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/18ee4869b93aab87/en.csv

@@ -0,0 +1,25 @@
+dataset,design,unit,set,cellset,distance,n_samples,n_cells_real,n_cells_gen,n_pcs,lb,ub,dif_mean,en,lb_exact,lb_queries,n_representative_rows,en_reps_at_lb,seconds
+imperial_eskd,scored,strict,real_R2,pc,sq,143,21395,21395,100,188.76717509428727,333.3601141132368,222.91438590836492,0.2361609843866754,True,"[21395, 21395]",,,15.7
+imperial_eskd,scored,strict,real_R2,pc,l2,143,21395,21395,100,13.52310104347431,17.849389899993515,14.620867738808174,0.25374327321664136,True,"[21395, 21395]",,,15.7
+imperial_eskd,scored,strict,real_R2,all,sq,143,238816,238891,100,154.3796639036006,270.5977411910587,185.9374395053448,0.2715393021318709,False,"[20000, 20000]",,,62.8
+imperial_eskd,scored,strict,real_R2,all,l2,143,238816,238891,100,12.23632835560116,16.16859463920437,13.388195243520798,0.2929269802308915,False,"[20000, 20000]",,,62.8
+imperial_eskd,scored,strict,lora,pc,sq,143,21395,21395,100,207.4685265765905,322.1453718945341,322.9065064521693,1.0066372122072678,True,"[21395, 21395]",,,16.5
+imperial_eskd,scored,strict,lora,pc,l2,143,21395,21395,100,14.19169550267499,17.56363089780548,17.683479105338083,1.0355428540255185,True,"[21395, 21395]",,,16.5
+imperial_eskd,scored,strict,lora,all,sq,143,477707,214500,100,164.53491155853254,259.5372923379825,265.93341059542905,1.0673258733620086,False,"[20000, 20000]",,,80.0
+imperial_eskd,scored,strict,lora,all,l2,143,477707,214500,100,12.62531315301172,15.855151678720466,16.079940976729585,1.0695976892404526,False,"[20000, 20000]",,,80.0
+imperial_eskd,scored,strict,pairedcal,pc,sq,143,21395,21395,100,200.75605659186397,320.6866393552535,340.2092308461472,1.162782428310298,True,"[21395, 21395]",,,15.6
+imperial_eskd,scored,strict,pairedcal,pc,l2,143,21395,21395,100,13.950497083399288,17.521973239548107,18.129053174204817,1.1699801169361115,True,"[21395, 21395]",,,15.6
+imperial_eskd,scored,strict,pairedcal,all,sq,143,477707,214500,100,160.0581893156612,258.86344982090804,276.98431207350836,1.183399772035802,False,"[20000, 20000]",,,76.7
+imperial_eskd,scored,strict,pairedcal,all,l2,143,477707,214500,100,12.45537386928526,15.836496913895612,16.42412996618209,1.173798186145041,False,"[20000, 20000]",,,76.7
+imperial_eskd,scored,strict,scsemi,pc,sq,143,21395,21395,100,136.86672574861132,320.0083089497558,442.2826379220178,1.6676491861379619,True,"[21395, 21395]",,,14.8
+imperial_eskd,scored,strict,scsemi,pc,l2,143,21395,21395,100,11.231663265476177,17.465372638214085,20.735677913251163,1.524616256468294,True,"[21395, 21395]",,,14.8
+imperial_eskd,scored,strict,scsemi,all,sq,143,477707,214500,100,119.09716681246633,256.7247936433485,395.9957441550396,2.0119403619654666,False,"[20000, 20000]",,,77.8
+imperial_eskd,scored,strict,scsemi,all,l2,143,477707,214500,100,10.430417887182593,15.744933165992508,19.610051474676933,1.7272757920360977,False,"[20000, 20000]",,,77.8
+imperial_eskd,scored,strict,raw,pc,sq,143,21395,21395,100,236.46346625381858,295.5106309495549,636.8352651609829,6.780542316811263,True,"[21395, 21395]",,,15.3
+imperial_eskd,scored,strict,raw,pc,l2,143,21395,21395,100,14.969671547110076,16.78666636661275,24.545850260171772,5.270339029190396,True,"[21395, 21395]",,,15.3
+imperial_eskd,scored,strict,raw,all,sq,143,477707,214500,100,173.71149373698444,249.87319471600978,485.8930983218987,4.0989316227441925,False,"[20000, 20000]",,,79.3
+imperial_eskd,scored,strict,raw,all,l2,143,477707,214500,100,12.885866609015476,15.554647648742204,21.57014240194467,3.2540233401157654,False,"[20000, 20000]",,,79.3
+imperial_eskd,scored,strict,refcal,pc,sq,143,21395,21395,100,192.998065246238,319.6449787583641,370.85951490077383,1.404388348062711,True,"[21395, 21395]",,,15.4
+imperial_eskd,scored,strict,refcal,pc,l2,143,21395,21395,100,13.674496231691283,17.48864817063922,18.93182096104882,1.3783731779724733,True,"[21395, 21395]",,,15.4
+imperial_eskd,scored,strict,refcal,all,sq,143,477707,214500,100,155.4956594398019,258.19272017867166,303.66428867059864,1.4427738064242033,False,"[20000, 20000]",,,76.9
+imperial_eskd,scored,strict,refcal,all,l2,143,477707,214500,100,12.278308890739828,15.81522484189862,17.209129784033927,1.3941017998119587,False,"[20000, 20000]",,,76.9

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/abb2a4efc3d569e5/support.json

@@ -0,0 +1,177 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "ji2025_chili",
+  "design": "disease_existing_draw",
+  "unit": "draw0_n5",
+  "n_pairs": 5,
+  "train_sample_ids": [
+    "N150_BC",
+    "N018_BC",
+    "N032_AC",
+    "N012_TOL",
+    "N138_TOL"
+  ],
+  "train_donor_ids": [
+    "N150",
+    "N018",
+    "N032",
+    "N012",
+    "N138"
+  ],
+  "test_sample_ids": [
+    "N064_TOL",
+    "N064_FU1",
+    "N038_BC",
+    "N038_AC",
+    "N055_AC",
+    "N136_TOL",
+    "N136_FU1",
+    "N128_BC",
+    "N128_AC",
+    "N129_BC",
+    "N129_AC",
+    "N147_TOL",
+    "N158_AC",
+    "N159_BC",
+    "N001_TOL",
+    "N001_FU1",
+    "N002_TOL",
+    "N002_FU1",
+    "N005_BC",
+    "N005_AC",
+    "N022_TOL",
+    "N022_FU1",
+    "N035_TOL",
+    "N043_TOL",
+    "N043_FU1"
+  ],
+  "test_donor_ids": [
+    "N064",
+    "N064",
+    "N038",
+    "N038",
+    "N055",
+    "N136",
+    "N136",
+    "N128",
+    "N128",
+    "N129",
+    "N129",
+    "N147",
+    "N158",
+    "N159",
+    "N001",
+    "N001",
+    "N002",
+    "N002",
+    "N005",
+    "N005",
+    "N022",
+    "N022",
+    "N035",
+    "N043",
+    "N043"
+  ],
+  "excluded_sample_ids": [
+    "N012_FU1",
+    "N018_AC",
+    "N032_BC",
+    "N138_FU1",
+    "N150_AC"
+  ],
+  "seed": null,
+  "selection_audit": [
+    {
+      "donor_id": "N150",
+      "assigned_stratum": false,
+      "selected_sample_id": "N150_BC",
+      "candidates": [
+        {
+          "sample_id": "N150_BC",
+          "time_value": 0.0,
+          "time_raw": "BC",
+          "time_field": "timepoint",
+          "group": "BC"
+        }
+      ]
+    },
+    {
+      "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": "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": "N012",
+      "assigned_stratum": true,
+      "selected_sample_id": "N012_TOL",
+      "candidates": [
+        {
+          "sample_id": "N012_TOL",
+          "time_value": 0.0,
+          "time_raw": "TOL",
+          "time_field": "timepoint",
+          "group": "TOL"
+        },
+        {
+          "sample_id": "N012_FU1",
+          "time_value": 1.0,
+          "time_raw": "FU1",
+          "time_field": "timepoint",
+          "group": "FU1"
+        }
+      ]
+    },
+    {
+      "donor_id": "N138",
+      "assigned_stratum": true,
+      "selected_sample_id": "N138_TOL",
+      "candidates": [
+        {
+          "sample_id": "N138_TOL",
+          "time_value": 0.0,
+          "time_raw": "TOL",
+          "time_field": "timepoint",
+          "group": "TOL"
+        },
+        {
+          "sample_id": "N138_FU1",
+          "time_value": 1.0,
+          "time_raw": "FU1",
+          "time_field": "timepoint",
+          "group": "FU1"
+        }
+      ]
+    }
+  ],
+  "sha256": "b361deccb2e2b5da9fc4fcf8d3b558dc4ebefa14390ebba15e419ff8c351b9b8"
+}

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/adb1b50de2749465/support.json

@@ -0,0 +1,187 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "giroux2022",
+  "design": "disease_existing_draw",
+  "unit": "draw3_n5",
+  "n_pairs": 5,
+  "train_sample_ids": [
+    "450905_d0",
+    "BAAF62_d0",
+    "7085CA_d0",
+    "180E1A_d0",
+    "B85D75_d0"
+  ],
+  "train_donor_ids": [
+    "450905",
+    "BAAF62",
+    "7085CA",
+    "180E1A",
+    "B85D75"
+  ],
+  "test_sample_ids": [
+    "0B943B_d0",
+    "0B943B_d14",
+    "2AD75E_d0",
+    "2AD75E_d7",
+    "2AD75E_d14",
+    "82CCF5_d0",
+    "82CCF5_d7",
+    "82CCF5_d14",
+    "0BF51C_d0",
+    "0BF51C_d7",
+    "0BF51C_d14"
+  ],
+  "test_donor_ids": [
+    "0B943B",
+    "0B943B",
+    "2AD75E",
+    "2AD75E",
+    "2AD75E",
+    "82CCF5",
+    "82CCF5",
+    "82CCF5",
+    "0BF51C",
+    "0BF51C",
+    "0BF51C"
+  ],
+  "excluded_sample_ids": [
+    "180E1A_d14",
+    "180E1A_d7",
+    "450905_d14",
+    "7085CA_d14",
+    "7085CA_d7",
+    "B85D75_d7",
+    "BAAF62_d14",
+    "BAAF62_d7"
+  ],
+  "seed": null,
+  "selection_audit": [
+    {
+      "donor_id": "450905",
+      "assigned_stratum": false,
+      "selected_sample_id": "450905_d0",
+      "candidates": [
+        {
+          "sample_id": "450905_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "450905_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "mild"
+        }
+      ]
+    },
+    {
+      "donor_id": "BAAF62",
+      "assigned_stratum": false,
+      "selected_sample_id": "BAAF62_d0",
+      "candidates": [
+        {
+          "sample_id": "BAAF62_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "BAAF62_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "BAAF62_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "mild"
+        }
+      ]
+    },
+    {
+      "donor_id": "7085CA",
+      "assigned_stratum": false,
+      "selected_sample_id": "7085CA_d0",
+      "candidates": [
+        {
+          "sample_id": "7085CA_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "7085CA_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "7085CA_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "mild"
+        }
+      ]
+    },
+    {
+      "donor_id": "180E1A",
+      "assigned_stratum": true,
+      "selected_sample_id": "180E1A_d0",
+      "candidates": [
+        {
+          "sample_id": "180E1A_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "severe"
+        },
+        {
+          "sample_id": "180E1A_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "severe"
+        },
+        {
+          "sample_id": "180E1A_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "severe"
+        }
+      ]
+    },
+    {
+      "donor_id": "B85D75",
+      "assigned_stratum": true,
+      "selected_sample_id": "B85D75_d0",
+      "candidates": [
+        {
+          "sample_id": "B85D75_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "severe"
+        },
+        {
+          "sample_id": "B85D75_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "severe"
+        }
+      ]
+    }
+  ],
+  "sha256": "6e7e31e9963228d5a291268fad234c49a14e285b7afa181e57d8d66d80195a15"
+}

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/b5d9d1d3a0f5af91/summary.json

@@ -0,0 +1,1887 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-12T16:19:09.807546+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "ye2026_sepsis",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/score",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/test_sample_ids.txt",
+  "--threads",
+  "4",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/lora.npz",
+  "--arm",
+  "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/pairedcal.npz",
+  "--arm",
+  "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/scsemi.npz",
+  "--arm",
+  "raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+  "--arm",
+  "refcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz",
+  "--case-groups",
+  "adult_sepsis,ped_sepsis",
+  "--control-groups",
+  "adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl"
+ ],
+ "arms": [
+  "lora",
+  "pairedcal",
+  "scsemi",
+  "raw",
+  "refcal"
+ ],
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Uri-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_donors": 77,
+ "reference": {
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