{
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  "status": "completed",
  "checkpoint": "ctx2048 E12 EMA",
  "contrast": "SLE minus HC; observational donor cohorts, not IFNa stimulation",
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  "cohort_SLE": 30,
  "cohort_HC": 12,
  "model_genes": 6000,
  "tested_genes": 2980,
  "fixed_global_BH_family": 17880,
  "label_order": [
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    "B cell",
    "Monocyte",
    "NK cell",
    "DC",
    "Other"
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  "eligible_HC": [
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  "cell_minimum": 20,
  "arm_minimum": 5,
  "eligibility": "Endpoint >=20 cells in both generated and real donor/type; matched donors fixed across all frames.",
  "labels": "Existing frozen AIFI scANVI endpoint annotations, validated to baseline NPZ row IDs; held fixed throughout.",
  "expression": "Continuous expm1(hard-gated clean log1p), summed per donor/type; no rounding or Poissonization for tests.",
  "effect": "log2[(mean donor CPM_SLE+1)/(mean donor CPM_HC+1)]",
  "test": "Welch unequal-variance t-test on donor log2(1+CPM)",
  "multiple_testing": "BH across all 6 types x 2,980 genes every frame; undefined/non-estimable p=1 with an explicit estimable flag. Within-type q also exported.",
  "statistics_files": [
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  "endpoint_primary": true,
  "earlier_frames": "Exploratory dependent visualizations; no across-time discovery claim.",
  "bootstrap": {
    "repeats": 1000,
    "interval": "Percentile95%",
    "unit": "donor",
    "resampling": "Within disease arm and adult/pediatric stratum; shared resamples for real/generated",
    "selection": "All measured IFNa Hallmark members, not selected by effect or p"
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    "null": "Disease labels permuted within adult/pediatric strata with preserved class counts; same permutations for real/generated",
    "statistic": "Absolute log2 CPM mean ratio",
    "correction": "Diagnostic empirical p with +1 correction; no discovery claim"
  },
  "clinical_confounding": "Welch tests remain unadjusted as in the benchmark; pediatric/adult composition and other clinical covariates preclude causal interpretation.",
  "hallmark": {
    "name": "HALLMARK_INTERFERON_ALPHA_RESPONSE",
    "source": "https://www.gsea-msigdb.org/gsea/msigdb/human/download_geneset.jsp?fileType=json&geneSetName=HALLMARK_INTERFERON_ALPHA_RESPONSE",
    "systematic_name": "M5911",
    "total_members": 97,
    "measured_members": 61,
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    "aliases_sha256": "94313e8a8a175d8b8e35d981d36f6ca0a06ca39b864a6585cf648b59aca02e90",
    "unmatched_symbols": [
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      "B2M",
      "BATF2",
      "BST2",
      "C1S",
      "CASP1",
      "CASP8",
      "CCRL2",
      "CD47",
      "CNP",
      "DHX58",
      "ELF1",
      "HLA-C",
      "IRF1",
      "IRF2",
      "IRF9",
      "LGALS3BP",
      "LY6E",
      "MVB12A",
      "NCOA7",
      "NMI",
      "NUB1",
      "OGFR",
      "PROCR",
      "PSMA3",
      "PSMB8",
      "PSMB9",
      "PSME1",
      "PSME2",
      "RTP4",
      "SLC25A28",
      "TAP1",
      "TRIM21",
      "TRIM26",
      "TXNIP",
      "UBE2L6"
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    "mapping": "Official source or current symbols only; ambiguous symbol-to-multiple-Ensembl mapping fails; actual and canonical symbols exported; no absent-gene zero-fill.",
    "attribution": "MSigDB / Broad Institute, MIT, Regents of the University of California; CC BY 4.0; Liberzon et al., PMID26771021"
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  "provenance": {
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    "checkpoint_sha256": "f634f0ef06d06cd547e7c53cef58942520f3d998b8d99eba4798ca53fb09f315"
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  "warnings": [
    "Generated-donor uncertainty conditions on one fixed sampling seed, checkpoint and endpoint annotation.",
    "These fixed-family tests and true fold changes differ from the legacy variable-family, mean-log-expression DEG benchmark."
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    "duration_seconds": 30.0,
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    "interpolation": "none",
    "full_decode_verified": true,
    "width": 1800,
    "height": 1000
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  "rendering": {
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    "point_unit": "gene",
    "test_replicate_unit": "donor",
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    "coordinate_validation": "All generated cached effects/q checked exactly against hash-verified CSV; all real endpoint effects/q loaded unchanged from CSV.",
    "validated_statistics_rows": 929760,
    "statistics_recomputed": false,
    "fixed_axes": "Original axis_limits and comparison_axis_limits preserved exactly.",
    "point_count": "All 2,980 gene entries drawn in each eligible panel; unsupported panels remain empty. Overlapping coordinates can conceal entries.",
    "color_rule": "Direction of estimable log2 fold change, not significance or membership of individual cells/donors in cohorts.",
    "color_legend": {
      "HC higher: estimable log2FC < 0": "#2563EB",
      "SLE higher: estimable log2FC > 0": "#DC2626",
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    "ifna_style": "61 measured Hallmark genes use larger markers with dark outlines; fill still encodes direction.",
    "ground_truth_insets": {
      "label": "Ground truth",
      "position": "Upper right of each cell-type panel",
      "source": "Hash-verified source=real, frame=endpoint_reference rows from existing statistics",
      "expression_source": "Observed raw UMI counts summed per donor/cell type; existing CPM/Welch/BH results",
      "donors": "Same matched eligible observed/generated donor subset for each cell type",
      "constant_across_frames": true,
      "generated_points_occluded": false,
      "axes": "Preserved comparison_axis_limits; same numerical scales",
      "unsupported_types": "N/A; no invented points",
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