Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_lora_n5__raw/README.md

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+# score_ft.py output: ye2026_sepsis, 82 scored donors
+
+Arms: within_lora_n5__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 82 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) (12300 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 0.9805, coverage 0.9997.
+   **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
+   0.9796, coverage 0.9998.
+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 = 61) vs control groups ['adult_HC', 'adult_ICU_ctrl', 'ped_HC', 'ped_ICU_ctrl'] (n = 21); 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 61 + 21
+   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/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_lora_n5__raw/arms/within_lora_n5__raw/deg_top50_lists.csv

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+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000123358
+T cell,observed,2,ENSG00000090382
+T cell,observed,3,ENSG00000143333
+T cell,observed,4,ENSG00000109321
+T cell,observed,5,ENSG00000124762
+T cell,observed,6,ENSG00000184113
+T cell,observed,7,ENSG00000144655
+T cell,observed,8,ENSG00000118515
+T cell,observed,9,ENSG00000184557
+T cell,observed,10,ENSG00000162772
+T cell,observed,11,ENSG00000232810
+T cell,observed,12,ENSG00000134531
+T cell,observed,13,ENSG00000277632
+T cell,observed,14,ENSG00000144290
+T cell,observed,15,ENSG00000112149
+T cell,observed,16,ENSG00000168497
+T cell,observed,17,ENSG00000062524
+T cell,observed,18,ENSG00000163563
+T cell,observed,19,ENSG00000113070
+T cell,observed,20,ENSG00000101162
+T cell,observed,21,ENSG00000168209
+T cell,observed,22,ENSG00000158813
+T cell,observed,23,ENSG00000173114
+T cell,observed,24,ENSG00000127920
+T cell,observed,25,ENSG00000120708
+T cell,observed,26,ENSG00000138166
+T cell,observed,27,ENSG00000168329
+T cell,observed,28,ENSG00000119508
+T cell,observed,29,ENSG00000085265
+T cell,observed,30,ENSG00000275302
+T cell,observed,31,ENSG00000100906
+T cell,observed,32,ENSG00000179388
+T cell,observed,33,ENSG00000108551
+T cell,observed,34,ENSG00000128016
+T cell,observed,35,ENSG00000160789
+T cell,observed,36,ENSG00000100079
+T cell,observed,37,ENSG00000121552
+T cell,observed,38,ENSG00000110848
+T cell,observed,39,ENSG00000150681
+T cell,observed,40,ENSG00000197728
+T cell,observed,41,ENSG00000110077
+T cell,observed,42,ENSG00000115607
+T cell,observed,43,ENSG00000134545
+T cell,observed,44,ENSG00000125968
+T cell,observed,45,ENSG00000091129
+T cell,observed,46,ENSG00000113088
+T cell,observed,47,ENSG00000106066
+T cell,observed,48,ENSG00000130844
+T cell,observed,49,ENSG00000117281
+T cell,observed,50,ENSG00000038427
+T cell,generated,1,ENSG00000163737
+T cell,generated,2,ENSG00000101162
+T cell,generated,3,ENSG00000127920
+T cell,generated,4,ENSG00000169704
+T cell,generated,5,ENSG00000196968
+T cell,generated,6,ENSG00000204420
+T cell,generated,7,ENSG00000188322
+T cell,generated,8,ENSG00000177570
+T cell,generated,9,ENSG00000167578
+T cell,generated,10,ENSG00000132964
+T cell,generated,11,ENSG00000173065
+T cell,generated,12,ENSG00000113319
+T cell,generated,13,ENSG00000088812
+T cell,generated,14,ENSG00000123607
+T cell,generated,15,ENSG00000064687
+T cell,generated,16,ENSG00000198728
+T cell,generated,17,ENSG00000059122
+T cell,generated,18,ENSG00000104880
+T cell,generated,19,ENSG00000100307
+T cell,generated,20,ENSG00000175216
+T cell,generated,21,ENSG00000088387
+T cell,generated,22,ENSG00000196329
+T cell,generated,23,ENSG00000100629
+T cell,generated,24,ENSG00000163606
+T cell,generated,25,ENSG00000109943
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+T cell,generated,28,ENSG00000127152
+T cell,generated,29,ENSG00000148154
+T cell,generated,30,ENSG00000180628
+T cell,generated,31,ENSG00000164466
+T cell,generated,32,ENSG00000108839
+T cell,generated,33,ENSG00000134490
+B cell,observed,1,ENSG00000123358
+B cell,observed,2,ENSG00000090382
+B cell,observed,3,ENSG00000184557
+B cell,observed,4,ENSG00000143333
+B cell,observed,5,ENSG00000125968
+B cell,observed,6,ENSG00000124762
+B cell,observed,7,ENSG00000162772
+B cell,observed,8,ENSG00000113088
+B cell,observed,9,ENSG00000066923
+B cell,observed,10,ENSG00000118515
+B cell,observed,11,ENSG00000158050
+B cell,observed,12,ENSG00000119508
+B cell,observed,13,ENSG00000168209
+B cell,observed,14,ENSG00000232810
+B cell,observed,15,ENSG00000168329
+B cell,observed,16,ENSG00000114315
+B cell,observed,17,ENSG00000112149
+B cell,observed,18,ENSG00000137441
+B cell,observed,19,ENSG00000138166
+B cell,observed,20,ENSG00000185022
+B cell,observed,21,ENSG00000090339
+B cell,observed,22,ENSG00000145649
+B cell,observed,23,ENSG00000130844
+B cell,observed,24,ENSG00000150625
+B cell,observed,25,ENSG00000153563
+B cell,observed,26,ENSG00000165949
+B cell,observed,27,ENSG00000180739
+B cell,observed,28,ENSG00000153234
+B cell,observed,29,ENSG00000160654
+B cell,observed,30,ENSG00000143603
+B cell,observed,31,ENSG00000103257
+B cell,observed,32,ENSG00000172673
+B cell,observed,33,ENSG00000110448
+B cell,observed,34,ENSG00000151090
+B cell,observed,35,ENSG00000111796
+B cell,observed,36,ENSG00000173114
+B cell,observed,37,ENSG00000166750
+B cell,observed,38,ENSG00000144655
+B cell,observed,39,ENSG00000172116
+B cell,observed,40,ENSG00000100906
+B cell,observed,41,ENSG00000099860
+B cell,observed,42,ENSG00000184613
+B cell,observed,43,ENSG00000271503
+B cell,observed,44,ENSG00000115523
+B cell,observed,45,ENSG00000085265
+B cell,observed,46,ENSG00000102245
+B cell,observed,47,ENSG00000120708
+B cell,observed,48,ENSG00000105374
+B cell,observed,49,ENSG00000101665
+B cell,observed,50,ENSG00000184545
+B cell,generated,1,ENSG00000133985
+B cell,generated,2,ENSG00000133812
+B cell,generated,3,ENSG00000065029
+B cell,generated,4,ENSG00000186918
+B cell,generated,5,ENSG00000178607
+B cell,generated,6,ENSG00000175857
+B cell,generated,7,ENSG00000259207
+B cell,generated,8,ENSG00000132635
+B cell,generated,9,ENSG00000270629
+B cell,generated,10,ENSG00000167476
+B cell,generated,11,ENSG00000137193
+B cell,generated,12,ENSG00000048052
+B cell,generated,13,ENSG00000179715
+B cell,generated,14,ENSG00000148429
+B cell,generated,15,ENSG00000185883
+B cell,generated,16,ENSG00000163534
+B cell,generated,17,ENSG00000104880
+B cell,generated,18,ENSG00000120875
+B cell,generated,19,ENSG00000088726
+B cell,generated,20,ENSG00000165209
+B cell,generated,21,ENSG00000171174
+B cell,generated,22,ENSG00000133789
+B cell,generated,23,ENSG00000140694
+B cell,generated,24,ENSG00000086300
+B cell,generated,25,ENSG00000145416
+B cell,generated,26,ENSG00000227507
+B cell,generated,27,ENSG00000075884
+B cell,generated,28,ENSG00000153064
+Monocyte,observed,1,ENSG00000087116
+Monocyte,observed,2,ENSG00000159189
+Monocyte,observed,3,ENSG00000115590
+Monocyte,observed,4,ENSG00000166428
+Monocyte,observed,5,ENSG00000173369
+Monocyte,observed,6,ENSG00000115009
+Monocyte,observed,7,ENSG00000113088
+Monocyte,observed,8,ENSG00000108950
+Monocyte,observed,9,ENSG00000123610
+Monocyte,observed,10,ENSG00000100079
+Monocyte,observed,11,ENSG00000146070
+Monocyte,observed,12,ENSG00000179639
+Monocyte,observed,13,ENSG00000145649
+Monocyte,observed,14,ENSG00000180644
+Monocyte,observed,15,ENSG00000137441
+Monocyte,observed,16,ENSG00000115523
+Monocyte,observed,17,ENSG00000153563
+Monocyte,observed,18,ENSG00000111796
+Monocyte,observed,19,ENSG00000100450
+Monocyte,observed,20,ENSG00000134539
+Monocyte,observed,21,ENSG00000073861
+Monocyte,observed,22,ENSG00000184613
+Monocyte,observed,23,ENSG00000163739
+Monocyte,observed,24,ENSG00000147138
+Monocyte,observed,25,ENSG00000139970
+Monocyte,observed,26,ENSG00000129538
+Monocyte,observed,27,ENSG00000155659
+Monocyte,observed,28,ENSG00000172116
+Monocyte,observed,29,ENSG00000013725
+Monocyte,observed,30,ENSG00000163734
+Monocyte,observed,31,ENSG00000180739
+Monocyte,observed,32,ENSG00000153823
+Monocyte,observed,33,ENSG00000163564
+Monocyte,observed,34,ENSG00000120262
+Monocyte,observed,35,ENSG00000198821
+Monocyte,observed,36,ENSG00000152495
+Monocyte,observed,37,ENSG00000183918
+Monocyte,observed,38,ENSG00000160856
+Monocyte,observed,39,ENSG00000081041
+Monocyte,observed,40,ENSG00000257017
+Monocyte,observed,41,ENSG00000120885
+Monocyte,observed,42,ENSG00000186810
+Monocyte,observed,43,ENSG00000172575
+Monocyte,observed,44,ENSG00000101096
+Monocyte,observed,45,ENSG00000168685
+Monocyte,observed,46,ENSG00000115085
+Monocyte,observed,47,ENSG00000100385
+Monocyte,observed,48,ENSG00000163508
+Monocyte,observed,49,ENSG00000205336
+Monocyte,observed,50,ENSG00000198851
+Monocyte,generated,1,ENSG00000129757
+Monocyte,generated,2,ENSG00000175857
+Monocyte,generated,3,ENSG00000104814
+Monocyte,generated,4,ENSG00000131196
+Monocyte,generated,5,ENSG00000186153
+Monocyte,generated,6,ENSG00000087338
+Monocyte,generated,7,ENSG00000179583
+Monocyte,generated,8,ENSG00000156831
+Monocyte,generated,9,ENSG00000007312
+Monocyte,generated,10,ENSG00000099308
+Monocyte,generated,11,ENSG00000100079
+Monocyte,generated,12,ENSG00000182578
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+Monocyte,generated,14,ENSG00000140386
+Monocyte,generated,15,ENSG00000147133
+Monocyte,generated,16,ENSG00000196511
+Monocyte,generated,17,ENSG00000112234
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+Monocyte,generated,19,ENSG00000183023
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+Monocyte,generated,21,ENSG00000132394
+Monocyte,generated,22,ENSG00000147459
+Monocyte,generated,23,ENSG00000131378
+Monocyte,generated,24,ENSG00000183508
+Monocyte,generated,25,ENSG00000122986
+Monocyte,generated,26,ENSG00000151466
+Monocyte,generated,27,ENSG00000197548
+Monocyte,generated,28,ENSG00000137841
+Monocyte,generated,29,ENSG00000188191
+Monocyte,generated,30,ENSG00000261371
+Monocyte,generated,31,ENSG00000197283
+Monocyte,generated,32,ENSG00000163935
+Monocyte,generated,33,ENSG00000196531
+NK cell,observed,1,ENSG00000090382
+NK cell,observed,2,ENSG00000085265
+NK cell,observed,3,ENSG00000123358
+NK cell,observed,4,ENSG00000185215
+NK cell,observed,5,ENSG00000110077
+NK cell,observed,6,ENSG00000038427
+NK cell,observed,7,ENSG00000119535
+NK cell,observed,8,ENSG00000163563
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+NK cell,observed,10,ENSG00000116701
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+NK cell,observed,17,ENSG00000144655
+NK cell,observed,18,ENSG00000109321
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+NK cell,observed,20,ENSG00000241399
+NK cell,observed,21,ENSG00000143333
+NK cell,observed,22,ENSG00000197249
+NK cell,observed,23,ENSG00000143546
+NK cell,observed,24,ENSG00000101336
+NK cell,observed,25,ENSG00000168497
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+NK cell,observed,27,ENSG00000160789
+NK cell,observed,28,ENSG00000126759
+NK cell,observed,29,ENSG00000171051
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+NK cell,observed,31,ENSG00000131042
+NK cell,observed,32,ENSG00000197467
+NK cell,observed,33,ENSG00000187164
+NK cell,observed,34,ENSG00000120594
+NK cell,observed,35,ENSG00000160593
+NK cell,observed,36,ENSG00000197766
+NK cell,observed,37,ENSG00000275302
+NK cell,observed,38,ENSG00000189292
+NK cell,observed,39,ENSG00000122877
+NK cell,observed,40,ENSG00000184731
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+NK cell,observed,42,ENSG00000163694
+NK cell,observed,43,ENSG00000106066
+NK cell,observed,44,ENSG00000127920
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+NK cell,observed,46,ENSG00000162444
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+NK cell,observed,48,ENSG00000111275
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+NK cell,observed,50,ENSG00000166592
+NK cell,generated,1,ENSG00000135362
+NK cell,generated,2,ENSG00000163508
+NK cell,generated,3,ENSG00000104299
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+NK cell,generated,5,ENSG00000115084
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+DC,observed,1,ENSG00000179639
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+DC,observed,4,ENSG00000163606
+DC,observed,5,ENSG00000008517
+DC,observed,6,ENSG00000158481
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+DC,observed,8,ENSG00000081059
+DC,observed,9,ENSG00000155974
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+DC,observed,12,ENSG00000271503
+DC,observed,13,ENSG00000107317
+DC,observed,14,ENSG00000138795
+DC,observed,15,ENSG00000139970
+DC,observed,16,ENSG00000160654
+DC,observed,17,ENSG00000109099
+DC,observed,18,ENSG00000112182
+DC,observed,19,ENSG00000156313
+DC,observed,20,ENSG00000153823
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+DC,observed,23,ENSG00000186854
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+DC,observed,25,ENSG00000136111
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+DC,observed,27,ENSG00000134326
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+DC,observed,29,ENSG00000157657
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+DC,observed,31,ENSG00000141337
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+DC,observed,38,ENSG00000198851
+DC,observed,39,ENSG00000062524
+DC,observed,40,ENSG00000013725
+DC,observed,41,ENSG00000171408
+DC,observed,42,ENSG00000177409
+DC,observed,43,ENSG00000172116
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+DC,observed,45,ENSG00000162869
+DC,observed,46,ENSG00000035664
+DC,observed,47,ENSG00000153563
+DC,observed,48,ENSG00000127920
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paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_lora_n5__raw/arms/within_lora_n5__raw/labels/labels.manifest.json

@@ -0,0 +1,156 @@
+{
+  "dataset_id": "Ye2026_sepsis",
+  "split": "generated",
+  "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_lora_n5__raw/arms/within_lora_n5__raw/query.h5ad",
+  "method": "within_lora_n5__raw",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_lora_n5__raw/arms/within_lora_n5__raw/labels/labels.parquet",
+  "training_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/reference/aifi_reference_f01common.h5ad",
+  "target_truth_used_for_fitting": false,
+  "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
+  "labels": [
+    "T cell",
+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
+    "Other"
+  ],
+  "l2_labels": [
+    "ASDC",
+    "CD14 monocyte",
+    "CD16 monocyte",
+    "CD56bright NK cell",
+    "CD56dim NK cell",
+    "CD8aa",
+    "DN T cell",
+    "Effector B cell",
+    "Erythrocyte",
+    "ILC",
+    "Intermediate monocyte",
+    "MAIT",
+    "Memory B cell",
+    "Memory CD4 T cell",
+    "Memory CD8 T cell",
+    "Naive B cell",
+    "Naive CD4 T cell",
+    "Naive CD8 T cell",
+    "Plasma cell",
+    "Platelet",
+    "Progenitor cell",
+    "Proliferating NK cell",
+    "Proliferating T cell",
+    "Transitional B cell",
+    "Treg",
+    "cDC1",
+    "cDC2",
+    "gdT",
+    "pDC"
+  ],
+  "n_cells": 123000,
+  "n_genes": 1005,
+  "note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
+  "label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
+  "query_train_epochs": 0,
+  "confidence_threshold": 0.0,
+  "subset": false,
+  "evaluator_aligned": true,
+  "gene_space": {
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+    "model_genes": 1005,
+    "query_genes": 1006,
+    "model_genes_missing_from_query_zero_padded": 0,
+    "query_genes_outside_model_dropped": 1,
+    "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
+  },
+  "readout": null,
+  "query_build": {
+    "kind": "generated_npz",
+    "poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
+    "readout": "poisson",
+    "seed": 20260916,
+    "set": "within_lora_n5__raw",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated_masked/ye2026_sepsis/hoL_ye2026_sepsis/within_lora_n5__raw.npz",
+    "source_sha256": "5af16db341ca18c9764d7bc3f5fc0005cd74db014d225d3e940cc386a74bb884"
+  },
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+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "model_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/MODEL_MANIFEST.json",
+    "held_out_summary": {
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+      "l1_macro_f1": 0.9715232379009036,
+      "pbmc5_other_accuracy": 0.9920886873267826,
+      "pbmc5_other_macro_f1": 0.9812088972148597
+    }
+  },
+  "label_counts": {
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+      "Monocyte": 21215,
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+      "Other": 3614,
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+      "Erythrocyte": 713,
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+      "Progenitor cell": 183
+    },
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+      "Naive B cell": 11446,
+      "gdT": 8287,
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+      "DN T cell": 4236,
+      "CD56dim NK cell": 3460,
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+      "CD16 monocyte": 3124,
+      "CD8aa": 3093,
+      "Effector B cell": 2533,
+      "Platelet": 2218,
+      "Intermediate monocyte": 2025,
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+      "Proliferating NK cell": 917,
+      "CD56bright NK cell": 779,
+      "Erythrocyte": 713,
+      "Plasma cell": 705,
+      "Proliferating T cell": 696,
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+      "ILC": 500,
+      "cDC2": 416,
+      "Progenitor cell": 183,
+      "pDC": 93,
+      "cDC1": 16,
+      "ASDC": 9
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.918043800132546,
+    "mean_l1_mass": 0.9859100580215454,
+    "frac_l2_max_prob_ge_0.5": 0.9700813008130081
+  },
+  "timings_s": {
+    "predict": 1.0,
+    "total": 1.8
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-05T10:52:38.923142+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_lora_n5__raw/contrast.csv

@@ -0,0 +1,14 @@
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