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/xcalL_K1000/per_donor.csv

@@ -0,0 +1,83 @@
+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
+xcalL_K1000,Abd-PS04,ped_sepsis,1500,5449,150,0.13466666666666666,0.14094329234721967,0.020666666666666667,0.17030647825289044,0.798,0.5608368507983116,0.023333333333333334,0.02147182969352175,0.012,0.003853918150119288,0.011333333333333334,0.10258763075793724,0.4943414693827614,0.8240358281801887,0.8686186453809633,5,False,0.9133333333333333,0.47333333333333333,0.9333333333333333,0.6533333333333333,79.80000000000001,56.083685079831156,2813.5,2716.0
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+xcalL_K1000,Abd-PS07,ped_sepsis,1500,3472,150,0.7646666666666667,0.8626152073732719,0.024666666666666667,0.023329493087557603,0.082,0.002304147465437788,0.118,0.09331797235023041,0.005333333333333333,0.0002880184331797235,0.005333333333333333,0.018145161290322582,0.2215207373271889,0.7909717817075781,0.8235182060765777,61,False,0.82,0.48,0.8666666666666667,0.62,8.200000000000001,0.2304147465437788,1307.5,1614.0
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+xcalL_K1000,Abd-S42,adult_sepsis,1500,6567,150,0.6566666666666666,0.5748439165524593,0.029333333333333333,0.09760925841327851,0.15133333333333332,0.17039744175422566,0.14333333333333334,0.05862646566164154,0.007333333333333333,0.0016750418760469012,0.012,0.0968478757423481,0.34437581848637117,0.2811971753944427,0.8716920704411917,13,False,0.9266666666666666,0.47333333333333333,0.96,0.6933333333333334,15.133333333333333,17.039744175422566,1829.5,1982.0
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+xcalL_K1000,Abd-S79,adult_sepsis,1500,8044,150,0.3413333333333333,0.5500994530084535,0.21533333333333332,0.30892590750870214,0.282,0.024365987071108902,0.12666666666666668,0.09373446046742914,0.004,0.00012431626056688214,0.030666666666666665,0.022749875683739432,0.604717387700978,0.43476793794453494,0.8605264706113658,54,False,0.88,0.24,0.8733333333333333,0.5733333333333334,28.199999999999996,2.4365987071108903,1744.0,2389.5
+xcalL_K1000,Abd-S83,adult_sepsis,1500,6209,150,0.21866666666666668,0.3924947656627476,0.034666666666666665,0.16991464003865356,0.688,0.049927524561120956,0.021333333333333333,0.3013367692059913,0.005333333333333333,0.0009663391850539539,0.032,0.0853599613464326,1.2848789391743167,0.5217899477442837,0.8141330889703888,61,False,0.9,0.5666666666666667,0.84,0.66,68.8,4.992752456112096,1789.5,1649.0
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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/xcalL_K1000/summary.json

@@ -0,0 +1,767 @@
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+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated_masked/ye2026_sepsis/hoL_ye2026_sepsis/xcalL_K1000.npz",
+   "npz_sha256": "ef516022b53748792448792f9e69475ca5d34164790ed5f9e62763f9560776f3",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+    "checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ye2026_sepsis/test_xcal_K1000.npz",
+    "input_condition_sha256": "b4c2b51f0669e2f0236e7981a6b5b5ddabcd22cbf9e3949384144fb55f5564ed",
+    "seed": 20260927,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/splits/hoL_ye2026_sepsis/test_xcal_K1000.npz",
+    "sha256": "b4c2b51f0669e2f0236e7981a6b5b5ddabcd22cbf9e3949384144fb55f5564ed"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 34017297,
+    "median_library_whole_npz_panel": 1628.0,
+    "n_rows_whole_npz": 123000
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 57674,
+     "Monocyte": 32509,
+     "B cell": 17496,
+     "NK cell": 11771,
+     "Other": 2743,
+     "DC": 807
+    },
+    "mean_l2_max_prob": 0.9375362153139298,
+    "predict_seconds": 4.7
+   },
+   "n_donors": 82,
+   "n_generated_cells": 123000,
+   "composition": {
+    "l1_mean": 0.4442804458742561,
+    "l1_median": 0.38480190266564623,
+    "l1_obs_loo_null_mean": 0.515468004498372,
+    "l1_generated_loo_mean_vs_observed_mean": 0.5284644836568292,
+    "composition_top1": 0.04878048780487805,
+    "mean_fraction_generated": {
+     "T cell": 0.468894,
+     "B cell": 0.142244,
+     "Monocyte": 0.264301,
+     "NK cell": 0.095699,
+     "DC": 0.006561,
+     "Other": 0.022301
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.484547,
+     "B cell": 0.172757,
+     "Monocyte": 0.208171,
+     "NK cell": 0.080723,
+     "DC": 0.005542,
+     "Other": 0.04826
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5975,
+    "r_median": 0.8655730812887326,
+    "r_mean": 0.8589778591163962,
+    "top1": 0.13414634146341464,
+    "n_top1": 11,
+    "own_rank_median": 12.0,
+    "chance_top1": 0.012195121951219513
+   },
+   "precision_coverage": {
+    "precision": 0.8947154471544716,
+    "coverage": 0.4608943089430894,
+    "density": 0.5601626016260163,
+    "n_query": 12300,
+    "n_reference": 12300
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.8973983739837398,
+    "coverage": 0.6535772357723577,
+    "density": 0.7638861788617886,
+    "detected_median_before": {
+     "R1": 411.0,
+     "Q": 268.0
+    },
+    "detected_median_after": {
+     "R1": 268.0,
+     "Q": 268.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 26.430081300813008,
+    "observed_mean_over_donors": 20.817070783198325,
+    "generated_pooled_cells": 26.430081300813008
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 1628.0,
+    "observed_pooled": 1967.0,
+    "generated_mean_of_donor_medians": 1667.53662109375,
+    "observed_mean_of_donor_medians": 2112.9146341463415
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.05627544679846157,
+       "r_broadcast": 0.2417280392439751,
+       "partial_r_generated_given_broadcast": -0.02050007691127722,
+       "r_generated_vs_broadcast": 0.31101491183217883,
+       "n_genes": 3258
+      },
+      "B cell": {
+       "r_generated": 0.14694432575237432,
+       "r_broadcast": 0.27652248568893345,
+       "partial_r_generated_given_broadcast": 0.08091701026075308,
+       "r_generated_vs_broadcast": 0.2598472854525099,
+       "n_genes": 3310
+      },
+      "Monocyte": {
+       "r_generated": 0.20638200160135267,
+       "r_broadcast": 0.5887447215431866,
+       "partial_r_generated_given_broadcast": 0.08132622220068925,
+       "r_generated_vs_broadcast": 0.2422135300656274,
+       "n_genes": 3289
+      },
+      "NK cell": {
+       "r_generated": -0.023935585548446603,
+       "r_broadcast": 0.16207395037992536,
+       "partial_r_generated_given_broadcast": -0.07618425739904247,
+       "r_generated_vs_broadcast": 0.2954533760541212,
+       "n_genes": 3240
+      }
+     },
+     "mean_r_generated": 0.09641654715093549,
+     "mean_r_broadcast": 0.3172672992140051,
+     "mean_partial_r": 0.01638972453778066
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.1558048510564581,
+       "r_broadcast": 0.21842986671424938,
+       "partial_r_generated_given_broadcast": 0.07422734836639464,
+       "r_generated_vs_broadcast": 0.41097799017014486,
+       "n_genes": 3258
+      },
+      "B cell": {
+       "r_generated": 0.2128052559867798,
+       "r_broadcast": 0.2766567545456621,
+       "partial_r_generated_given_broadcast": 0.1484568988172587,
+       "r_generated_vs_broadcast": 0.2731468692632431,
+       "n_genes": 3310
+      },
+      "Monocyte": {
+       "r_generated": 0.1377099791029595,
+       "r_broadcast": 0.6208124073714443,
+       "partial_r_generated_given_broadcast": -0.09504346483962818,
+       "r_generated_vs_broadcast": 0.334911445045998,
+       "n_genes": 3289
+      },
+      "NK cell": {
+       "r_generated": -0.06324276116255552,
+       "r_broadcast": 0.05311099002810362,
+       "partial_r_generated_given_broadcast": -0.08283174254191039,
+       "r_generated_vs_broadcast": 0.29656618824951697,
+       "n_genes": 3240
+      }
+     },
+     "mean_r_generated": 0.11076933124591047,
+     "mean_r_broadcast": 0.29225250466486485,
+     "mean_partial_r": 0.01120225995052869
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.010101010101010102,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 4,
+      "top50_jaccard_broadcast": 0.041666666666666664,
+      "n_cells_obs": 298117,
+      "n_cells_gen": 57674
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.010101010101010102,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 3,
+      "top50_jaccard_broadcast": 0.030927835051546393,
+      "n_cells_obs": 99729,
+      "n_cells_gen": 17496
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 8,
+      "top50_jaccard": 0.08695652173913043,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 14,
+      "top50_jaccard_broadcast": 0.16279069767441862,
+      "n_cells_obs": 111269,
+      "n_cells_gen": 32509
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 4,
+      "top50_jaccard_broadcast": 0.041666666666666664,
+      "n_cells_obs": 47832,
+      "n_cells_gen": 11771
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 3300,
+      "n_cells_gen": 807
+     }
+    },
+    "sum": 10,
+    "sum_4type": 10,
+    "max": 250,
+    "mean": 2.0,
+    "sum_broadcast": 27,
+    "sum_broadcast_4type": 25,
+    "broadcast_n_significant": 1714,
+    "seconds": 0.34
+   },
+   "seconds": 18.3
+  }
+ },
+ "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": 27.3
+}

paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/zs_K1000/README.md

@@ -0,0 +1,73 @@
+# score_ft.py output: ye2026_sepsis, 82 scored donors
+
+Arms: zs_K1000.  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/zs_K1000/arms/zs_K1000/deg_top50_lists.csv

@@ -0,0 +1,519 @@
+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,ENSG00000213402
+T cell,generated,2,ENSG00000058673
+T cell,generated,3,ENSG00000132465
+T cell,generated,4,ENSG00000143546
+T cell,generated,5,ENSG00000165949
+T cell,generated,6,ENSG00000233276
+T cell,generated,7,ENSG00000142089
+T cell,generated,8,ENSG00000038427
+T cell,generated,9,ENSG00000165168
+T cell,generated,10,ENSG00000203896
+T cell,generated,11,ENSG00000163563
+T cell,generated,12,ENSG00000154146
+T cell,generated,13,ENSG00000119917
+T cell,generated,14,ENSG00000103150
+T cell,generated,15,ENSG00000101019
+T cell,generated,16,ENSG00000180573
+T cell,generated,17,ENSG00000112799
+T cell,generated,18,ENSG00000205784
+T cell,generated,19,ENSG00000170476
+T cell,generated,20,ENSG00000177575
+T cell,generated,21,ENSG00000133056
+T cell,generated,22,ENSG00000160318
+T cell,generated,23,ENSG00000223865
+T cell,generated,24,ENSG00000183691
+T cell,generated,25,ENSG00000127951
+T cell,generated,26,ENSG00000197249
+T cell,generated,27,ENSG00000135218
+T cell,generated,28,ENSG00000145416
+T cell,generated,29,ENSG00000178904
+T cell,generated,30,ENSG00000163220
+T cell,generated,31,ENSG00000125740
+T cell,generated,32,ENSG00000184678
+T cell,generated,33,ENSG00000225528
+T cell,generated,34,ENSG00000165025
+T cell,generated,35,ENSG00000185864
+T cell,generated,36,ENSG00000030582
+T cell,generated,37,ENSG00000285437
+T cell,generated,38,ENSG00000099910
+T cell,generated,39,ENSG00000120738
+T cell,generated,40,ENSG00000015532
+T cell,generated,41,ENSG00000163736
+T cell,generated,42,ENSG00000170458
+T cell,generated,43,ENSG00000144290
+T cell,generated,44,ENSG00000168461
+T cell,generated,45,ENSG00000073605
+T cell,generated,46,ENSG00000163131
+T cell,generated,47,ENSG00000081189
+T cell,generated,48,ENSG00000105325
+T cell,generated,49,ENSG00000067840
+T cell,generated,50,ENSG00000011600
+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,ENSG00000026751
+B cell,generated,2,ENSG00000075420
+B cell,generated,3,ENSG00000048462
+B cell,generated,4,ENSG00000165272
+B cell,generated,5,ENSG00000150961
+B cell,generated,6,ENSG00000173334
+B cell,generated,7,ENSG00000099958
+B cell,generated,8,ENSG00000027075
+B cell,generated,9,ENSG00000132465
+B cell,generated,10,ENSG00000213658
+B cell,generated,11,ENSG00000118985
+B cell,generated,12,ENSG00000057657
+B cell,generated,13,ENSG00000105325
+B cell,generated,14,ENSG00000163694
+B cell,generated,15,ENSG00000239264
+B cell,generated,16,ENSG00000122188
+B cell,generated,17,ENSG00000184678
+B cell,generated,18,ENSG00000165949
+B cell,generated,19,ENSG00000133195
+B cell,generated,20,ENSG00000092529
+B cell,generated,21,ENSG00000100629
+B cell,generated,22,ENSG00000130653
+B cell,generated,23,ENSG00000176658
+B cell,generated,24,ENSG00000170476
+B cell,generated,25,ENSG00000111640
+B cell,generated,26,ENSG00000111885
+B cell,generated,27,ENSG00000132199
+B cell,generated,28,ENSG00000213402
+B cell,generated,29,ENSG00000139193
+B cell,generated,30,ENSG00000165632
+B cell,generated,31,ENSG00000165716
+B cell,generated,32,ENSG00000189233
+B cell,generated,33,ENSG00000070214
+B cell,generated,34,ENSG00000158158
+B cell,generated,35,ENSG00000144445
+B cell,generated,36,ENSG00000103257
+B cell,generated,37,ENSG00000175265
+B cell,generated,38,ENSG00000182774
+B cell,generated,39,ENSG00000156017
+B cell,generated,40,ENSG00000112195
+B cell,generated,41,ENSG00000091409
+B cell,generated,42,ENSG00000177084
+B cell,generated,43,ENSG00000154358
+B cell,generated,44,ENSG00000007264
+B cell,generated,45,ENSG00000171488
+B cell,generated,46,ENSG00000136143
+B cell,generated,47,ENSG00000184574
+B cell,generated,48,ENSG00000179909
+B cell,generated,49,ENSG00000159753
+B cell,generated,50,ENSG00000154016
+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,ENSG00000165949
+Monocyte,generated,2,ENSG00000129538
+Monocyte,generated,3,ENSG00000120885
+Monocyte,generated,4,ENSG00000138821
+Monocyte,generated,5,ENSG00000121716
+Monocyte,generated,6,ENSG00000138621
+Monocyte,generated,7,ENSG00000197353
+Monocyte,generated,8,ENSG00000123358
+Monocyte,generated,9,ENSG00000188312
+Monocyte,generated,10,ENSG00000158050
+Monocyte,generated,11,ENSG00000163737
+Monocyte,generated,12,ENSG00000232810
+Monocyte,generated,13,ENSG00000162804
+Monocyte,generated,14,ENSG00000182853
+Monocyte,generated,15,ENSG00000104880
+Monocyte,generated,16,ENSG00000186654
+Monocyte,generated,17,ENSG00000101162
+Monocyte,generated,18,ENSG00000152217
+Monocyte,generated,19,ENSG00000185291
+Monocyte,generated,20,ENSG00000138166
+Monocyte,generated,21,ENSG00000154447
+Monocyte,generated,22,ENSG00000256525
+Monocyte,generated,23,ENSG00000135362
+Monocyte,generated,24,ENSG00000129757
+Monocyte,generated,25,ENSG00000104918
+Monocyte,generated,26,ENSG00000169385
+Monocyte,generated,27,ENSG00000133985
+Monocyte,generated,28,ENSG00000115590
+Monocyte,generated,29,ENSG00000188290
+Monocyte,generated,30,ENSG00000132635
+Monocyte,generated,31,ENSG00000141337
+Monocyte,generated,32,ENSG00000159788
+Monocyte,generated,33,ENSG00000058673
+Monocyte,generated,34,ENSG00000021762
+Monocyte,generated,35,ENSG00000166428
+Monocyte,generated,36,ENSG00000124243
+Monocyte,generated,37,ENSG00000153234
+Monocyte,generated,38,ENSG00000168497
+Monocyte,generated,39,ENSG00000132478
+Monocyte,generated,40,ENSG00000127920
+Monocyte,generated,41,ENSG00000136878
+Monocyte,generated,42,ENSG00000120738
+Monocyte,generated,43,ENSG00000148356
+Monocyte,generated,44,ENSG00000198393
+Monocyte,generated,45,ENSG00000163629
+Monocyte,generated,46,ENSG00000169704
+Monocyte,generated,47,ENSG00000126464
+Monocyte,generated,48,ENSG00000058453
+Monocyte,generated,49,ENSG00000203666
+Monocyte,generated,50,ENSG00000283782
+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
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+NK cell,observed,11,ENSG00000172243
+NK cell,observed,12,ENSG00000121552
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+NK cell,observed,14,ENSG00000163220
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+NK cell,observed,16,ENSG00000100079
+NK cell,observed,17,ENSG00000144655
+NK cell,observed,18,ENSG00000109321
+NK cell,observed,19,ENSG00000120708
+NK cell,observed,20,ENSG00000241399
+NK cell,observed,21,ENSG00000143333
+NK cell,observed,22,ENSG00000197249
+NK cell,observed,23,ENSG00000143546
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+NK cell,observed,25,ENSG00000168497
+NK cell,observed,26,ENSG00000277632
+NK cell,observed,27,ENSG00000160789
+NK cell,observed,28,ENSG00000126759
+NK cell,observed,29,ENSG00000171051
+NK cell,observed,30,ENSG00000232810
+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
+NK cell,observed,41,ENSG00000165061
+NK cell,observed,42,ENSG00000163694
+NK cell,observed,43,ENSG00000106066
+NK cell,observed,44,ENSG00000127920
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+NK cell,observed,46,ENSG00000162444
+NK cell,observed,47,ENSG00000204472
+NK cell,observed,48,ENSG00000111275
+NK cell,observed,49,ENSG00000186407
+NK cell,observed,50,ENSG00000166592
+NK cell,generated,1,ENSG00000213402
+NK cell,generated,2,ENSG00000102804
+NK cell,generated,3,ENSG00000058673
+NK cell,generated,4,ENSG00000170476
+NK cell,generated,5,ENSG00000119917
+NK cell,generated,6,ENSG00000184381
+NK cell,generated,7,ENSG00000130559
+NK cell,generated,8,ENSG00000106992
+NK cell,generated,9,ENSG00000198393
+NK cell,generated,10,ENSG00000143546
+NK cell,generated,11,ENSG00000163736
+NK cell,generated,12,ENSG00000117475
+NK cell,generated,13,ENSG00000120885
+NK cell,generated,14,ENSG00000156500
+NK cell,generated,15,ENSG00000038427
+NK cell,generated,16,ENSG00000132635
+NK cell,generated,17,ENSG00000243716
+NK cell,generated,18,ENSG00000233276
+NK cell,generated,19,ENSG00000104689
+NK cell,generated,20,ENSG00000132600
+NK cell,generated,21,ENSG00000163221
+NK cell,generated,22,ENSG00000099910
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+NK cell,generated,24,ENSG00000161010
+NK cell,generated,25,ENSG00000197249
+NK cell,generated,26,ENSG00000274211
+NK cell,generated,27,ENSG00000164970
+NK cell,generated,28,ENSG00000158555
+NK cell,generated,29,ENSG00000185344
+NK cell,generated,30,ENSG00000147586
+NK cell,generated,31,ENSG00000266714
+NK cell,generated,32,ENSG00000101104
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+NK cell,generated,41,ENSG00000183542
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+NK cell,generated,44,ENSG00000107331
+NK cell,generated,45,ENSG00000198933
+NK cell,generated,46,ENSG00000168818
+NK cell,generated,47,ENSG00000067840
+NK cell,generated,48,ENSG00000198131
+NK cell,generated,49,ENSG00000089123
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+DC,observed,1,ENSG00000179639
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+DC,observed,26,ENSG00000149131
+DC,observed,27,ENSG00000134326
+DC,observed,28,ENSG00000113263
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+DC,observed,48,ENSG00000127920
+DC,observed,49,ENSG00000162654
+DC,observed,50,ENSG00000075223
+DC,generated,1,ENSG00000185989
+DC,generated,2,ENSG00000143878
+DC,generated,3,ENSG00000203485
+DC,generated,4,ENSG00000177606
+DC,generated,5,ENSG00000198467
+DC,generated,6,ENSG00000109436
+DC,generated,7,ENSG00000163029
+DC,generated,8,ENSG00000151466
+DC,generated,9,ENSG00000196684
+DC,generated,10,ENSG00000136826
+DC,generated,11,ENSG00000033327
+DC,generated,12,ENSG00000204267
+DC,generated,13,ENSG00000254772
+DC,generated,14,ENSG00000122025
+DC,generated,15,ENSG00000048052
+DC,generated,16,ENSG00000161638
+DC,generated,17,ENSG00000213445
+DC,generated,18,ENSG00000130522
+all (input bulk),broadcast,1,ENSG00000244734
+all (input bulk),broadcast,2,ENSG00000188536
+all (input bulk),broadcast,3,ENSG00000087116
+all (input bulk),broadcast,4,ENSG00000158578
+all (input bulk),broadcast,5,ENSG00000206172
+all (input bulk),broadcast,6,ENSG00000115590
+all (input bulk),broadcast,7,ENSG00000159189
+all (input bulk),broadcast,8,ENSG00000108950
+all (input bulk),broadcast,9,ENSG00000004939
+all (input bulk),broadcast,10,ENSG00000100985
+all (input bulk),broadcast,11,ENSG00000173369
+all (input bulk),broadcast,12,ENSG00000179639
+all (input bulk),broadcast,13,ENSG00000133742
+all (input bulk),broadcast,14,ENSG00000257017
+all (input bulk),broadcast,15,ENSG00000125740
+all (input bulk),broadcast,16,ENSG00000223609
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+all (input bulk),broadcast,23,ENSG00000123610
+all (input bulk),broadcast,24,ENSG00000138772
+all (input bulk),broadcast,25,ENSG00000276085
+all (input bulk),broadcast,26,ENSG00000132170
+all (input bulk),broadcast,27,ENSG00000137869
+all (input bulk),broadcast,28,ENSG00000184792
+all (input bulk),broadcast,29,ENSG00000118520
+all (input bulk),broadcast,30,ENSG00000170298
+all (input bulk),broadcast,31,ENSG00000162747
+all (input bulk),broadcast,32,ENSG00000120885
+all (input bulk),broadcast,33,ENSG00000177606
+all (input bulk),broadcast,34,ENSG00000153234
+all (input bulk),broadcast,35,ENSG00000182885
+all (input bulk),broadcast,36,ENSG00000078053
+all (input bulk),broadcast,37,ENSG00000165682
+all (input bulk),broadcast,38,ENSG00000042062
+all (input bulk),broadcast,39,ENSG00000115414
+all (input bulk),broadcast,40,ENSG00000144290
+all (input bulk),broadcast,41,ENSG00000166428
+all (input bulk),broadcast,42,ENSG00000079215
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+all (input bulk),broadcast,47,ENSG00000105610
+all (input bulk),broadcast,48,ENSG00000117281
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+all (input bulk),broadcast,50,ENSG00000166947