Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paired_finetune_intradataset_20260927/scores_contrast/ye2026_sepsis/scsemi_cv_20261002/pooled/rbo.csv

@@ -0,0 +1,11 @@
+dataset,design,unit,arm,predictor,celltype,p,rbo_ext_t_desc,rbo_ext_t_asc,rbo_ext_mean_up_down,pred_defined,len_obs,len_pred
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,T cell,0.98,0.026662246700349702,0.044101048164336895,0.0353816474323433,True,5810,4349
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@3b2d8ef2,T cell,0.98,0.01424985895863068,0.11706981397966511,0.0656598364691479,True,5810,5858
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,B cell,0.98,0.15709519307441,0.012315036769672383,0.08470511492204119,True,5752,2582
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@3b2d8ef2,B cell,0.98,0.03252386873033706,0.03844765030774369,0.03548575951904037,True,5752,5858
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,Monocyte,0.98,0.14198610790458535,0.03186324515499303,0.08692467652978919,True,5754,3320
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@3b2d8ef2,Monocyte,0.98,0.22054619685578747,0.0868213040504805,0.15368375045313398,True,5754,5858
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,NK cell,0.98,0.023252492206409087,0.014348867653262452,0.01880067992983577,True,5623,2558
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@3b2d8ef2,NK cell,0.98,0.016691479245490817,0.03383434206541271,0.025262910655451765,True,5623,5858
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,DC,0.98,0.007529514404051855,0.08779534161546865,0.04766242800976025,True,5330,963
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@3b2d8ef2,DC,0.98,0.06699510250310538,0.134187322599656,0.10059121255138068,True,5330,5858

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/protocol/PROTOCOL.json

@@ -0,0 +1,37 @@
+{
+  "schema": "pbisc.paper-figures-strictpairs.v1",
+  "project_id": "pbisc-diffusion",
+  "figure6": "waiting_user_data_no_execution",
+  "n_pairs": [
+    5,
+    10,
+    20,
+    40
+  ],
+  "strict_pairs": "one_sample_per_unique_donor",
+  "healthy_cohort": "immicro",
+  "disease_cohorts": [
+    "ye2026_sepsis",
+    "imperial_eskd",
+    "giroux2022",
+    "ji2025_chili"
+  ],
+  "outer_folds": 5,
+  "healthy_seed_base": 20261012,
+  "disease_seed_base": 20260928,
+  "lora_rank": 16,
+  "lora_fixed_steps": 3000,
+  "K_cond": 1000,
+  "rho_reference": 3869.603120208939,
+  "N_gen": 1500,
+  "sampling_steps": 50,
+  "external_reference": "AIFI",
+  "external_reference_anchor": "all_unlabelled_target_bulks",
+  "primary_gene_masks": "existing_cohort_scoring_genes; Giroux disease excludes sex-linked",
+  "pretraining_cost_excluded": true,
+  "rare_zero_draws": "include",
+  "git_push": false,
+  "overleaf_sync": false,
+  "source_model": "f01_6k_1x_seed20260627 E16 EMA",
+  "manuscript_start_head": "132cfc93c3c14ff6e9c1940f4a3b5e188c5cf512"
+}

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/protocol/splits/ye2026_sepsis/disease/draw0/support.json

@@ -0,0 +1,254 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "ye2026_sepsis",
+  "design": "disease_existing_draw",
+  "unit": "draw0_n5",
+  "n_pairs": 5,
+  "train_sample_ids": [
+    "HC07",
+    "Abd-S66",
+    "Res-S150",
+    "Skin-S74",
+    "Res-S77"
+  ],
+  "train_donor_ids": [
+    "HC07",
+    "Abd-S66",
+    "Res-S150",
+    "Skin-S74",
+    "Res-S77"
+  ],
+  "test_sample_ids": [
+    "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-S79",
+    "Abd-S83",
+    "Abd-S98",
+    "HC01",
+    "HC05",
+    "HC09",
+    "HC12",
+    "HC13",
+    "HC16",
+    "IC10",
+    "IC15",
+    "IC16",
+    "IC19",
+    "IC22",
+    "IC23",
+    "PHC01",
+    "PHC02",
+    "PHC03",
+    "PHC05",
+    "PIC01",
+    "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-S136",
+    "Res-S139",
+    "Res-S146",
+    "Res-S149",
+    "Res-S164",
+    "Res-S166",
+    "Res-S174",
+    "Res-S177",
+    "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"
+  ],
+  "test_donor_ids": [
+    "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-S79",
+    "Abd-S83",
+    "Abd-S98",
+    "HC01",
+    "HC05",
+    "HC09",
+    "HC12",
+    "HC13",
+    "HC16",
+    "IC10",
+    "IC15",
+    "IC16",
+    "IC19",
+    "IC22",
+    "IC23",
+    "PHC01",
+    "PHC02",
+    "PHC03",
+    "PHC05",
+    "PIC01",
+    "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-S136",
+    "Res-S139",
+    "Res-S146",
+    "Res-S149",
+    "Res-S164",
+    "Res-S166",
+    "Res-S174",
+    "Res-S177",
+    "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"
+  ],
+  "excluded_sample_ids": [],
+  "seed": null,
+  "selection_audit": [
+    {
+      "donor_id": "HC07",
+      "assigned_stratum": false,
+      "selected_sample_id": "HC07",
+      "candidates": [
+        {
+          "sample_id": "HC07",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_HC"
+        }
+      ]
+    },
+    {
+      "donor_id": "Abd-S66",
+      "assigned_stratum": true,
+      "selected_sample_id": "Abd-S66",
+      "candidates": [
+        {
+          "sample_id": "Abd-S66",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    },
+    {
+      "donor_id": "Res-S150",
+      "assigned_stratum": true,
+      "selected_sample_id": "Res-S150",
+      "candidates": [
+        {
+          "sample_id": "Res-S150",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    },
+    {
+      "donor_id": "Skin-S74",
+      "assigned_stratum": true,
+      "selected_sample_id": "Skin-S74",
+      "candidates": [
+        {
+          "sample_id": "Skin-S74",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    },
+    {
+      "donor_id": "Res-S77",
+      "assigned_stratum": true,
+      "selected_sample_id": "Res-S77",
+      "candidates": [
+        {
+          "sample_id": "Res-S77",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    }
+  ],
+  "sha256": "ad30daaf76d46edb695df2ae02cb67f8d8b3ae709630e8ec7ae87056258f9bda"
+}

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/protocol/splits/ye2026_sepsis/disease/draw1/support.json

@@ -0,0 +1,254 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "ye2026_sepsis",
+  "design": "disease_existing_draw",
+  "unit": "draw1_n5",
+  "n_pairs": 5,
+  "train_sample_ids": [
+    "HC12",
+    "Uri-S134",
+    "Uri-S147",
+    "Res-S164",
+    "Res-S166"
+  ],
+  "train_donor_ids": [
+    "HC12",
+    "Uri-S134",
+    "Uri-S147",
+    "Res-S164",
+    "Res-S166"
+  ],
+  "test_sample_ids": [
+    "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",
+    "HC13",
+    "HC16",
+    "IC10",
+    "IC15",
+    "IC16",
+    "IC19",
+    "IC22",
+    "IC23",
+    "PHC01",
+    "PHC02",
+    "PHC03",
+    "PHC05",
+    "PIC01",
+    "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-S136",
+    "Res-S139",
+    "Res-S146",
+    "Res-S149",
+    "Res-S150",
+    "Res-S174",
+    "Res-S177",
+    "Res-S184",
+    "Res-S19",
+    "Res-S26",
+    "Res-S40",
+    "Res-S77",
+    "Res-S87",
+    "Skin-S140",
+    "Skin-S142",
+    "Skin-S152",
+    "Skin-S38",
+    "Skin-S43",
+    "Skin-S46",
+    "Skin-S52",
+    "Skin-S74",
+    "Uri-S157",
+    "Uri-S20",
+    "Uri-S93"
+  ],
+  "test_donor_ids": [
+    "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",
+    "HC13",
+    "HC16",
+    "IC10",
+    "IC15",
+    "IC16",
+    "IC19",
+    "IC22",
+    "IC23",
+    "PHC01",
+    "PHC02",
+    "PHC03",
+    "PHC05",
+    "PIC01",
+    "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-S136",
+    "Res-S139",
+    "Res-S146",
+    "Res-S149",
+    "Res-S150",
+    "Res-S174",
+    "Res-S177",
+    "Res-S184",
+    "Res-S19",
+    "Res-S26",
+    "Res-S40",
+    "Res-S77",
+    "Res-S87",
+    "Skin-S140",
+    "Skin-S142",
+    "Skin-S152",
+    "Skin-S38",
+    "Skin-S43",
+    "Skin-S46",
+    "Skin-S52",
+    "Skin-S74",
+    "Uri-S157",
+    "Uri-S20",
+    "Uri-S93"
+  ],
+  "excluded_sample_ids": [],
+  "seed": null,
+  "selection_audit": [
+    {
+      "donor_id": "HC12",
+      "assigned_stratum": false,
+      "selected_sample_id": "HC12",
+      "candidates": [
+        {
+          "sample_id": "HC12",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_HC"
+        }
+      ]
+    },
+    {
+      "donor_id": "Uri-S134",
+      "assigned_stratum": true,
+      "selected_sample_id": "Uri-S134",
+      "candidates": [
+        {
+          "sample_id": "Uri-S134",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    },
+    {
+      "donor_id": "Uri-S147",
+      "assigned_stratum": true,
+      "selected_sample_id": "Uri-S147",
+      "candidates": [
+        {
+          "sample_id": "Uri-S147",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    },
+    {
+      "donor_id": "Res-S164",
+      "assigned_stratum": true,
+      "selected_sample_id": "Res-S164",
+      "candidates": [
+        {
+          "sample_id": "Res-S164",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    },
+    {
+      "donor_id": "Res-S166",
+      "assigned_stratum": true,
+      "selected_sample_id": "Res-S166",
+      "candidates": [
+        {
+          "sample_id": "Res-S166",
+          "time_value": 0.0,
+          "time_raw": "none (single sample per donor)",
+          "time_field": "timepoint",
+          "group": "adult_sepsis"
+        }
+      ]
+    }
+  ],
+  "sha256": "b85d386f59fff3c35b7beb041528403ab3fde9abf06af2bdd0b3b63c1bb8d99f"
+}