Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T175437Z-deck-supplementary-other-tissues-review/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec10_other_tissues_slide_text.json

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+{
+ "section": "10-other-tissues",
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/sec10_other_tissues.py"
+ ],
+ "generated_from": "tools/sec10_other_tissues.py (rerun to refresh; do not edit by hand)",
+ "slides": [
+  {
+   "title": "Next: other tissues from a few dozen pairs",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec10_other_tissues.png"
+   ],
+   "keywords": [
+    "Pretrained: a 3-min LoRA works from 5 pairs",
+    "Scratch: 58 pairs + recipes come close (86 min)",
+    "Next: test this route on other tissues"
+   ],
+   "footnote_short": "Pilots: sepsis fold 0 (17 donors); last row held-out sepsis (82). Folds 1–4 and a second cohort pending.",
+   "footnote": "Discussion point; the from-scratch evidence is in the Supplementary. Same cohort, same pairs: sepsis fold 0, 17 held-out donors; every run also early-stops on the same 7 inner-validation pairs. From scratch = the same denoiser at random initialisation, full training (lr 2e-4, inner-val selection, cap 100k steps; the 58-pair and 58-pair + recipes runs were still improving at the cap). It still took the architecture, the diffusion settings, the 6k gene panel, the value scaler and the bulk z-score constants from the PBMC checkpoint, so a corpus-free setup (panel and scalers built from the pairs alone) is untested. Recipes = 50% of each batch is pseudobulk built from the training donors' own cells, K from the pretraining grid (250–4,000). Bold = higher by 0.05 or more (one fold, no interval), or less training time per cohort; the pretraining row is not scored. Rare states: mean |log2 gen/obs| over 13 states, scratch minus pretrained -0.09 [-0.38, +0.18] (donor bootstrap, n.s.); per-state calls = significant, marker states only, excluding states that both arms miss by more than 4-fold. Protocol dependence: recipes, the step budget, and the gene space - a scratch model learns only genes measured in its training pairs (trained on other cohorts, it put 91–94% of its UMI on the 46 genes that none of those cohorts measured). Pairs from other cohorts do not replace the target cohort's own: own-cohort LoRA coverage 0.83 on held-out sepsis. Pilot only: folds 1–4 and a second cohort are needed before the claim. Pretraining (15.9 h on 33.1 M train cells of the 41.4 M-cell corpus) is done once and reused by every cohort.",
+   "say": "Pretraining is what makes PBISC practical: a LoRA of a few minutes on as few as five pairs. In a one-fold sepsis pilot, though, with enough compute, a few dozen paired bulk and single-cell samples plus pseudobulk recipes came close to the same results without corpus pretraining, and the outcome depends on the training protocol. This does not weaken the pretraining result. It suggests that a PBISC-like bulk-to-single-cell model could be built for other organs and tissues that have no large single-cell corpus yet. Folds 1 to 4 and a second cohort will test this first.",
+   "numbers": [
+    {
+     "value": "Corpus pretraining: pretrained 33.1 M train cells, 15.9 h, once / scratch none",
+     "source": "data/sec01_model_numbers.csv train_split_cells; sec06_ft_method.csv pretrain_wall_hours"
+    },
+    {
+     "value": "Training, sepsis fold 0 (one GPU): pretrained 3–5 min / scratch 61–86 min",
+     "source": "data/sec07_no_pretraining.csv minutes"
+    },
+    {
+     "value": "5 pairs: donor composition r: pretrained 0.70 / scratch 0.17",
+     "source": "data/sec07_no_pretraining.csv comp_r"
+    },
+    {
+     "value": "58 pairs + recipes: donor composition r: pretrained 0.80 / scratch 0.77",
+     "source": "data/sec07_no_pretraining.csv comp_r"
+    },
+    {
+     "value": "58 pairs + recipes: coverage: pretrained 0.87 / scratch 0.88",
+     "source": "data/sec07_no_pretraining.csv coverage"
+    },
+    {
+     "value": "58 pairs + recipes: disease logFC r: pretrained 0.45 / scratch 0.54",
+     "source": "data/sec07_no_pretraining.csv logfc_r"
+    },
+    {
+     "value": "58 pairs + recipes: 13 rare states, n.s. on average: pretrained closer on ISG-high T / scratch closer on DN2 B",
+     "source": "data/secS_scratch_rare_states_bootstrap.csv"
+    },
+    {
+     "value": "Other cohorts' pairs only (sepsis held out): coverage: pretrained 0.34 (LoRA r16) / scratch 0.33",
+     "source": "data/sec08_cross_scratch.csv coverage (masked)"
+    }
+   ]
+  }
+ ]
+}

paper-releases/pbisc-diffusion/updates/20261005T175437Z-deck-supplementary-other-tissues-review/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/secS_scratch_rare_states_slide_text.json

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+{
+ "section": "S-scratch-rare-states",
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/secS_scratch_rare_states.py"
+ ],
+ "generated_from": "tools/secS_scratch_rare_states.py (rerun to refresh; do not edit by hand)",
+ "slides": [
+  {
+   "title": "Rare states: from scratch vs pretrained",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_scratch_rare_states.png"
+   ],
+   "keywords": [
+    "Same pairs: no significant difference on average",
+    "Cycling T/NK: pretrained closer, 8 of 8",
+    "C1Q-high needs the cohort's own pairs"
+   ],
+   "footnote_short": "Pilot, one seed: sepsis fold 0 (17 donors), held-out sepsis (82, masked). 1 = observed rate; grey = within 2-fold.",
+   "footnote": "Supplementary. Rare-state screen (plans/rare_states_screen_20261004): 13 rare states plus two controls, marker rules from the literature (tools/states.json) or scANVI labels; per arm, generated state % of its parent / observed % (1 = same rate; grey band = within 2-fold). For marker states the observed cells are thinned to the arm's generated depth; the two label states (plasmablast, proliferating T) are not thinned. The figure shows 8 of the 13 states; every average uses all 13 (data/secS_scratch_rare_states_bootstrap.csv). Same cohort: sepsis fold 0, 17 held-out donors, the same training pairs, conditions and sampling seed for both initialisations; from scratch = random initialisation, full training (lr 2e-4, cap 100k steps). Other cohorts: all 82 sepsis donors held out, trained on ImMicro + Imperial + Giroux + Liu pairs; the 46 genes that no training cohort measured are zeroed in every arm (the scratch model is never trained on them). Donor bootstrap of D = |log2| scratch - |log2| pretrained, mean of the 13 rare states (D > 0 = pretrained closer): same cohort 5 pairs +0.22 [-0.08, +0.41]; 58 pairs +0.02 [-0.35, +0.25]; 58 pairs, full FT +0.14 [-0.14, +0.41]; 58 pairs + recipes -0.09 [-0.38, +0.18]; other cohorts, scratch final vs LoRA r16 -0.04 [-0.20, +0.18]; LoRA r64 +0.06 [-0.08, +0.22]; Full FT +0.29 [+0.07, +0.57]; Calibration +0.72 [+0.57, +0.95]; scratch 50k vs LoRA r16 -0.31 [-0.45, -0.11]; LoRA r64 -0.21 [-0.37, -0.02]; Full FT +0.02 [-0.19, +0.30]; Calibration +0.44 [+0.30, +0.66]. A non-significant average is not a shown equivalence (intervals about +/-0.3 log2). Cycling T/NK: pretrained closer in 4 of 4 same-cohort settings (1 significant) and 4 of 4 other-cohort comparisons (4 significant; scratch 0.08x). ISG-high T: pretrained closer in 4 of 4 same-cohort settings (1 significant) but scratch closer in 4 of 4 other-cohort comparisons (0 significant; scratch 1.10x vs pretrained 1.54–1.98x). Same-cohort state-level calls (13 states x 4 settings): pretrained closer 3, scratch closer 7 of 52; of the scratch calls 4 are label over-calls by the pretrained arms (Plasmablast, Proliferating T), 2 are states where both arms are more than 4-fold off (Granulocyte-like), and 1 is DN2 B (58 pairs + recipes -0.70 [-1.21, -0.08]); scratch is also closer on MS1 at 58 pairs (-0.97 [-1.44, +0.03], n.s.). C1Q-high: 0.47x or more with the cohort's own pairs (both initialisations), 0.10x or less without them. Fold 0 is the own-pair LoRA's best fold for C1Q-high and cycling T/NK (58 pairs: 1.03x and 1.00x vs 0.27–0.82x and 0.32–0.64x in folds 1–4); scratch has not been run on folds 1–4. One fold, one held-out cohort, one seed; no multiplicity correction. Full analysis: plans/rare_states_screen_20261004/README.md and out/scratch_vs_lora_20261005/REPORT.md (two verification passes on the same-cohort and unmasked analyses); the masked cross-cohort numbers here come from the REPORT addendum and masked_cross_bootstrap.csv, which supersede the unmasked cross-cohort readings in the REPORT body.",
+   "numbers": [
+    {
+     "value": "C1Q-high mono: same cohort 5 pairs LoRA 1.07 / scratch 1.01, 58 pairs LoRA 1.05 / scratch 0.47, 58 pairs + recipes LoRA 0.63 / scratch 0.53; other cohorts Own-cohort LoRA (reference) 0.51, Calibration 0.08, LoRA r16 0.04, Full FT 0.08, From scratch 0.07",
+     "source": "data/secS_scratch_rare_states.csv"
+    },
+    {
+     "value": "MS1 mono: same cohort 5 pairs LoRA 0.15 / scratch 0.10, 58 pairs LoRA 0.21 / scratch 0.40, 58 pairs + recipes LoRA 0.30 / scratch 0.46; other cohorts Own-cohort LoRA (reference) 0.72, Calibration 0.73, LoRA r16 0.12, Full FT 0.27, From scratch 0.16",
+     "source": "data/secS_scratch_rare_states.csv"
+    },
+    {
+     "value": "Cycling mono: same cohort 5 pairs LoRA 0.11 / scratch 0.06, 58 pairs LoRA 0.09 / scratch 0.09, 58 pairs + recipes LoRA 0.10 / scratch 0.09; other cohorts Own-cohort LoRA (reference) 0.24, Calibration 0.26, LoRA r16 0.07, Full FT 0.12, From scratch 0.04",
+     "source": "data/secS_scratch_rare_states.csv"
+    },
+    {
+     "value": "Cycling T/NK: same cohort 5 pairs LoRA 1.15 / scratch 0.51, 58 pairs LoRA 0.93 / scratch 0.42, 58 pairs + recipes LoRA 0.99 / scratch 0.48; other cohorts Own-cohort LoRA (reference) 0.52, Calibration 0.48, LoRA r16 0.13, Full FT 0.36, From scratch 0.08",
+     "source": "data/secS_scratch_rare_states.csv"
+    },
+    {
+     "value": "ISG-high T: same cohort 5 pairs LoRA 0.46 / scratch 0.15, 58 pairs LoRA 0.37 / scratch 0.17, 58 pairs + recipes LoRA 0.53 / scratch 0.18; other cohorts Own-cohort LoRA (reference) 0.58, Calibration 1.54, LoRA r16 1.71, Full FT 1.98, From scratch 1.10",
+     "source": "data/secS_scratch_rare_states.csv"
+    },
+    {
+     "value": "Plasmablast (label): same cohort 5 pairs LoRA 1.87 / scratch 1.12, 58 pairs LoRA 3.47 / scratch 1.24, 58 pairs + recipes LoRA 2.30 / scratch 1.18; other cohorts Own-cohort LoRA (reference) 0.76, Calibration 0.78, LoRA r16 1.38, Full FT 2.21, From scratch 0.87",
+     "source": "data/secS_scratch_rare_states.csv"
+    },
+    {
+     "value": "DN2 B: same cohort 5 pairs LoRA 1.11 / scratch 1.63, 58 pairs LoRA 0.35 / scratch 0.63, 58 pairs + recipes LoRA 0.28 / scratch 0.46; other cohorts Own-cohort LoRA (reference) 0.29, Calibration 0.28, LoRA r16 0.14, Full FT 0.29, From scratch 0.27",
+     "source": "data/secS_scratch_rare_states.csv"
+    },
+    {
+     "value": "Granulocyte-like: same cohort 5 pairs LoRA 0.05 / scratch 0.13, 58 pairs LoRA 0.04 / scratch 0.04, 58 pairs + recipes LoRA 0.03 / scratch 0.06; other cohorts Own-cohort LoRA (reference) 0.06, Calibration 0.07, LoRA r16 0.02, Full FT 0.01, From scratch 0.02",
+     "source": "data/secS_scratch_rare_states.csv"
+    }
+   ]
+  }
+ ]
+}

paper-releases/pbisc-diffusion/updates/20261005T175437Z-deck-supplementary-other-tissues-review/diffusion/metadata/request.json

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+  "project_id": "pbisc-diffusion",
+  "summary": "Paper summary deck 2026-09-30 (presentations/2026-09-30--paper-summary--r00): English slides over the ten paper sections plus Supplementary and Appendix blocks (slide list in README.md). Deck, PDF, frozen 12:00 draft, builder, figure scripts, figures and every plotted/quoted number table. CPU only; no new checkpoint or inference. || 2026-10-06 deck update (45 slides). The from-scratch (no pretraining) results move to a new Supplementary block: 'No pretraining: same cohort / other cohorts, from scratch' plus a new 'Rare states: from scratch vs pretrained' slide (rare-state screen, donor bootstrap, masked cross-cohort scoring). New section-10 slide 'Next: other tissues from a few dozen pairs' (Discussion framing: with enough compute, a few dozen paired samples plus pseudobulk recipes come close to the pretrained result in a one-fold pilot; a route to other tissues). 'Longer training on other cohorts: gap stays' with training minutes to saturation from RUN.json. A 5-agent review's 39 confirmed issues are fixed (33.1 M train cells, significance-based rare-state wording with the fold-0 caveat, receipt-derived UMI shares and stopping settings, cohort-mean speed-up keywords, slide pointers by title). CPU only; no new checkpoint or inference. The scSemiProfiler sepsis CV queue still running on server_1 is not part of this delta."
+}