
+    "dropped": [
+      {
+        "gene_id": "ENSG00000124343",
+        "symbol": "XG"
+      },
+      {
+        "gene_id": "ENSG00000183943",
+        "symbol": "PRKX"
+      },
+      {
+        "gene_id": "ENSG00000146938",
+        "symbol": "NLGN4X"
+      },
+      {
+        "gene_id": "ENSG00000130021",
+        "symbol": "PUDP"
+      },
+      {
+        "gene_id": "ENSG00000101846",
+        "symbol": "STS"
+      },
+      {
+        "gene_id": "ENSG00000011201",
+        "symbol": "ANOS1"
+      },
+      {
+        "gene_id": "ENSG00000177138",
+        "symbol": "FAM9B"
+      },
+      {
+        "gene_id": "ENSG00000101849",
+        "symbol": "TBL1X"
+      },
+      {
+        "gene_id": "ENSG00000146950",
+        "symbol": "SHROOM2"
+      },
+      {
+        "gene_id": "ENSG00000182287",
+        "symbol": "AP1S2"
+      },
+      {
+        "gene_id": "ENSG00000047230",
+        "symbol": "CTPS2"
+      },
+      {
+        "gene_id": "ENSG00000086712",
+        "symbol": "TXLNG"
+      },
+      {
+        "gene_id": "ENSG00000188158",
+        "symbol": "NHS"
+      },
+      {
+        "gene_id": "ENSG00000177324",
+        "symbol": "BEND2"
+      },
+      {
+        "gene_id": "ENSG00000086717",
+        "symbol": "PPEF1"
+      },
+      {
+        "gene_id": "ENSG00000149970",
+        "symbol": "CNKSR2"
+      },
+      {
+        "gene_id": "ENSG00000102174",
+        "symbol": "PHEX"
+      },
+      {
+        "gene_id": "ENSG00000165186",
+        "symbol": "PTCHD1"
+      },
+      {
+        "gene_id": "ENSG00000169306",
+        "symbol": "IL1RAPL1"
+      },
+      {
+        "gene_id": "ENSG00000147036",
+        "symbol": "LANCL3"
+      },
+      {
+        "gene_id": "ENSG00000047597",
+        "symbol": "XK"
+      },
+      {
+        "gene_id": "ENSG00000180182",
+        "symbol": "MED14"
+      },
+      {
+        "gene_id": "ENSG00000183690",
+        "symbol": "EFHC2"
+      },
+      {
+        "gene_id": "ENSG00000147050",
+        "symbol": "KDM6A"
+      },
+      {
+        "gene_id": "ENSG00000147117",
+        "symbol": "ZNF157"
+      },
+      {
+        "gene_id": "ENSG00000102265",
+        "symbol": "TIMP1"
+      },
+      {
+        "gene_id": "ENSG00000158423",
+        "symbol": "RIBC1"
+      },
+      {
+        "gene_id": "ENSG00000155659",
+        "symbol": "VSIG4"
+      },
+      {
+        "gene_id": "ENSG00000204165",
+        "symbol": "CXorf65"
+      },
+      {
+        "gene_id": "ENSG00000204131",
+        "symbol": "NHSL2"
+      },
+      {
+        "gene_id": "ENSG00000078589",
+        "symbol": "P2RY10"
+      },
+      {
+        "gene_id": "ENSG00000147138",
+        "symbol": "GPR174"
+      },
+      {
+        "gene_id": "ENSG00000198157",
+        "symbol": "HMGN5"
+      },
+      {
+        "gene_id": "ENSG00000147180",
+        "symbol": "ZNF711"
+      },
+      {
+        "gene_id": "ENSG00000124429",
+        "symbol": "POF1B"
+      },
+      {
+        "gene_id": "ENSG00000126733",
+        "symbol": "DACH2"
+      },
+      {
+        "gene_id": "ENSG00000102290",
+        "symbol": "PCDH11X"
+      },
+      {
+        "gene_id": "ENSG00000102362",
+        "symbol": "SYTL4"
+      },
+      {
+        "gene_id": "ENSG00000182489",
+        "symbol": "XKRX"
+      },
+      {
+        "gene_id": "ENSG00000166432",
+        "symbol": "ZMAT1"
+      },
+      {
+        "gene_id": "ENSG00000189108",
+        "symbol": "IL1RAPL2"
+      },
+      {
+        "gene_id": "ENSG00000198088",
+        "symbol": "NUP62CL"
+      },
+      {
+        "gene_id": "ENSG00000147234",
+        "symbol": "FRMPD3"
+      },
+      {
+        "gene_id": "ENSG00000080561",
+        "symbol": "MID2"
+      },
+      {
+        "gene_id": "ENSG00000197565",
+        "symbol": "COL4A6"
+      },
+      {
+        "gene_id": "ENSG00000072315",
+        "symbol": "TRPC5"
+      },
+      {
+        "gene_id": "ENSG00000187823",
+        "symbol": "RTL4"
+      },
+      {
+        "gene_id": "ENSG00000125675",
+        "symbol": "GRIA3"
+      },
+      {
+        "gene_id": "ENSG00000183918",
+        "symbol": "SH2D1A"
+      },
+      {
+        "gene_id": "ENSG00000056277",
+        "symbol": "ZNF280C"
+      },
+      {
+        "gene_id": "ENSG00000171004",
+        "symbol": "HS6ST2"
+      },
+      {
+        "gene_id": "ENSG00000170965",
+        "symbol": "PLAC1"
+      },
+      {
+        "gene_id": "ENSG00000022267",
+        "symbol": "FHL1"
+      },
+      {
+        "gene_id": "ENSG00000102245",
+        "symbol": "CD40LG"
+      },
+      {
+        "gene_id": "ENSG00000129682",
+        "symbol": "FGF13"
+      },
+      {
+        "gene_id": "ENSG00000155966",
+        "symbol": "AFF2"
+      },
+      {
+        "gene_id": "ENSG00000011677",
+        "symbol": "GABRA3"
+      },
+      {
+        "gene_id": "ENSG00000183837",
+        "symbol": "PNMA3"
+      },
+      {
+        "gene_id": "ENSG00000067646",
+        "symbol": "ZFY"
+      },
+      {
+        "gene_id": "ENSG00000099715",
+        "symbol": "PCDH11Y"
+      },
+      {
+        "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"
+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/949e48ae87458341/summary.json

@@ -0,0 +1,1010 @@
+{
+  "schema": "paired_ft_scores.v1",
+  "dataset": "imperial_eskd",
+  "written_utc": "2026-10-15T07:25:58.792404+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",
+    "imperial_eskd",
+    "--out",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/imperial_eskd/draw4/score",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw4/lora.npz",
+    "--condition",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw4/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/imperial_eskd/draw4/test_samples.txt",
+    "--threads",
+    "2",
+    "--case-groups",
+    "covid_positive",
+    "--control-groups",
+    "covid_negative"
+  ],
+  "arms": [
+    "lora"
+  ],
+  "donors": [
+    "C20_1004",
+    "C20_1404",
+    "C21_1004",
+    "C21_1704",
+    "C21_2504",
+    "C23_2204",
+    "C31_1304",
+    "C31_2004",
+    "C31_2704",
+    "C34_1404",
+    "C34_2104",
+    "C34_2504",
+    "C40_1504",
+    "C40_2204",
+    "C40_0105",
+    "C42_1504",
+    "C42_2204",
+    "C42_2704",
+    "C58_1604",
+    "C58_2501",
+    "C58_2901",
+    "C58_0102",
+    "C58_0402",
+    "C58_1003",
+    "C60_2504",
+    "C63_1704",
+    "C63_2404",
+    "C63_2904",
+    "C65_1704",
+    "C65_2104",
+    "C65_2504",
+    "C69_1804",
+    "C82_2504",
+    "C85_2004",
+    "C93_2104",
+    "C93_2704",
+    "C93_0405",
+    "C101_0601",
+    "C101_1101",
+    "C101_1301",
+    "C101_1801",
+    "C101_2001",
+    "C101_2502",
+    "C103_2204",
+    "C104_2204",
+    "C106_2204",
+    "C108_2204",
+    "C108_1501",
+    "C108_1801",
+    "C108_2201",
+    "C113_0605",
+    "C123_2404",
+    "C123_2904",
+    "C123_0505",
+    "C124_2404",
+    "C124_2704",
+    "C124_0105",
+    "C126_2504",
+    "C126_3004",
+    "C126_0605",
+    "C127_2504",
+    "C127_0405",
+    "C127_1105",
+    "C128_2504",
+    "C128_0405",
+    "C128_1105",
+    "C132_2804",
+    "C132_0205",
+    "C132_1105",
+    "C138_3004",
+    "C138_2301",
+    "C138_3001",
+    "C138_0202",
+    "C138_0402",
+    "C140_3004",
+    "C140_2801",
+    "C140_3001",
+    "C140_0202",
+    "C140_0402",
+    "C140_0602",
+    "C140_0902",
+    "C140_1103",
+    "C141_2001",
+    "C141_2201",
+    "C141_3001",
+    "C141_0202",
+    "C142_3004",
+    "C145_3004",
+    "C145_0701",
+    "C145_1201",
+    "C145_1401",
+    "C145_1901",
+    "C145_2301",
+    "C146_3004",
+    "C146_1201",
+    "C146_1401",
+    "C146_1601",
+    "C146_1901",
+    "C146_2301",
+    "C146_2701",
+    "C146_2502",
+    "C147_3004",
+    "C147_1401",
+    "C147_1901",
+    "C161_1105",
+    "C164_1105",
+    "C167_1205",
+    "C168_1205",
+    "C168_2001",
+    "C168_2301",
+    "C168_3001",
+    "C168_0202",
+    "C168_0403",
+    "C169_1205",
+    "C169_2001",
+    "C169_2301",
+    "C169_0202",
+    "C169_0403",
+    "C187_2605",
+    "C187_1201",
+    "C187_1401",
+    "C187_1901",
+    "C187_2301",
+    "C187_2502",
+    "C190_2605",
+    "C190_2901",
+    "C190_0102",
+    "C190_0302",
+    "C190_0502",
+    "C190_0802",
+    "C190_1002",
+    "C190_0903",
+    "C193_2605",
+    "C195_2605",
+    "C197_2605",
+    "C212_2705",
+    "C214_2705",
+    "C234_2805",
+    "C237_2805",
+    "C238_2905",
+    "C240_2905",
+    "C246_2905",
+    "C251_2905"
+  ],
+  "n_donors": 143,
+  "reference": {
+    "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd",
+    "reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
+    "features_sha256": "e46e5bb1a24eae045efe75125d20e3accaa8f68a1006eb2f60d24159013d4aa7",
+    "n_r1_cells": 21382,
+    "pca": {
+      "n_components": 50,
+      "explained_variance_ratio_sum": 0.26274892687797546,
+      "n_fit_cells": 21382
+    },
+    "r2_control": {
+      "precision": 0.9695538303245721,
+      "coverage": 0.9998129267608269,
+      "density": 1.2846225797399682,
+      "n_query": 21382,
+      "depth_matched": {
+        "precision": 0.9684313908895332,
+        "coverage": 0.999672621831447,
+        "density": 1.28349546347395
+      }
+    },
+    "observed_l1_loo_null_mean": 0.5095285177538514
+  },
+  "contrast_definition": {
+    "enabled": true,
+    "rule": "explicit --case-groups / --control-groups",
+    "group_source": "features groups",
+    "case_groups": [
+      "covid_positive"
+    ],
+    "control_groups": [
+      "covid_negative"
+    ],
+    "n_case_donors": 104,
+    "n_control_donors": 31,
+    "n_donors_in_neither": 8,
+    "case": [
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      true,
+      true,
+      true,
+      true,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      true,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      true,
+      true,
+      true,
+      true,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      true,
+      true,
+      true,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ],
+    "ctrl": [
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true,
+      true
+    ],
+    "groups": [
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_negative",
+      "covid_positive",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_negative",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_negative",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "covid_positive",
+      "recovery",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative",
+      "covid_negative"
+    ]
+  },
+  "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": 5927,
+    "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/imperial_eskd/deg_reference.npz",
+    "aggregates_sha256": "8fada1ace7530b79bfc5c5201b9cb60399ff77d083dd8b53b13cfbe900cda55c",
+    "aggregates_note": null,
+    "types_not_scored_observed": [],
+    "observed": {
+      "T cell": {
+        "n_significant": 1194,
+        "n_tested": 5743,
+        "n_case_donors": 104,
+        "n_control_donors": 31,
+        "n_cells": 244943,
+        "top_list_size": 50
+      },
+      "B cell": {
+        "n_significant": 310,
+        "n_tested": 5634,
+        "n_case_donors": 104,
+        "n_control_donors": 31,
+        "n_cells": 46230,
+        "top_list_size": 50
+      },
+      "Monocyte": {
+        "n_significant": 305,
+        "n_tested": 5624,
+        "n_case_donors": 103,
+        "n_control_donors": 31,
+        "n_cells": 77634,
+        "top_list_size": 50
+      },
+      "NK cell": {
+        "n_significant": 431,
+        "n_tested": 5565,
+        "n_case_donors": 104,
+        "n_control_donors": 31,
+        "n_cells": 65766,
+        "top_list_size": 50
+      },
+      "DC": {
+        "n_significant": 295,
+        "n_tested": 5419,
+        "n_case_donors": 104,
+        "n_control_donors": 31,
+        "n_cells": 12690,
+        "top_list_size": 50
+      }
+    },
+    "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": {
+    "lora": {
+      "comp_l1": 0.5164213271978368,
+      "comp_l1_obs_loo_null": 0.5095285177538514,
+      "precision": 0.860396595267047,
+      "coverage": 0.6640164624450472,
+      "precision_dm": 0.88293892058741,
+      "coverage_dm": 0.8046020016836591,
+      "pb_r_median": 0.8700606941085695,
+      "pb_top1": 0.04895104895104895,
+      "mono_pct_gen": 12.722144522144523,
+      "mono_pct_obs": 17.567899313806723,
+      "median_umi_gen": 1189.0,
+      "median_umi_obs": 1367.0,
+      "contrast_mean_cp10k_r_gen": 0.7149080892885361,
+      "contrast_pseudobulk_log1p_cpm_r_gen": 0.5294718303742492,
+      "contrast_mean_cp10k_r_broadcast": 0.6565426449733607,
+      "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.6057327733142364,
+      "deg_top50_T": 31,
+      "deg_top50_B": 27,
+      "deg_top50_Mono": 23,
+      "deg_top50_NK": 20,
+      "deg_top50_DC": 18,
+      "deg_top50_sum": 119,
+      "deg_top50_max": 250,
+      "deg_top50_sum_4type": 101,
+      "deg_top50_sum_broadcast": 76,
+      "seconds": 33.5
+    }
+  },
+  "per_arm": {
+    "lora": {
+      "arm": "lora",
+      "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/imperial_eskd/disease/draw4/lora.npz",
+      "npz_sha256": "b675a0e816dfe73aea961f990fdd194f292ce693073025d62f05a393914d178d",
+      "receipt_verified": true,
+      "generation": {
+        "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/imperial_eskd/disease/draw4/lora/checkpoint_ft.pt",
+        "checkpoint_sha256": "e26c0174875e75879837cfd9cb90a6b6f6b09404c4052c6ebd681fe5f860274d",
+        "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw4/test_raw.npz",
+        "input_condition_sha256": "55970c18927ba5d8e151bf797760d36017fffd360229507c346e39c3c6759f69",
+        "seed": 20260928,
+        "steps": 50,
+        "support_readout": "bernoulli",
+        "weights": "ema"
+      },
+      "condition_for_broadcast": {
+        "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/imperial_eskd/disease/draw4/test_raw.npz",
+        "sha256": "55970c18927ba5d8e151bf797760d36017fffd360229507c346e39c3c6759f69"
+      },
+      "poisson": {
+        "seed": 20260916,
+        "rule": "whole NPZ, rows in NPZ order",
+        "nnz_whole_npz": 53791177,
+        "median_library_whole_npz_panel": 1189.0,
+        "n_rows_whole_npz": 214500
+      },
+      "annotation": {
+        "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+        "zero_padded_model_genes": 0,
+        "label_counts": {
+          "T cell": 130847,
+          "B cell": 28688,
+          "Monocyte": 27289,
+          "NK cell": 20472,
+          "DC": 4343,
+          "Other": 2861
+        },
+        "mean_l2_max_prob": 0.9178270972906015,
+        "predict_seconds": 4.9
+      },
+      "n_donors": 143,
+      "n_generated_cells": 214500,
+      "composition": {
+        "l1_mean": 0.5164213271978368,
+        "l1_median": 0.4842995319812792,
+        "l1_obs_loo_null_mean": 0.5095285177538514,
+        "l1_generated_loo_mean_vs_observed_mean": 0.5210780278582823,
+        "composition_top1": 0.027972027972027972,
+        "mean_fraction_generated": {
+          "T cell": 0.610009,
+          "B cell": 0.133744,
+          "Monocyte": 0.127221,
+          "NK cell": 0.095441,
+          "DC": 0.020247,
+          "Other": 0.013338
+        },
+        "mean_fraction_observed": {
+          "T cell": 0.491688,
+          "B cell": 0.123343,
+          "Monocyte": 0.175679,
+          "NK cell": 0.163061,
+          "DC": 0.03105,
+          "Other": 0.015178
+        }
+      },
+      "pseudobulk": {
+        "n_genes": 5927,
+        "r_median": 0.8700606941085695,
+        "r_mean": 0.8684062028753599,
+        "top1": 0.04895104895104895,
+        "n_top1": 7,
+        "own_rank_median": 40.0,
+        "chance_top1": 0.006993006993006993
+      },
+      "precision_coverage": {
+        "precision": 0.860396595267047,
+        "coverage": 0.6640164624450472,
+        "density": 0.6965204377513797,
+        "n_query": 21382,
+        "n_reference": 21382
+      },
+      "precision_coverage_depth_matched": {
+        "precision": 0.88293892058741,
+        "coverage": 0.8046020016836591,
+        "density": 0.8277710223552521,
+        "detected_median_before": {
+          "R1": 346.0,
+          "Q": 245.0
+        },
+        "detected_median_after": {
+          "R1": 245.0,
+          "Q": 245.0
+        }
+      },
+      "monocyte_pct": {
+        "generated_mean_over_donors": 12.722144522144523,
+        "observed_mean_over_donors": 17.567899313806723,
+        "generated_pooled_cells": 12.722144522144522
+      },
+      "median_umi_per_cell_scoring_genes": {
+        "generated_pooled": 1189.0,
+        "observed_pooled": 1367.0,
+        "generated_mean_of_donor_medians": 1232.3671875,
+        "observed_mean_of_donor_medians": 1292.7272727272727
+      },
+      "contrast": {
+        "mean_cp10k": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.7970499282609055,
+              "r_broadcast": 0.6232824935145761,
+              "partial_r_generated_given_broadcast": 0.7269183436949467,
+              "r_generated_vs_broadcast": 0.4774244938858088,
+              "n_genes": 3032
+            },
+            "B cell": {
+              "r_generated": 0.6895939143486651,
+              "r_broadcast": 0.6315018114438883,
+              "partial_r_generated_given_broadcast": 0.5790240531173816,
+              "r_generated_vs_broadcast": 0.46116080237098056,
+              "n_genes": 3180
+            },
+            "Monocyte": {
+              "r_generated": 0.7048353267995291,
+              "r_broadcast": 0.7121111596726496,
+              "partial_r_generated_given_broadcast": 0.45450934173155594,
+              "r_generated_vs_broadcast": 0.6487971064619436,
+              "n_genes": 2878
+            },
+            "NK cell": {
+              "r_generated": 0.6681531877450451,
+              "r_broadcast": 0.6592751152623284,
+              "partial_r_generated_given_broadcast": 0.5019482671277837,
+              "r_generated_vs_broadcast": 0.52691207848407,
+              "n_genes": 2963
+            }
+          },
+          "mean_r_generated": 0.7149080892885361,
+          "mean_r_broadcast": 0.6565426449733607,
+          "mean_partial_r": 0.565600001417917
+        },
+        "pseudobulk_log1p_cpm": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.6929722140777046,
+              "r_broadcast": 0.6213005296240948,
+              "partial_r_generated_given_broadcast": 0.55229970605803,
+              "r_generated_vs_broadcast": 0.5206743468722275,
+              "n_genes": 3032
+            },
+            "B cell": {
+              "r_generated": 0.38088910000951054,
+              "r_broadcast": 0.49592343727839516,
+              "partial_r_generated_given_broadcast": 0.24756529823968326,
+              "r_generated_vs_broadcast": 0.3643479116329454,
+              "n_genes": 3180
+            },
+            "Monocyte": {
+              "r_generated": 0.5743730910543564,
+              "r_broadcast": 0.7117946294640722,
+              "partial_r_generated_given_broadcast": 0.29574510067544163,
+              "r_generated_vs_broadcast": 0.5664314233050853,
+              "n_genes": 2878
+            },
+            "NK cell": {
+              "r_generated": 0.4696529163554252,
+              "r_broadcast": 0.5939124968903833,
+              "partial_r_generated_given_broadcast": 0.2852947067093613,
+              "r_generated_vs_broadcast": 0.44460925000813334,
+              "n_genes": 2963
+            }
+          },
+          "mean_r_generated": 0.5294718303742492,
+          "mean_r_broadcast": 0.6057327733142364,
+          "mean_partial_r": 0.3452262029206291
+        }
+      },
+      "deg_top50": {
+        "types_scored": [
+          "T cell",
+          "B cell",
+          "Monocyte",
+          "NK cell",
+          "DC"
+        ],
+        "types_not_scored": {},
+        "per_type": {
+          "T cell": {
+            "deg_scored": true,
+            "top50_overlap": 31,
+            "top50_jaccard": 0.4492753623188406,
+            "obs_top_list_size": 50,
+            "gen_top_list_size": 50,
+            "top50_overlap_broadcast": 15,
+            "top50_jaccard_broadcast": 0.17647058823529413,
+            "n_cells_obs": 244943,
+            "n_cells_gen": 123137
+          },
+          "B cell": {
+            "deg_scored": true,
+            "top50_overlap": 27,
+            "top50_jaccard": 0.3698630136986301,
+            "obs_top_list_size": 50,
+            "gen_top_list_size": 50,
+            "top50_overlap_broadcast": 12,
+            "top50_jaccard_broadcast": 0.13636363636363635,
+            "n_cells_obs": 46230,
+            "n_cells_gen": 27046
+          },
+          "Monocyte": {
+            "deg_scored": true,
+            "top50_overlap": 23,
+            "top50_jaccard": 0.2987012987012987,
+            "obs_top_list_size": 50,
+            "gen_top_list_size": 50,
+            "top50_overlap_broadcast": 21,
+            "top50_jaccard_broadcast": 0.26582278481012656,
+            "n_cells_obs": 77634,
+            "n_cells_gen": 25984
+          },
+          "NK cell": {
+            "deg_scored": true,
+            "top50_overlap": 20,
+            "top50_jaccard": 0.25,
+            "obs_top_list_size": 50,
+            "gen_top_list_size": 50,
+            "top50_overlap_broadcast": 14,
+            "top50_jaccard_broadcast": 0.16279069767441862,
+            "n_cells_obs": 65766,
+            "n_cells_gen": 19507
+          },
+          "DC": {
+            "deg_scored": true,
+            "top50_overlap": 18,
+            "top50_jaccard": 0.21951219512195122,
+            "obs_top_list_size": 50,
+            "gen_top_list_size": 50,
+            "top50_overlap_broadcast": 14,
+            "top50_jaccard_broadcast": 0.16279069767441862,
+            "n_cells_obs": 12690,
+            "n_cells_gen": 4124
+          }
+        },
+        "sum": 119,
+        "sum_4type": 101,
+        "max": 250,
+        "mean": 23.8,
+        "sum_broadcast": 76,
+        "sum_broadcast_4type": 62,
+        "broadcast_n_significant": 2055,
+        "seconds": 0.37
+      },
+      "seconds": 33.5
+    }
+  },
+  "code_sha256": {
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+  },
+  "seconds": 48.0,
+  "core_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/imperial_eskd/draw4/score"
+}