Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_plan.json

@@ -0,0 +1,308 @@
+{
+ "source": "Nature Style Manuscript Writing.pdf (paper-release-20260928/reference-papers, 2026-10-06): six main figures, up to 17 supplementary; short abstract and introduction, descriptive results, short discussion with limitations, detailed methods. User decisions of 2026-10-06: no PBISC-VAE (scSemiProfiler, a VAE-based method, is the comparison); LoRA performance first on the healthy cohort with the realism metrics, the disease-cohort comparison later; CYBERSORTx and other bulk deconvolution methods only in the Supplementary (PBISC generates single cells); Figs 4 and 6 left empty until their analyses are done.",
+ "status_legend": {
+  "Ready": "slide exists and fits the panel",
+  "Adapt": "slide exists; change its scope or style",
+  "Draft": "new draft exists, not yet approved",
+  "Build": "results exist; no slide yet",
+  "Run": "needs a new analysis or experiment",
+  "Plan": "not planned yet"
+ },
+ "figures": [
+  {
+   "n": 1,
+   "title": "Design and performance of PBISC",
+   "claim": "Diffusion on each gene's value and detection, conditioned on bulk, writes realistic blood cells.",
+   "panels": [
+    {
+     "p": "a",
+     "content": "Backbones compared: scDiffusion, SDD, PBISC-Diffusion",
+     "evidence": [
+      "Backbone: SDD → PBISC-Diffusion"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "b",
+     "content": "Overview: pretraining, diffusion, generation",
+     "evidence": [
+      "Overview draft (Nature style)"
+     ],
+     "status": "Draft"
+    },
+    {
+     "p": "c",
+     "content": "What the bulk condition contains",
+     "evidence": [
+      "Bulk conditioning"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "d",
+     "content": "Pretraining corpus: assays, conditions, cell types",
+     "evidence": [
+      "Pretraining corpus"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "e",
+     "content": "Width and context: lower loss, same biology",
+     "evidence": [
+      "Width & context ablation: loss saturation",
+      "Width & context ablation: benchmark"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "f",
+     "content": "Gene panel: 2k, 3k, 6k, 15k",
+     "evidence": [
+      "Gene context: 2k / 3k / 6k / 15k"
+     ],
+     "status": "Ready"
+    }
+   ],
+   "candidates": [],
+   "details": [
+    "PBISC-Diffusion: bulk in, cells out",
+    "Denoiser: joint value + support diffusion"
+   ]
+  },
+  {
+   "n": 2,
+   "title": "Fine-tuning PBISC with LoRA",
+   "claim": "On a healthy cohort, a few paired samples and a LoRA of minutes give cells close to the real ones.",
+   "panels": [
+    {
+     "p": "a",
+     "content": "Real bulk differs from the training input",
+     "evidence": [
+      "Real bulk ≠ pseudobulk (model input)",
+      "Same shift in three paired cohorts"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "b",
+     "content": "Without fine-tuning, cells fall off the real manifold",
+     "evidence": [
+      "Consequence: cells off-manifold"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "c",
+     "content": "LoRA on paired bulk and cells; how it is tested",
+     "evidence": [
+      "Fine-tuning with paired bulk + sc",
+      "Evaluation design"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "d",
+     "content": "How generated cells are scored (the metric suite)",
+     "evidence": [
+      "How we score generated cells"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "e",
+     "content": "Healthy cohort: precision, coverage, composition",
+     "evidence": [
+      "5-fold CV: train on the other 4 folds"
+     ],
+     "status": "Adapt",
+     "note": "ImMicro only; LoRA vs zero-shot and calibration"
+    },
+    {
+     "p": "f",
+     "content": "Healthy cohort: classifier AUROC, MMD, E_N",
+     "evidence": [
+      "5-fold: realism beyond precision/coverage"
+     ],
+     "status": "Adapt",
+     "note": "ImMicro only"
+    },
+    {
+     "p": "g",
+     "content": "Full, LoRA and condition-encoder fine-tuning",
+     "evidence": [
+      "Full vs LoRA vs cond.-encoder-only"
+     ],
+     "status": "Adapt",
+     "note": "ImMicro only"
+    },
+    {
+     "p": "h",
+     "content": "How many pairs are needed",
+     "evidence": [
+      "Pairs needed: composition, coverage, training steps"
+     ],
+     "status": "Adapt",
+     "note": "ImMicro only"
+    },
+    {
+     "p": "i",
+     "content": "LoRA rank and K choices",
+     "evidence": [
+      "LoRA rank: r = 4, 16, 64",
+      "K diversification: no gain"
+     ],
+     "status": "Ready",
+     "note": "supplementary candidate"
+    }
+   ],
+   "candidates": [],
+   "details": []
+  },
+  {
+   "n": 3,
+   "title": "Comparison with scSemiProfiler",
+   "claim": "PBISC gives better cells than scSemiProfiler, a VAE-based method, for far less compute.",
+   "panels": [
+    {
+     "p": "a",
+     "content": "Lupus benchmark against scSemiProfiler",
+     "evidence": [
+      "SLE benchmark: PBISC vs scSemiProfiler",
+      "SLE benchmark: per cell type",
+      "Bulk broadcast baseline"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "b",
+     "content": "Five paired cohorts",
+     "evidence": [
+      "Five paired cohorts"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "c",
+     "content": "Five donors: generated cells",
+     "evidence": [
+      "5 donors: LoRA vs scSemiProfiler — cells",
+      "5 donors: realism beyond precision/coverage",
+      "5 donors: precision/coverage at k = 3, 5, 10"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "d",
+     "content": "scSemiProfiler copies its representative",
+     "evidence": [
+      "scSemiProfiler copies its representative"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "e",
+     "content": "Same training pairs, 5-fold",
+     "evidence": [
+      "Same training pairs: LoRA vs scSemiProfiler"
+     ],
+     "status": "Ready",
+     "note": "scSemiProfiler CV: Imperial still running"
+    },
+    {
+     "p": "f",
+     "content": "Time to apply to a new cohort",
+     "evidence": [
+      "5 donors: time to apply"
+     ],
+     "status": "Ready"
+    }
+   ],
+   "candidates": [],
+   "details": []
+  },
+  {
+   "n": 4,
+   "title": "Disease signal and rare cell states",
+   "claim": "Open until the disease-cohort analyses are done, including LoRA on the disease cohort.",
+   "panels": [],
+   "candidates": [
+    "Pairs needed: donor and disease signal",
+    "5 donors: LoRA vs scSemiProfiler — disease signal",
+    "Disease genes at every list length (CAT)"
+   ],
+   "details": []
+  },
+  {
+   "n": 5,
+   "title": "Datasets outside training",
+   "claim": "PBISC applies to cohorts it never saw, and needs their own pairs to do it well.",
+   "panels": [
+    {
+     "p": "a",
+     "content": "Other cohorts' pairs do not replace a cohort's own",
+     "evidence": [
+      "Pairs from other cohorts do not transfer",
+      "Longer training on other cohorts: gap stays"
+     ],
+     "status": "Ready"
+    },
+    {
+     "p": "b",
+     "content": "Behçet: disease direction from real bulk",
+     "evidence": [
+      "Consequence: disease direction flips"
+     ],
+     "status": "Adapt",
+     "note": "add the LoRA-3 result (C1Q-high BD > HC)"
+    },
+    {
+     "p": "c",
+     "content": "Influenza exposure from raw clinical bulk (Randolph)",
+     "evidence": [],
+     "status": "Build",
+     "note": "manuscript result"
+    },
+    {
+     "p": "d",
+     "content": "Diseases absent from the corpus vs present",
+     "evidence": [],
+     "status": "Build",
+     "note": "Kawasaki, SLE vs DRESS (2026-10-04)"
+    }
+   ],
+   "candidates": [],
+   "details": []
+  },
+  {
+   "n": 6,
+   "title": "Discovery from public bulk-only data",
+   "claim": "Analysis not started; to be planned.",
+   "panels": [],
+   "candidates": [
+    "Next: cohorts with a paired subset (planned)"
+   ],
+   "details": []
+  }
+ ],
+ "supplementary": {
+  "slides": [
+   "No pretraining: same cohort, from scratch",
+   "No pretraining: other cohorts, from scratch",
+   "Rare states: from scratch vs pretrained",
+   "Deconvolution with the same pairs: composition",
+   "Deconvolution with the same pairs: disease signal"
+  ],
+  "planned": [],
+  "notes": {
+   "Deconvolution with the same pairs: composition": "reference only: PBISC generates single cells",
+   "Deconvolution with the same pairs: disease signal": "reference only: PBISC generates single cells"
+  }
+ },
+ "appendix": [
+  "Appendix: scSemiProfiler without output threshold"
+ ],
+ "discussion": [
+  "Next: other tissues from a few dozen pairs"
+ ]
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_plan_slide_text.json

@@ -0,0 +1,132 @@
+{
+ "section": "figure-plan",
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/figure_plan.py"
+ ],
+ "generated_from": "tools/figure_plan.py (rerun to refresh; do not edit by hand)",
+ "slides": [
+  {
+   "title": "Manuscript plan: six main figures",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_overview.png"
+   ],
+   "keywords": [],
+   "footnote_short": "Nature style: short abstract and introduction, descriptive results, short discussion, detailed methods; up to 17 supplementary figures.",
+   "footnote": "Nature Style Manuscript Writing.pdf (paper-release-20260928/reference-papers, 2026-10-06): six main figures, up to 17 supplementary; short abstract and introduction, descriptive results, short discussion with limitations, detailed methods. User decisions of 2026-10-06: no PBISC-VAE (scSemiProfiler, a VAE-based method, is the comparison); LoRA performance first on the healthy cohort with the realism metrics, the disease-cohort comparison later; CYBERSORTx and other bulk deconvolution methods only in the Supplementary (PBISC generates single cells); Figs 4 and 6 left empty until their analyses are done. Status: Ready = slide exists and fits the panel; Adapt = slide exists; change its scope or style; Draft = new draft exists, not yet approved; Build = results exist; no slide yet; Run = needs a new analysis or experiment; Plan = not planned yet.",
+   "numbers": []
+  },
+  {
+   "title": "Figure 1 plan: Design and performance of PBISC",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_fig1.png"
+   ],
+   "keywords": [],
+   "footnote_short": "Diffusion on each gene's value and detection, conditioned on bulk, writes realistic blood cells. 5 of 6 panels ready.",
+   "footnote": "Panels: a) Backbones compared: scDiffusion, SDD, PBISC-Diffusion [Ready]. b) Overview: pretraining, diffusion, generation [Draft]. c) What the bulk condition contains [Ready]. d) Pretraining corpus: assays, conditions, cell types [Ready]. e) Width and context: lower loss, same biology [Ready]. f) Gene panel: 2k, 3k, 6k, 15k [Ready]. Details in this section: PBISC-Diffusion: bulk in, cells out; Denoiser: joint value + support diffusion.",
+   "numbers": []
+  },
+  {
+   "title": "Figure 2 plan: Fine-tuning PBISC with LoRA",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_fig2.png"
+   ],
+   "keywords": [],
+   "footnote_short": "On a healthy cohort, a few paired samples and a LoRA of minutes give cells close to the real ones. 5 of 9 panels ready.",
+   "footnote": "Panels: a) Real bulk differs from the training input [Ready]. b) Without fine-tuning, cells fall off the real manifold [Ready]. c) LoRA on paired bulk and cells; how it is tested [Ready]. d) How generated cells are scored (the metric suite) [Ready]. e) Healthy cohort: precision, coverage, composition [Adapt; ImMicro only; LoRA vs zero-shot and calibration]. f) Healthy cohort: classifier AUROC, MMD, E_N [Adapt; ImMicro only]. g) Full, LoRA and condition-encoder fine-tuning [Adapt; ImMicro only]. h) How many pairs are needed [Adapt; ImMicro only]. i) LoRA rank and K choices [Ready; supplementary candidate].",
+   "numbers": []
+  },
+  {
+   "title": "Figure 3 plan: Comparison with scSemiProfiler",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_fig3.png"
+   ],
+   "keywords": [],
+   "footnote_short": "PBISC gives better cells than scSemiProfiler, a VAE-based method, for far less compute. 6 of 6 panels ready.",
+   "footnote": "Panels: a) Lupus benchmark against scSemiProfiler [Ready]. b) Five paired cohorts [Ready]. c) Five donors: generated cells [Ready]. d) scSemiProfiler copies its representative [Ready]. e) Same training pairs, 5-fold [Ready; scSemiProfiler CV: Imperial still running]. f) Time to apply to a new cohort [Ready].",
+   "numbers": []
+  },
+  {
+   "title": "Figure 4 plan: Disease signal and rare cell states",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_fig4.png"
+   ],
+   "keywords": [],
+   "footnote_short": "Open until the disease-cohort analyses are done, including LoRA on the disease cohort.",
+   "footnote": "Panels:  Slides kept in this section until it is planned: Pairs needed: donor and disease signal; 5 donors: LoRA vs scSemiProfiler — disease signal; Disease genes at every list length (CAT).",
+   "numbers": []
+  },
+  {
+   "title": "Figure 5 plan: Datasets outside training",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_fig5.png"
+   ],
+   "keywords": [],
+   "footnote_short": "PBISC applies to cohorts it never saw, and needs their own pairs to do it well. 1 of 4 panels ready.",
+   "footnote": "Panels: a) Other cohorts' pairs do not replace a cohort's own [Ready]. b) Behçet: disease direction from real bulk [Adapt; add the LoRA-3 result (C1Q-high BD > HC)]. c) Influenza exposure from raw clinical bulk (Randolph) [Build; manuscript result]. d) Diseases absent from the corpus vs present [Build; Kawasaki, SLE vs DRESS (2026-10-04)].",
+   "numbers": []
+  },
+  {
+   "title": "Figure 6 plan: Discovery from public bulk-only data",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_fig6.png"
+   ],
+   "keywords": [],
+   "footnote_short": "Analysis not started; to be planned.",
+   "footnote": "Panels:  Slides kept in this section until it is planned: Next: cohorts with a paired subset (planned).",
+   "numbers": []
+  },
+  {
+   "title": "Supplementary plan",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figplan_supp.png"
+   ],
+   "keywords": [],
+   "footnote_short": "Bulk deconvolution methods appear here only: PBISC generates single cells, a different task.",
+   "footnote": "Supplementary: No pretraining: same cohort, from scratch; No pretraining: other cohorts, from scratch; Rare states: from scratch vs pretrained; Deconvolution with the same pairs: composition; Deconvolution with the same pairs: disease signal. Appendix: Appendix: scSemiProfiler without output threshold.",
+   "numbers": []
+  },
+  {
+   "title": "Overview draft (Nature style)",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig1b_overview_nature.png"
+   ],
+   "keywords": [
+    "Each cell is learned with its own bulk",
+    "Diffusion on each gene's value and detection",
+    "One bulk in, K cells out; optional LoRA"
+   ],
+   "footnote_short": "Draft for Fig. 1b; schematic, no data. Plan: manuscript editorial/fig1_nature_redesign_plan.",
+   "footnote": "Candidate replacement for the engineering diagram (kept in this section as details and for Methods). Source: paper-release-20260928/manuscript/figures/fig01_architecture_nature.svg (scripts/build_figure1_architecture_nature.py).",
+   "numbers": []
+  },
+  {
+   "title": "Pretraining corpus",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig1d_corpus.png"
+   ],
+   "keywords": [
+    "41.4 M cells, 22 datasets, 3,199 donors",
+    "88.5% healthy donors; 23.6% cultured in vitro",
+    "Labels describe the corpus; never model input"
+   ],
+   "footnote_short": "Detailed version: Supplementary Fig. S1 of the manuscript.",
+   "footnote": "Source: paper-release-20260928/manuscript/source_data/corpus/ (build_corpus_tables.py) and figures/fig01_corpus_nature.png (build_figure1_corpus.py).",
+   "numbers": [
+    {
+     "value": "41,395,184 cells; 22 datasets; 3,199 donors; healthy 88.5%; in vitro 23.6%",
+     "source": "manuscript/source_data/corpus/corpus_summary.json"
+    }
+   ]
+  }
+ ]
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_same_pairs_budget.csv

@@ -0,0 +1,9 @@
+dataset,n,scsemi_l1,lora_l1,scsemi_cov,lora_cov
+immicro,5,0.218449,0.171451,0.0381931,0.83919
+immicro,10,0.226932,0.187881,0.0380062,0.78567
+immicro,20,0.223249,0.172324,0.0371963,0.755202
+immicro,40,0.221315,0.171385,0.0384424,0.778442
+ye2026_sepsis,5,0.521487,0.428061,0.0969106,0.766667
+ye2026_sepsis,10,0.535812,0.389665,0.103008,0.785854
+ye2026_sepsis,20,0.531893,0.380257,0.100569,0.806667
+ye2026_sepsis,40,0.516498,0.364757,0.0960163,0.817561

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/secS_deconvolution.csv

@@ -0,0 +1,6 @@
+cohort,f_lora_l1,f_bp_l1,f_cx_l1,c_lora_l1,c_bp_l1,c_cx_l1,c_scsemi_l1,f_lora_r,f_lora_partial,f_lora_deg,f_bp_r,f_bp_partial,f_bp_deg,f_cx_r,f_cx_partial,f_cx_deg,f_broadcast_r,f_broadcast_partial,f_broadcast_deg
+ImMicro,0.1755595893035838,0.5374450557106532,0.49140827856730807,0.1617289035078621,0.5745628784374615,0.5065033643252109,0.2170087237986556,,,,,,,,,,,,
+Sepsis,0.4661935856958568,0.4461497190936295,0.5821898971787263,0.3618246783833512,0.4750523423944086,0.607149641152929,0.5022299158951089,0.3501183786066874,0.30469762374899834,16.4,0.24118586866067449,0.09459917525726311,27.0,0.0691472644717398,-0.00988830062408914,25.4,0.3200255010646996,,20.0
+Ji ChILI,0.5130875970575781,0.8932363204937289,0.8267482537726828,0.5044992874562503,0.8832571878464304,0.914073829946989,0.575388570715078,0.33313865479653937,0.3004989267312548,0.2,0.19324923766266502,0.03175063444356422,2.0,0.15848363999937304,0.0048928823034919515,0.0,0.23359889293846758,,1.0
+Imperial,0.5029703261097016,0.8445385293550187,0.6455487576081367,0.3763856087574566,0.8870870830413495,0.5918271288164071,,0.7491552706205521,0.6028412048970822,113.6,0.5976127405567618,0.1866076529400855,72.4,0.2834999227020752,0.06094785618071251,30.8,0.6564998400670289,,74.8
+Giroux,0.25643971843189417,1.4554372974895542,0.6693819873634712,0.2580442754044374,0.8778647964495544,0.5914100321768722,0.2430769027717485,0.2965942782817652,0.18857337655691103,0.2,0.3714147659649227,0.11665014209738915,0.2,0.09549187007462323,0.0286423958767148,0.0,0.4924984776861333,,0.0