Archive 4 checkpoints (1-4)

.gitattributes

@@ -69,3 +69,5 @@ paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-
 paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pdf filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx filter=lfs diff=lfs merge=lfs -text
+paper-releases/pbisc-diffusion/updates/20261002T002920Z-deck-extra-metrics-scsemi-prep/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pdf filter=lfs diff=lfs merge=lfs -text
+paper-releases/pbisc-diffusion/updates/20261002T002920Z-deck-extra-metrics-scsemi-prep/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx filter=lfs diff=lfs merge=lfs -text

paper-releases/pbisc-diffusion/updates/20261002T002920Z-deck-extra-metrics-scsemi-prep/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pdf

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paper-releases/pbisc-diffusion/updates/20261002T002920Z-deck-extra-metrics-scsemi-prep/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx

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paper-releases/pbisc-diffusion/updates/20261002T002920Z-deck-extra-metrics-scsemi-prep/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/README.md

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+# PBISC-Diffusion paper summary deck (2026-09-30, r00)
+
+32-slide English summary of the PBISC-Diffusion (Model 8) paper experiments: title,
+outline, 10 sections (24 content slides), then a Backup divider and 6 backup slides.
+Short keyword lines only; the figures carry the results. Section 10 is planned work.
+
+- `PBISC-Diffusion_paper_summary_20260930.pptx`: the deck
+- `PBISC-Diffusion_paper_summary_20260930.pdf`: LibreOffice PDF of the deck
+- `data/slides_spec.json`: slide order, titles, keywords, footnotes, speaker-note text
+- `generate_deck.py`: builds the pptx from `data/slides_spec.json` only (python-pptx)
+- `figures/`: all slide figures (PNG + PDF), made by `tools/sec*.py`
+- `data/sec*.csv`, `data/sec09_slide_text.json`, `data/sec09_extra_slide_text.json`,
+  `data/sec07_rank_sweep_slide_text.json`: every plotted or quoted number with its source path
+- `render/`: PDF and 70-dpi slide JPGs for checking
+
+## Rebuild
+
+Everything is CPU only; no GPU or checkpoint is touched.
+
+```bash
+cd /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00
+# figures + data tables (sec03_common.py, style.py and scsemi_results.py are shared helpers, not run directly)
+for f in sec01_overview sec02_backbone sec03_width_loss sec03_width_bench sec03_panel \
+         sec04_sle_benchmark sec05_condition_space sec05_cells_offmanifold \
+         sec05_behcet_direction sec05_shift_cohorts sec06_finetune_method sec07_ft_modes \
+         sec07_k_aug sec07_rank_sweep sec08_pairs_needed sec09_paired_validation sec09_extra_metrics \
+         sec10_paired_subset_cohorts; do
+  python3 "tools/$f.py" || break
+done
+python3 tools/sync_sec09_text.py      # copy generated slide text (sec09, sec09_extra, sec07_rank_sweep) into the spec
+python3 generate_deck.py              # -> PBISC-Diffusion_paper_summary_20260930.pptx
+soffice --headless --convert-to pdf --outdir render PBISC-Diffusion_paper_summary_20260930.pptx
+pdftoppm -jpeg -r 70 render/PBISC-Diffusion_paper_summary_20260930.pdf render/slide
+cp render/PBISC-Diffusion_paper_summary_20260930.pdf .
+```
+
+`generate_deck.py` stops with an error if a figure is missing, a title does not fit on one
+line, a footnote needs more than 2 lines, or any text contains Korean or placeholder words.
+
+## Notes
+
+- Section 9 (few-pair scSemiProfiler comparison) uses all 25 scSemiProfiler draws
+  (5 cohorts x 5 draws). If scores change, rerun `tools/sec09_paired_validation.py`, then
+  `tools/sync_sec09_text.py`, then check the short footnotes it lists and rebuild.
+- Section 9 update (user decisions 2026-10-01): (1) the gene-wise calibration comparator is back,
+  named "Zero-shot + calibration" (few-pair `zs_cal`, alpha from the same 5 donors; 5-fold `zs__cal`)
+  and the sc-only control is "sc-only fine-tune (+ calibration)" (`pseudo_full__cal`); (2) Giroux's
+  disease metrics (logFC r, partial r, top-50 DEG, broadcast) exclude 196 sex-linked genes because its
+  severity is confounded with sex, read from `plans/paired_finetune_intradataset_20260927/scores_nosex/`
+  (see its README). Both are stated in the slide footnotes.
+- On-slide footnotes are one short line; the full source and method text is in the speaker
+  notes (`footnote_full` in the spec).
+- `DRAFT_1150_*`: frozen copy shown at the 2026-09-30 12:00 meeting (23/25 scSemiProfiler
+  draws, long footnotes). Superseded by the files above.
+- Story rule (user decision 2026-09-30): the deck and paper do not mention PBISC-VAE, reference
+  calibration (refcal), the TPM input variant or any calibration arm (calibration arm reinstated
+  2026-10-01 as "Zero-shot + calibration"; never "refcal"). The no-fine-tune baseline is
+  zero-shot on real bulk as measured; the sc-only control is the sc-only fine-tune fed raw bulk.
+  `tools/sec04_immicro.py` (refcal vs scSemiProfiler on ImMicro) is kept but no longer in the deck.
+  The pre-revision deck, scripts and figures are in `_archive/2026-09-30_before_no_vae_refcal/`.
+
+- Added 2026-10-02 (from `plans/paired_finetune_intradataset_20260927/scores_extra/` and `scores/<cohort>/rankcal_20261001.*`):
+  slide 23 "5 donors: realism beyond precision/coverage" (classifier AUC, MMD², scSemiProfiler's E_N per cohort;
+  few-pair arms, mean ± SD over draws) and three backups: slide 30 LoRA rank r = 4 / 16 / 64 (ImMicro, sepsis),
+  slide 31 the same realism metrics for the 5-fold pooled design, slide 32 precision/coverage at k = 3 / 5 / 10
+  (few-pair; the 5-fold k ranking is in the speaker notes). Scripts: `tools/sec09_extra_metrics.py` (checks every
+  value against `scores_extra/{fewshot,pooled}_headline.csv`) and `tools/sec07_rank_sweep.py` (checks
+  `rankcal_20261001.json` against the scoring calls). Their slide text is generated (`text_source` in the spec) and
+  synced by `tools/sync_sec09_text.py`. Pre-update deck: `_archive/2026-10-01_before_extra_metrics/`.
+- scSemiProfiler 5-fold and equal-budget results are picked up automatically when they appear
+  (`tools/scsemi_results.py`: arm `scsemi__raw` in `scores/<cohort>/scsemi_cv_20261002/pooled*/`, arms
+  `scsemi_n{5,10,20,40}__raw` in `scores/<cohort>/scsemi_budget_20261002/pooled*/`, extra metrics below
+  `scores_extra/<cohort>/scsemi_cv_20261002/`; a call is used only for the same donors and reference cells as the
+  main pooled call). When present: a "scSemiProfiler, all training pairs" bar on slide 24 (Giroux disease metrics only
+  after a `scores_nosex/giroux2022/scsemi_cv_20261002/` rescore, else "rescore pending"), a scSemiProfiler line across
+  n on slides 18–19 ("all" = the 5-fold run), and a scSemiProfiler row on slide 31. When absent, each script prints a
+  NOTE and the figures are unchanged. After they arrive: rerun the four scripts, sync, check the hand-written keywords
+  of slides 18–19 (not generated) and rebuild. The presence path was tested with synthetic arms in a scratch copy
+  (`DECK_SCSEMI_PLAN_ROOT`, `DECK_FIGDIR`, `DECK_OUTDATA` redirect the lookup and outputs).
+
+## Sources
+
+Final model: `runs/f01_6k_1x_seed20260627` (epoch 16, EMA). Scores and receipts come from
+`plans/utility_studies_final6k_20260925/`, `plans/paired_finetune_intradataset_20260927/`,
+`plans/immicro_scsemi_comparison_20260927/`, `plans/floor01_campaign_20260923/`,
+`analysis/scsemi_benchmark_diffusion_20260913/` and the run folders named in each
+`data/sec*.csv`. Manuscript: `/home/sj_server_1/PBISC/paper-release-20260928/manuscript/`.

paper-releases/pbisc-diffusion/updates/20261002T002920Z-deck-extra-metrics-scsemi-prep/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/tools/scsemi_results.py

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+"""Where the scSemiProfiler 5-fold (CV) and equal-budget results will appear, and a tolerant lookup for them.
+
+Shared helper of the 2026-09-30 paper-summary deck (not run directly). CPU only; reads files, never writes.
+
+Planned locations (2026-10-02; the GPU runs are prepared by another agent and may not exist yet):
+  CV           arm  scsemi__raw                 <PLAN>/scores/<ds>/scsemi_cv_20261002/{fold<k>,pooled}/
+  equal budget arms scsemi_n{5,10,20,40}__raw   <PLAN>/scores/<ds>/scsemi_budget_20261002/{fold<k>,pooled}/
+               (ImMicro and sepsis only)
+  extra metrics (classifier AUC, MMD^2, E_N, P/C at k = 3/5/10)
+               <PLAN>/scores_extra/<ds>/scsemi_cv_20261002/ and .../scsemi_budget_20261002/ (any depth below)
+  Giroux disease metrics without sex-linked genes, if rescored:
+               <PLAN>/scores_nosex/giroux2022/scsemi_cv_20261002/...
+
+The deck uses cross-fitted pooled calls only: directories below <exp>/ with a path part starting with "pooled"
+(pooled, pooled_deg, ...), never fold<k>/ or arms/. A call is accepted only if it scores the same donors with the
+same reference cells as the main pooled call and its generation receipt is not marked unverified (accept()).
+
+Every script that uses this module prints a note and draws nothing for scSemiProfiler when no accepted call exists.
+DECK_SCSEMI_PLAN_ROOT overrides <PLAN> for these lookups only (the synthetic presence test in a scratch copy).
+"""
+from __future__ import annotations
+
+import json
+import os
+import re
+from pathlib import Path
+
+PLAN_DEFAULT = Path("/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/"
+                    "paired_finetune_intradataset_20260927")
+CV_EXP = "scsemi_cv_20261002"
+BUDGET_EXP = "scsemi_budget_20261002"
+CV_ARM = "scsemi__raw"
+BUDGET_RE = re.compile(r"^scsemi_n(\d+)__raw$")
+FOLD_RE = re.compile(r"^fold\d+$")
+LABEL_CV = "scSemiProfiler, all training pairs"
+
+
+def plan_root() -> Path:
+    return Path(os.environ.get("DECK_SCSEMI_PLAN_ROOT", str(PLAN_DEFAULT)))
+
+
+def is_test_root() -> bool:
+    return plan_root() != PLAN_DEFAULT
+
+
+def _pooled_dir(rel: Path) -> bool:
+    parts = rel.parts
+    return (not any(FOLD_RE.match(p) or p == "arms" for p in parts)) and any(p.startswith("pooled") for p in parts)
+
+
+def pooled_dirs(ds: str, exp: str, tree: str = "scores") -> list[Path]:
+    """Directories with a summary.json of the pooled calls of one experiment, 'pooled' before 'pooled_deg' etc."""
+    root = plan_root() / tree / ds / exp
+    if not root.is_dir():
+        return []
+    out = [sp.parent for sp in root.rglob("summary.json") if _pooled_dir(sp.parent.relative_to(root))]
+    return sorted(out, key=lambda p: (len(p.relative_to(root).parts), p.name != "pooled", str(p)))
+
+
+def _arms(d: Path) -> list[str]:
+    try:
+        return list(json.loads((d / "summary.json").read_text()).get("arms") or [])
+    except (OSError, ValueError):
+        return []
+
+
+def cv_calls(ds: str, tree: str = "scores") -> list[Path]:
+    """Pooled call directories that contain the CV arm."""
+    return [d for d in pooled_dirs(ds, CV_EXP, tree) if CV_ARM in _arms(d)]
+
+
+def budget_calls(ds: str, tree: str = "scores") -> dict[int, list[tuple[str, Path]]]:
+    """n -> [(arm, pooled call dir)] for the equal-budget arms scsemi_n<n>__raw."""
+    out: dict[int, list[tuple[str, Path]]] = {}
+    for d in pooled_dirs(ds, BUDGET_EXP, tree):
+        for a in _arms(d):
+            m = BUDGET_RE.match(a)
+            if m:
+                out.setdefault(int(m.group(1)), []).append((a, d))
+    return out
+
+
+def accept(summary: dict, ref_summary: dict, arm: str) -> list[str]:
+    """Reasons to reject one scSemiProfiler arm of a call against the main pooled call ([] = accepted)."""
+    why = []
+    if arm not in (summary.get("arms") or []):
+        why.append(f"arm {arm} not in the call")
+    if set(map(str, summary.get("donors", []))) != set(map(str, ref_summary.get("donors", []))):
+        why.append(f"donor set differs ({len(summary.get('donors', []))} vs {len(ref_summary.get('donors', []))})")
+    rs = summary.get("reference", {}).get("reference_sha256")
+    if rs != ref_summary.get("reference", {}).get("reference_sha256"):
+        why.append("reference cells differ (reference_sha256)")
+    if summary.get("per_arm", {}).get(arm, {}).get("receipt_verified", True) is False:
+        why.append("generation receipt not verified")
+    return why
+
+
+def extra_units(ds: str, exp: str) -> list[Path]:
+    """Extra-metric unit directories (metrics.csv + en.csv) below scores_extra/<ds>/<exp>/, pooled ones first;
+    fold<k>/ units are skipped (the deck shows the pooled design)."""
+    root = plan_root() / "scores_extra" / ds / exp
+    if not root.is_dir():
+        return []
+    out = []
+    for mp in root.rglob("metrics.csv"):
+        d = mp.parent
+        rel = d.relative_to(root)
+        if any(FOLD_RE.match(p) for p in rel.parts) or not (d / "en.csv").is_file():
+            continue
+        out.append(d)
+    return sorted(out, key=lambda p: (not any(x.startswith("pooled") for x in p.relative_to(root).parts),
+                                      len(p.relative_to(root).parts), str(p)))