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/zs_K1000/arms/zs_K1000/labels/labels.manifest.json

@@ -0,0 +1,156 @@
+{
+  "dataset_id": "Ye2026_sepsis",
+  "split": "generated",
+  "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/zs_K1000/arms/zs_K1000/query.h5ad",
+  "method": "zs_K1000",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/zs_K1000/arms/zs_K1000/labels/labels.parquet",
+  "training_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/reference/aifi_reference_f01common.h5ad",
+  "target_truth_used_for_fitting": false,
+  "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
+  "labels": [
+    "T cell",
+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
+    "Other"
+  ],
+  "l2_labels": [
+    "ASDC",
+    "CD14 monocyte",
+    "CD16 monocyte",
+    "CD56bright NK cell",
+    "CD56dim NK cell",
+    "CD8aa",
+    "DN T cell",
+    "Effector B cell",
+    "Erythrocyte",
+    "ILC",
+    "Intermediate monocyte",
+    "MAIT",
+    "Memory B cell",
+    "Memory CD4 T cell",
+    "Memory CD8 T cell",
+    "Naive B cell",
+    "Naive CD4 T cell",
+    "Naive CD8 T cell",
+    "Plasma cell",
+    "Platelet",
+    "Progenitor cell",
+    "Proliferating NK cell",
+    "Proliferating T cell",
+    "Transitional B cell",
+    "Treg",
+    "cDC1",
+    "cDC2",
+    "gdT",
+    "pDC"
+  ],
+  "n_cells": 123000,
+  "n_genes": 1005,
+  "note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
+  "label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
+  "query_train_epochs": 0,
+  "confidence_threshold": 0.0,
+  "subset": false,
+  "evaluator_aligned": true,
+  "gene_space": {
+    "join_key": "ensembl_id",
+    "model_genes": 1005,
+    "query_genes": 1006,
+    "model_genes_missing_from_query_zero_padded": 0,
+    "query_genes_outside_model_dropped": 1,
+    "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
+  },
+  "readout": null,
+  "query_build": {
+    "kind": "generated_npz",
+    "poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
+    "readout": "poisson",
+    "seed": 20260916,
+    "set": "zs_K1000",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated_masked/ye2026_sepsis/hoL_ye2026_sepsis/zs_K1000.npz",
+    "source_sha256": "3631bfcd45dd8bf6111547c2dd41f7cd0e4baefe7d1070fa8a5f46aee499ad75"
+  },
+  "model": {
+    "scanvi_model_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_model",
+    "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": {
+      "l2_accuracy": 0.8692869740488788,
+      "l2_macro_f1": 0.8500925599737216,
+      "l1_accuracy": 0.9918367346938776,
+      "l1_macro_f1": 0.9715232379009036,
+      "pbmc5_other_accuracy": 0.9920886873267826,
+      "pbmc5_other_macro_f1": 0.9812088972148597
+    }
+  },
+  "label_counts": {
+    "celltype_l1_pred": {
+      "Monocyte": 45219,
+      "T cell": 43708,
+      "B cell": 18509,
+      "NK cell": 11342,
+      "Other": 3067,
+      "DC": 1155
+    },
+    "aifi_l1": {
+      "Monocyte": 45219,
+      "T cell": 43708,
+      "B cell": 18509,
+      "NK cell": 11342,
+      "Erythrocyte": 1503,
+      "Platelet": 1249,
+      "DC": 1155,
+      "ILC": 178,
+      "Progenitor cell": 137
+    },
+    "aifi_l2": {
+      "CD14 monocyte": 35996,
+      "Memory CD8 T cell": 13473,
+      "Naive B cell": 12299,
+      "Memory CD4 T cell": 7368,
+      "Naive CD4 T cell": 6533,
+      "CD56dim NK cell": 5851,
+      "gdT": 5391,
+      "Proliferating NK cell": 4919,
+      "Intermediate monocyte": 4664,
+      "CD16 monocyte": 4559,
+      "DN T cell": 3879,
+      "Naive CD8 T cell": 2660,
+      "Memory B cell": 2138,
+      "Treg": 1826,
+      "Effector B cell": 1782,
+      "Transitional B cell": 1590,
+      "Erythrocyte": 1503,
+      "Proliferating T cell": 1353,
+      "Platelet": 1249,
+      "MAIT": 872,
+      "Plasma cell": 700,
+      "cDC2": 644,
+      "CD56bright NK cell": 572,
+      "CD8aa": 353,
+      "pDC": 267,
+      "cDC1": 217,
+      "ILC": 178,
+      "Progenitor cell": 137,
+      "ASDC": 27
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9339999258905891,
+    "mean_l1_mass": 0.9838707447052002,
+    "frac_l2_max_prob_ge_0.5": 0.9790162601626017
+  },
+  "timings_s": {
+    "predict": 1.2,
+    "total": 2.0
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-05T10:27:39.232608+00:00"
+}

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

@@ -0,0 +1,14 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+zs_K1000,T cell,mean_cp10k,3258,-0.10626920236197915,0.2548893770824626,-0.17698878918901748,0.23561381867716125,61,21,61,21,298117,43708,,,,,,,,,,,
+zs_K1000,T cell,pseudobulk_log1p_cpm,3258,-0.018419428478047662,0.2164745523777111,-0.08253693265610379,0.2730081644174592,61,21,61,21,298117,43708,,,,,,,,,,,
+zs_K1000,B cell,mean_cp10k,3310,0.04537596618840693,0.27458639801653467,-0.014759442158262217,0.21572058927497456,61,21,61,21,99729,18509,,,,,,,,,,,
+zs_K1000,B cell,pseudobulk_log1p_cpm,3310,0.10752880906580575,0.2711145517540278,0.04874634056941341,0.2281148672966534,61,21,61,21,99729,18509,,,,,,,,,,,
+zs_K1000,Monocyte,mean_cp10k,3289,0.05684088300852428,0.5481103923782986,-0.07970337628471502,0.22228627688989985,61,21,61,21,111269,45219,,,,,,,,,,,
+zs_K1000,Monocyte,pseudobulk_log1p_cpm,3289,0.19368907067202545,0.6203629305570988,-0.05013992002847866,0.37108389204694464,61,21,61,21,111269,45219,,,,,,,,,,,
+zs_K1000,NK cell,mean_cp10k,3240,-0.07855574199823576,0.1861970975708186,-0.13744267652926595,0.2753231247041104,61,21,61,21,47832,11342,,,,,,,,,,,
+zs_K1000,NK cell,pseudobulk_log1p_cpm,3240,-0.054486761116555926,0.05592238177293225,-0.07220341783799075,0.26772780139477986,61,21,61,21,47832,11342,,,,,,,,,,,
+zs_K1000,T cell,welch_top50_deg,5975,,,,,61,21,61,21,298117,43708,True,3,0.030927835051546393,50,50,1578,733,3,0.030927835051546393,50,1378
+zs_K1000,B cell,welch_top50_deg,5975,,,,,61,21,61,21,99729,18509,True,2,0.02040816326530612,50,50,1102,547,2,0.02040816326530612,50,1378
+zs_K1000,Monocyte,welch_top50_deg,5975,,,,,61,21,61,21,111269,45219,True,4,0.041666666666666664,50,50,2459,964,13,0.14942528735632185,50,1378
+zs_K1000,NK cell,welch_top50_deg,5975,,,,,61,21,61,21,47832,11342,True,4,0.041666666666666664,50,50,1235,323,2,0.02040816326530612,50,1378
+zs_K1000,DC,welch_top50_deg,5975,,,,,57,21,60,21,3300,1155,True,0,0.0,50,18,1572,18,1,0.010101010101010102,50,1378

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/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
+zs_K1000,Abd-PS04,ped_sepsis,1500,5449,150,0.06533333333333333,0.14094329234721967,0.022,0.17030647825289044,0.854,0.5608368507983116,0.029333333333333333,0.02147182969352175,0.006666666666666667,0.003853918150119288,0.02266666666666667,0.10258763075793724,0.6076748027160946,0.8240358281801887,0.8753057338921635,5,False,0.7266666666666667,0.06,0.7533333333333333,0.06,85.39999999999999,56.083685079831156,1412.0,2716.0
+zs_K1000,Abd-PS05,ped_sepsis,1500,6924,150,0.3486666666666667,0.30387059503177355,0.18133333333333335,0.5060658578856152,0.28733333333333333,0.07019064124783363,0.11533333333333333,0.0891103408434431,0.0,0.008954361640670132,0.06733333333333333,0.021808203350664357,0.667373772385904,0.6987393915367811,0.8308855305677671,68,False,0.8733333333333333,0.07333333333333333,0.82,0.06,28.733333333333334,7.0190641247833625,380.0,2313.0
+zs_K1000,Abd-PS07,ped_sepsis,1500,3472,150,0.5733333333333334,0.8626152073732719,0.048666666666666664,0.023329493087557603,0.17,0.002304147465437788,0.19066666666666668,0.09331797235023041,0.0033333333333333335,0.0002880184331797235,0.014,0.018145161290322582,0.5868540706605223,0.7909717817075781,0.82863424272524,71,False,0.7933333333333333,0.06,0.8266666666666667,0.04666666666666667,17.0,0.2304147465437788,508.0,1614.0
+zs_K1000,Abd-PS19,ped_sepsis,1500,7984,150,0.35333333333333333,0.4622995991983968,0.164,0.11209919839679358,0.3373333333333333,0.2937124248496994,0.11,0.05586172344689379,0.009333333333333334,0.0156563126252505,0.026,0.06037074148296593,0.2993199732798931,0.218193607618059,0.8788786094069906,22,False,0.7266666666666667,0.09333333333333334,0.7133333333333334,0.11333333333333333,33.733333333333334,29.37124248496994,611.0,2111.0
+zs_K1000,Abd-PS20,ped_sepsis,1500,7286,150,0.2773333333333333,0.30496843261048584,0.6733333333333333,0.5780949766675817,0.01,0.08770244304144935,0.03,0.007823222618720834,0.0033333333333333335,0.0005489980785067252,0.006,0.02086192698325556,0.24039893860371483,0.8206851316278935,0.8783225908958909,2,False,0.3333333333333333,0.03333333333333333,0.38,0.03333333333333333,1.0,8.770244304144935,1590.5,1820.0
+zs_K1000,Abd-PS23,ped_sepsis,1500,4309,150,0.37466666666666665,0.2529589231840334,0.138,0.3272220932931075,0.26866666666666666,0.32142028312833604,0.086,0.013460199582269667,0.0026666666666666666,0.002088651659317707,0.13,0.08284984915293572,0.48395141950955367,0.6120732295054894,0.8591228228169108,32,False,0.78,0.03333333333333333,0.7133333333333334,0.05333333333333334,26.866666666666667,32.1420283128336,358.0,1832.0
+zs_K1000,Abd-PS27,ped_sepsis,1500,9427,150,0.664,0.6126021003500584,0.08066666666666666,0.06078285774901877,0.14133333333333334,0.13196138750397793,0.08266666666666667,0.010289593720165482,0.0026666666666666666,0.0029701920016972526,0.028666666666666667,0.1813938686750822,0.3060614546868923,0.5288253850706728,0.8692219939536855,41,False,0.5733333333333334,0.04,0.5533333333333333,0.02666666666666667,14.133333333333335,13.196138750397793,1310.5,2356.0
+zs_K1000,Abd-S102,adult_sepsis,1500,9512,150,0.14933333333333335,0.47981497056349875,0.07133333333333333,0.39318755256518084,0.6253333333333333,0.0053616484440706475,0.10533333333333333,0.095878889823381,0.004666666666666667,0.0007359125315391085,0.044,0.02502102607232969,1.304671712924026,0.47699080006140543,0.7802567026580056,73,False,0.7,0.04666666666666667,0.74,0.07333333333333333,62.53333333333333,0.5361648444070648,768.5,1646.0
+zs_K1000,Abd-S103,adult_sepsis,1500,9423,150,0.35333333333333333,0.4813753581661891,0.11066666666666666,0.14782977820227103,0.28933333333333333,0.0024408362517245037,0.16,0.04393505253104107,0.004666666666666667,0.00021224663058473945,0.082,0.3242067282181895,0.8148237291732994,0.5587060076493682,0.808234768273432,76,False,0.74,0.05333333333333334,0.7666666666666667,0.07333333333333333,28.933333333333334,0.24408362517245036,394.5,971.0
+zs_K1000,Abd-S120,adult_sepsis,1500,5783,150,0.23133333333333334,0.3140238630468615,0.06933333333333333,0.11049628220646723,0.5993333333333334,0.46446481065191075,0.07066666666666667,0.07297250561992046,0.010666666666666666,0.0008646031471554556,0.018666666666666668,0.03717793532768459,0.2893411724018675,0.5189164550921991,0.8933198169793556,4,False,0.6466666666666666,0.05333333333333334,0.6533333333333333,0.06,59.93333333333334,46.44648106519107,878.5,2845.0
+zs_K1000,Abd-S123,adult_sepsis,1500,6299,150,0.222,0.16986823305286552,0.03,0.08779171297031275,0.632,0.5027782187648833,0.07,0.10938244165740593,0.004,0.0007937767899666614,0.042,0.1293856167645658,0.369119542784569,0.8187693250726966,0.8842358328792861,8,False,0.6533333333333333,0.09333333333333334,0.7466666666666667,0.09333333333333334,63.2,50.277821876488325,725.5,2261.0
+zs_K1000,Abd-S156,adult_sepsis,1500,7004,150,0.09333333333333334,0.3343803540833809,0.02266666666666667,0.08209594517418618,0.7846666666666666,0.39406053683609366,0.06066666666666667,0.0910908052541405,0.006666666666666667,0.0012849800114220445,0.032,0.0970873786407767,0.7919756329716353,0.4962206922485184,0.8777262184073864,18,False,0.6133333333333333,0.10666666666666667,0.6266666666666667,0.11333333333333333,78.46666666666667,39.406053683609365,1616.0,1821.0
+zs_K1000,Abd-S39,adult_sepsis,1500,4291,150,0.152,0.13819622465625728,0.03,0.06152412025168958,0.7146666666666667,0.6933115823817292,0.048,0.049638778839431366,0.004666666666666667,0.0013982754602656724,0.050666666666666665,0.05593101841062689,0.07685450167016236,0.9977910325594677,0.8877370405118872,5,False,0.6266666666666667,0.12666666666666668,0.62,0.14,71.46666666666667,69.33115823817292,1101.5,3523.0
+zs_K1000,Abd-S42,adult_sepsis,1500,6567,150,0.3446666666666667,0.5748439165524593,0.07133333333333333,0.09760925841327851,0.358,0.17039744175422566,0.198,0.05862646566164154,0.017333333333333333,0.0016750418760469012,0.010666666666666666,0.0968478757423481,0.6852687680828384,0.2811971753944427,0.8812583910522853,27,False,0.5066666666666667,0.04666666666666667,0.49333333333333335,0.03333333333333333,35.8,17.039744175422566,1425.0,1982.0
+zs_K1000,Abd-S47,adult_sepsis,1500,7971,150,0.5846666666666667,0.7027976414502571,0.33,0.20474219044034625,0.02,0.03224187680341237,0.051333333333333335,0.019069125580228326,0.004,0.0006272738677706687,0.01,0.040521891857985194,0.32178948688997616,0.5066504444101315,0.8742768154060635,7,False,0.32666666666666666,0.013333333333333334,0.36666666666666664,0.02,2.0,3.224187680341237,1526.5,2030.0
+zs_K1000,Abd-S51,adult_sepsis,1500,6865,150,0.156,0.25273124544792425,0.16666666666666666,0.269482884195193,0.5573333333333333,0.3551347414420976,0.07666666666666666,0.03670793882010197,0.024,0.0014566642388929353,0.019333333333333334,0.08448652585579024,0.529401310997815,0.566744289390268,0.8782518125584124,31,False,0.5933333333333334,0.06,0.5933333333333334,0.04666666666666667,55.733333333333334,35.51347414420976,1436.0,1849.0
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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/zs_K1000/summary.json

@@ -0,0 +1,767 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-05T10:27:44.703604+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "ye2026_sepsis",
+  "--threads",
+  "8",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/usable_samples.txt",
+  "--arm",
+  "zs_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated_masked/ye2026_sepsis/hoL_ye2026_sepsis/zs_K1000.npz",
+  "--case-groups",
+  "adult_sepsis,ped_sepsis",
+  "--control-groups",
+  "adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/zs_K1000"
+ ],
+ "arms": [
+  "zs_K1000"
+ ],
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
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+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
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+  "Uri-S20",
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+ ],
+ "n_donors": 82,
+ "reference": {
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+  "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+  "features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
+  "n_r1_cells": 12300,
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