Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T060837Z-deck-new-figure-split-time/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_plan_slide_text.json

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+{
+ "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): six main figures, up to 17 supplementary. User decisions of 2026-10-06: no PBISC-VAE; scSemiProfiler, a VAE-based method, is the comparison. User decisions of 2026-10-08 (supersede the earlier figure split): Fig. 2 shows no disease metrics; Fig. 3 compares with scSemiProfiler on healthy samples, with time as a main result; Figs 4-6 use the disease cohorts: Fig. 4 disease benchmarks (PBISC versions, scSemiProfiler, and BayesPrism / CIBERSORTx labelled as cell-type deconvolution), Fig. 5 rare-cell fractions and detection, Fig. 6 new findings from the bulk-only sepsis and COVID samples (K = 1,000 and 4,000). 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 pairs and a LoRA of minutes give cells close to the real ones. No disease metrics. 2 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 [Adapt; design example: ImMicro instead of sepsis]. d) How generated cells are scored (cells and composition) [Adapt; disease rows move to Fig. 4]. e) Healthy cohort: precision, coverage, composition [Adapt; ImMicro only; drop the disease columns]. f) Healthy cohort: classifier AUROC, MMD, E_N [Adapt; ImMicro only]. g) Full, LoRA and condition-encoder fine-tuning [Adapt; ImMicro only; no logFC]. h) How many pairs are needed [Adapt; ImMicro only; scSemiProfiler diamonds go to Fig. 3]. i) LoRA rank and K choices [Adapt; ImMicro only; supplementary candidate].",
+   "numbers": []
+  },
+  {
+   "title": "Figure 3 plan: PBISC vs scSemiProfiler on healthy donors",
+   "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": "On healthy donors, LoRA cells are closer to the real ones than scSemiProfiler's, in minutes instead of days. 1 of 4 panels ready.",
+   "footnote": "Panels: a) Five donors: generated cells and realism [Adapt; ImMicro only]. b) Same training pairs (5-fold) and equal pair budget (5-40) [Adapt; ImMicro only; add the n = 5-40 budget runs]. c) scSemiProfiler copies its representative [Adapt; ImMicro only]. d) Time: GPU hours and days per experiment [Ready; all cohorts shown: time is a property of the method].",
+   "numbers": []
+  },
+  {
+   "title": "Figure 4 plan: Disease signal on paired cohorts",
+   "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": "LoRA cells recover the paired single cells' disease signal; compared with other PBISC versions, scSemiProfiler and deconvolution. 3 of 6 panels ready.",
+   "footnote": "Panels: a) Five paired cohorts [Ready]. b) PBISC versions on the disease benchmarks: LoRA best [Build; zero-shot, calibration, sc-only, full FT, ranks, multi-K; data exist]. c) LoRA vs scSemiProfiler: disease logFC, DEG [Adapt; add the 5-fold same-pairs disease columns]. d) Disease genes at every list length (CAT) [Ready]. e) vs BayesPrism and CIBERSORTx (cell-type deconvolution) [Adapt; label as cell-type deconvolution in the title]. f) Lupus benchmark (sc-pseudobulk input) and the bulk broadcast [Ready; moved from Fig. 3]. Details in this section: Deconvolution with the same pairs: composition.",
+   "numbers": []
+  },
+  {
+   "title": "Figure 5 plan: Rare cell states in disease cohorts",
+   "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": "LoRA cells carry rare disease states near their observed fractions, in the donors that have them. 0 of 4 panels ready.",
+   "footnote": "Panels: a) Rare-state fractions, generated vs observed, four paired cohorts [Run; LoRA, scSemiProfiler, zero-shot; BayesPrism states where defined]. b) Finding rare states: per-donor detection [Run; donors with vs without the state]. c) Behçet: C1Q-high monocytes from real bulk [Adapt; add the LoRA-3 result (C1Q-high BD > HC)]. d) Diseases absent from the corpus: Kawasaki MS1, SLE ISG-high T [Build; rare_states_screen_20261004 results].",
+   "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": "New findings from LoRA cells of bulk-only sepsis and COVID dialysis samples (K = 1,000 and 4,000). 0 of 2 panels ready.",
+   "footnote": "Panels: a) Bulk-only samples generated: sepsis 122, COVID dialysis 164 [Adapt; update: K = 1,000 and 4,000 done]. b) New findings [Run; earlier screen: 0 confirmed beyond the bulk].",
+   "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: Pairs from other cohorts do not transfer; Longer training on other cohorts: gap stays; No pretraining: same cohort, from scratch; No pretraining: other cohorts, from scratch; Rare states: from scratch vs pretrained. Planned: Influenza exposure from raw clinical bulk (Randolph) [Build; manuscript result; placement open]. 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/20261008T060837Z-deck-new-figure-split-time/diffusion/metadata/inference_locations.json

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+{
+  "locations": [],
+  "project_id": "pbisc-diffusion",
+  "update_id": "20261008T060837Z-deck-new-figure-split-time"
+}

paper-releases/pbisc-diffusion/updates/20261008T060837Z-deck-new-figure-split-time/diffusion/metadata/request.json

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+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_arch4x_v1/effective_config.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_arch4x_v1/history.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_archctx2048_v1/RUN_STATUS.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_archctx2048_v1/effective_config.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_archctx2048_v1/history.json",
+      "state": "completed"
+    }
+  ],
+  "inference_locations": [],
+  "project_id": "pbisc-diffusion",
+  "summary": "2026-10-08 paper-summary deck: new six-figure split (user decision: Fig. 2 no disease metrics; Fig. 3 PBISC vs scSemiProfiler on healthy donors with time as a main result; Fig. 4 disease benchmarks incl. PBISC versions, scSemiProfiler and BayesPrism/CIBERSORTx as cell-type deconvolution; Fig. 5 rare cells; Fig. 6 bulk-only findings). New slide 'Time: days for scSemiProfiler, minutes for LoRA' (tools/fig3_time_days.py). 65 slides."
+}