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/locoL_scratchsat_s100000_K1000/arms/locoL_scratchsat_s100000_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/locoL_scratchsat_s100000_K1000/arms/locoL_scratchsat_s100000_K1000/query.h5ad",
+  "method": "locoL_scratchsat_s100000_K1000",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/locoL_scratchsat_s100000_K1000/arms/locoL_scratchsat_s100000_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": "locoL_scratchsat_s100000_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/locoL_scratchsat_s100000_K1000.npz",
+    "source_sha256": "7650cc28aee5b4a1ce9f992c2f4286799adf9d02953f58cf1e68ad684c0803be"
+  },
+  "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": {
+      "T cell": 53015,
+      "B cell": 24575,
+      "Monocyte": 22887,
+      "NK cell": 17666,
+      "DC": 2729,
+      "Other": 2128
+    },
+    "aifi_l1": {
+      "T cell": 53015,
+      "B cell": 24575,
+      "Monocyte": 22887,
+      "NK cell": 17666,
+      "DC": 2729,
+      "Platelet": 887,
+      "Progenitor cell": 543,
+      "ILC": 393,
+      "Erythrocyte": 305
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 16252,
+      "Naive B cell": 14527,
+      "CD14 monocyte": 14183,
+      "CD56dim NK cell": 13392,
+      "Memory CD4 T cell": 11923,
+      "gdT": 8196,
+      "Naive CD4 T cell": 6823,
+      "Intermediate monocyte": 4713,
+      "Memory B cell": 4432,
+      "CD16 monocyte": 3991,
+      "Naive CD8 T cell": 3079,
+      "Effector B cell": 2534,
+      "CD8aa": 2243,
+      "Proliferating NK cell": 2165,
+      "CD56bright NK cell": 2109,
+      "cDC2": 2079,
+      "Transitional B cell": 1896,
+      "DN T cell": 1717,
+      "Treg": 1579,
+      "Plasma cell": 1186,
+      "Platelet": 887,
+      "MAIT": 739,
+      "Progenitor cell": 543,
+      "pDC": 517,
+      "Proliferating T cell": 464,
+      "ILC": 393,
+      "Erythrocyte": 305,
+      "cDC1": 112,
+      "ASDC": 21
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9340392905252008,
+    "mean_l1_mass": 0.9912149906158447,
+    "frac_l2_max_prob_ge_0.5": 0.9820894308943089
+  },
+  "timings_s": {
+    "predict": 1.2,
+    "total": 2.1
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-05T10:21:53.955156+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/locoL_scratchsat_s100000_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
+locoL_scratchsat_s100000_K1000,T cell,mean_cp10k,3258,0.1506609840846157,0.2548893770824626,0.1635634219569782,-0.02916055044154397,61,21,61,21,298117,53015,,,,,,,,,,,
+locoL_scratchsat_s100000_K1000,T cell,pseudobulk_log1p_cpm,3258,0.03812744245391077,0.2164745523777111,0.02459556564465728,0.06544212236430581,61,21,61,21,298117,53015,,,,,,,,,,,
+locoL_scratchsat_s100000_K1000,B cell,mean_cp10k,3310,0.26400127490221825,0.27458639801653467,0.22835436966426148,0.17398202759275022,61,21,61,21,99729,24575,,,,,,,,,,,
+locoL_scratchsat_s100000_K1000,B cell,pseudobulk_log1p_cpm,3310,0.23942631271880677,0.2711145517540278,0.19914421747133174,0.18880665130530896,61,21,61,21,99729,24575,,,,,,,,,,,
+locoL_scratchsat_s100000_K1000,Monocyte,mean_cp10k,3289,0.3470171932693454,0.5481103923782986,0.22951841507707277,0.29888454900543526,61,21,61,21,111269,22887,,,,,,,,,,,
+locoL_scratchsat_s100000_K1000,Monocyte,pseudobulk_log1p_cpm,3289,0.22109287834714436,0.6203629305570988,0.046288333024338324,0.30057738792973804,61,21,61,21,111269,22887,,,,,,,,,,,
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+locoL_scratchsat_s100000_K1000,NK cell,pseudobulk_log1p_cpm,3240,0.11666785021657361,0.05592238177293225,0.11169441901029249,0.10257988314577984,61,21,61,21,47832,17666,,,,,,,,,,,
+locoL_scratchsat_s100000_K1000,T cell,welch_top50_deg,5975,,,,,61,21,61,21,298117,53015,True,0,0.0,50,11,1578,11,3,0.030927835051546393,50,1378
+locoL_scratchsat_s100000_K1000,B cell,welch_top50_deg,5975,,,,,61,21,61,21,99729,24575,True,0,0.0,50,6,1102,6,2,0.02040816326530612,50,1378
+locoL_scratchsat_s100000_K1000,Monocyte,welch_top50_deg,5975,,,,,61,21,61,21,111269,22887,True,1,0.013157894736842105,50,27,2459,27,13,0.14942528735632185,50,1378
+locoL_scratchsat_s100000_K1000,NK cell,welch_top50_deg,5975,,,,,61,21,61,21,47832,17666,True,0,0.0,50,4,1235,4,2,0.02040816326530612,50,1378
+locoL_scratchsat_s100000_K1000,DC,welch_top50_deg,5975,,,,,57,21,61,21,3300,2729,True,0,0.0,50,1,1572,1,1,0.010101010101010102,50,1378

paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/locoL_scratchsat_s100000_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
+locoL_scratchsat_s100000_K1000,Abd-PS04,ped_sepsis,1500,5449,150,0.3413333333333333,0.14094329234721967,0.14733333333333334,0.17030647825289044,0.3453333333333333,0.5608368507983116,0.10466666666666667,0.02147182969352175,0.029333333333333333,0.003853918150119288,0.032,0.10258763075793724,0.6181285862849453,0.8240358281801887,0.9084055789361325,23,False,0.84,0.31333333333333335,0.8066666666666666,0.66,34.53333333333333,56.083685079831156,1252.0,2716.0
+locoL_scratchsat_s100000_K1000,Abd-PS05,ped_sepsis,1500,6924,150,0.3626666666666667,0.30387059503177355,0.39666666666666667,0.5060658578856152,0.11133333333333334,0.07019064124783363,0.1,0.0891103408434431,0.015333333333333332,0.008954361640670132,0.014,0.021808203350664357,0.2344147891392258,0.6987393915367811,0.917860036500896,2,False,0.84,0.49333333333333335,0.9133333333333333,0.64,11.133333333333335,7.0190641247833625,1584.5,2313.0
+locoL_scratchsat_s100000_K1000,Abd-PS07,ped_sepsis,1500,3472,150,0.6366666666666667,0.8626152073732719,0.15466666666666667,0.023329493087557603,0.044,0.002304147465437788,0.11933333333333333,0.09331797235023041,0.028666666666666667,0.0002880184331797235,0.016666666666666666,0.018145161290322582,0.45485407066052225,0.7909717817075781,0.8706877116726812,68,False,0.7533333333333333,0.43333333333333335,0.84,0.6666666666666666,4.3999999999999995,0.2304147465437788,1136.0,1614.0
+locoL_scratchsat_s100000_K1000,Abd-PS19,ped_sepsis,1500,7984,150,0.21533333333333332,0.4622995991983968,0.32,0.11209919839679358,0.26466666666666666,0.2937124248496994,0.14333333333333334,0.05586172344689379,0.04066666666666666,0.0156563126252505,0.016,0.06037074148296593,0.6407655310621243,0.218193607618059,0.9087440463339392,6,False,0.8866666666666667,0.3466666666666667,0.8,0.5733333333333334,26.466666666666665,29.37124248496994,973.5,2111.0
+locoL_scratchsat_s100000_K1000,Abd-PS20,ped_sepsis,1500,7286,150,0.22333333333333333,0.30496843261048584,0.49266666666666664,0.5780949766675817,0.14666666666666667,0.08770244304144935,0.09533333333333334,0.007823222618720834,0.030666666666666665,0.0005489980785067252,0.011333333333333334,0.02086192698325556,0.35318400585597953,0.8206851316278935,0.872290628601111,26,False,0.8466666666666667,0.24,0.8133333333333334,0.4866666666666667,14.666666666666666,8.770244304144935,816.5,1820.0
+locoL_scratchsat_s100000_K1000,Abd-PS23,ped_sepsis,1500,4309,150,0.21133333333333335,0.2529589231840334,0.32866666666666666,0.3272220932931075,0.258,0.32142028312833604,0.16466666666666666,0.013460199582269667,0.015333333333333332,0.002088651659317707,0.022,0.08284984915293572,0.33179144426394364,0.6120732295054894,0.8933711990468495,41,False,0.8,0.24,0.7933333333333333,0.37333333333333335,25.8,32.1420283128336,905.5,1832.0
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+locoL_scratchsat_s100000_K1000,Abd-S42,adult_sepsis,1500,6567,150,0.76,0.5748439165524593,0.07333333333333333,0.09760925841327851,0.07066666666666667,0.17039744175422566,0.082,0.05862646566164154,0.008666666666666666,0.0016750418760469012,0.005333333333333333,0.0968478757423481,0.431042485153038,0.2811971753944427,0.897543583249603,10,False,0.8066666666666666,0.36666666666666664,0.9,0.6533333333333333,7.066666666666667,17.039744175422566,1492.0,1982.0
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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/locoL_scratchsat_s100000_K1000/summary.json

@@ -0,0 +1,767 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-05T10:22:00.018665+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",
+  "locoL_scratchsat_s100000_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/locoL_scratchsat_s100000_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/locoL_scratchsat_s100000_K1000"
+ ],
+ "arms": [
+  "locoL_scratchsat_s100000_K1000"
+ ],
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
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+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC01",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
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