Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/fold0/arms/scsemi__raw/deg_top50_lists.csv

@@ -0,0 +1,251 @@
+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000110077
+T cell,observed,2,ENSG00000163606
+T cell,observed,3,ENSG00000102245
+T cell,observed,4,ENSG00000171115
+T cell,observed,5,ENSG00000262655
+T cell,observed,6,ENSG00000216937
+T cell,observed,7,ENSG00000135426
+T cell,observed,8,ENSG00000145687
+T cell,observed,9,ENSG00000173208
+T cell,observed,10,ENSG00000166750
+T cell,observed,11,ENSG00000167106
+T cell,observed,12,ENSG00000070190
+T cell,observed,13,ENSG00000115415
+T cell,observed,14,ENSG00000082512
+T cell,observed,15,ENSG00000166432
+T cell,observed,16,ENSG00000160593
+T cell,observed,17,ENSG00000116138
+T cell,observed,18,ENSG00000156299
+T cell,observed,19,ENSG00000185621
+T cell,observed,20,ENSG00000133805
+T cell,observed,21,ENSG00000137992
+T cell,observed,22,ENSG00000174123
+T cell,observed,23,ENSG00000178562
+T cell,observed,24,ENSG00000071575
+T cell,observed,25,ENSG00000107863
+T cell,observed,26,ENSG00000116525
+T cell,observed,27,ENSG00000121289
+T cell,observed,28,ENSG00000181722
+T cell,observed,29,ENSG00000188641
+T cell,observed,30,ENSG00000124459
+T cell,observed,31,ENSG00000197548
+T cell,observed,32,ENSG00000138641
+T cell,observed,33,ENSG00000152683
+T cell,observed,34,ENSG00000183337
+T cell,observed,35,ENSG00000172575
+T cell,observed,36,ENSG00000171817
+T cell,observed,37,ENSG00000173065
+T cell,observed,38,ENSG00000100242
+T cell,observed,39,ENSG00000011523
+T cell,observed,40,ENSG00000173214
+T cell,observed,41,ENSG00000177272
+T cell,observed,42,ENSG00000158623
+T cell,observed,43,ENSG00000128513
+T cell,observed,44,ENSG00000100351
+T cell,observed,45,ENSG00000070269
+T cell,observed,46,ENSG00000104689
+T cell,observed,47,ENSG00000133103
+T cell,observed,48,ENSG00000065413
+T cell,observed,49,ENSG00000134146
+T cell,observed,50,ENSG00000170581
+B cell,observed,1,ENSG00000113088
+B cell,observed,2,ENSG00000066923
+B cell,observed,3,ENSG00000102245
+B cell,observed,4,ENSG00000184613
+B cell,observed,5,ENSG00000058866
+B cell,observed,6,ENSG00000215788
+B cell,observed,7,ENSG00000127152
+B cell,observed,8,ENSG00000081059
+B cell,observed,9,ENSG00000171643
+B cell,observed,10,ENSG00000172673
+B cell,observed,11,ENSG00000010610
+B cell,observed,12,ENSG00000182489
+B cell,observed,13,ENSG00000156052
+B cell,observed,14,ENSG00000163689
+B cell,observed,15,ENSG00000248905
+B cell,observed,16,ENSG00000091129
+B cell,observed,17,ENSG00000109943
+B cell,observed,18,ENSG00000066294
+B cell,observed,19,ENSG00000188322
+B cell,observed,20,ENSG00000174123
+B cell,observed,21,ENSG00000162804
+B cell,observed,22,ENSG00000172164
+B cell,observed,23,ENSG00000152495
+B cell,observed,24,ENSG00000153898
+B cell,observed,25,ENSG00000104490
+B cell,observed,26,ENSG00000122223
+B cell,observed,27,ENSG00000196975
+B cell,observed,28,ENSG00000137766
+B cell,observed,29,ENSG00000172575
+B cell,observed,30,ENSG00000126821
+B cell,observed,31,ENSG00000114013
+B cell,observed,32,ENSG00000140853
+B cell,observed,33,ENSG00000203710
+B cell,observed,34,ENSG00000216937
+B cell,observed,35,ENSG00000188906
+B cell,observed,36,ENSG00000147138
+B cell,observed,37,ENSG00000100351
+B cell,observed,38,ENSG00000135426
+B cell,observed,39,ENSG00000151490
+B cell,observed,40,ENSG00000186814
+B cell,observed,41,ENSG00000197548
+B cell,observed,42,ENSG00000140750
+B cell,observed,43,ENSG00000197385
+B cell,observed,44,ENSG00000035403
+B cell,observed,45,ENSG00000115956
+B cell,observed,46,ENSG00000100242
+B cell,observed,47,ENSG00000071575
+B cell,observed,48,ENSG00000071073
+B cell,observed,49,ENSG00000140548
+B cell,observed,50,ENSG00000058091
+Monocyte,observed,1,ENSG00000115590
+Monocyte,observed,2,ENSG00000087116
+Monocyte,observed,3,ENSG00000100079
+Monocyte,observed,4,ENSG00000155659
+Monocyte,observed,5,ENSG00000166428
+Monocyte,observed,6,ENSG00000140545
+Monocyte,observed,7,ENSG00000113088
+Monocyte,observed,8,ENSG00000173369
+Monocyte,observed,9,ENSG00000138821
+Monocyte,observed,10,ENSG00000081059
+Monocyte,observed,11,ENSG00000138795
+Monocyte,observed,12,ENSG00000168685
+Monocyte,observed,13,ENSG00000078053
+Monocyte,observed,14,ENSG00000146122
+Monocyte,observed,15,ENSG00000179344
+Monocyte,observed,16,ENSG00000184613
+Monocyte,observed,17,ENSG00000186810
+Monocyte,observed,18,ENSG00000100385
+Monocyte,observed,19,ENSG00000174705
+Monocyte,observed,20,ENSG00000152495
+Monocyte,observed,21,ENSG00000109321
+Monocyte,observed,22,ENSG00000013725
+Monocyte,observed,23,ENSG00000172575
+Monocyte,observed,24,ENSG00000153823
+Monocyte,observed,25,ENSG00000172543
+Monocyte,observed,26,ENSG00000147138
+Monocyte,observed,27,ENSG00000110448
+Monocyte,observed,28,ENSG00000115085
+Monocyte,observed,29,ENSG00000160856
+Monocyte,observed,30,ENSG00000173114
+Monocyte,observed,31,ENSG00000168209
+Monocyte,observed,32,ENSG00000111796
+Monocyte,observed,33,ENSG00000008517
+Monocyte,observed,34,ENSG00000167286
+Monocyte,observed,35,ENSG00000198851
+Monocyte,observed,36,ENSG00000102245
+Monocyte,observed,37,ENSG00000143184
+Monocyte,observed,38,ENSG00000113263
+Monocyte,observed,39,ENSG00000073861
+Monocyte,observed,40,ENSG00000172673
+Monocyte,observed,41,ENSG00000173372
+Monocyte,observed,42,ENSG00000183918
+Monocyte,observed,43,ENSG00000198821
+Monocyte,observed,44,ENSG00000027869
+Monocyte,observed,45,ENSG00000178562
+Monocyte,observed,46,ENSG00000065675
+Monocyte,observed,47,ENSG00000124181
+Monocyte,observed,48,ENSG00000106178
+Monocyte,observed,49,ENSG00000141384
+Monocyte,observed,50,ENSG00000196935
+NK cell,observed,1,ENSG00000185215
+NK cell,observed,2,ENSG00000100079
+NK cell,observed,3,ENSG00000106066
+NK cell,observed,4,ENSG00000110077
+NK cell,observed,5,ENSG00000171916
+NK cell,observed,6,ENSG00000170298
+NK cell,observed,7,ENSG00000124507
+NK cell,observed,8,ENSG00000010610
+NK cell,observed,9,ENSG00000121552
+NK cell,observed,10,ENSG00000196159
+NK cell,observed,11,ENSG00000197629
+NK cell,observed,12,ENSG00000172243
+NK cell,observed,13,ENSG00000120708
+NK cell,observed,14,ENSG00000126759
+NK cell,observed,15,ENSG00000172322
+NK cell,observed,16,ENSG00000140749
+NK cell,observed,17,ENSG00000120594
+NK cell,observed,18,ENSG00000137393
+NK cell,observed,19,ENSG00000184731
+NK cell,observed,20,ENSG00000197467
+NK cell,observed,21,ENSG00000121807
+NK cell,observed,22,ENSG00000169744
+NK cell,observed,23,ENSG00000104093
+NK cell,observed,24,ENSG00000241399
+NK cell,observed,25,ENSG00000151474
+NK cell,observed,26,ENSG00000087253
+NK cell,observed,27,ENSG00000102349
+NK cell,observed,28,ENSG00000100154
+NK cell,observed,29,ENSG00000101842
+NK cell,observed,30,ENSG00000140543
+NK cell,observed,31,ENSG00000261371
+NK cell,observed,32,ENSG00000198223
+NK cell,observed,33,ENSG00000136205
+NK cell,observed,34,ENSG00000138119
+NK cell,observed,35,ENSG00000101542
+NK cell,observed,36,ENSG00000095637
+NK cell,observed,37,ENSG00000168329
+NK cell,observed,38,ENSG00000219481
+NK cell,observed,39,ENSG00000035403
+NK cell,observed,40,ENSG00000161638
+NK cell,observed,41,ENSG00000147576
+NK cell,observed,42,ENSG00000135426
+NK cell,observed,43,ENSG00000170989
+NK cell,observed,44,ENSG00000123636
+NK cell,observed,45,ENSG00000185697
+NK cell,observed,46,ENSG00000100385
+NK cell,observed,47,ENSG00000160991
+NK cell,observed,48,ENSG00000172575
+NK cell,observed,49,ENSG00000006530
+NK cell,observed,50,ENSG00000185989
+DC,observed,1,ENSG00000179639
+DC,observed,2,ENSG00000153823
+DC,observed,3,ENSG00000163606
+DC,observed,4,ENSG00000198561
+DC,observed,5,ENSG00000081059
+DC,observed,6,ENSG00000118922
+DC,observed,7,ENSG00000150054
+DC,observed,8,ENSG00000106034
+DC,observed,9,ENSG00000112182
+DC,observed,10,ENSG00000154229
+DC,observed,11,ENSG00000074964
+DC,observed,12,ENSG00000123607
+DC,observed,13,ENSG00000165983
+DC,observed,14,ENSG00000013725
+DC,observed,15,ENSG00000136111
+DC,observed,16,ENSG00000171408
+DC,observed,17,ENSG00000104361
+DC,observed,18,ENSG00000134852
+DC,observed,19,ENSG00000100105
+DC,observed,20,ENSG00000120162
+DC,observed,21,ENSG00000150636
+DC,observed,22,ENSG00000186260
+DC,observed,23,ENSG00000111846
+DC,observed,24,ENSG00000133059
+DC,observed,25,ENSG00000104228
+DC,observed,26,ENSG00000186854
+DC,observed,27,ENSG00000114982
+DC,observed,28,ENSG00000149292
+DC,observed,29,ENSG00000171843
+DC,observed,30,ENSG00000135362
+DC,observed,31,ENSG00000109099
+DC,observed,32,ENSG00000100890
+DC,observed,33,ENSG00000187912
+DC,observed,34,ENSG00000130023
+DC,observed,35,ENSG00000116852
+DC,observed,36,ENSG00000012174
+DC,observed,37,ENSG00000269713
+DC,observed,38,ENSG00000113761
+DC,observed,39,ENSG00000137942
+DC,observed,40,ENSG00000171617
+DC,observed,41,ENSG00000135040
+DC,observed,42,ENSG00000066651
+DC,observed,43,ENSG00000120262
+DC,observed,44,ENSG00000146373
+DC,observed,45,ENSG00000115594
+DC,observed,46,ENSG00000151422
+DC,observed,47,ENSG00000151014
+DC,observed,48,ENSG00000141447
+DC,observed,49,ENSG00000115998
+DC,observed,50,ENSG00000152315

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled/README.md

@@ -0,0 +1,79 @@
+# score_ft.py output: giroux2022, 24 scored donors
+
+Arms: scsemi__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/giroux2022/reference.npz` (sha dd0152f7bde4), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022;
+  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/giroux2022/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 (5563 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 24 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) (3600 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 0.9981, 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
+   0.9981, 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 ['severe'] (n = 11) vs control groups ['mild'] (n = 13); 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 5563 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/giroux2022/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 11 + 13
+   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).
+
+## Gene exclusion (--exclude-genes)
+`/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv` (sha e3a0f3f225d9): 196 genes listed, 65 of them scoring genes (XG, PRKX, NLGN4X, PUDP, STS, ANOS1, FAM9B, TBL1X, SHROOM2, AP1S2, CTPS2, TXLNG, NHS, BEND2, PPEF1, CNKSR2, PHEX, PTCHD1, IL1RAPL1, LANCL3, XK, MED14, EFHC2, KDM6A, ZNF157, TIMP1, RIBC1, VSIG4, CXorf65, NHSL2, P2RY10, GPR174, HMGN5, ZNF711, POF1B, DACH2, PCDH11X, SYTL4, XKRX, ZMAT1, IL1RAPL2, NUP62CL, FRMPD3, MID2, COL4A6, TRPC5, RTL4, GRIA3, SH2D1A, ZNF280C, HS6ST2, PLAC1, FHL1, CD40LG, FGF13, AFF2, GABRA3, PNMA3, ZFY, PCDH11Y, USP9Y, DDX3Y, UTY, NLGN4Y, KDM5D). Applies to: group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene. Definitions 5 and 6 above therefore run on 5498 of the 5563 scoring genes.
+
+## Labels
+Frozen scANVI labels reused from `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/pooled` (same reference, NPZ sha256 and scored donors; checked per arm); predict_scanvi.py was not run.

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled/per_donor.csv

@@ -0,0 +1,25 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
+scsemi__raw,450905_d0,mild,1500,5914,150,0.21533333333333332,0.30943523841731485,0.023333333333333334,0.036185322962461956,0.5913333333333334,0.4293202570172472,0.16133333333333333,0.12089956036523504,0.002,0.009976327358809604,0.006666666666666667,0.09418329387893135,0.4048936985683689,0.6266504923198378,0.6187504078474927,1,True,0.9466666666666667,0.41333333333333333,0.41333333333333333,0.32666666666666666,59.13333333333334,42.93202570172472,481.0,574.5
+scsemi__raw,450905_d14,mild,1500,7407,150,0.484,0.4422843256379101,0.035333333333333335,0.02929661131362225,0.24133333333333334,0.27420008100445525,0.21,0.15782368030241664,0.01,0.02983664101525584,0.019333333333333334,0.06655866072633995,0.1998574321587687,0.36155260046011806,0.5878660853992073,3,False,0.76,0.24666666666666667,0.3333333333333333,0.18,24.133333333333333,27.420008100445525,481.0,558.0
+scsemi__raw,0B943B_d0,mild,1500,11344,150,0.49666666666666665,0.6220028208744711,0.028,0.08312764456981664,0.2846666666666667,0.12588152327221439,0.168,0.11865303244005641,0.010666666666666666,0.023977433004231313,0.012,0.026357545839210156,0.41626422190879186,0.1791278384873501,0.5930900079662251,18,False,0.7933333333333333,0.2,0.36,0.08666666666666667,28.46666666666667,12.588152327221438,457.0,539.0
+scsemi__raw,0B943B_d14,mild,1500,15650,150,0.528,0.5652396166134185,0.126,0.11175718849840256,0.18866666666666668,0.17086261980830672,0.10466666666666667,0.09789137380191694,0.0026666666666666666,0.009968051118210863,0.05,0.04428115015974441,0.08908200212992537,0.10063602424453227,0.6581692262493687,7,False,0.8733333333333333,0.44,0.25333333333333335,0.12666666666666668,18.866666666666667,17.08626198083067,458.0,461.0
+scsemi__raw,7085CA_d0,mild,1500,12585,150,0.21666666666666667,0.21660707191100517,0.020666666666666667,0.024791418355184745,0.6073333333333333,0.5874453714739769,0.126,0.13198251887167262,0.002,0.017719507350019866,0.027333333333333334,0.021454112038140644,0.051653555820421124,0.8829287440863147,0.665253870794892,1,True,0.9666666666666667,0.5,0.4666666666666667,0.4,60.73333333333333,58.74453714739769,459.0,640.0
+scsemi__raw,7085CA_d7,mild,1500,9515,150,0.5226666666666666,0.521492380451918,0.03133333333333333,0.0722017866526537,0.20733333333333334,0.10110352075669994,0.21466666666666667,0.2725170782974251,0.009333333333333334,0.019863373620599055,0.014666666666666666,0.012821860220704152,0.21849781047468902,0.3632282731474772,0.6151883643710102,1,True,0.8133333333333334,0.36666666666666664,0.34,0.11333333333333333,20.733333333333334,10.110352075669994,460.0,502.0
+scsemi__raw,7085CA_d14,mild,1500,11887,150,0.54,0.472533019264743,0.03333333333333333,0.07133843694792631,0.21266666666666667,0.16210986792294102,0.19266666666666668,0.24270211155043325,0.008,0.018591738874400604,0.013333333333333334,0.032724825439555814,0.2360475589579653,0.2993283707516418,0.6396572707706992,1,True,0.9066666666666666,0.3466666666666667,0.31333333333333335,0.17333333333333334,21.266666666666666,16.2109867922941,459.0,536.0
+scsemi__raw,2AD75E_d0,mild,1500,7693,150,0.6733333333333333,0.6034056934875861,0.03666666666666667,0.06408423241908229,0.164,0.14064734173924348,0.10866666666666666,0.15949564539191471,0.0013333333333333333,0.025347718705316522,0.016,0.007019368256856883,0.20452185969929376,0.20681142084856263,0.5917595856033825,3,False,0.9,0.28,0.47333333333333333,0.10666666666666667,16.400000000000002,14.064734173924348,487.0,532.0
+scsemi__raw,2AD75E_d7,mild,1500,10499,150,0.6953333333333334,0.5808172206876845,0.04066666666666666,0.14372797409277074,0.14066666666666666,0.10277169254214687,0.10333333333333333,0.14715687208305553,0.006666666666666667,0.013715591961139155,0.013333333333333334,0.011810648633203162,0.30786754294059765,0.27874882058987843,0.6062670315494059,1,True,0.9533333333333334,0.5066666666666667,0.4533333333333333,0.18666666666666668,14.066666666666666,10.277169254214687,487.0,443.0
+scsemi__raw,2AD75E_d14,mild,1500,13692,150,0.6933333333333334,0.5811422728600643,0.043333333333333335,0.12503651767455448,0.15066666666666667,0.14198071866783524,0.08733333333333333,0.12496348232544552,0.007333333333333333,0.016579024247735902,0.018,0.010297984224364592,0.25715804849547186,0.19762923258298543,0.591443566405085,2,False,0.8866666666666667,0.56,0.46,0.14,15.066666666666666,14.198071866783524,487.0,428.0
+scsemi__raw,B85D75_d0,severe,1500,11441,150,0.5506666666666666,0.7173324010138974,0.014666666666666666,0.031203566121842496,0.30666666666666664,0.11441307578008915,0.10933333333333334,0.06039681845992483,0.015333333333333332,0.016519535005681322,0.0033333333333333335,0.06013460361856481,0.48238021151997207,0.35882358586377083,0.6563597480766664,17,False,0.9533333333333334,0.32666666666666666,0.52,0.07333333333333333,30.666666666666664,11.441307578008916,482.0,347.0
+scsemi__raw,B85D75_d7,severe,1500,12328,150,0.668,0.6435756002595717,0.06733333333333333,0.06448734587929916,0.16733333333333333,0.13741077222582737,0.07066666666666667,0.04201817001946788,0.007333333333333333,0.027741726151849447,0.019333333333333334,0.08476638546398442,0.17168288989833444,0.28301793033829503,0.6302182367785831,5,False,0.8666666666666667,0.5,0.2733333333333333,0.18,16.733333333333334,13.741077222582737,481.0,363.0
+scsemi__raw,180E1A_d0,severe,1500,7157,150,0.6233333333333333,0.7019700992035769,0.09733333333333333,0.04135811094033813,0.162,0.13175911694844208,0.098,0.0655302501047925,0.004666666666666667,0.013273718038284197,0.014666666666666666,0.04610870476456616,0.23737171067952123,0.31372800769589615,0.6142210890148238,17,False,0.8266666666666667,0.26,0.24666666666666667,0.14,16.2,13.175911694844208,485.0,433.0
+scsemi__raw,180E1A_d7,severe,1500,10591,150,0.542,0.7348692285903126,0.034666666666666665,0.04909829100179398,0.214,0.09064299877254273,0.18066666666666667,0.08280615617033331,0.010666666666666666,0.010480596733075253,0.018,0.03210272873194221,0.44280716331476416,0.37628768415060193,0.6136145963010454,13,False,0.8266666666666667,0.26,0.29333333333333333,0.11333333333333333,21.4,9.064299877254273,486.0,408.0
+scsemi__raw,180E1A_d14,severe,1500,12511,150,0.6673333333333333,0.680840860043162,0.10066666666666667,0.05147470226200943,0.12266666666666666,0.12277196067460634,0.08066666666666666,0.0800095915594277,0.006666666666666667,0.009831348413396212,0.022,0.05507153704739829,0.0996980790237924,0.28939519394073066,0.6596975131129077,2,False,0.9066666666666666,0.30666666666666664,0.34,0.15333333333333332,12.266666666666666,12.277196067460634,487.0,342.0
+scsemi__raw,82CCF5_d0,severe,1500,10125,150,0.576,0.5422222222222223,0.114,0.11832098765432099,0.18533333333333332,0.1539753086419753,0.108,0.09303703703703704,0.004,0.016691358024691356,0.012666666666666666,0.07575308641975309,0.1601975308641974,0.18419072822032903,0.6209799784948123,11,False,0.8933333333333333,0.31333333333333335,0.18666666666666668,0.19333333333333333,18.53333333333333,15.397530864197531,470.0,390.0
+scsemi__raw,82CCF5_d7,severe,1500,10860,150,0.668,0.619060773480663,0.05533333333333333,0.09972375690607735,0.14666666666666667,0.14152854511970533,0.08866666666666667,0.09410681399631676,0.0026666666666666666,0.013627992633517496,0.03866666666666667,0.03195211786372008,0.12158379373848988,0.19419086678828923,0.6863528219387598,1,True,0.8933333333333333,0.4066666666666667,0.18666666666666668,0.16666666666666666,14.666666666666666,14.152854511970533,471.0,497.0
+scsemi__raw,82CCF5_d14,severe,1500,11056,150,0.7046666666666667,0.6330499276410999,0.042666666666666665,0.10121201157742403,0.128,0.11369392185238784,0.08733333333333333,0.06828871201157742,0.0033333333333333335,0.014562228654124458,0.034,0.0691931982633864,0.20993487698986968,0.2787071044352101,0.6807957009382283,2,False,0.8666666666666667,0.36,0.22,0.14,12.8,11.369392185238784,470.0,394.0
+scsemi__raw,BAAF62_d0,mild,1500,14741,150,0.5066666666666667,0.5279153381724442,0.07133333333333333,0.0384641476154942,0.11266666666666666,0.1854690997897022,0.2946666666666667,0.1717658232141646,0.008,0.023132758971575875,0.006666666666666667,0.053252832236618954,0.3115400583406824,0.14602913946264867,0.6342838428340984,6,False,0.8066666666666666,0.37333333333333335,0.22,0.14,11.266666666666666,18.54690997897022,470.0,449.0
+scsemi__raw,BAAF62_d7,mild,1500,7297,150,0.578,0.6932986158695355,0.11533333333333333,0.04070165821570509,0.15266666666666667,0.13389063998903658,0.138,0.0941482801151158,0.010666666666666666,0.016033986569823216,0.005333333333333333,0.021926819240783883,0.2745188433602851,0.25991971231178185,0.6395238527372827,10,False,0.9333333333333333,0.18666666666666668,0.30666666666666664,0.11333333333333333,15.266666666666667,13.389063998903659,470.0,580.0
+scsemi__raw,BAAF62_d14,mild,1500,11923,150,0.596,0.5431518913025245,0.104,0.019206575526293717,0.15133333333333332,0.2843244149962258,0.14,0.10416841398976767,0.005333333333333333,0.032793759959741674,0.0033333333333333335,0.016354944225446616,0.3469462383628282,0.2201331132920326,0.6389247386136839,3,False,0.9266666666666666,0.3466666666666667,0.31333333333333335,0.22,15.133333333333333,28.43244149962258,471.0,513.0
+scsemi__raw,0BF51C_d0,severe,1500,6510,150,0.286,0.4012288786482335,0.03333333333333333,0.01674347158218126,0.49933333333333335,0.4609831029185868,0.13933333333333334,0.07726574500768049,0.0006666666666666666,0.006144393241167435,0.04133333333333333,0.03763440860215054,0.24141321044546854,0.5556611725994968,0.6574799900593404,1,True,0.8466666666666667,0.29333333333333333,0.38,0.32,49.93333333333334,46.09831029185868,457.0,628.0
+scsemi__raw,0BF51C_d7,severe,1500,10105,150,0.6053333333333333,0.612370113805047,0.050666666666666665,0.05700148441365661,0.24466666666666667,0.1607125185551707,0.04533333333333334,0.05294408708560119,0.004666666666666667,0.0073231073725878275,0.04933333333333333,0.10964868876793667,0.167908296222992,0.22247826940326798,0.5683029857384005,8,False,0.8,0.35333333333333333,0.5,0.12,24.46666666666667,16.071251855517072,457.0,509.0
+scsemi__raw,0BF51C_d14,severe,1500,11419,150,0.6713333333333333,0.6330676941938874,0.04133333333333333,0.07960416849111131,0.20333333333333334,0.151589456169542,0.04733333333333333,0.07907872843506436,0.005333333333333333,0.010508801120938787,0.03133333333333333,0.04615115158945617,0.18001903260647456,0.1611535225979176,0.6209535406481763,6,False,0.7866666666666666,0.35333333333333333,0.4066666666666667,0.13333333333333333,20.333333333333332,15.1589456169542,456.0,541.0

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled/summary.json

@@ -0,0 +1,807 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "giroux2022",
+ "written_utc": "2026-10-08T01:57:36.531860+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",
+  "giroux2022",
+  "--threads",
+  "8",
+  "--arm",
+  "scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled_scsemi_cv_20261002/scsemi__raw.npz",
+  "--case-groups",
+  "severe",
+  "--control-groups",
+  "mild",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled",
+  "--exclude-genes",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv",
+  "--reuse-labels",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/pooled"
+ ],
+ "arms": [
+  "scsemi__raw"
+ ],
+ "donors": [
+  "450905_d0",
+  "450905_d14",
+  "0B943B_d0",
+  "0B943B_d14",
+  "7085CA_d0",
+  "7085CA_d7",
+  "7085CA_d14",
+  "2AD75E_d0",
+  "2AD75E_d7",
+  "2AD75E_d14",
+  "B85D75_d0",
+  "B85D75_d7",
+  "180E1A_d0",
+  "180E1A_d7",
+  "180E1A_d14",
+  "82CCF5_d0",
+  "82CCF5_d7",
+  "82CCF5_d14",
+  "BAAF62_d0",
+  "BAAF62_d7",
+  "BAAF62_d14",
+  "0BF51C_d0",
+  "0BF51C_d7",
+  "0BF51C_d14"
+ ],
+ "n_donors": 24,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
+  "reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
+  "features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
+  "n_r1_cells": 3600,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.23158283531665802,
+   "n_fit_cells": 3600
+  },
+  "r2_control": {
+   "precision": 0.9980555555555556,
+   "coverage": 1.0,
+   "density": 3.7886666666666664,
+   "n_query": 3600,
+   "depth_matched": {
+    "precision": 0.9980555555555556,
+    "coverage": 1.0,
+    "density": 3.7033611111111115
+   }
+  },
+  "observed_l1_loo_null_mean": 0.30584824369245694
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "severe"
+  ],
+  "control_groups": [
+   "mild"
+  ],
+  "n_case_donors": 11,
+  "n_control_donors": 13,
+  "n_donors_in_neither": 0,
+  "case": [
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "mild",
+   "mild",
+   "mild",
+   "severe",
+   "severe",
+   "severe"
+  ]
+ },
+ "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": 5498,
+  "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/giroux2022/deg_reference.npz",
+  "aggregates_sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
+  "observed": {
+   "T cell": {
+    "n_significant": 274,
+    "n_tested": 5295,
+    "n_case_donors": 11,
+    "n_control_donors": 13,
+    "n_cells": 145034,
+    "top_list_size": 50
+   },
+   "B cell": {
+    "n_significant": 0,
+    "n_tested": 5087,
+    "n_case_donors": 11,
+    "n_control_donors": 13,
+    "n_cells": 17383,
+    "top_list_size": 0
+   },
+   "Monocyte": {
+    "n_significant": 1,
+    "n_tested": 5239,
+    "n_case_donors": 11,
+    "n_control_donors": 13,
+    "n_cells": 47311,
+    "top_list_size": 1
+   },
+   "NK cell": {
+    "n_significant": 62,
+    "n_tested": 5103,
+    "n_case_donors": 11,
+    "n_control_donors": 13,
+    "n_cells": 29061,
+    "top_list_size": 50
+   },
+   "DC": {
+    "n_significant": 0,
+    "n_tested": 4914,
+    "n_case_donors": 11,
+    "n_control_donors": 13,
+    "n_cells": 4328,
+    "top_list_size": 0
+   }
+  },
+  "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": {
+  "scsemi__raw": {
+   "comp_l1": 0.24307690277174857,
+   "comp_l1_obs_loo_null": 0.30584824369245694,
+   "precision": 0.8722222222222222,
+   "coverage": 0.3541666666666667,
+   "precision_dm": 0.3441666666666667,
+   "coverage_dm": 0.1686111111111111,
+   "pb_r_median": 0.6255991076366978,
+   "pb_top1": 0.2916666666666667,
+   "mono_pct_gen": 23.272222222222226,
+   "mono_pct_obs": 19.247866360995445,
+   "median_umi_gen": 472.0,
+   "median_umi_obs": 471.0,
+   "contrast_mean_cp10k_r_gen": 0.5372927269740906,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.33150450117197183,
+   "contrast_mean_cp10k_r_broadcast": 0.5752659929360795,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5705382227795629,
+   "deg_top50_T": 0,
+   "deg_top50_B": 0,
+   "deg_top50_Mono": 0,
+   "deg_top50_NK": 0,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 0,
+   "deg_top50_max": 101,
+   "deg_top50_sum_4type": 0,
+   "deg_top50_sum_broadcast": 5,
+   "seconds": 2.8
+  }
+ },
+ "per_arm": {
+  "scsemi__raw": {
+   "arm": "scsemi__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled_scsemi_cv_20261002/scsemi__raw.npz",
+   "npz_sha256": "4c2f9e7c193605a0f6c5bda6a759730190e40bb3a4d4210e86c7cb0bdb9a7dd9",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled_scsemi_cv_20261002/conditions_pooled_raw.npz",
+    "input_condition_sha256": "1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015",
+    "seed": null,
+    "steps": null,
+    "support_readout": null,
+    "weights": null
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled_scsemi_cv_20261002/conditions_pooled_raw.npz",
+    "sha256": "1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 4025738,
+    "median_library_whole_npz_panel": 472.0,
+    "n_rows_whole_npz": 36000
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 19963,
+     "Monocyte": 8378,
+     "NK cell": 4657,
+     "B cell": 2042,
+     "Other": 736,
+     "DC": 224
+    },
+    "mean_l2_max_prob": 0.8491351462010708,
+    "predict_seconds": 3.2,
+    "reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/pooled/arms/scsemi__raw/labels",
+    "reused_labels_sha256": "23223713098301087649b703a06a4ab470080a101fec7d7b72198208db32e3e7"
+   },
+   "n_donors": 24,
+   "n_generated_cells": 36000,
+   "composition": {
+    "l1_mean": 0.24307690277174857,
+    "l1_median": 0.22727268471632717,
+    "l1_obs_loo_null_mean": 0.30584824369245694,
+    "l1_generated_loo_mean_vs_observed_mean": 0.3381459188674268,
+    "composition_top1": 0.125,
+    "mean_fraction_generated": {
+     "T cell": 0.554528,
+     "B cell": 0.056722,
+     "Monocyte": 0.232722,
+     "NK cell": 0.129361,
+     "DC": 0.006222,
+     "Other": 0.020444
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.566621,
+     "B cell": 0.065423,
+     "Monocyte": 0.192479,
+     "NK cell": 0.114152,
+     "DC": 0.016843,
+     "Other": 0.044482
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5563,
+    "r_median": 0.6255991076366978,
+    "r_mean": 0.6287147521768157,
+    "top1": 0.2916666666666667,
+    "n_top1": 7,
+    "own_rank_median": 3.0,
+    "chance_top1": 0.041666666666666664
+   },
+   "precision_coverage": {
+    "precision": 0.8722222222222222,
+    "coverage": 0.3541666666666667,
+    "density": 0.38472222222222224,
+    "n_query": 3600,
+    "n_reference": 3600
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.3441666666666667,
+    "coverage": 0.1686111111111111,
+    "density": 0.11599999999999999,
+    "detected_median_before": {
+     "R1": 254.0,
+     "Q": 110.0
+    },
+    "detected_median_after": {
+     "R1": 110.0,
+     "Q": 110.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 23.272222222222226,
+    "observed_mean_over_donors": 19.247866360995445,
+    "generated_pooled_cells": 23.272222222222222
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 472.0,
+    "observed_pooled": 471.0,
+    "generated_mean_of_donor_medians": 472.0416564941406,
+    "observed_mean_of_donor_medians": 483.6458333333333
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.5896983572148723,
+       "r_broadcast": 0.5864764503055301,
+       "partial_r_generated_given_broadcast": 0.41608350514079784,
+       "r_generated_vs_broadcast": 0.5118253037060416,
+       "n_genes": 2886
+      },
+      "B cell": {
+       "r_generated": 0.4023801437336676,
+       "r_broadcast": 0.48025603753384744,
+       "partial_r_generated_given_broadcast": 0.2748298277172872,
+       "r_generated_vs_broadcast": 0.37190657777381525,
+       "n_genes": 3030
+      },
+      "Monocyte": {
+       "r_generated": 0.6055701581942391,
+       "r_broadcast": 0.6794468550874515,
+       "partial_r_generated_given_broadcast": 0.4504975396560621,
+       "r_generated_vs_broadcast": 0.45907721684011676,
+       "n_genes": 3034
+      },
+      "NK cell": {
+       "r_generated": 0.5515222487535836,
+       "r_broadcast": 0.554884628817489,
+       "partial_r_generated_given_broadcast": 0.41146669564200294,
+       "r_generated_vs_broadcast": 0.43994589539010526,
+       "n_genes": 2931
+      }
+     },
+     "mean_r_generated": 0.5372927269740906,
+     "mean_r_broadcast": 0.5752659929360795,
+     "mean_partial_r": 0.38821939203903755
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.47668856642514423,
+       "r_broadcast": 0.6077451868574512,
+       "partial_r_generated_given_broadcast": 0.3059147485870827,
+       "r_generated_vs_broadcast": 0.421948813227649,
+       "n_genes": 2886
+      },
+      "B cell": {
+       "r_generated": 0.199437720590521,
+       "r_broadcast": 0.4644022343428308,
+       "partial_r_generated_given_broadcast": 0.09440310101549665,
+       "r_generated_vs_broadcast": 0.2553919598939267,
+       "n_genes": 3030
+      },
+      "Monocyte": {
+       "r_generated": 0.30911861040995087,
+       "r_broadcast": 0.6731923266540611,
+       "partial_r_generated_given_broadcast": 0.1674763590975495,
+       "r_generated_vs_broadcast": 0.28272449437038877,
+       "n_genes": 3034
+      },
+      "NK cell": {
+       "r_generated": 0.34077310726227117,
+       "r_broadcast": 0.5368131432639086,
+       "partial_r_generated_given_broadcast": 0.22347878449113212,
+       "r_generated_vs_broadcast": 0.2997164391765415,
+       "n_genes": 2931
+      }
+     },
+     "mean_r_generated": 0.33150450117197183,
+     "mean_r_broadcast": 0.5705382227795629,
+     "mean_partial_r": 0.19781824829781525
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 3,
+      "top50_jaccard_broadcast": 0.05454545454545454,
+      "n_cells_obs": 145034,
+      "n_cells_gen": 19963
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": null,
+      "obs_top_list_size": 0,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 17383,
+      "n_cells_gen": 2042
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 1,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 1,
+      "top50_jaccard_broadcast": 0.125,
+      "n_cells_obs": 47311,
+      "n_cells_gen": 8378
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 1,
+      "top50_jaccard_broadcast": 0.017543859649122806,
+      "n_cells_obs": 29061,
+      "n_cells_gen": 4657
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": null,
+      "obs_top_list_size": 0,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 4328,
+      "n_cells_gen": 224
+     }
+    },
+    "sum": 0,
+    "sum_4type": 0,
+    "max": 101,
+    "mean": 0.0,
+    "sum_broadcast": 5,
+    "sum_broadcast_4type": 5,
+    "broadcast_n_significant": 8,
+    "seconds": 0.04
+   },
+   "seconds": 2.8
+  }
+ },
+ "code_sha256": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+ },
+ "seconds": 4.0,
+ "gene_exclusion": {
+  "file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv",
+  "sha256": "e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de",
+  "n_listed": 196,
+  "n_scoring_genes": 5563,
+  "n_dropped_from_scoring_genes": 65,
+  "n_scoring_genes_kept": 5498,
+  "dropped": [
+   {
+    "gene_id": "ENSG00000124343",
+    "symbol": "XG"
+   },
+   {
+    "gene_id": "ENSG00000183943",
+    "symbol": "PRKX"
+   },
+   {
+    "gene_id": "ENSG00000146938",
+    "symbol": "NLGN4X"
+   },
+   {
+    "gene_id": "ENSG00000130021",
+    "symbol": "PUDP"
+   },
+   {
+    "gene_id": "ENSG00000101846",
+    "symbol": "STS"
+   },
+   {
+    "gene_id": "ENSG00000011201",
+    "symbol": "ANOS1"
+   },
+   {
+    "gene_id": "ENSG00000177138",
+    "symbol": "FAM9B"
+   },
+   {
+    "gene_id": "ENSG00000101849",
+    "symbol": "TBL1X"
+   },
+   {
+    "gene_id": "ENSG00000146950",
+    "symbol": "SHROOM2"
+   },
+   {
+    "gene_id": "ENSG00000182287",
+    "symbol": "AP1S2"
+   },
+   {
+    "gene_id": "ENSG00000047230",
+    "symbol": "CTPS2"
+   },
+   {
+    "gene_id": "ENSG00000086712",
+    "symbol": "TXLNG"
+   },
+   {
+    "gene_id": "ENSG00000188158",
+    "symbol": "NHS"
+   },
+   {
+    "gene_id": "ENSG00000177324",
+    "symbol": "BEND2"
+   },
+   {
+    "gene_id": "ENSG00000086717",
+    "symbol": "PPEF1"
+   },
+   {
+    "gene_id": "ENSG00000149970",
+    "symbol": "CNKSR2"
+   },
+   {
+    "gene_id": "ENSG00000102174",
+    "symbol": "PHEX"
+   },
+   {
+    "gene_id": "ENSG00000165186",
+    "symbol": "PTCHD1"
+   },
+   {
+    "gene_id": "ENSG00000169306",
+    "symbol": "IL1RAPL1"
+   },
+   {
+    "gene_id": "ENSG00000147036",
+    "symbol": "LANCL3"
+   },
+   {
+    "gene_id": "ENSG00000047597",
+    "symbol": "XK"
+   },
+   {
+    "gene_id": "ENSG00000180182",
+    "symbol": "MED14"
+   },
+   {
+    "gene_id": "ENSG00000183690",
+    "symbol": "EFHC2"
+   },
+   {
+    "gene_id": "ENSG00000147050",
+    "symbol": "KDM6A"
+   },
+   {
+    "gene_id": "ENSG00000147117",
+    "symbol": "ZNF157"
+   },
+   {
+    "gene_id": "ENSG00000102265",
+    "symbol": "TIMP1"
+   },
+   {
+    "gene_id": "ENSG00000158423",
+    "symbol": "RIBC1"
+   },
+   {
+    "gene_id": "ENSG00000155659",
+    "symbol": "VSIG4"
+   },
+   {
+    "gene_id": "ENSG00000204165",
+    "symbol": "CXorf65"
+   },
+   {
+    "gene_id": "ENSG00000204131",
+    "symbol": "NHSL2"
+   },
+   {
+    "gene_id": "ENSG00000078589",
+    "symbol": "P2RY10"
+   },
+   {
+    "gene_id": "ENSG00000147138",
+    "symbol": "GPR174"
+   },
+   {
+    "gene_id": "ENSG00000198157",
+    "symbol": "HMGN5"
+   },
+   {
+    "gene_id": "ENSG00000147180",
+    "symbol": "ZNF711"
+   },
+   {
+    "gene_id": "ENSG00000124429",
+    "symbol": "POF1B"
+   },
+   {
+    "gene_id": "ENSG00000126733",
+    "symbol": "DACH2"
+   },
+   {
+    "gene_id": "ENSG00000102290",
+    "symbol": "PCDH11X"
+   },
+   {
+    "gene_id": "ENSG00000102362",
+    "symbol": "SYTL4"
+   },
+   {
+    "gene_id": "ENSG00000182489",
+    "symbol": "XKRX"
+   },
+   {
+    "gene_id": "ENSG00000166432",
+    "symbol": "ZMAT1"
+   },
+   {
+    "gene_id": "ENSG00000189108",
+    "symbol": "IL1RAPL2"
+   },
+   {
+    "gene_id": "ENSG00000198088",
+    "symbol": "NUP62CL"
+   },
+   {
+    "gene_id": "ENSG00000147234",
+    "symbol": "FRMPD3"
+   },
+   {
+    "gene_id": "ENSG00000080561",
+    "symbol": "MID2"
+   },
+   {
+    "gene_id": "ENSG00000197565",
+    "symbol": "COL4A6"
+   },
+   {
+    "gene_id": "ENSG00000072315",
+    "symbol": "TRPC5"
+   },
+   {
+    "gene_id": "ENSG00000187823",
+    "symbol": "RTL4"
+   },
+   {
+    "gene_id": "ENSG00000125675",
+    "symbol": "GRIA3"
+   },
+   {
+    "gene_id": "ENSG00000183918",
+    "symbol": "SH2D1A"
+   },
+   {
+    "gene_id": "ENSG00000056277",
+    "symbol": "ZNF280C"
+   },
+   {
+    "gene_id": "ENSG00000171004",
+    "symbol": "HS6ST2"
+   },
+   {
+    "gene_id": "ENSG00000170965",
+    "symbol": "PLAC1"
+   },
+   {
+    "gene_id": "ENSG00000022267",
+    "symbol": "FHL1"
+   },
+   {
+    "gene_id": "ENSG00000102245",
+    "symbol": "CD40LG"
+   },
+   {
+    "gene_id": "ENSG00000129682",
+    "symbol": "FGF13"
+   },
+   {
+    "gene_id": "ENSG00000155966",
+    "symbol": "AFF2"
+   },
+   {
+    "gene_id": "ENSG00000011677",
+    "symbol": "GABRA3"
+   },
+   {
+    "gene_id": "ENSG00000183837",
+    "symbol": "PNMA3"
+   },
+   {
+    "gene_id": "ENSG00000067646",
+    "symbol": "ZFY"
+   },
+   {
+    "gene_id": "ENSG00000099715",
+    "symbol": "PCDH11Y"
+   },
+   {
+    "gene_id": "ENSG00000114374",
+    "symbol": "USP9Y"
+   },
+   {
+    "gene_id": "ENSG00000067048",
+    "symbol": "DDX3Y"
+   },
+   {
+    "gene_id": "ENSG00000183878",
+    "symbol": "UTY"
+   },
+   {
+    "gene_id": "ENSG00000165246",
+    "symbol": "NLGN4Y"
+   },
+   {
+    "gene_id": "ENSG00000012817",
+    "symbol": "KDM5D"
+   }
+  ],
+  "applies_to": "group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene"
+ },
+ "labels_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/pooled"
+}