Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261006T121425Z-fig1-architecture-plus-corpus/diffusion/dataset/server_1/manuscript/source_data/corpus/README.md

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+# Pretraining corpus tables (Figure 1 corpus panels)
+
+Built 2026-10-06 by `scripts/corpus/build_corpus_tables.py` (CPU only). `scripts/corpus/build_figure1_corpus.py`
+draws two figures from these files only: `figures/fig01_corpus.*`, the 38 mm strip that is Fig. 1c under the
+architecture (both authored at 180 mm; `sections/overview_figure.tex` places them at 1.05\textwidth), and
+`figures/figS_corpus.*`, the detailed version for the Supplementary (overview, the 22 datasets, L1/L2 cell types,
+per-cell record; not yet placed in `supplementary.tex`).
+
+| File | Content |
+|---|---|
+| `corpus_summary.json` | totals and checks: 41,395,184 cells (41,270,779 base + 124,405 overlay), 22 datasets, 6,507 samples, split, condition, assay, cell-type totals, split-leakage check |
+| `corpus_datasets.csv` | one row per dataset: cells, samples, donors, assay, cells per split, cells per condition |
+| `corpus_samples.csv` | one row per registered sample (hashed `sample_key` only): platform, assay, split, majority condition |
+| `corpus_cellgroups.csv` | cells per sample x condition x handling (cell-level condition) |
+| `corpus_celltypes.csv` | cells per dataset x L1 x L2 (source labels mapped to the shared hierarchy) |
+| `corpus_assay_condition.csv` | cells per assay x condition |
+| `dataset_info.csv` | hand-written display names, accessions, enrichment and metadata notes |
+| `geo/` | GEO series matrices used to complete metadata missing from the source obs |
+
+Rules (all in the script): CMV-seropositive healthy donors (recorded as "cytomegalovirus infection") and
+post-vaccination draws count as Healthy. GSE274680 groups come from the GEO sample-title suffix (CON1/CON2
+control, ARI/LONG ACPA+ at risk, ERA early RA) and its donors from the GEO subject id. GSE132802 has one DRESS
+patient and one healthy volunteer. Parse 10M donors are healthy per the vendor description. In vitro = Parse
+cytokine panel (incl. PBS), GSE314010 (IL-36 or PBS, 7 h) and the GSE132802 cultured samples. Cell types are the
+block's harmonized source labels for base cells; overlay cells have no label ("Unlabelled").
+
+Split check: every sample sits in exactly one split (no sample-level overlap). At donor level,
+27 of 3,199 donors have samples in more than one split: 26 GSE274680 subjects, whose corpus donor key is the per-visit
+sample id (the GEO subject id is the person), and the GSE132802 patient, whose samples are separate time points and
+cultures. 38 val/test samples (659,112 cells; val 331,377, test 327,735) come from a person who also has
+training samples. Other datasets' donor ids were checked against the source person ids (e.g. Sound Life: 868 samples,
+96 people) and match.
+
+## Fig. 1c caption (as in `sections/overview_figure.tex`)
+
+**c**, Pretraining corpus: share of cells by assay (Other: Seq-Well and 10x of unreported chemistry), condition
+shares within each assay by disease family (Healthy includes CMV-seropositive donors, post-vaccination draws and
+cultured healthy-donor cells) and cell-type shares from each dataset's labels. The model never receives condition or
+cell-type labels.

paper-releases/pbisc-diffusion/updates/20261006T121425Z-fig1-architecture-plus-corpus/diffusion/dataset/server_1/manuscript/source_data/corpus/corpus_datasets.csv

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+dataset_prefix,short_name,accession,enrichment,dataset_id,platform,assay,n_cells,n_samples,n_donors,train_cells,val_cells,test_cells,in_vitro_cells,conditions
+065_A,Sound Life,GSE271896,PBMC,065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immune_profiling,10x,10x 3' v3,13789548,868,96,11138182,1445231,1206135,0,Healthy 13789548
+304_A,Parse 10M cytokines,Parse Biosciences,PBMC,304_A_Parse_10M_PBMC_12donor_90cytokines,Parse,Parse,9697974,1092,12,7711697,1054708,931569,9697974,Healthy 9697974
+061_A,RA at-risk cohort,GSE274680,PBMC,061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progression_PBMC_multi-omic_cohort,10x,10x 3' (hashed),4117384,239,120,3253619,438733,425032,0,Healthy 2113388; ACPA+ at risk of RA 1792129; RA 211867
+200_A,Immunobiology of Aging,GSE275067,PBMC,200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling,10x,10x Flex,3758514,234,234,3014412,402041,342061,0,Healthy 3758514
+009_A,Human Immune Health Atlas,AIFI HIHA,PBMC,009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AIFI_immune_dynamics_across_healthy_age,10x,10x 3' v3,1821725,108,108,1443923,191363,186439,0,Healthy 1821725
+006_A,AIDA,CELLxGENE ced320a1,PBMC,006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asian_Immune_Diversity_Atlas,10x,10x 5' v2,1265624,625,625,991970,138032,135622,0,Healthy 1265624
+001_A,Perez SLE,CELLxGENE 436154da,PBMC,001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et_al._lupus_PBMC_cell-type-specific_molecular_genetic_associations_to_lup,10x,10x 3' v2,1263676,1391,261,996252,131345,136079,0,SLE 777258; Healthy 486418
+005_A,OneK1K,CELLxGENE dde06e0f,PBMC,005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Yazar_et_al._single-cell_eQTL_mapping,10x,10x 3' v2,1248980,981,981,995251,127741,125988,0,Healthy 1248980
+204_B,Circulating HSPC (aging/MDS),CELLxGENE,HSPC-enriched,204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoietic_stem_and_progenitor_cells_in_aging_cytopenia_and,10x,10x 3' v3,1011884,239,206,808473,82481,120930,0,Healthy 605236; MDS 176233; MDS/MPN 130268; Cytopenia 100147
+074_A,COMBAT,CELLxGENE COMBAT,PBMC,074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collection,10x,10x 5' v1,836148,140,124,657262,92959,85927,0,COVID-19 724710; Healthy 92205; Influenza 19233
+010_A,ScaleBio PBMC,CELLxGENE 4a9fd4d7,PBMC,010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio_single-cell_RNA_sequencing_of_human_PBMCs,ScaleBio,ScaleBio,685024,1,1,685024,0,0,0,Healthy 685024
+203_B,Indonesia diversity,CELLxGENE 665714af,PBMC,203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversity_shape_the_immune_landscape_in_Indonesia,10x,10x 5' v2,462034,199,199,363636,47577,50821,0,Healthy 462034
+093_C,SARS-CoV-2 local and systemic,CELLxGENE,PBMC,093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_and_systemic_SARS-CoV-2_response_CELLxGENE,10x,10x 5' v1,422220,80,75,336885,48503,36832,0,Healthy 173684; COVID-19 151312; Post-COVID-19 97224
+202_B,COVID-19 time course,GSE161918,PBMC,202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_Late_Juncture_Linked_to_Fatal_COVID-1,10x,10x 5' v1,372081,92,46,281960,60564,29557,0,COVID-19 277957; Healthy 94124
+053_B,CITE-seq PBMC,CELLxGENE b0cf0afa,PBMC,053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrated_analysis_of_multimodal_single-cell_data_CITE-seq_PBMC,10x,10x 3' v3,161764,24,8,114082,25871,21811,0,Healthy 161764
+007_A,Miao RA,CELLxGENE e1a9ca56,PBMC,007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_al._RA_PBMC_disease_activity-associated_PBMC_subsets,10x,10x 3' v3,108717,36,36,85902,12841,9974,0,Healthy 60080; RA 48637
+071_C,JDM CITE-seq,CELLxGENE,PBMC,071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGENE,10x,10x 3' v3,105827,106,20,81787,15216,8824,0,JDM 82666; Healthy 23161
+058_B,COVID-19 immunodeficiency,CELLxGENE eb735cc9,PBMC,058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PBMC_nasal_swab_donors_with_immunodeficiencies_and_autoimmune_conditions,10x,10x 5' v1,97499,22,22,75412,11634,10453,0,COVID-19 97499
+302_A,IL-36 stimulation,GSE314010,PBMC,302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq,10x,10x (version n.r.),64752,5,5,37807,14473,12472,64752,Healthy 64752
+081_B,SARS-CoV-2 Seq-Well,CELLxGENE,PBMC,081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-cell_atlas_of_peripheral_immune_response_to_SARS-CoV-2,Seq-Well,Seq-Well,44721,13,13,33040,6545,5136,0,COVID-19 28094; Healthy 16627
+300b_A,DRESS,GSE132802,PBMC,300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq,10x,10x v2 (3'/5'),34051,7,2,19816,7660,6575,11037,DRESS 25272; Healthy 8779
+301_A,SLE B cells,GSE163121,B-cell enriched,301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq,10x,10x 3' v2,25037,5,5,14988,5514,4535,0,SLE 15402; Healthy 9635

paper-releases/pbisc-diffusion/updates/20261006T121425Z-fig1-architecture-plus-corpus/diffusion/dataset/server_1/manuscript/source_data/corpus/corpus_summary.json

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+{
+ "cells": 41395184,
+ "base_cells": 41270779,
+ "overlay_cells": 124405,
+ "datasets": 22,
+ "samples": 6507,
+ "donors": 3199,
+ "split_cells": {
+  "test": 3892772,
+  "train": 33141380,
+  "val": 4361032
+ },
+ "split_samples": {
+  "train": 5232,
+  "val": 648,
+  "test": 627
+ },
+ "condition_cells": {
+  "ACPA+ at risk of RA": 1792129,
+  "COVID-19": 1279572,
+  "Cytopenia": 100147,
+  "DRESS": 25272,
+  "Healthy": 36639276,
+  "Influenza": 19233,
+  "JDM": 82666,
+  "MDS": 176233,
+  "MDS/MPN": 130268,
+  "Post-COVID-19": 97224,
+  "RA": 260504,
+  "SLE": 792660
+ },
+ "family_cells": {
+  "Autoimmune": 2927959,
+  "Drug reaction": 25272,
+  "Haematological": 406648,
+  "Healthy": 36639276,
+  "Infection": 1396029
+ },
+ "handling_cells": {
+  "ex vivo": 31621421,
+  "in vitro": 9773763
+ },
+ "cmv_seropositive_healthy_cells": 9215690,
+ "assay_cells": {
+  "10x (version n.r.)": 64752,
+  "10x 3' (hashed)": 4117384,
+  "10x 3' v2": 2537693,
+  "10x 3' v3": 16999465,
+  "10x 5' v1": 1727948,
+  "10x 5' v2": 1727658,
+  "10x Flex": 3758514,
+  "10x v2 (3'/5')": 34051,
+  "Parse": 9697974,
+  "ScaleBio": 685024,
+  "Seq-Well": 44721
+ },
+ "platform_cells": {
+  "10x": 30967465,
+  "Parse": 9697974,
+  "ScaleBio": 685024,
+  "Seq-Well": 44721
+ },
+ "celltype_l1_cells": {
+  "B cell": 3744614,
+  "DC": 472529,
+  "Erythrocyte": 27504,
+  "Granulocyte": 1331,
+  "ILC": 19329,
+  "Mast cell": 65,
+  "Monocyte": 7373579,
+  "NK cell": 3369999,
+  "NKT cell": 2494,
+  "Neutrophil": 600,
+  "No label (overlay)": 124405,
+  "Platelet": 121626,
+  "Progenitor cell": 1206741,
+  "T cell": 24772208,
+  "__unknown__": 158160
+ },
+ "corpus_vs_block_donor_id_mismatch_rows": 0,
+ "samples_in_more_than_one_split": 0,
+ "donors_in_more_than_one_split": 27,
+ "cells_of_those_donors": 1743549,
+ "val_test_cells_whose_donor_has_train_samples": {
+  "test": 327735,
+  "val": 331377
+ },
+ "val_test_samples_whose_donor_has_train_samples": 38,
+ "donors_in_more_than_one_split_by_dataset": {
+  "061_A_": 26,
+  "300b_A": 1
+ },
+ "conditions_order": [
+  "Healthy",
+  "SLE",
+  "RA",
+  "ACPA+ at risk of RA",
+  "JDM",
+  "COVID-19",
+  "Post-COVID-19",
+  "Influenza",
+  "MDS",
+  "MDS/MPN",
+  "Cytopenia",
+  "DRESS"
+ ],
+ "condition_family": {
+  "Healthy": "Healthy",
+  "SLE": "Autoimmune",
+  "RA": "Autoimmune",
+  "ACPA+ at risk of RA": "Autoimmune",
+  "JDM": "Autoimmune",
+  "COVID-19": "Infection",
+  "Post-COVID-19": "Infection",
+  "Influenza": "Infection",
+  "MDS": "Haematological",
+  "MDS/MPN": "Haematological",
+  "Cytopenia": "Haematological",
+  "DRESS": "Drug reaction"
+ },
+ "inputs": {
+  "corpus_obs": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source/metadata/obs_sc.parquet",
+  "block_obs": "/home/sj_server_1/PBISC/PBISC-data/single-cell-data-block-blood/metadata/obs_sc.parquet",
+  "sample_index": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/metadata/sample_index.parquet",
+  "source_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source/dataset_manifest.json",
+  "geo": [
+   "GSE132802_series_matrix.txt.gz",
+   "GSE163121_series_matrix.txt.gz",
+   "GSE274680_series_matrix.txt.gz",
+   "GSE314010_series_matrix.txt.gz"
+  ]
+ },
+ "script": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/scripts/corpus/build_corpus_tables.py"
+}

paper-releases/pbisc-diffusion/updates/20261006T121425Z-fig1-architecture-plus-corpus/diffusion/metadata/request.json

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+{
+  "assets": [
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.pdf",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.png",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "config",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.provenance.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_corpus.svg",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.pdf",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.png",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "config",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.provenance.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "figure",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/figS_corpus.svg",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/main.pdf",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/scripts/corpus/build_corpus_tables.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/scripts/corpus/build_figure1_corpus.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "document",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/overview_figure.tex",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "document",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/README.md",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_assay_condition.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_cellgroups.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_celltypes.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_datasets.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_samples.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "config",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_summary.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/dataset_info.csv",
+      "state": "completed"
+    }
+  ],
+  "inference_locations": [],
+  "project_id": "pbisc-diffusion",
+  "summary": "Figure 1 now holds the architecture (a, b) and a compact pretraining-corpus strip (c: assay shares, disease-family shares per assay, L1 cell-type shares) at one scale (1.05 textwidth) on one float page; caption a-b condensed without dropping content claims. The detailed corpus figure moved to figures/figS_corpus.* (Supplementary candidate, not yet placed). Corpus tables corrected: GSE274680 person ids are under 'subject id' or 'subject' in GEO, so donors are 3,199 (RA at-risk 120); no sample is in more than one split; 27 donors (26 GSE274680 subjects + the GSE132802 patient) have samples in more than one split, giving 38 val/test samples (659,112 cells) whose person also has training samples. main.pdf rebuilt with tectonic (line breaks differ slightly from the earlier pdfLaTeX build)."
+}