Archive 4 checkpoints (1-4)

.gitattributes

@@ -85,3 +85,5 @@ paper-releases/pbisc-diffusion/updates/20261003T105229Z-deck-cross-cohort-loco-k
 paper-releases/pbisc-diffusion/updates/20261003T105229Z-deck-cross-cohort-loco-k1000/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/20261003T224927Z-deck-appendix-scsemi-readout/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/20261003T224927Z-deck-appendix-scsemi-readout/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/20261005T133325Z-deck-scratch-samepairs-tracking/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/20261005T133325Z-deck-scratch-samepairs-tracking/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/20261005T133325Z-deck-scratch-samepairs-tracking/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/20261005T133325Z-deck-scratch-samepairs-tracking/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/20261005T133325Z-deck-scratch-samepairs-tracking/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; restructured 2026-10-02)
+
+42-slide English summary of the PBISC-Diffusion (Model 8) paper experiments: title, outline, 10 sections and an
+appendix (divider + 1 slide). There is no Backup section: every main slide sits in the section it supports. The
+appendix (user decision 2026-10-04) holds only supplementary results that use a modified method and must not be
+read as main evidence. Short keyword lines
+only; the figures carry the results. Every slide that uses a published method, metric or baseline has a one-line
+"References:" footer; full citations are in the speaker notes. 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, references, speaker-note text
+- `generate_deck.py`: builds the pptx from `data/slides_spec.json` only (python-pptx)
+- `figures/`: exactly the figures the slides show (PNG + PDF), made by `tools/sec*.py`. Intermediate panels go to a
+  temporary folder; superseded figures are deleted, not kept (2026-10-02, user request; every deleted file was
+  checked to be in the paper archive by sha256 first).
+- `data/sec*.csv` and `data/*_slide_text.json`: every plotted or quoted number with its source path
+- `render/`: PDF and 70-dpi slide JPGs for checking
+
+## Slide order
+
+| section | slides |
+|---|---|
+| 1 Model overview | bulk in, cells out; denoiser |
+| 2 Backbone | SDD → PBISC-Diffusion; bulk conditioning |
+| 3 Architecture ablation | width & context (loss, benchmark); gene panel |
+| 4 Metrics + SLE benchmark | **how we score generated cells** (metric table with references); SLE benchmark; per cell type; bulk broadcast baseline |
+| 5 Real bulk vs pseudobulk | input shift; same shift in three cohorts; cells off-manifold; disease direction flips |
+| 6 Paired fine-tuning | method; evaluation design |
+| 7 LoRA ablations | full vs LoRA vs cond.-encoder-only; LoRA rank r = 4 / 16 / 64; K diversification; no pretraining, same cohort (pilot) |
+| 8 Pairs needed | composition / coverage / steps (with scSemiProfiler at the same n); donor and disease signal; pairs from other cohorts; longer training on them; no pretraining, other cohorts (pilot) |
+| 9 Paired validation | cohorts; 5 donors: cells, realism beyond P/C, P/C at k = 3 / 5 / 10, scSemiProfiler copies its representative, disease signal, CAT curves, time to apply; 5-fold CV (with scSemiProfiler on the same pairs); same training pairs: LoRA vs scSemiProfiler; 5-fold realism metrics |
+| 10 Paired-subset cohorts | planned |
+| Appendix | scSemiProfiler without its output threshold (sensitivity; modified read-out, not the official output) |
+
+## Rebuild
+
+Everything is CPU only; no GPU or checkpoint is touched.
+
+```bash
+# prerequisites (plan folder plans/paired_finetune_intradataset_20260927/, CPU):
+#   scsemi/tools/representative_dependence.py      -> scsemi/analysis/representative_dependence_20261002/
+#   tools/contrast_extra.py (+ tools/contrast_extra_tables.py) -> scores_contrast/   (Spearman, ceiling, limma, CAT, RBO)
+#   tools/build_tpm_zeroshot.py + tools/score_tpm_zeroshot.sh -> scores/<ds>/zeroshot_tpm_20261002/pooled/
+#     (the length-corrected zero-shot arm needs one GPU sampling step: tools/sample_lockwait.sh, coordinator only)
+cd /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00
+# shared helpers, not run directly: style.py, sec03_common.py, scsemi_results.py, fold_sizes.py
+for f in sec01_overview sec02_backbone sec03_width_loss sec03_width_bench sec03_panel \
+         sec04_metrics_overview 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 sec08_cross_cohort sec09_paired_validation sec09_extra_metrics \
+         sec09_time_to_apply sec09_scsemi_representative sec09_cat_curves sec10_paired_subset_cohorts \
+         secA_scsemi_readout sec07_no_pretraining sec08_cross_scratch sec09_same_pairs; do
+  python3 "tools/$f.py" || break
+done
+python3 tools/sync_sec09_text.py      # copy every generated slide text (sec09_index / text_source) 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 (1 line when the slide has references), the reference line needs more than 1 line, or any text
+contains Korean or placeholder words. `tools/restructure_20261002.py` is the one-off script that produced the current
+slide order and the references (it refuses to run twice).
+
+## Notes
+
+- **No "all" label (2026-10-02).** The 5-fold arm trains each fold model on the other four folds minus 7–8
+  inner-validation donors; its test fold is never trained on (RUN.json `test_rows_never_loaded_for_training`). Figures
+  label it "5-fold CV (other 4 folds)" and learning-curve ticks show the training-pair count per fold (78–79 ImMicro,
+  58–59 sepsis), read by `tools/fold_sizes.py`.
+- **Learning curve x = 0 uses no pairs (2026-10-02).** It shows the zero-shot model fed the real bulk as measured
+  and after exon-length correction (counts / Ensembl union-exon kb, then the same fixed-depth arithmetic;
+  `plans/.../tools/build_tpm_zeroshot.py`, scored in `scores/<ds>/zeroshot_tpm_20261002/pooled`). The old x = 0
+  calibration point, whose alpha used every training pair of the fold, is gone; calibration appears only fitted on the
+  same n pairs as the LoRA point (squares; `cal_budget_20261001`).
+- **Disease metrics (2026-10-02).** Next to Pearson logFC r and the Welch top-50 DEG overlap: Spearman r, the
+  split-half ceiling (observed vs observed, Spearman–Brown), limma-voom top-50 DEG, each arm's chance overlap, and
+  CAT curves with the k / 2G chance line (`plans/.../scores_contrast/`, tools/contrast_extra.py; every Pearson r and
+  Welch count reproduced exactly). Repeated samples of one patient (Imperial, Giroux, Ji) count as separate samples in
+  both DE tests, as in the scorer (footnote).
+- Section 9 text is generated: `tools/sec09_paired_validation.py`, `sec09_extra_metrics.py`, `sec07_rank_sweep.py`,
+  `sec09_time_to_apply.py`, `sec09_scsemi_representative.py`, `sec09_cat_curves.py` write slide text JSON; sync copies
+  it. Hand-written: the keywords of the two "Pairs needed" slides (section 8) and of every slide in sections 1–7 and 10.
+- Giroux's disease metrics exclude 196 sex-linked genes (severity is confounded with sex), from
+  `plans/.../scores_nosex/`. The calibration comparator is "Zero-shot + calibration" (user decision 2026-10-01).
+- Story rule (user decision 2026-09-30): no PBISC-VAE and no reference calibration (refcal). The exon-length-corrected
+  input is used only as the no-pair x = 0 point of the learning curve (user decision 2026-10-02).
+  `tools/sec04_immicro.py` (refcal vs scSemiProfiler on ImMicro) is kept but is not part of the deck or the rebuild.
+- 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*/`, `scsemi_n{5,10,20,40}__raw` in
+  `scores/<cohort>/scsemi_budget_20261002/pooled*/`; same donors and reference cells as the main pooled call only).
+  Then rerun sections 8 and 9, sync, recheck the section 8 keywords and rebuild.
+- Earlier versions: `_archive/2026-09-30_before_no_vae_refcal/`, `_archive/2026-10-01_before_extra_metrics/`,
+  `_archive/2026-10-02_before_time_to_apply/`, `_archive/2026-10-02_before_restructure/` (pptx, PDF, spec; their
+  figures are in the paper archive). `DRAFT_1150_*`: the copy shown at the 2026-09-30 12:00 meeting.
+
+- Added 2026-10-03 (user decision: the cross-cohort experiment is reported at K = 1000 only and is the figure that explains
+  why PBISC fits LoRA on a few pairs of each cohort): slides 25-26 in section 8, `tools/sec08_cross_cohort.py`.
+  - Slide 25 "Pairs from other cohorts do not transfer": per held-out cohort, composition L1 / coverage / disease logFC r of
+    zero-shot, calibration fitted on the other cohorts, LoRA r16 / r64 / full fine-tune trained on the other cohorts
+    (+ Liu 2021) at step saturation, and LoRA on the cohort's own pairs (5-fold pooled).
+  - Slide 26 "Longer training on other cohorts: no gain": the same metrics at every 20k-step milestone.
+  - Source plan: `plans/paired_crosscohort_20261002/` (README; same-reference and same-sample checks in the script).
+    Agenda item 8 now reads "How many pairs, and do other cohorts' pairs transfer". The deck has 37 slides.
+    Pre-update copy: `_archive/2026-10-03_before_cross_cohort/`.
+
+## 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`. Reference PDFs:
+`/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/` (INDEX.md). Manuscript:
+`/home/sj_server_1/PBISC/paper-release-20260928/manuscript/`.
+- 2026-10-04 appendix (user decision: supplementary, appendix only, because it changes scSemiProfiler's official
+  output). Slide 38 is the divider "Appendix" and slide 39 is "Appendix: scSemiProfiler without output threshold"
+  (`tools/secA_scsemi_readout.py`, `data/secA_scsemi_readout{.csv,_slide_text.json}`).
+  - Inputs: `plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/`. The script checks
+    that its LoRA-5 and official scSemiProfiler values equal the section 9 slide data draw by draw.
+  - Result: without upstream's output threshold, scSemiProfiler's coverage rises in 5/5 cohorts, and 23/23 LoRA-5
+    comparisons (coverage, precision, composition, logFC r, DEG) keep their winner.
+  - The outline keeps its 10 sections (the builder requires 10). The pre-change copy is in
+    `_archive/2026-10-04_before_appendix/`. The deck has 39 slides.
+- 2026-10-05 update (user request: put the results so far into the deck). Pre-change copy: `_archive/2026-10-05_before_scratch_cv/`.
+  - New slide 23, "No pretraining: same cohort, from scratch" (`tools/sec07_no_pretraining.py`). Pilot on sepsis fold 0
+    (17 donors). Reads `fold0_scratch_20261005/` and the runs' RUN.json. The donor composition r is recomputed from
+    per_donor.csv and reproduces ablation_extra_donor.csv.
+  - New slide 28, "No pretraining: other cohorts, from scratch" (`tools/sec08_cross_scratch.py`). Held-out sepsis pilot.
+    Every arm is read from `paired_crosscohort_20261002/scores_masked/`: genes no training cohort measured are zeroed
+    in all arms, because the unmasked scratch arm puts ~91 % of its UMI there.
+  - New slide 38, "Same training pairs: LoRA vs scSemiProfiler" (`tools/sec09_same_pairs.py`). scSemiProfiler 5-fold
+    CV with LoRA's own training pairs, plus GPU hours per fold from the receipts on either host. Cohorts that are still
+    running show "in progress"; rerun the script as they finish.
+  - These two slides now draw the scSemiProfiler CV / budget runs automatically:
+    - Slide 24, "Pairs needed" (diamonds; ImMicro so far): keyword 2 reworded, footnote extended.
+    - Slide 37, "5-fold CV" (yellow bar; ImMicro and Ji so far).
+  - `tools/sec09_paired_validation.py` reads the scSemiProfiler CV arm's Spearman / limma values from
+    `scores_contrast/<cohort>/scsemi_cv_20261002/pooled/` (contrast_extra.py --design scored). Pearson r and the Welch
+    DEG must match the scorer; the values stay blank until computed. Cohorts not yet run say "in progress".
+  - Agenda item 7 now reads "LoRA: compute, rank, K; training from scratch". The deck has 42 slides.
+  - New helper: `tools/grouped_bars.py`.

paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/tools/grouped_bars.py

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+"""Grouped vertical bars for the 2026-10-05 slides (no-pretraining ablations, same-pairs scSemiProfiler).
+
+Shared helper of the 2026-09-30 paper-summary deck (not run directly). CPU only, plotting only.
+"""
+from __future__ import annotations
+
+import numpy as np
+
+
+def grouped_bars(ax, groups, arms, value, fs, edge="#333333", sub="#595959", na_text="n/a", fmt=None, log=False,
+                 width=0.8):
+    """groups: x labels; arms: [(key, label, colour, hatch)]; value(group_index, arm_key) -> float (nan = no bar).
+    fmt: optional callable(v) -> str printed above each bar."""
+    n = len(arms)
+    w = width / n
+    x = np.arange(len(groups))
+    tops = []
+    for k, (key, _lab, col, hatch) in enumerate(arms):
+        xs = x + (k - (n - 1) / 2) * w
+        for i, xi in enumerate(xs):
+            v = value(i, key)
+            if v is None or np.isnan(v):
+                ax.text(xi, 0.5, na_text, transform=ax.get_xaxis_transform(), ha="center", va="center",
+                        fontsize=fs - 5, color=sub, rotation=90)
+                continue
+            ax.bar(xi, v, w * 0.92, color=col, edgecolor=edge if hatch else "none", linewidth=0.6, hatch=hatch,
+                   zorder=2)
+            tops.append(v)
+            if fmt is not None:
+                ax.text(xi, v * (1.08 if log else 1.0) + (0 if log else 0.01), fmt(v), ha="center", va="bottom",
+                        fontsize=fs - 6, color=sub, rotation=0)
+    ax.set_xticks(x, groups, fontsize=fs - 3)
+    if log:
+        ax.set_yscale("log")
+    ax.tick_params(axis="y", labelsize=fs - 3)
+    ax.grid(axis="y", color="#E3E3E3", linewidth=0.8, zorder=0)
+    ax.set_axisbelow(True)
+    return tops