Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261012T233237Z-figure-layout-todo/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/layout_preview_20261013/PROVENANCE.json

@@ -0,0 +1,246 @@
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+  "experiments_started": false,
+  "panels": [
+    {
+      "figure": 1,
+      "panel": "a-e",
+      "title": "Complete training-to-inference concept",
+      "state": "AVAILABLE",
+      "dependency": "fig1_overview.pdf"
+    },
+    {
+      "figure": 2,
+      "panel": "a-c",
+      "title": "Architecture and gene-panel comparisons",
+      "state": "AVAILABLE",
+      "dependency": "fig2_ablation_and_support.pdf, top row"
+    },
+    {
+      "figure": 2,
+      "panel": "d-f",
+      "title": "Full fine-tuning and LoRA rank selection",
+      "state": "HISTORICAL 5-FOLD",
+      "dependency": "fig2_ablation_and_support.pdf, middle row"
+    },
+    {
+      "figure": 2,
+      "panel": "g",
+      "title": "Precision curve",
+      "state": "TODO",
+      "dependency": "Exact n = 5 / 10 / 20 / 40\nFive outer folds\n2/20 units scored\nLoRA, same-n calibration and scSemiProfiler; raw/ref-cal control lines."
+    },
+    {
+      "figure": 2,
+      "panel": "h",
+      "title": "Coverage curve",
+      "state": "TODO",
+      "dependency": "Exact n = 5 / 10 / 20 / 40\nFive outer folds\n2/20 units scored\nLoRA, same-n calibration and scSemiProfiler; raw/ref-cal control lines."
+    },
+    {
+      "figure": 2,
+      "panel": "i",
+      "title": "Composition curve",
+      "state": "TODO",
+      "dependency": "Exact n = 5 / 10 / 20 / 40\nFive outer folds\n2/20 units scored\nLoRA, same-n calibration and scSemiProfiler; raw/ref-cal control lines."
+    },
+    {
+      "figure": 3,
+      "panel": "a",
+      "title": "Common-reference UMAP",
+      "state": "TODO",
+      "dependency": "Real | PBISC-LoRA | scSemiProfiler | external ref-cal | same-pair calibration\nReal-reference coordinates only; shared cell-type colors; no forced integration."
+    },
+    {
+      "figure": 3,
+      "panel": "b",
+      "title": "Canonical marker profiles",
+      "state": "TODO",
+      "dependency": "Heatmap + dot plot\nFixed marker list, gene order and expression scale; dot size = detection fraction."
+    },
+    {
+      "figure": 3,
+      "panel": "c",
+      "title": "Cell-type composition",
+      "state": "TODO",
+      "dependency": "Observed and generated fractions\nPer-donor composition error, with the same cell-type ordering across methods."
+    },
+    {
+      "figure": 3,
+      "panel": "d",
+      "title": "Primary quality metrics",
+      "state": "TODO",
+      "dependency": "Precision | coverage | composition L1\nMatched reference, donors and output cell budget."
+    },
+    {
+      "figure": 3,
+      "panel": "e",
+      "title": "Additional realism",
+      "state": "TODO",
+      "dependency": "C2ST | MMD2 | E_N\nReal-versus-real control; no interpretation of UMAP overlap as a score."
+    },
+    {
+      "figure": 3,
+      "panel": "f",
+      "title": "Operating time and compute",
+      "state": "TODO",
+      "dependency": "Small supporting panel: adaptation time + target-generation time.\nExclude the supplied pretraining cost, GPU queue waits and evaluation time."
+    },
+    {
+      "figure": 4,
+      "panel": "a",
+      "title": "Exact-five-pair comparison",
+      "state": "TODO",
+      "dependency": "Five draws per cohort; one pair per donor.\nPearson / Spearman logFC, partial correlation and top-DEG overlap; patient-level uncertainty."
+    },
+    {
+      "figure": 4,
+      "panel": "b",
+      "title": "Existing disease five-fold contrasts",
+      "state": "HISTORICAL ESTIMATOR",
+      "dependency": "fig4_historical_5fold_separate.pdf, logFC + partial-r rows"
+    },
+    {
+      "figure": 4,
+      "panel": "c",
+      "title": "Gene-level validation",
+      "state": "TODO",
+      "dependency": "Observed-generated scatter / heatmap, CAT curves and patient-aware DEG sensitivity."
+    },
+    {
+      "figure": 4,
+      "panel": "d",
+      "title": "Matched deconvolution",
+      "state": "TODO",
+      "dependency": "BayesPrism / CIBERSORTx on the same support pairs; supported expression/composition endpoints."
+    },
+    {
+      "figure": 5,
+      "panel": "a",
+      "title": "State-frequency and detection map",
+      "state": "TODO",
+      "dependency": "All predefined state x cohort combinations; observed frequency, donor support and explicit zero detections."
+    },
+    {
+      "figure": 5,
+      "panel": "b",
+      "title": "State identity and location",
+      "state": "TODO",
+      "dependency": "Common UMAP with rare-state zoom; marker heatmap, dot plot and same-cell co-detection."
+    },
+    {
+      "figure": 5,
+      "panel": "c",
+      "title": "Patient-level reproduction",
+      "state": "TODO",
+      "dependency": "Observed-generated abundance scatter, missed-state frequency and disease direction."
+    },
+    {
+      "figure": 5,
+      "panel": "d",
+      "title": "All-state robustness",
+      "state": "TODO",
+      "dependency": "Retain zero draws and real donor IDs; common-depth / equal-cell-budget sensitivity; required markers."
+    },
+    {
+      "figure": 5,
+      "panel": "e",
+      "title": "Any C1Q versus multi-gene C1Q rule",
+      "state": "DESCRIPTIVE",
+      "dependency": "fig5_behcet_rules_diagnostic.pdf"
+    },
+    {
+      "figure": 6,
+      "panel": "a",
+      "title": "Dataset and reproduction design",
+      "state": "TODO",
+      "dependency": "Place the cohort, published target finding, paired-adaptation subset and held-out evaluation here after data preparation."
+    },
+    {
+      "figure": 6,
+      "panel": "b",
+      "title": "Reproduction and validation",
+      "state": "TODO",
+      "dependency": "Place the reproduction result and independent supporting evidence here. No Figure 6 analysis is started by this layout task."
+    }
+  ]
+}

paper-releases/pbisc-diffusion/updates/20261012T233237Z-figure-layout-todo/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/layout_preview_20261013/README.md

@@ -0,0 +1,12 @@
+# PBISC Figure placement preview
+
+Figure 1–5 placement first, with explicit TODO slots for running experiments; Figure 6 is reserved.
+
+- `PBISC_Figure_layout_TODO_20261013.pdf`: eight-page vector review package.
+- `PBISC_Figure_layout_TODO_20261013.pptx`: same layout, editable labels and TODO boxes.
+- `panels/`: individual figure PDF/SVG/PNG exports.
+- `PANEL_MAP.csv`: available panels and experiment TODOs.
+- `STATUS_SNAPSHOT.json`: point-in-time execution counts, not live status.
+- `PROVENANCE.json`: stable source copies and file hashes.
+
+No new experiment or statistical analysis was run. The incomplete strict curves were replaced by TODO boxes. Historical five-fold and descriptive Behcet evidence retain their scope labels. This package is separate from the running campaign outputs and does not modify manuscript source.

paper-releases/pbisc-diffusion/updates/20261012T233237Z-figure-layout-todo/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/layout_preview_20261013/STATUS_SNAPSHOT.json

@@ -0,0 +1,297 @@
+{
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+  "units": [
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+      "cohort": "giroux2022",
+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "074d1cf9ca3951ef1a032239eabb9d3a13f0f9a2030b030dcbe425ac71d46700"
+    },
+    {
+      "unit": "giroux2022-disease-draw1",
+      "cohort": "giroux2022",
+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "1a20024ce53f3aeb268784fed7fed630ef326f8ffa89fa9bc150661c1506b7e2"
+    },
+    {
+      "unit": "giroux2022-disease-draw2",
+      "cohort": "giroux2022",
+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "c9ac2355733aaf62165d452aaa3f2a4ee95874fc15e983c8c06cec01a9b0abb5"
+    },
+    {
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+      "n_pairs": 5,
+      "score_completed": false,
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+    },
+    {
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+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "df74fb20effc23b7784248bf76e32951803075e492251168f3d5f83dfdec81ea"
+    },
+    {
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+      "cohort": "immicro",
+      "n_pairs": 10,
+      "score_completed": false,
+      "support_sha256": "b76459a585604c60e588279b889094c972e621e2aa6c28ecf5aa163ffe5481bf"
+    },
+    {
+      "unit": "immicro-healthy-fold0-n20",
+      "cohort": "immicro",
+      "n_pairs": 20,
+      "score_completed": false,
+      "support_sha256": "52b20ff9322e8bf850bd0092fb61a1ad1bdbf6304ddd2b7b654ef90fe8009e7e"
+    },
+    {
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+      "support_sha256": "2418da2d8050f3ec761109aa5c1e5da234d88bc8bd7ed5f540dc44c10d046252"
+    },
+    {
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+      "cohort": "immicro",
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+      "support_sha256": "85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4"
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+    {
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+      "cohort": "immicro",
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+      "score_completed": false,
+      "support_sha256": "92447ba4a03867ba6b52a7739bf4db0eecf05fd367e725c0dbe07ae927b6f511"
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+      "cohort": "immicro",
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+      "score_completed": false,
+      "support_sha256": "e8d557be6f2e1d807f043f68ed8c2ff803dd04fe18f928167741079279d57ae6"
+    },
+    {
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+      "cohort": "immicro",
+      "n_pairs": 40,
+      "score_completed": false,
+      "support_sha256": "e4909b732024af62d8332b9fc37adb0f7bda2024884b74ac3b4059ecf371d2c5"
+    },
+    {
+      "unit": "immicro-healthy-fold1-n5",
+      "cohort": "immicro",
+      "n_pairs": 5,
+      "score_completed": true,
+      "support_sha256": "84d7e7a40992a7f24ceb5017c7534e2897d89246de9747c0a683442ad506e155"
+    },
+    {
+      "unit": "immicro-healthy-fold2-n10",
+      "cohort": "immicro",
+      "n_pairs": 10,
+      "score_completed": false,
+      "support_sha256": "6b42beb22dbd81bfe90a640c7061888be83ef668d4ba6fbbe7943e5a1b3d7a33"
+    },
+    {
+      "unit": "immicro-healthy-fold2-n20",
+      "cohort": "immicro",
+      "n_pairs": 20,
+      "score_completed": false,
+      "support_sha256": "9f6a9cc2d9c261a63f2c81229ca55961fdb44352ddc03c479e260dd238557168"
+    },
+    {
+      "unit": "immicro-healthy-fold2-n40",
+      "cohort": "immicro",
+      "n_pairs": 40,
+      "score_completed": false,
+      "support_sha256": "190cb65c7367580cc8d33aece9c90ac0d5c5129e6fce7b1c205b46bacb949b2f"
+    },
+    {
+      "unit": "immicro-healthy-fold2-n5",
+      "cohort": "immicro",
+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "bd9c9fcca2102a403eec20242ecd5e3184be33095e3d37a60e0bca1c32c06c7d"
+    },
+    {
+      "unit": "immicro-healthy-fold3-n10",
+      "cohort": "immicro",
+      "n_pairs": 10,
+      "score_completed": false,
+      "support_sha256": "6c96dd0aa52a33a7104c5f9396953beecd5a93bf1832486be95fb2c9ce2f86fb"
+    },
+    {
+      "unit": "immicro-healthy-fold3-n20",
+      "cohort": "immicro",
+      "n_pairs": 20,
+      "score_completed": false,
+      "support_sha256": "ae96bceb313de5c71379681084098d5d1288078b47cc602f229d39829510d522"
+    },
+    {
+      "unit": "immicro-healthy-fold3-n40",
+      "cohort": "immicro",
+      "n_pairs": 40,
+      "score_completed": false,
+      "support_sha256": "457ae60d867da300d96362599a9f620a09620452e46bbc389594819508e14958"
+    },
+    {
+      "unit": "immicro-healthy-fold3-n5",
+      "cohort": "immicro",
+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "da5bd0ca62732497c449a00693622c21fdd07445fbcb1b6ca86bb59b5802636e"
+    },
+    {
+      "unit": "immicro-healthy-fold4-n10",
+      "cohort": "immicro",
+      "n_pairs": 10,
+      "score_completed": false,
+      "support_sha256": "71350ef0e193641d9f260d1758377a3de64dc12ad169c130a0293e33711a48ac"
+    },
+    {
+      "unit": "immicro-healthy-fold4-n20",
+      "cohort": "immicro",
+      "n_pairs": 20,
+      "score_completed": false,
+      "support_sha256": "b070c6f6f9e0b95b4cb3951c76263c6a19981e0a8dbd635410ae99a94c2dd212"
+    },
+    {
+      "unit": "immicro-healthy-fold4-n40",
+      "cohort": "immicro",
+      "n_pairs": 40,
+      "score_completed": false,
+      "support_sha256": "33938ffd402679c4e3bc90489e4891da3f72101bf5a52e3a479a3ee9db212dae"
+    },
+    {
+      "unit": "immicro-healthy-fold4-n5",
+      "cohort": "immicro",
+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "e0c6712ab61af431d22b7cd8aeff0d39b2400e0c266649d045acc42c75889449"
+    },
+    {
+      "unit": "imperial_eskd-disease-draw0",
+      "cohort": "imperial_eskd",
+      "n_pairs": 5,
+      "score_completed": false,
+      "support_sha256": "4733416ac0e4142bc928aa91f4fbe75c852492f55832470684fd9d41b56ef716"
+    },
+    {
+      "unit": "imperial_eskd-disease-draw1",
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paper-releases/pbisc-diffusion/updates/20261012T233237Z-figure-layout-todo/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/layout_preview_20261013/VERIFICATION.json

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