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/corpus/condition_counts.csv

@@ -0,0 +1,13 @@
+condition,n_cells,corpus_fraction,detail_fraction,overview_group,interpretation,color
+Healthy,36639276,0.8851096301444149,,Healthy,healthy donor status; stimulation/vaccination/CMV context retained,#A9B8CC
+SLE,792660,0.019148604340060427,0.166668488961519,Disease / at-risk,source disease/history annotation,#7A4F6E
+RA,260504,0.006293099216565869,0.054774819025094686,Disease / at-risk,source disease/history annotation,#B5655E
+ACPA+ at risk of RA,1792129,0.04329317632698528,0.37682162901384975,Disease / at-risk,"at risk, not confirmed RA",#DDA59B
+JDM,82666,0.001996995592530764,0.017381749184382875,Disease / at-risk,source disease/history annotation,#A58BB0
+COVID-19,1279572,0.03091113207758661,0.26904893870949564,Disease / at-risk,source disease/history annotation,#D08C3C
+Post-COVID-19,97224,0.002348679015413967,0.020442784006755386,Disease / at-risk,source disease/history annotation,#E8C68E
+Influenza,19233,0.0004646192658546946,0.004044022718690101,Disease / at-risk,source disease/history annotation,#9C6B2A
+MDS,176233,0.004257330997731523,0.03705559485170865,Disease / at-risk,source disease/history annotation,#3F7A73
+MDS/MPN,130268,0.003146936126675992,0.02739077374919784,Disease / at-risk,source disease/history annotation,#6FA39B
+Cytopenia,100147,0.002419291094345661,0.02105738798984337,Disease / at-risk,source disease/history annotation,#A9D0C8
+DRESS,25272,0.000610505801834339,0.005313811789462706,Disease / at-risk,source disease/history annotation,#5F5F5F

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/hashes.json

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+      "host": "server_1",
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+      "role": "registered source corpus, split unit, K and platform recipe quotas"
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+    {
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+      "host": "server_1",
+      "sha256": "461b46107f75984000747877a11823ec15042b5c2104b4b979729dcee10ee30f",
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+      "role": "final Model8 all-cell training coverage and emitted targets"
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+    {
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+      "host": "server_1",
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+      "bytes": 4772,
+      "role": "registered recipe unique coverage and sampling semantics"
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+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data_e2.py",
+      "host": "server_1",
+      "sha256": "6f6db69002ae01857a0f1882b2e6e98552f3ee00aa1116e4fd4a308cbf761b71",
+      "bytes": 58198,
+      "role": "K distinct cells sampled within a sample; count-sum pseudobulk"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/ladder_experiment.py",
+      "host": "server_1",
+      "sha256": "872bf059e14f0042eec64d290cb84685dafd9705ae364125462d1d8e06e14314",
+      "bytes": 51067,
+      "role": "all-K plus top-up training contract implementation"
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+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/full_recipe_allcells_6k_broad_20260909/topup_v1/topup_recipes.csv",
+      "host": "server_1",
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+      "bytes": 966455,
+      "role": "saved explicit top-up recipe sizes and split"
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+    {
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+      "bytes": 2058,
+      "role": "method palette; biological category colors exempt"
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+      "bytes": 27130,
+      "role": "reproducible metadata-only figure builder"
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+  "outputs": [
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+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/condition_counts.csv",
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+      "sha256": "0bf08bf81801ad46c6a96f5422230cc6666dfc002358f39be9470a2a6d307c49"
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+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/celltype_counts.csv",
+      "sha256": "10e38e1925b5e135e3ab4a6be55fa2fb8aaa7742d43ca96eee48fabb6d9344e1"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/split_counts.csv",
+      "sha256": "7d71e0ea0887ede72f28d2ceb60f22c30bfafd210ce5a751fc84ae29477c2fb8"
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+      "sha256": "6671e2d445ee28caf664a4edff9bb67c095efbeb393d091b389d1ee2b007e47e"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/strengthening_20261013/corpus/healthy_disease_overview.png",
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+      "sha256": "fd2a32268ba906e3231cc03237600c77a4cb2e656b010b6ba19130941216413e"
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+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/strengthening_20261013/corpus/healthy_disease_overview.svg",
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+    {
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+      "sha256": "2a35f5fbd061e6d0a11dc5c29e861e2d5b1c2da6ad5cd80ff22ce9a3e760b02d"
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+    {
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+      "sha256": "ff67b348d3229cb4ea4733bd36eea6619e81e7bc7f46c3100dec592461c5dd6d"
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+  ]
+}

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/recipe_counts.csv

@@ -0,0 +1,7 @@
+recipe_kind,K,recipes_per_part,target_occurrences_per_part,parts,source
+registered,250,745,186250,16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/dataset_manifest.json
+registered,500,1489,744500,16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/dataset_manifest.json
+registered,1000,2234,2234000,16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/dataset_manifest.json
+registered,2000,2979,5958000,16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/dataset_manifest.json
+registered,4000,745,2980000,16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/dataset_manifest.json
+coverage top-up,"1–4000, actual tail size",196–283,124158–127329,16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/ALLCELL_DATA_CONTRACT.json

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/result.json

@@ -0,0 +1,1346 @@
+{
+  "schema": "pbisc.strengthening.corpus.v1",
+  "panels": [
+    {
+      "key": "corpus_conditions",
+      "kind": "content",
+      "title": "Corpus composition: health, disease risk and cell types",
+      "subtitle": "Two-level condition view with the existing cell-type statistics",
+      "figure": "figures/strengthening_20261013/corpus/healthy_disease_overview.png",
+      "figures": [
+        "figures/strengthening_20261013/corpus/healthy_disease_overview.png"
+      ],
+      "section": "Figure 1",
+      "section_label": "Figure 1 support",
+      "keywords": [],
+      "footnote": "Source-cell shares. Disease / at-risk includes ACPA+ at-risk, not confirmed RA. Healthy includes stimulation, vaccination and CMV contexts.",
+      "note": "Saved corpus metadata and final f01_6k_1x_seed20260627 E16 training contract; no raw expression arrays or new model runs. Biological condition/split colors retain their existing meanings, independent of the method palette. Left denominator41,395,184; Healthy36,639,276(88.51%); disease/at-risk4,755,908(11.49%). Detail contains11 source conditions, including ACPA+ at-risk1,792,129; disease/history subtotal excluding at-risk2,963,779. Post-COVID remains a history/post-infection label and Cytopenia is retained verbatim, not called a confirmed malignancy. Counts derive from cell-level groups, not per-sample majority condition. Healthy includes9,762,726 in-vitro cells: Parse9,697,974 (90 cytokines or PBS) and IL-36/PBS healthy-donor cells64,752. CMV-seropositive healthy cells9,215,690; post-vaccination source draws remain Healthy. These are donor/handling context, not inferred active disease. Right donut preserves original harmonized L1 source cell-type counts and colors: NKT/Granulocyte/Neutrophil/Mast\u2192Other, unknown/overlay labels\u2192Unlabelled, matching the source figure merge rules. Total source-cell denominator is checked again. The model receives no disease/cell-type labels in this final base run.",
+      "footnote_full": "Saved corpus metadata and final f01_6k_1x_seed20260627 E16 training contract; no raw expression arrays or new model runs. Biological condition/split colors retain their existing meanings, independent of the method palette. Left denominator41,395,184; Healthy36,639,276(88.51%); disease/at-risk4,755,908(11.49%). Detail contains11 source conditions, including ACPA+ at-risk1,792,129; disease/history subtotal excluding at-risk2,963,779. Post-COVID remains a history/post-infection label and Cytopenia is retained verbatim, not called a confirmed malignancy. Counts derive from cell-level groups, not per-sample majority condition. Healthy includes9,762,726 in-vitro cells: Parse9,697,974 (90 cytokines or PBS) and IL-36/PBS healthy-donor cells64,752. CMV-seropositive healthy cells9,215,690; post-vaccination source draws remain Healthy. These are donor/handling context, not inferred active disease. Right donut preserves original harmonized L1 source cell-type counts and colors: NKT/Granulocyte/Neutrophil/Mast\u2192Other, unknown/overlay labels\u2192Unlabelled, matching the source figure merge rules. Total source-cell denominator is checked again. The model receives no disease/cell-type labels in this final base run.",
+      "palette": "biological",
+      "source_refs": [
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_summary.json",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_cellgroups.csv",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_datasets.csv",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_samples.csv",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_assay_condition.csv",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_celltypes.csv",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/README.md",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/dataset_info.csv",
+        "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/scripts/corpus/build_corpus_tables.py",
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+      "kind": "content",
+      "title": "Recipe K and training exposure are different counts",
+      "subtitle": "All training cells are covered after explicit top-up recipes",
+      "figure": "figures/strengthening_20261013/corpus/recipe_coverage_and_exposure.png",
+      "figures": [
+        "figures/strengthening_20261013/corpus/recipe_coverage_and_exposure.png"
+      ],
+      "section": "Figure 1",
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+      "footnote": "Saved all-cell audit: 33,141,380 unique training cells covered. K defines recipe membership; 195,639,930 target occurrences include reuse.",
+      "note": "Saved corpus metadata and final f01_6k_1x_seed20260627 E16 training contract; no raw expression arrays or new model runs. Biological condition/split colors retain their existing meanings, independent of the method palette. Registered K250/500/1000/2000/4000 has recipe quotas745/1489/2234/2979/745 per part (weights1/2/3/4/1);8192recipes/part\u00d716parts=131072. All K members are targets because cells_per_block4000 is at least maxK. Registered recipes alone cover31,145,450 unique train cells (93.9775%); top-up3658recipes adds1,995,930 previously unseen train cells once, totaling33,141,380(100%). Top-upK1\u20134000 preserves small tails without padding; total134730recipes. Total195,639,930target occurrences across16parts include repeated source cells and do not imply195Munique cells. Platform quotas10x4691,Parse2625,ScaleBio698,Seq-Well178 per part derive from square-root source-cell counts, not natural corpus prevalence. Disease-specific exposure proportions are not available in these figures. K is distinct from N_gen, the number of cells sampled at inference.",
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+      "key": "corpus_conditions",
+      "kind": "content",
+      "title": "Corpus composition: health, disease risk and cell types",
+      "subtitle": "Two-level condition view with the existing cell-type statistics",
+      "figure": "figures/strengthening_20261013/corpus/healthy_disease_overview.png",
+      "figures": [
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+      "section": "Figure 1",
+      "section_label": "Figure 1 support",
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+      "footnote": "Source-cell shares. Disease / at-risk includes ACPA+ at-risk, not confirmed RA. Healthy includes stimulation, vaccination and CMV contexts.",
+      "note": "Saved corpus metadata and final f01_6k_1x_seed20260627 E16 training contract; no raw expression arrays or new model runs. Biological condition/split colors retain their existing meanings, independent of the method palette. Left denominator41,395,184; Healthy36,639,276(88.51%); disease/at-risk4,755,908(11.49%). Detail contains11 source conditions, including ACPA+ at-risk1,792,129; disease/history subtotal excluding at-risk2,963,779. Post-COVID remains a history/post-infection label and Cytopenia is retained verbatim, not called a confirmed malignancy. Counts derive from cell-level groups, not per-sample majority condition. Healthy includes9,762,726 in-vitro cells: Parse9,697,974 (90 cytokines or PBS) and IL-36/PBS healthy-donor cells64,752. CMV-seropositive healthy cells9,215,690; post-vaccination source draws remain Healthy. These are donor/handling context, not inferred active disease. Right donut preserves original harmonized L1 source cell-type counts and colors: NKT/Granulocyte/Neutrophil/Mast\u2192Other, unknown/overlay labels\u2192Unlabelled, matching the source figure merge rules. Total source-cell denominator is checked again. The model receives no disease/cell-type labels in this final base run.",
+      "footnote_full": "Saved corpus metadata and final f01_6k_1x_seed20260627 E16 training contract; no raw expression arrays or new model runs. Biological condition/split colors retain their existing meanings, independent of the method palette. Left denominator41,395,184; Healthy36,639,276(88.51%); disease/at-risk4,755,908(11.49%). Detail contains11 source conditions, including ACPA+ at-risk1,792,129; disease/history subtotal excluding at-risk2,963,779. Post-COVID remains a history/post-infection label and Cytopenia is retained verbatim, not called a confirmed malignancy. Counts derive from cell-level groups, not per-sample majority condition. Healthy includes9,762,726 in-vitro cells: Parse9,697,974 (90 cytokines or PBS) and IL-36/PBS healthy-donor cells64,752. CMV-seropositive healthy cells9,215,690; post-vaccination source draws remain Healthy. These are donor/handling context, not inferred active disease. Right donut preserves original harmonized L1 source cell-type counts and colors: NKT/Granulocyte/Neutrophil/Mast\u2192Other, unknown/overlay labels\u2192Unlabelled, matching the source figure merge rules. Total source-cell denominator is checked again. The model receives no disease/cell-type labels in this final base run.",
+      "palette": "biological",
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+      "title": "Recipe K and training exposure are different counts",
+      "subtitle": "All training cells are covered after explicit top-up recipes",
+      "figure": "figures/strengthening_20261013/corpus/recipe_coverage_and_exposure.png",
+      "figures": [
+        "figures/strengthening_20261013/corpus/recipe_coverage_and_exposure.png"
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+      "note": "Saved corpus metadata and final f01_6k_1x_seed20260627 E16 training contract; no raw expression arrays or new model runs. Biological condition/split colors retain their existing meanings, independent of the method palette. Registered K250/500/1000/2000/4000 has recipe quotas745/1489/2234/2979/745 per part (weights1/2/3/4/1);8192recipes/part\u00d716parts=131072. All K members are targets because cells_per_block4000 is at least maxK. Registered recipes alone cover31,145,450 unique train cells (93.9775%); top-up3658recipes adds1,995,930 previously unseen train cells once, totaling33,141,380(100%). Top-upK1\u20134000 preserves small tails without padding; total134730recipes. Total195,639,930target occurrences across16parts include repeated source cells and do not imply195Munique cells. Platform quotas10x4691,Parse2625,ScaleBio698,Seq-Well178 per part derive from square-root source-cell counts, not natural corpus prevalence. Disease-specific exposure proportions are not available in these figures. K is distinct from N_gen, the number of cells sampled at inference.",
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+  "verified_data": {
+    "source_total": 41395184,
+    "healthy": 36639276,
+    "disease_or_at_risk": 4755908,
+    "at_risk": 1792129,
+    "disease_history_without_at_risk": 2963779,
+    "condition_cells": {
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+      "Healthy": 36639276,
+      "RA": 260504,
+      "COVID-19": 1279572,
+      "ACPA+ at risk of RA": 1792129,
+      "JDM": 82666,
+      "Influenza": 19233,
+      "Post-COVID-19": 97224,
+      "MDS/MPN": 130268,
+      "Cytopenia": 100147,
+      "MDS": 176233,
+      "DRESS": 25272
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+      "val": 648,
+      "test": 627
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+    "celltype_display_counts": {
+      "B cell": 3744614,
+      "DC": 472529,
+      "Monocyte": 7373579,
+      "NK cell": 3369999,
+      "Unlabelled": 282565,
+      "Progenitor cell": 1206741,
+      "T cell": 24772208,
+      "Erythrocyte": 27504,
+      "ILC": 19329,
+      "Platelet": 121626,
+      "Other": 4490
+    },
+    "healthy_in_vitro": 9762726,
+    "healthy_cmv_seropositive": 9215690,
+    "k_values": [
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+      500,
+      1000,
+      2000,
+      4000
+    ],
+    "recipe_quotas": {
+      "1000": 2234,
+      "2000": 2979,
+      "250": 745,
+      "4000": 745,
+      "500": 1489
+    },
+    "original_unique_train_covered": 31145450,
+    "unique_topup_cells": 1995930,
+    "final_unique_train_covered": 33141380,
+    "target_occurrences": 195639930,
+    "final_run_corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
+    "checks": {
+      "cellgroup_dataset_assay_totals_equal": true,
+      "split_crosschecks_equal": true,
+      "sample_keys_unique": true,
+      "condition_counts_match_source_summary": true,
+      "topup_k_sum_matches_coverage": true,
+      "expected_observed_targets_equal": true,
+      "final_training_coverage_100pct": true,
+      "nontrain_targets_zero": true
+    },
+    "limitations": [
+      "Disease / at-risk is not synonymous with confirmed active disease. ACPA+ risk, Post-COVID history and Cytopenia remain explicit.",
+      "Donor and source-cell proportions are different. Disease/cell-type annotations are descriptive only and were not supplied to the final base model.",
+      "Source-cell composition is not the distribution of training-target occurrences. No disease-exposure frequencies are inferred.",
+      "Dataset-donor split keys did not ensure strict biological-donor separation for27 internal donors. External target overlap requires separate linkage.",
+      "The source validation/test totals do not equal cells used by fixed validation/test recipes. These figures make no performance/generalization claim.",
+      "All-cell coverage is a verified saved contract, not a fresh audit of raw cell-ID arrays. Existing cell-type corpus panels are untouched."
+    ]
+  },
+  "recommendations": [
+    "Keep the two-level disease / at-risk design on one slide.",
+    "Keep original cell-type statistics elsewhere.",
+    "Do not claim donor-disjoint evaluation from sample-level split separation."
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "raw_expression_payload_read": false
+}