Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/COMPARISON_RECEIPT.json

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+{
+  "draw": 0,
+  "support_sha256": "ad30daaf76d46edb695df2ae02cb67f8d8b3ae709630e8ec7ae87056258f9bda",
+  "sources": {
+    "current_f01": {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw0/lora.npz",
+      "sha256": "823ee652c0cb8be8f822bd48bbdb4d4368b8aca5a075f423159acc3c66be8842"
+    },
+    "scsemi": {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw0/scsemi.npz",
+      "sha256": "80d99f5363d0fd7b967070fe1e8e716a05c86869edd31757c4e7cac5bf7ef29f"
+    }
+  },
+  "reference_ready_sha256": "8364f8c9d7dc8ed868034811c04d9f2157275a477b351e9e1699d65d99bac5c5",
+  "score_code_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+  "note": "Native common-axis readout; donor-aware Welch benchmark DEG. Draws are overlapping, not independent biological replicates."
+}

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/README.md

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+# score_ft.py output: ye2026_sepsis, 77 scored donors
+
+Arms: current_f01, scsemi.  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/trunk4x_lora_sepsis_20261013/reference/reference.npz` (sha 8c5f2d794d13), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/evaluation_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/trunk4x_lora_sepsis_20261013/reference/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 (4243 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 77 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) (11550 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 0.9800, coverage 0.9999.
+   **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
+   0.9786, coverage 0.9999.
+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 = 57) vs control groups ['adult_HC', 'adult_ICU_ctrl', 'ped_HC', 'ped_ICU_ctrl'] (n = 20); 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 4243 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/trunk4x_lora_sepsis_20261013/reference/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 57 + 20
+   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/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/current_f01/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,ENSG00000124762
+T cell,observed,5,ENSG00000109321
+T cell,observed,6,ENSG00000184557
+T cell,observed,7,ENSG00000118515
+T cell,observed,8,ENSG00000144655
+T cell,observed,9,ENSG00000134531
+T cell,observed,10,ENSG00000232810
+T cell,observed,11,ENSG00000162772
+T cell,observed,12,ENSG00000113070
+T cell,observed,13,ENSG00000158813
+T cell,observed,14,ENSG00000277632
+T cell,observed,15,ENSG00000144290
+T cell,observed,16,ENSG00000168497
+T cell,observed,17,ENSG00000101162
+T cell,observed,18,ENSG00000173114
+T cell,observed,19,ENSG00000163563
+T cell,observed,20,ENSG00000168209
+T cell,observed,21,ENSG00000112149
+T cell,observed,22,ENSG00000168329
+T cell,observed,23,ENSG00000127920
+T cell,observed,24,ENSG00000120708
+T cell,observed,25,ENSG00000197728
+T cell,observed,26,ENSG00000138166
+T cell,observed,27,ENSG00000100906
+T cell,observed,28,ENSG00000134545
+T cell,observed,29,ENSG00000085265
+T cell,observed,30,ENSG00000160789
+T cell,observed,31,ENSG00000115607
+T cell,observed,32,ENSG00000275302
+T cell,observed,33,ENSG00000091129
+T cell,observed,34,ENSG00000119508
+T cell,observed,35,ENSG00000179388
+T cell,observed,36,ENSG00000128016
+T cell,observed,37,ENSG00000150681
+T cell,observed,38,ENSG00000110077
+T cell,observed,39,ENSG00000180875
+T cell,observed,40,ENSG00000117281
+T cell,observed,41,ENSG00000113088
+T cell,observed,42,ENSG00000221869
+T cell,observed,43,ENSG00000121552
+T cell,observed,44,ENSG00000163508
+T cell,observed,45,ENSG00000100079
+T cell,observed,46,ENSG00000106066
+T cell,observed,47,ENSG00000110848
+T cell,observed,48,ENSG00000030419
+T cell,observed,49,ENSG00000182253
+T cell,observed,50,ENSG00000172215
+T cell,generated,1,ENSG00000132465
+T cell,generated,2,ENSG00000170476
+T cell,generated,3,ENSG00000140968
+T cell,generated,4,ENSG00000137265
+T cell,generated,5,ENSG00000133985
+T cell,generated,6,ENSG00000104921
+T cell,generated,7,ENSG00000168209
+T cell,generated,8,ENSG00000239264
+T cell,generated,9,ENSG00000160593
+T cell,generated,10,ENSG00000144802
+T cell,generated,11,ENSG00000204681
+T cell,generated,12,ENSG00000136068
+T cell,generated,13,ENSG00000109943
+T cell,generated,14,ENSG00000099860
+T cell,generated,15,ENSG00000123552
+T cell,generated,16,ENSG00000197008
+T cell,generated,17,ENSG00000070718
+T cell,generated,18,ENSG00000029639
+T cell,generated,19,ENSG00000122547
+T cell,generated,20,ENSG00000115687
+T cell,generated,21,ENSG00000171522
+T cell,generated,22,ENSG00000197329
+T cell,generated,23,ENSG00000166432
+T cell,generated,24,ENSG00000115590
+T cell,generated,25,ENSG00000158467
+T cell,generated,26,ENSG00000034693
+T cell,generated,27,ENSG00000130066
+T cell,generated,28,ENSG00000168685
+T cell,generated,29,ENSG00000115239
+T cell,generated,30,ENSG00000140379
+T cell,generated,31,ENSG00000011523
+T cell,generated,32,ENSG00000178971
+T cell,generated,33,ENSG00000184588
+T cell,generated,34,ENSG00000003400
+T cell,generated,35,ENSG00000155657
+T cell,generated,36,ENSG00000188171
+T cell,generated,37,ENSG00000167261
+T cell,generated,38,ENSG00000099958
+T cell,generated,39,ENSG00000198911
+T cell,generated,40,ENSG00000215788
+T cell,generated,41,ENSG00000139083
+T cell,generated,42,ENSG00000138439
+T cell,generated,43,ENSG00000142459
+T cell,generated,44,ENSG00000185883
+T cell,generated,45,ENSG00000166225
+T cell,generated,46,ENSG00000213402
+T cell,generated,47,ENSG00000135426
+T cell,generated,48,ENSG00000062716
+T cell,generated,49,ENSG00000180628
+T cell,generated,50,ENSG00000112699
+B cell,observed,1,ENSG00000123358
+B cell,observed,2,ENSG00000090382
+B cell,observed,3,ENSG00000184557
+B cell,observed,4,ENSG00000066923
+B cell,observed,5,ENSG00000143333
+B cell,observed,6,ENSG00000118515
+B cell,observed,7,ENSG00000113088
+B cell,observed,8,ENSG00000124762
+B cell,observed,9,ENSG00000125968
+B cell,observed,10,ENSG00000162772
+B cell,observed,11,ENSG00000158050
+B cell,observed,12,ENSG00000168209
+B cell,observed,13,ENSG00000168329
+B cell,observed,14,ENSG00000232810
+B cell,observed,15,ENSG00000137441
+B cell,observed,16,ENSG00000119508
+B cell,observed,17,ENSG00000145649
+B cell,observed,18,ENSG00000185022
+B cell,observed,19,ENSG00000153563
+B cell,observed,20,ENSG00000112149
+B cell,observed,21,ENSG00000180739
+B cell,observed,22,ENSG00000090339
+B cell,observed,23,ENSG00000138166
+B cell,observed,24,ENSG00000172673
+B cell,observed,25,ENSG00000160654
+B cell,observed,26,ENSG00000150625
+B cell,observed,27,ENSG00000130844
+B cell,observed,28,ENSG00000165949
+B cell,observed,29,ENSG00000166750
+B cell,observed,30,ENSG00000110448
+B cell,observed,31,ENSG00000103257
+B cell,observed,32,ENSG00000163508
+B cell,observed,33,ENSG00000136250
+B cell,observed,34,ENSG00000271503
+B cell,observed,35,ENSG00000173114
+B cell,observed,36,ENSG00000111796
+B cell,observed,37,ENSG00000100450
+B cell,observed,38,ENSG00000184613
+B cell,observed,39,ENSG00000102245
+B cell,observed,40,ENSG00000151090
+B cell,observed,41,ENSG00000074706
+B cell,observed,42,ENSG00000172116
+B cell,observed,43,ENSG00000105374
+B cell,observed,44,ENSG00000184545
+B cell,observed,45,ENSG00000100906
+B cell,observed,46,ENSG00000120708
+B cell,observed,47,ENSG00000153234
+B cell,observed,48,ENSG00000116824
+B cell,observed,49,ENSG00000197728
+B cell,observed,50,ENSG00000144655
+B cell,generated,1,ENSG00000239264
+B cell,generated,2,ENSG00000057657
+B cell,generated,3,ENSG00000026751
+B cell,generated,4,ENSG00000173334
+B cell,generated,5,ENSG00000118985
+B cell,generated,6,ENSG00000170476
+B cell,generated,7,ENSG00000184557
+B cell,generated,8,ENSG00000103257
+B cell,generated,9,ENSG00000123352
+B cell,generated,10,ENSG00000132465
+B cell,generated,11,ENSG00000137265
+B cell,generated,12,ENSG00000116741
+B cell,generated,13,ENSG00000143333
+B cell,generated,14,ENSG00000160789
+B cell,generated,15,ENSG00000118515
+B cell,generated,16,ENSG00000186818
+B cell,generated,17,ENSG00000183508
+B cell,generated,18,ENSG00000075420
+B cell,generated,19,ENSG00000165948
+B cell,generated,20,ENSG00000099958
+B cell,generated,21,ENSG00000155090
+B cell,generated,22,ENSG00000065308
+B cell,generated,23,ENSG00000169136
+B cell,generated,24,ENSG00000139514
+B cell,generated,25,ENSG00000101057
+B cell,generated,26,ENSG00000142892
+B cell,generated,27,ENSG00000135604
+B cell,generated,28,ENSG00000135916
+B cell,generated,29,ENSG00000153094
+B cell,generated,30,ENSG00000070214
+B cell,generated,31,ENSG00000138709
+B cell,generated,32,ENSG00000065485
+B cell,generated,33,ENSG00000136682
+B cell,generated,34,ENSG00000135541
+B cell,generated,35,ENSG00000150961
+B cell,generated,36,ENSG00000096060
+B cell,generated,37,ENSG00000161010
+B cell,generated,38,ENSG00000013375
+B cell,generated,39,ENSG00000029639
+B cell,generated,40,ENSG00000164687
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+B cell,generated,42,ENSG00000004468
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+B cell,generated,46,ENSG00000144791
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+B cell,generated,48,ENSG00000142065
+B cell,generated,49,ENSG00000142197
+B cell,generated,50,ENSG00000116824
+Monocyte,observed,1,ENSG00000115590
+Monocyte,observed,2,ENSG00000166428
+Monocyte,observed,3,ENSG00000173369
+Monocyte,observed,4,ENSG00000113088
+Monocyte,observed,5,ENSG00000146070
+Monocyte,observed,6,ENSG00000108950
+Monocyte,observed,7,ENSG00000123610
+Monocyte,observed,8,ENSG00000100079
+Monocyte,observed,9,ENSG00000153563
+Monocyte,observed,10,ENSG00000145649
+Monocyte,observed,11,ENSG00000172116
+Monocyte,observed,12,ENSG00000184613
+Monocyte,observed,13,ENSG00000179639
+Monocyte,observed,14,ENSG00000180644
+Monocyte,observed,15,ENSG00000147138
+Monocyte,observed,16,ENSG00000100450
+Monocyte,observed,17,ENSG00000073861
+Monocyte,observed,18,ENSG00000115523
+Monocyte,observed,19,ENSG00000137441
+Monocyte,observed,20,ENSG00000139970
+Monocyte,observed,21,ENSG00000153823
+Monocyte,observed,22,ENSG00000111796
+Monocyte,observed,23,ENSG00000134539
+Monocyte,observed,24,ENSG00000013725
+Monocyte,observed,25,ENSG00000163734
+Monocyte,observed,26,ENSG00000120262
+Monocyte,observed,27,ENSG00000152495
+Monocyte,observed,28,ENSG00000160856
+Monocyte,observed,29,ENSG00000183918
+Monocyte,observed,30,ENSG00000163564
+Monocyte,observed,31,ENSG00000180739
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+Monocyte,observed,34,ENSG00000198821
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+Monocyte,observed,37,ENSG00000172673
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+Monocyte,observed,39,ENSG00000100385
+Monocyte,observed,40,ENSG00000163508
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+Monocyte,observed,42,ENSG00000173114
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+Monocyte,observed,46,ENSG00000115085
+Monocyte,observed,47,ENSG00000198851
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+Monocyte,observed,49,ENSG00000168685
+Monocyte,observed,50,ENSG00000138795
+Monocyte,generated,1,ENSG00000115590
+Monocyte,generated,2,ENSG00000198848
+Monocyte,generated,3,ENSG00000100079
+Monocyte,generated,4,ENSG00000169385
+Monocyte,generated,5,ENSG00000149131
+Monocyte,generated,6,ENSG00000126262
+Monocyte,generated,7,ENSG00000122483
+Monocyte,generated,8,ENSG00000143344
+Monocyte,generated,9,ENSG00000090924
+Monocyte,generated,10,ENSG00000160201
+Monocyte,generated,11,ENSG00000115159
+Monocyte,generated,12,ENSG00000163220
+Monocyte,generated,13,ENSG00000122025
+Monocyte,generated,14,ENSG00000184357
+Monocyte,generated,15,ENSG00000102181
+Monocyte,generated,16,ENSG00000142655
+Monocyte,generated,17,ENSG00000047634
+Monocyte,generated,18,ENSG00000170293
+Monocyte,generated,19,ENSG00000089157
+Monocyte,generated,20,ENSG00000142937
+Monocyte,generated,21,ENSG00000186468
+Monocyte,generated,22,ENSG00000140988
+Monocyte,generated,23,ENSG00000164587
+Monocyte,generated,24,ENSG00000198712
+Monocyte,generated,25,ENSG00000231500
+Monocyte,generated,26,ENSG00000162688
+Monocyte,generated,27,ENSG00000109475
+Monocyte,generated,28,ENSG00000142676
+Monocyte,generated,29,ENSG00000198938
+Monocyte,generated,30,ENSG00000105640
+Monocyte,generated,31,ENSG00000171863
+Monocyte,generated,32,ENSG00000138326
+Monocyte,generated,33,ENSG00000167526
+Monocyte,generated,34,ENSG00000161016
+Monocyte,generated,35,ENSG00000130255
+Monocyte,generated,36,ENSG00000182899
+Monocyte,generated,37,ENSG00000136942
+Monocyte,generated,38,ENSG00000145425
+Monocyte,generated,39,ENSG00000162244
+Monocyte,generated,40,ENSG00000198918
+Monocyte,generated,41,ENSG00000149806
+Monocyte,generated,42,ENSG00000115268
+NK cell,observed,1,ENSG00000090382
+NK cell,observed,2,ENSG00000085265
+NK cell,observed,3,ENSG00000185215
+NK cell,observed,4,ENSG00000123358
+NK cell,observed,5,ENSG00000110077
+NK cell,observed,6,ENSG00000119535
+NK cell,observed,7,ENSG00000038427
+NK cell,observed,8,ENSG00000163563
+NK cell,observed,9,ENSG00000116701
+NK cell,observed,10,ENSG00000197629
+NK cell,observed,11,ENSG00000172243
+NK cell,observed,12,ENSG00000169429
+NK cell,observed,13,ENSG00000125538
+NK cell,observed,14,ENSG00000109321
+NK cell,observed,15,ENSG00000121552
+NK cell,observed,16,ENSG00000120708
+NK cell,observed,17,ENSG00000163220
+NK cell,observed,18,ENSG00000100079
+NK cell,observed,19,ENSG00000144655
+NK cell,observed,20,ENSG00000241399
+NK cell,observed,21,ENSG00000101336
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paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/current_f01/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/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/current_f01/query.h5ad",
+  "method": "current_f01",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/current_f01/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": 115500,
+  "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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+  },
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+  "query_build": {
+    "kind": "generated_npz",
+    "poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
+    "readout": "poisson",
+    "seed": 20260916,
+    "set": "current_f01",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw0/current_f01.npz",
+    "source_sha256": "1fdcf1a90209aa916ab0389642e3d7fda6234031ae5e0b6275f76ddff4a57c21"
+  },
+  "model": {
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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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+  "label_counts": {
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+      "pDC": 55,
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+  },
+  "confidence": {
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+    "mean_l1_mass": 0.9870825409889221,
+    "frac_l2_max_prob_ge_0.5": 0.9733593073593073
+  },
+  "timings_s": {
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+    "total": 3.1
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+  "versions": {
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+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-13T12:36:22.987566+00:00"
+}