Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T100456Z-figure1-diffusion-readable-corpus/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/display_aggregations.csv

@@ -0,0 +1,15 @@
+panel,display_label,members,n_cells,denominator_cells,percentage,color
+healthy_disease,Healthy,Healthy,29304952,33141380,88.42405476175102,#A9B8CC
+healthy_disease,Disease / at-risk,ACPA+ at risk of RA|COVID-19|Cytopenia|DRESS|Influenza|JDM|MDS|MDS/MPN|Post-COVID-19|RA|SLE,3836428,33141380,11.57594523824898,#94776F
+disease_detail,ACPA+ at risk of RA,ACPA+ at risk of RA,1488898,3836428,38.809486324257875,#DDA59B
+disease_detail,COVID-19,COVID-19,999716,3836428,26.058510677119447,#D08C3C
+disease_detail,SLE,SLE,619230,3836428,16.140795552529593,#7A4F6E
+disease_detail,RA,RA,226113,3836428,5.893841875828245,#B5655E
+disease_detail,Other conditions / history,Cytopenia|DRESS|Influenza|JDM|MDS|MDS/MPN|Post-COVID-19,502471,3836428,13.09736557026484,#7C9B91
+celltype,T cell,T cell,19846978,33141380,59.88579232367512,#4C6E91
+celltype,Monocyte,Monocyte,5953356,33141380,17.963512684142906,#5E8C6A
+celltype,B cell,B cell,2891493,33141380,8.724721179383598,#C98A4B
+celltype,NK cell,NK cell,2720293,33141380,8.208146432043566,#8FB0CF
+celltype,DC,DC,385387,33141380,1.1628574308010107,#A8C79C
+celltype,Other cell types,Progenitor cell|Erythrocyte|ILC|Platelet|Other,1106444,33141380,3.338557416740039,#9787A0
+celltype,Unlabelled,Unlabelled,237429,33141380,0.7164125332137647,#E2E2E2

paper-releases/pbisc-diffusion/updates/20261015T100456Z-figure1-diffusion-readable-corpus/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/numeric_checks.json

@@ -0,0 +1,10 @@
+{
+  "source_verified_data_equals_prior_result": true,
+  "saved_condition_and_celltype_csv_counts_match": true,
+  "prior_verified_data_and_provenance_roster_hashes_match": true,
+  "each_chart_sums_to_its_exact_denominator": true,
+  "each_source_category_appears_once_per_chart": true,
+  "unlabelled_not_merged_into_known_types": true,
+  "at_risk_not_merged_into_confirmed_RA": true,
+  "count_differences_from_saved_source": 0
+}

paper-releases/pbisc-diffusion/updates/20261015T100456Z-figure1-diffusion-readable-corpus/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/result.json

@@ -0,0 +1,281 @@
+{
+  "schema": "pbisc.figure1-focused-corpus.v1",
+  "status": "verified",
+  "slides": [
+    {
+      "key": "main_figure1_training_corpus_focused",
+      "kind": "content",
+      "title": "Pretraining data: 33.14 million training cells",
+      "subtitle": "Main proportions; full category counts are retained in Figure 1 support",
+      "figure": "figures/figure1_focus_20261015/corpus/training_corpus_main.png",
+      "figures": [
+        "figures/figure1_focus_20261015/corpus/training_corpus_main.png"
+      ],
+      "section": "Figure 1",
+      "section_label": "Figure 1 · main panel",
+      "keywords": [],
+      "footnote": "Disease / at-risk includes ACPA+ risk. Proportions count each training-source cell once.",
+      "note": "Exact 33,141,380-cell training universe: 22 datasets, 2,572 corrected biological donor identities, 5,232 samples. Counts unchanged from the verified 2026-10-14 train-corpus bundle. Healthy 29,304,952 (88.4241%); disease/at-risk 3,836,428. Disease-detail percentages use only the disease/at-risk subset as denominator. ACPA+ at risk of RA is kept separate from RA. Other conditions/history comprises Cytopenia, DRESS, Influenza, JDM, MDS, MDS/MPN, Post-COVID-19. Other cell types comprises Progenitor cell, Erythrocyte, ILC, Platelet, Other. Unlabelled remains a separate category including all 99,769 training overlay cells and other unlabelled cells. Original unmerged counts and full category labels are retained on the Figure 1 support panel. Healthy includes stimulated, CMV-seropositive healthy and post-vaccination samples. Post-COVID-19 is historical/post-infection, and cytopenia is not equated with confirmed malignancy. Unique source-cell composition is not recipe-weighted exposure. The original 27-donor internal corpus cross-split caveat remains; this chart makes no new donor-disjoint validation claim.",
+      "footnote_full": "Exact 33,141,380-cell training universe: 22 datasets, 2,572 corrected biological donor identities, 5,232 samples. Counts unchanged from the verified 2026-10-14 train-corpus bundle. Healthy 29,304,952 (88.4241%); disease/at-risk 3,836,428. Disease-detail percentages use only the disease/at-risk subset as denominator. ACPA+ at risk of RA is kept separate from RA. Other conditions/history comprises Cytopenia, DRESS, Influenza, JDM, MDS, MDS/MPN, Post-COVID-19. Other cell types comprises Progenitor cell, Erythrocyte, ILC, Platelet, Other. Unlabelled remains a separate category including all 99,769 training overlay cells and other unlabelled cells. Original unmerged counts and full category labels are retained on the Figure 1 support panel. Healthy includes stimulated, CMV-seropositive healthy and post-vaccination samples. Post-COVID-19 is historical/post-infection, and cytopenia is not equated with confirmed malignancy. Unique source-cell composition is not recipe-weighted exposure. The original 27-donor internal corpus cross-split caveat remains; this chart makes no new donor-disjoint validation claim.",
+      "palette": "biological",
+      "source_refs": [
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/verified_data.json",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_condition_counts.csv",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_celltype_counts.csv",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/result.json",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/source_hashes.json",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/figure1_corpus_main_20261015.py",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/display_aggregations.csv"
+      ],
+      "source_bindings": [
+        {
+          "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/verified_data.json",
+          "host": "server_1",
+          "sha256": "bda56b4c2a3670a0be4be56bd3f79e74269c05e22296004b033f6cdcf96fc925",
+          "bytes": 2704,
+          "role": "verified previous training-corpus source"
+        },
+        {
+          "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_condition_counts.csv",
+          "host": "server_1",
+          "sha256": "0acef1318304a5075de225d57533a555be677cb65c76dd45215d0293c1c52447",
+          "bytes": 840,
+          "role": "verified previous training-corpus source"
+        },
+        {
+          "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_celltype_counts.csv",
+          "host": "server_1",
+          "sha256": "12f68e88b01350071bc16eb89627cdf829f0652c6e52c19d61aad9a2448a3fce",
+          "bytes": 538,
+          "role": "verified previous training-corpus source"
+        },
+        {
+          "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/result.json",
+          "host": "server_1",
+          "sha256": "44a6a52adbf52f77a971e407209e9946bc19684450b06cb970953f667ba79f20",
+          "bytes": 440958,
+          "role": "verified previous training-corpus source"
+        },
+        {
+          "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/source_hashes.json",
+          "host": "server_1",
+          "sha256": "b6e37c602ed324b2a26c17b2ba90be269b9a60ba81bc49d219b873ca2fea7a6e",
+          "bytes": 424246,
+          "role": "verified previous training-corpus source"
+        },
+        {
+          "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/figure1_corpus_main_20261015.py",
+          "host": "server_1",
+          "sha256": "8d6259544c255421ed8f45409331cb490f10b04f05aa883afd2b384de4278cd2",
+          "bytes": 10942,
+          "role": "CPU-only main-panel renderer"
+        },
+        {
+          "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/display_aggregations.csv",
+          "host": "server_1",
+          "sha256": "dc96d88d64b4390452d7417a8e8eb333a32457875a9b185dd6ce32701ac024bd",
+          "bytes": 1290,
+          "role": "explicit main-panel category aggregation"
+        }
+      ]
+    }
+  ],
+  "assets": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure1_focus_20261015/corpus/training_corpus_main.png",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure1_focus_20261015/corpus/training_corpus_main.pdf",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure1_focus_20261015/corpus/training_corpus_main.svg"
+  ],
+  "sources": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/verified_data.json",
+      "host": "server_1",
+      "sha256": "bda56b4c2a3670a0be4be56bd3f79e74269c05e22296004b033f6cdcf96fc925",
+      "bytes": 2704,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_condition_counts.csv",
+      "host": "server_1",
+      "sha256": "0acef1318304a5075de225d57533a555be677cb65c76dd45215d0293c1c52447",
+      "bytes": 840,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_celltype_counts.csv",
+      "host": "server_1",
+      "sha256": "12f68e88b01350071bc16eb89627cdf829f0652c6e52c19d61aad9a2448a3fce",
+      "bytes": 538,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/result.json",
+      "host": "server_1",
+      "sha256": "44a6a52adbf52f77a971e407209e9946bc19684450b06cb970953f667ba79f20",
+      "bytes": 440958,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/source_hashes.json",
+      "host": "server_1",
+      "sha256": "b6e37c602ed324b2a26c17b2ba90be269b9a60ba81bc49d219b873ca2fea7a6e",
+      "bytes": 424246,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/figure1_corpus_main_20261015.py",
+      "host": "server_1",
+      "sha256": "8d6259544c255421ed8f45409331cb490f10b04f05aa883afd2b384de4278cd2",
+      "bytes": 10942,
+      "role": "CPU-only main-panel renderer"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/display_aggregations.csv",
+      "host": "server_1",
+      "sha256": "dc96d88d64b4390452d7417a8e8eb333a32457875a9b185dd6ce32701ac024bd",
+      "bytes": 1290,
+      "role": "explicit main-panel category aggregation"
+    }
+  ],
+  "checks": {
+    "source_verified_data_equals_prior_result": true,
+    "saved_condition_and_celltype_csv_counts_match": true,
+    "prior_verified_data_and_provenance_roster_hashes_match": true,
+    "each_chart_sums_to_its_exact_denominator": true,
+    "each_source_category_appears_once_per_chart": true,
+    "unlabelled_not_merged_into_known_types": true,
+    "at_risk_not_merged_into_confirmed_RA": true,
+    "count_differences_from_saved_source": 0
+  },
+  "display_aggregations": [
+    {
+      "panel": "healthy_disease",
+      "display_label": "Healthy",
+      "members": "Healthy",
+      "n_cells": 29304952,
+      "denominator_cells": 33141380,
+      "percentage": 88.42405476175102,
+      "color": "#A9B8CC"
+    },
+    {
+      "panel": "healthy_disease",
+      "display_label": "Disease / at-risk",
+      "members": "ACPA+ at risk of RA|COVID-19|Cytopenia|DRESS|Influenza|JDM|MDS|MDS/MPN|Post-COVID-19|RA|SLE",
+      "n_cells": 3836428,
+      "denominator_cells": 33141380,
+      "percentage": 11.57594523824898,
+      "color": "#94776F"
+    },
+    {
+      "panel": "disease_detail",
+      "display_label": "ACPA+ at risk of RA",
+      "members": "ACPA+ at risk of RA",
+      "n_cells": 1488898,
+      "denominator_cells": 3836428,
+      "percentage": 38.809486324257875,
+      "color": "#DDA59B"
+    },
+    {
+      "panel": "disease_detail",
+      "display_label": "COVID-19",
+      "members": "COVID-19",
+      "n_cells": 999716,
+      "denominator_cells": 3836428,
+      "percentage": 26.058510677119447,
+      "color": "#D08C3C"
+    },
+    {
+      "panel": "disease_detail",
+      "display_label": "SLE",
+      "members": "SLE",
+      "n_cells": 619230,
+      "denominator_cells": 3836428,
+      "percentage": 16.140795552529593,
+      "color": "#7A4F6E"
+    },
+    {
+      "panel": "disease_detail",
+      "display_label": "RA",
+      "members": "RA",
+      "n_cells": 226113,
+      "denominator_cells": 3836428,
+      "percentage": 5.893841875828245,
+      "color": "#B5655E"
+    },
+    {
+      "panel": "disease_detail",
+      "display_label": "Other conditions / history",
+      "members": "Cytopenia|DRESS|Influenza|JDM|MDS|MDS/MPN|Post-COVID-19",
+      "n_cells": 502471,
+      "denominator_cells": 3836428,
+      "percentage": 13.09736557026484,
+      "color": "#7C9B91"
+    },
+    {
+      "panel": "celltype",
+      "display_label": "T cell",
+      "members": "T cell",
+      "n_cells": 19846978,
+      "denominator_cells": 33141380,
+      "percentage": 59.88579232367512,
+      "color": "#4C6E91"
+    },
+    {
+      "panel": "celltype",
+      "display_label": "Monocyte",
+      "members": "Monocyte",
+      "n_cells": 5953356,
+      "denominator_cells": 33141380,
+      "percentage": 17.963512684142906,
+      "color": "#5E8C6A"
+    },
+    {
+      "panel": "celltype",
+      "display_label": "B cell",
+      "members": "B cell",
+      "n_cells": 2891493,
+      "denominator_cells": 33141380,
+      "percentage": 8.724721179383598,
+      "color": "#C98A4B"
+    },
+    {
+      "panel": "celltype",
+      "display_label": "NK cell",
+      "members": "NK cell",
+      "n_cells": 2720293,
+      "denominator_cells": 33141380,
+      "percentage": 8.208146432043566,
+      "color": "#8FB0CF"
+    },
+    {
+      "panel": "celltype",
+      "display_label": "DC",
+      "members": "DC",
+      "n_cells": 385387,
+      "denominator_cells": 33141380,
+      "percentage": 1.1628574308010107,
+      "color": "#A8C79C"
+    },
+    {
+      "panel": "celltype",
+      "display_label": "Other cell types",
+      "members": "Progenitor cell|Erythrocyte|ILC|Platelet|Other",
+      "n_cells": 1106444,
+      "denominator_cells": 33141380,
+      "percentage": 3.338557416740039,
+      "color": "#9787A0"
+    },
+    {
+      "panel": "celltype",
+      "display_label": "Unlabelled",
+      "members": "Unlabelled",
+      "n_cells": 237429,
+      "denominator_cells": 33141380,
+      "percentage": 0.7164125332137647,
+      "color": "#E2E2E2"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "raw_metadata_read": false,
+  "new_statistical_analysis": false
+}

paper-releases/pbisc-diffusion/updates/20261015T100456Z-figure1-diffusion-readable-corpus/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/source_hashes.json

@@ -0,0 +1,53 @@
+{
+  "sources": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/verified_data.json",
+      "host": "server_1",
+      "sha256": "bda56b4c2a3670a0be4be56bd3f79e74269c05e22296004b033f6cdcf96fc925",
+      "bytes": 2704,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_condition_counts.csv",
+      "host": "server_1",
+      "sha256": "0acef1318304a5075de225d57533a555be677cb65c76dd45215d0293c1c52447",
+      "bytes": 840,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/training_celltype_counts.csv",
+      "host": "server_1",
+      "sha256": "12f68e88b01350071bc16eb89627cdf829f0652c6e52c19d61aad9a2448a3fce",
+      "bytes": 538,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/result.json",
+      "host": "server_1",
+      "sha256": "44a6a52adbf52f77a971e407209e9946bc19684450b06cb970953f667ba79f20",
+      "bytes": 440958,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/source_hashes.json",
+      "host": "server_1",
+      "sha256": "b6e37c602ed324b2a26c17b2ba90be269b9a60ba81bc49d219b873ca2fea7a6e",
+      "bytes": 424246,
+      "role": "verified previous training-corpus source"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/figure1_corpus_main_20261015.py",
+      "host": "server_1",
+      "sha256": "8d6259544c255421ed8f45409331cb490f10b04f05aa883afd2b384de4278cd2",
+      "bytes": 10942,
+      "role": "CPU-only main-panel renderer"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/display_aggregations.csv",
+      "host": "server_1",
+      "sha256": "dc96d88d64b4390452d7417a8e8eb333a32457875a9b185dd6ce32701ac024bd",
+      "bytes": 1290,
+      "role": "explicit main-panel category aggregation"
+    }
+  ]
+}