Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/README.md

@@ -0,0 +1,73 @@
+# score_ft.py output: ye2026_sepsis, 17 scored donors
+
+Arms: zs__raw, lora_n5__raw, real_lora__raw, lora_recipe__raw, real_full__raw, scratch_full__raw, scratch_n5__raw, scratch_recipe__raw.  Every arm is scored on the same donors against the same observed reference.
+
+## Inputs and fixed contracts
+- Observed reference: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/reference.npz` (sha bac12da8a241), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis;
+  observed cells sum exactly to the features pseudobulk of every donor. Observed labels: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/observed_labels/labels/labels.parquet.
+- Generated cells: `generated_counts` read out once with Poisson(seed 20260916) over the **whole NPZ in row order**
+  (`poisson_readout.poisson_integerise`), then the scored donors' rows. These integer counts are used for labels, embedding,
+  depth and the contrast. Pseudobulk uses the summed `generated_counts` (rates), as `score_generated.py`.
+- Labels: frozen f01common scANVI (`predict_scanvi.py`, CPU, zero query epochs), six-type gate ['T cell', 'B cell', 'Monocyte', 'NK cell', 'DC', 'Other']; query genes =
+  the 1,006-gene annotation list minus genes the dataset's sc assay did not measure in every sample (1006 genes).
+- Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (5975 genes).
+
+## Definitions
+1. **Composition**: fraction of each donor's cells per six-type label (all generated cells; all observed QC cells).
+   `comp_l1` = sum over the six labels of |generated - observed| (immicro_common.l1). `comp_l1_obs_loo_null` = L1 of the
+   donor's observed composition to the mean of the *other scored donors'* observed compositions. `composition_top1` =
+   fraction of donors whose generated composition is closest (L1) to their own observed composition.
+2. **Pseudobulk**: `pb_r` = Pearson r of CPM-log1p(summed generated_counts) vs CPM-log1p(observed pseudobulk) on the scoring
+   genes (evaluate_realbulk.cpm_log1p / paired_r). `pb_top1` = the donor's generated pseudobulk is closest (Pearson) to its own
+   observed pseudobulk among the 17 scored donors (immicro_common.retrieval = evaluate_realbulk.top1 arithmetic).
+3. **Precision / coverage / density** (stage_b_embed.py functions): per-cell CP10K over the scoring genes + log1p; PCA-50
+   (randomized, random_state 20260925) and k = 10 real-real k-NN balls fitted on **R1 of the scored donors only**.
+   Reference rule (independent of fold and arm): per donor, cells in canonical order (library_id+barcode), one
+   permutation from `default_rng([20260925, uint64(sha256(donor)[:8])])`; R1 = first n, R2 = next n,
+   n = min(150, n_cells // 2) (2550 R1 cells here). Generated query: per donor n cells (the donor's R1 size),
+   without replacement, `default_rng([20260926, same key])`. Precision = fraction of generated cells inside any R1 ball
+   (Kynkaanniemi 2019); coverage = fraction of R1 cells whose ball holds a generated cell; density = Naeem 2020.
+   Per-donor precision = that donor's generated cells; per-donor coverage = that donor's R1 cells (the pooled values are
+   their n-weighted means; plain means when every donor has 150 reference cells). R2 (held-out real cells of the same donors) is the
+   perfect-generator control: precision 0.9969, coverage 1.0000.
+   **Depth matched**: stage_b_embed depth matching run pairwise (R1 vs this arm): per donor and within-donor rank of detected
+   genes, both cells are thinned by UMI sampling without replacement to the smaller detected-gene count; PCA kept from
+   un-thinned R1, radii recomputed on thinned R1; fresh rng(20260929) per arm. R2 control: precision
+   0.9961, coverage 1.0000.
+4. **Monocyte %** = 100 x Monocyte fraction (all cells) per donor; **median UMI per cell** = median over cells of the
+   Poisson-read (generated) / observed counts summed over the scoring genes (per donor, and pooled).
+5. **Group contrast** (T, B, Monocyte, NK): case groups ['adult_sepsis', 'ped_sepsis'] (n = 12) vs control groups ['adult_HC', 'adult_ICU_ctrl', 'ped_HC', 'ped_ICU_ctrl'] (n = 5); rule: explicit --case-groups / --control-groups; groups from features groups.
+   Genes per type = scoring genes detected (count > 0) in >= 1 % of the scored donors' observed
+   cells of that type. Primary statistic `mean_cp10k`: per-cell CP10K over the scoring genes; per donor the mean over its
+   cells of the type (donors with >= 1 such cell); group mean = mean over the group's donors (donor-balanced);
+   logFC = log2(case mean + 1) - log2(control mean + 1). Secondary `pseudobulk_log1p_cpm`: the SLE benchmark evaluator's
+   statistic (donor x type summed counts, log1p CPM over the scoring genes, mean case - mean control;
+   evaluate_generated_vs_truth.group_log_fold_change). Both are computed on the generated cells (their frozen labels) and on
+   the observed cells; `r_generated` = Pearson r of the two logFC vectors. Broadcast baseline `r_broadcast`: the same
+   observed vector against the logFC of the input bulk (condition NPZ `bulk_counts` of the arm, scoring genes, per-donor
+   CP10K resp. log1p CPM, group means). `partial_r_generated_given_broadcast`: r of the OLS residuals of observed and
+   generated logFC on the bulk logFC (residual_specificity.py).
+6. **Top-50 DEG overlap** (contrast.csv rows `statistic = welch_top50_deg`; summary `deg_top50`): the SLE benchmark's score (`total_top50_overlap` of
+   `bulk2sc-paper/scripts/evaluate_generated_vs_truth.py`, Welch backend: the "top-50 DEG 81 / 84" of the final model), run
+   with the evaluator's own functions on the same donor x type pseudobulks as the contrast. Per cell type, observed and
+   generated separately: donor x type summed counts on all 5975 scoring genes (donors of the two groups with
+   >= 1 cell of the type) -> `welch_bh_deg` (log1p CPM, two-sided Welch t-test case vs control, Benjamini-Hochberg over the
+   genes with a defined p-value; needs >= 2 donors per group) -> `top_deg_genes` (FDR < 0.05, descending |logFC|,
+   first 50; shorter when fewer genes pass). `top50_overlap` = |observed list & generated list|; `top50_jaccard`
+   the evaluator's Jaccard. Summary `sum` = total over the scored types (the quantity reported as 81), `max` = the sum of
+   the observed list lengths (the "of 262"), `sum_4type` = T + B + Monocyte + NK. A type is scored when its observed test
+   is defined; an arm whose generated test is undefined for a scored type gets overlap 0. Types: T cell, B cell, Monocyte, NK cell, DC
+   (aggregates: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz).
+   **Broadcast analogue** (`top50_overlap_broadcast`, as `sle_broadcast.py` `broadcast_input_bulk`; not part of the
+   published benchmark): the same test on the arm's condition bulk_counts (scoring genes, the 12 + 5
+   donors), one whole-PBMC top-50 list, compared with every type's observed list.
+
+## Files
+- `per_donor.csv`: one row per arm x donor (all per-donor quantities above).
+- `summary.json`: per arm the donor means / pooled values, provenance (NPZ sha, receipt check, generation metadata,
+  Poisson nnz of the whole NPZ, annotation contract), and the reference block (PCA, R2 control).
+- `contrast.csv`: per arm x cell type x statistic (`mean_cp10k`, `pseudobulk_log1p_cpm`: logFC r; `welch_top50_deg`:
+  top-50 DEG overlap, T / B / Monocyte / NK / DC; columns of the other kind are empty).
+- `arms/<arm>/labels/` (predict_scanvi.py labels + manifest), `arms/<arm>/generated_cells.parquet` (NPZ row, donor, label,
+  UMI on the scoring genes, P/C subsample flag), `arms/<arm>/deg_top50_lists.csv` (observed, generated and broadcast
+  top-50 gene lists, Ensembl ids, rank order).

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/contrast.csv

@@ -0,0 +1,105 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+zs__raw,T cell,mean_cp10k,3276,-0.08242955650705179,0.3932774345878696,-0.1461007206093643,0.12910515351620933,12,5,12,5,61162,8631,,,,,,,,,,,
+zs__raw,T cell,pseudobulk_log1p_cpm,3276,0.034755918484185265,0.34430236190429087,-0.03884876053396737,0.20463859925136924,12,5,12,5,61162,8631,,,,,,,,,,,
+zs__raw,B cell,mean_cp10k,3261,0.06104255822583509,0.47022569734381875,-0.0195454319562281,0.16599051400456835,12,5,12,5,21022,4425,,,,,,,,,,,
+zs__raw,B cell,pseudobulk_log1p_cpm,3261,0.12700585699495992,0.4467015184665126,0.060117663106738106,0.16557362901051695,12,5,12,5,21022,4425,,,,,,,,,,,
+zs__raw,Monocyte,mean_cp10k,3260,0.2711932147865901,0.7018160115879556,0.09533996656220628,0.2939186750501527,12,5,12,5,31471,9506,,,,,,,,,,,
+zs__raw,Monocyte,pseudobulk_log1p_cpm,3260,0.29987864903155775,0.7631886901658,0.04430622094856255,0.357900320466039,12,5,12,5,31471,9506,,,,,,,,,,,
+zs__raw,NK cell,mean_cp10k,3269,0.006878874503327891,0.3607355096498457,-0.07066347156694662,0.19814440789820298,12,5,12,5,10457,1983,,,,,,,,,,,
+zs__raw,NK cell,pseudobulk_log1p_cpm,3269,0.04946261932674456,0.2468852852573835,0.008556945776732057,0.1672328498545464,12,5,12,5,10457,1983,,,,,,,,,,,
+zs__raw,T cell,welch_top50_deg,5975,,,,,12,5,12,5,61162,8631,True,0,0.0,50,50,113,263,0,0.0,0,0
+zs__raw,B cell,welch_top50_deg,5975,,,,,12,5,12,5,21022,4425,True,0,0.0,50,50,164,137,0,0.0,0,0
+zs__raw,Monocyte,welch_top50_deg,5975,,,,,12,5,12,5,31471,9506,True,0,0.0,50,6,932,6,0,0.0,0,0
+zs__raw,NK cell,welch_top50_deg,5975,,,,,12,5,12,5,10457,1983,True,0,0.0,50,7,122,7,0,0.0,0,0
+zs__raw,DC,welch_top50_deg,5975,,,,,12,5,11,5,1035,220,True,0,0.0,50,2,152,2,0,0.0,0,0
+lora_n5__raw,T cell,mean_cp10k,3276,0.20364511678286898,0.3932774345878696,0.11886261772566048,0.24866175096039972,12,5,12,5,61162,12396,,,,,,,,,,,
+lora_n5__raw,T cell,pseudobulk_log1p_cpm,3276,0.13471990320658844,0.34430236190429087,0.02869413783773733,0.3170766870751248,12,5,12,5,61162,12396,,,,,,,,,,,
+lora_n5__raw,B cell,mean_cp10k,3261,0.2870438199867317,0.47022569734381875,0.1938690556858803,0.2589889284065375,12,5,12,5,21022,3997,,,,,,,,,,,
+lora_n5__raw,B cell,pseudobulk_log1p_cpm,3261,0.2380007593352334,0.4467015184665126,0.14965982239054437,0.24195364234876673,12,5,12,5,21022,3997,,,,,,,,,,,
+lora_n5__raw,Monocyte,mean_cp10k,3260,0.354062750068399,0.7018160115879556,0.17590754138588435,0.3363479114322682,12,5,12,5,31471,7183,,,,,,,,,,,
+lora_n5__raw,Monocyte,pseudobulk_log1p_cpm,3260,0.35261107996494273,0.7631886901658,0.09218021613743108,0.39016194564940465,12,5,12,5,31471,7183,,,,,,,,,,,
+lora_n5__raw,NK cell,mean_cp10k,3269,0.08592847939245817,0.3607355096498457,0.03109554111192825,0.1588277196598059,12,5,12,5,10457,964,,,,,,,,,,,
+lora_n5__raw,NK cell,pseudobulk_log1p_cpm,3269,0.027407018717002376,0.2468852852573835,-0.007609840470908461,0.14058374875819812,12,5,12,5,10457,964,,,,,,,,,,,
+lora_n5__raw,T cell,welch_top50_deg,5975,,,,,12,5,12,5,61162,12396,True,0,0.0,50,0,113,0,0,0.0,0,0
+lora_n5__raw,B cell,welch_top50_deg,5975,,,,,12,5,12,5,21022,3997,True,0,0.0,50,2,164,2,0,0.0,0,0
+lora_n5__raw,Monocyte,welch_top50_deg,5975,,,,,12,5,12,5,31471,7183,True,0,0.0,50,3,932,3,0,0.0,0,0
+lora_n5__raw,NK cell,welch_top50_deg,5975,,,,,12,5,12,5,10457,964,True,0,0.0,50,1,122,1,0,0.0,0,0
+lora_n5__raw,DC,welch_top50_deg,5975,,,,,12,5,12,5,1035,119,True,1,0.017543859649122806,50,8,152,8,0,0.0,0,0
+real_lora__raw,T cell,mean_cp10k,3276,0.5197650726962013,0.3932774345878696,0.4578725168310507,0.3007491328724024,12,5,12,5,61162,14147,,,,,,,,,,,
+real_lora__raw,T cell,pseudobulk_log1p_cpm,3276,0.4346250414734638,0.34430236190429087,0.3780956486173911,0.2694640128824917,12,5,12,5,61162,14147,,,,,,,,,,,
+real_lora__raw,B cell,mean_cp10k,3261,0.5466043803673709,0.47022569734381875,0.4896357744441666,0.28029071751113604,12,5,12,5,21022,4903,,,,,,,,,,,
+real_lora__raw,B cell,pseudobulk_log1p_cpm,3261,0.4058131060671425,0.4467015184665126,0.3439295341711949,0.23970387299122686,12,5,12,5,21022,4903,,,,,,,,,,,
+real_lora__raw,Monocyte,mean_cp10k,3260,0.4987781592088495,0.7018160115879556,0.3407267767681704,0.39262302868141774,12,5,12,5,31471,3891,,,,,,,,,,,
+real_lora__raw,Monocyte,pseudobulk_log1p_cpm,3260,0.49959647615788155,0.7631886901658,0.3474474792286492,0.38285452510633905,12,5,12,5,31471,3891,,,,,,,,,,,
+real_lora__raw,NK cell,mean_cp10k,3269,0.38226976045895433,0.3607355096498457,0.3523740094281199,0.16044903545529676,12,5,12,5,10457,1504,,,,,,,,,,,
+real_lora__raw,NK cell,pseudobulk_log1p_cpm,3269,0.2490124660577032,0.2468852852573835,0.24031703941125349,0.06750382286712334,12,5,12,5,10457,1504,,,,,,,,,,,
+real_lora__raw,T cell,welch_top50_deg,5975,,,,,12,5,12,5,61162,14147,True,0,0.0,50,0,113,0,0,0.0,0,0
+real_lora__raw,B cell,welch_top50_deg,5975,,,,,12,5,12,5,21022,4903,True,0,0.0,50,0,164,0,0,0.0,0,0
+real_lora__raw,Monocyte,welch_top50_deg,5975,,,,,12,5,12,5,31471,3891,True,0,0.0,50,1,932,1,0,0.0,0,0
+real_lora__raw,NK cell,welch_top50_deg,5975,,,,,12,5,12,5,10457,1504,True,0,0.0,50,3,122,3,0,0.0,0,0
+real_lora__raw,DC,welch_top50_deg,5975,,,,,12,5,11,5,1035,122,True,1,0.015625,50,15,152,15,0,0.0,0,0
+lora_recipe__raw,T cell,mean_cp10k,3276,0.4555266853105178,0.3932774345878696,0.38216575780195905,0.3083859981562977,12,5,12,5,61162,13851,,,,,,,,,,,
+lora_recipe__raw,T cell,pseudobulk_log1p_cpm,3276,0.4230503174190799,0.34430236190429087,0.3715848274752333,0.24680963259407077,12,5,12,5,61162,13851,,,,,,,,,,,
+lora_recipe__raw,B cell,mean_cp10k,3261,0.5137446232745543,0.47022569734381875,0.46200411631745336,0.25383333747312137,12,5,12,5,21022,5157,,,,,,,,,,,
+lora_recipe__raw,B cell,pseudobulk_log1p_cpm,3261,0.4232486679858749,0.4467015184665126,0.36817332085564036,0.22983695376805993,12,5,12,5,21022,5157,,,,,,,,,,,
+lora_recipe__raw,Monocyte,mean_cp10k,3260,0.49716921214169785,0.7018160115879556,0.3246797808312777,0.40744234519798106,12,5,12,5,31471,3965,,,,,,,,,,,
+lora_recipe__raw,Monocyte,pseudobulk_log1p_cpm,3260,0.4561616879554607,0.7631886901658,0.2779414503415366,0.3800338405090842,12,5,12,5,31471,3965,,,,,,,,,,,
+lora_recipe__raw,NK cell,mean_cp10k,3269,0.3275390673134424,0.3607355096498457,0.2785757400278991,0.20267675299372456,12,5,12,5,10457,1350,,,,,,,,,,,
+lora_recipe__raw,NK cell,pseudobulk_log1p_cpm,3269,0.1792109700734274,0.2468852852573835,0.16160294829161012,0.09441654750001419,12,5,12,5,10457,1350,,,,,,,,,,,
+lora_recipe__raw,T cell,welch_top50_deg,5975,,,,,12,5,12,5,61162,13851,True,0,0.0,50,3,113,3,0,0.0,0,0
+lora_recipe__raw,B cell,welch_top50_deg,5975,,,,,12,5,12,5,21022,5157,True,0,0.0,50,1,164,1,0,0.0,0,0
+lora_recipe__raw,Monocyte,welch_top50_deg,5975,,,,,12,5,12,5,31471,3965,True,0,0.0,50,0,932,0,0,0.0,0,0
+lora_recipe__raw,NK cell,welch_top50_deg,5975,,,,,12,5,12,5,10457,1350,True,1,0.01694915254237288,50,10,122,10,0,0.0,0,0
+lora_recipe__raw,DC,welch_top50_deg,5975,,,,,12,5,12,5,1035,138,True,0,0.0,50,50,152,59,0,0.0,0,0
+real_full__raw,T cell,mean_cp10k,3276,0.5263102943181304,0.3932774345878696,0.45127555880717013,0.3499780738167342,12,5,12,5,61162,13435,,,,,,,,,,,
+real_full__raw,T cell,pseudobulk_log1p_cpm,3276,0.40624622280985906,0.34430236190429087,0.35074031401629346,0.25515402161872536,12,5,12,5,61162,13435,,,,,,,,,,,
+real_full__raw,B cell,mean_cp10k,3261,0.5426543195826619,0.47022569734381875,0.48415232131251346,0.2823063933608265,12,5,12,5,21022,5233,,,,,,,,,,,
+real_full__raw,B cell,pseudobulk_log1p_cpm,3261,0.4032232759945149,0.4467015184665126,0.34216248235836716,0.23686482429708647,12,5,12,5,21022,5233,,,,,,,,,,,
+real_full__raw,Monocyte,mean_cp10k,3260,0.5665441003109477,0.7018160115879556,0.36950922282939214,0.4777701165533974,12,5,12,5,31471,4120,,,,,,,,,,,
+real_full__raw,Monocyte,pseudobulk_log1p_cpm,3260,0.4936522974370248,0.7631886901658,0.296855344471577,0.4185637861494763,12,5,12,5,31471,4120,,,,,,,,,,,
+real_full__raw,NK cell,mean_cp10k,3269,0.32177879507554924,0.3607355096498457,0.26624729689539317,0.2205924370280916,12,5,12,5,10457,1380,,,,,,,,,,,
+real_full__raw,NK cell,pseudobulk_log1p_cpm,3269,0.1535891570442277,0.2468852852573835,0.14278380300719962,0.06277474092711705,12,5,12,5,10457,1380,,,,,,,,,,,
+real_full__raw,T cell,welch_top50_deg,5975,,,,,12,5,12,5,61162,13435,True,0,0.0,50,0,113,0,0,0.0,0,0
+real_full__raw,B cell,welch_top50_deg,5975,,,,,12,5,12,5,21022,5233,True,0,0.0,50,0,164,0,0,0.0,0,0
+real_full__raw,Monocyte,welch_top50_deg,5975,,,,,12,5,12,5,31471,4120,True,0,0.0,50,0,932,0,0,0.0,0,0
+real_full__raw,NK cell,welch_top50_deg,5975,,,,,12,5,12,5,10457,1380,True,0,0.0,50,0,122,0,0,0.0,0,0
+real_full__raw,DC,welch_top50_deg,5975,,,,,12,5,12,5,1035,163,True,0,0.0,50,43,152,43,0,0.0,0,0
+scratch_full__raw,T cell,mean_cp10k,3276,0.6405324701134752,0.3932774345878696,0.5915938851441552,0.31696646283284663,12,5,12,5,61162,13443,,,,,,,,,,,
+scratch_full__raw,T cell,pseudobulk_log1p_cpm,3276,0.4251290040363076,0.34430236190429087,0.38461192744840716,0.20918005110538934,12,5,12,5,61162,13443,,,,,,,,,,,
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paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/per_donor.csv

@@ -0,0 +1,137 @@
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+scratch_recipe__raw,PHC03,ped_HC,1500,9638,150,0.6106666666666667,0.6757626063498651,0.232,0.17804523760116206,0.10066666666666667,0.055613197758871136,0.03333333333333333,0.07273293214359826,0.002,0.011516912222452791,0.021333333333333333,0.006329113924050633,0.2280249014318323,0.5245802286446084,0.9112956727089853,5,False,0.9933333333333333,0.9266666666666666,0.9933333333333333,0.9866666666666667,10.066666666666666,5.561319775887114,1741.0,1660.5
+scratch_recipe__raw,PIC04,ped_ICU_ctrl,1500,11535,150,0.508,0.36341569137407886,0.14266666666666666,0.08253142609449501,0.24866666666666667,0.4273948851322063,0.074,0.03233636757693975,0.006666666666666667,0.006501950585175552,0.02,0.08781967923710446,0.49309579540528825,0.46601933835481935,0.9163903845107353,5,False,1.0,0.94,0.9733333333333334,0.9933333333333333,24.866666666666667,42.73948851322063,1952.5,1144.0
+scratch_recipe__raw,Res-PS25,ped_sepsis,1500,6203,150,0.35,0.3562792197323876,0.5653333333333334,0.42447202966306624,0.059333333333333335,0.18458810253103336,0.011333333333333334,0.0095115266806384,0.0006666666666666666,0.005642431081734645,0.013333333333333334,0.01950669031113977,0.28536622064592404,0.5472774959628155,0.9089528588206979,1,True,0.9933333333333333,0.8266666666666667,0.9733333333333334,0.9333333333333333,5.933333333333334,18.458810253103337,1632.5,2342.0
+scratch_recipe__raw,Res-S139,adult_sepsis,1500,2657,150,0.6173333333333333,0.3522770041400075,0.14333333333333334,0.06925103500188182,0.06533333333333333,0.26345502446368085,0.15466666666666667,0.29055325555137373,0.0013333333333333333,0.00978547233722243,0.018,0.014678208505833647,0.6849208380378873,0.4788067877633468,0.8971589636674242,13,False,0.9933333333333333,0.8333333333333334,0.9866666666666667,0.96,6.533333333333332,26.345502446368087,1366.5,1637.0
+scratch_recipe__raw,Res-S26,adult_sepsis,1500,6036,150,0.736,0.6973161033797217,0.16133333333333333,0.145791915175613,0.012,0.023028495692511596,0.072,0.11911862160371106,0.0,0.0001656726308813784,0.018666666666666668,0.0145791915175613,0.11662557985420803,0.608009358576924,0.9181202001930207,1,True,0.98,0.9733333333333334,0.98,0.9866666666666667,1.2,2.3028495692511597,1764.0,3953.0
+scratch_recipe__raw,Res-S77,adult_sepsis,1500,7804,150,0.574,0.685033316248078,0.3353333333333333,0.20861096873398258,0.01,0.04651460789338801,0.058666666666666666,0.023193234238851872,0.0,0.0012813941568426447,0.022,0.035366478728856995,0.32439159405433116,0.5993076173488051,0.9093666692270634,3,False,0.9933333333333333,0.9733333333333334,0.98,0.9733333333333334,1.0,4.651460789338801,1670.0,2095.0
+scratch_recipe__raw,Skin-S140,adult_sepsis,1500,7668,150,0.43533333333333335,0.2646061554512259,0.27066666666666667,0.23735002608242045,0.118,0.3272039645279082,0.134,0.042383933229003655,0.0013333333333333333,0.0003912363067292645,0.04066666666666666,0.12806468440271257,0.5932039645279082,0.48827750640154627,0.9245405562213258,2,False,1.0,0.8333333333333334,0.9933333333333333,0.92,11.799999999999999,32.720396452790816,1569.0,2069.5
+scratch_recipe__raw,Uri-S147,adult_sepsis,1500,7529,150,0.6133333333333333,0.5427015539912339,0.17933333333333334,0.20268295922433258,0.11266666666666666,0.18262717492362865,0.07133333333333333,0.031212644441492896,0.0033333333333333335,0.004648691725328729,0.02,0.036126975693983265,0.22150493646787972,0.28425560234500524,0.9244107164405855,1,True,1.0,0.96,0.9933333333333333,0.9866666666666667,11.266666666666666,18.262717492362864,1872.0,2024.0

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/summary.json

@@ -0,0 +1,2500 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-05T04:58:55.587617+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "ye2026_sepsis",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005",
+  "--threads",
+  "8",
+  "--arm",
+  "zs__raw=/tmp/claude-1000/-home-sj-server-1/79519e81-f10b-453d-b06f-e70ccb0d836a/scratchpad/f0_compare/zs__raw.npz",
+  "--arm",
+  "lora_n5__raw=/tmp/claude-1000/-home-sj-server-1/79519e81-f10b-453d-b06f-e70ccb0d836a/scratchpad/f0_compare/lora_n5__raw.npz",
+  "--arm",
+  "real_lora__raw=/tmp/claude-1000/-home-sj-server-1/79519e81-f10b-453d-b06f-e70ccb0d836a/scratchpad/f0_compare/real_lora__raw.npz",
+  "--arm",
+  "lora_recipe__raw=/tmp/claude-1000/-home-sj-server-1/79519e81-f10b-453d-b06f-e70ccb0d836a/scratchpad/f0_compare/lora_recipe__raw.npz",
+  "--arm",
+  "real_full__raw=/tmp/claude-1000/-home-sj-server-1/79519e81-f10b-453d-b06f-e70ccb0d836a/scratchpad/f0_compare/real_full__raw.npz",
+  "--arm",
+  "scratch_full__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/scratch_full__raw.npz",
+  "--arm",
+  "scratch_n5__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/scratch_n5__raw.npz",
+  "--arm",
+  "scratch_recipe__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/scratch_recipe__raw.npz",
+  "--case-groups",
+  "adult_sepsis,ped_sepsis",
+  "--control-groups",
+  "adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl"
+ ],
+ "arms": [
+  "zs__raw",
+  "lora_n5__raw",
+  "real_lora__raw",
+  "lora_recipe__raw",
+  "real_full__raw",
+  "scratch_full__raw",
+  "scratch_n5__raw",
+  "scratch_recipe__raw"
+ ],
+ "donors": [
+  "Abd-PS19",
+  "Abd-PS23",
+  "Abd-S123",
+  "Abd-S39",
+  "Abd-S47",
+  "Abd-S66",
+  "HC01",
+  "HC07",
+  "IC23",
+  "PHC03",
+  "PIC04",
+  "Res-PS25",
+  "Res-S139",
+  "Res-S26",
+  "Res-S77",
+  "Skin-S140",
+  "Uri-S147"
+ ],
+ "n_donors": 17,
+ "reference": {
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+  "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+  "features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
+  "n_r1_cells": 2550,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.3596964478492737,
+   "n_fit_cells": 2550
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+  "r2_control": {
+   "precision": 0.9968627450980392,
+   "coverage": 1.0,
+   "density": 2.1749019607843136,
+   "n_query": 2550,
+   "depth_matched": {
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+    "coverage": 1.0,
+    "density": 2.1365882352941177
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+  },
+  "observed_l1_loo_null_mean": 0.5132314215340571
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 12,
+  "n_control_donors": 5,
+  "n_donors_in_neither": 0,
+  "case": [
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_HC",
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis"
+  ]
+ },
+ "deg_definition": {
+  "enabled": true,
+  "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
+  "functions": [
+   "welch_bh_deg",
+   "top_deg_genes",
+   "jaccard"
+  ],
+  "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
+  "top_n": 50,
+  "fdr": 0.05,
+  "n_genes": 5975,
+  "types": [
+   "T cell",
+   "B cell",
+   "Monocyte",
+   "NK cell",
+   "DC"
+  ],
+  "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz",
+  "aggregates_sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
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+    "top_list_size": 50
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+    "n_case_donors": 12,
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+    "top_list_size": 50
+   },
+   "Monocyte": {
+    "n_significant": 932,
+    "n_tested": 5587,
+    "n_case_donors": 12,
+    "n_control_donors": 5,
+    "n_cells": 31471,
+    "top_list_size": 50
+   },
+   "NK cell": {
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+    "n_tested": 5322,
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+    "n_control_donors": 5,
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+    "top_list_size": 50
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+   "DC": {
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+    "n_control_donors": 5,
+    "n_cells": 1035,
+    "top_list_size": 50
+   }
+  },
+  "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
+ },
+ "headline": {
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