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  1. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/arms/within_real_lora__raw/labels/labels.manifest.json +156 -0
  2. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/contrast.csv +14 -0
  3. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/per_donor.csv +83 -0
  4. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/summary.json +769 -0
paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/arms/within_real_lora__raw/labels/labels.manifest.json ADDED
@@ -0,0 +1,156 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
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+ "dataset_id": "Ye2026_sepsis",
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+ "split": "generated",
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+ "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/arms/within_real_lora__raw/query.h5ad",
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+ "method": "within_real_lora__raw",
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+ "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/arms/within_real_lora__raw/labels/labels.parquet",
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+ "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",
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+ "target_truth_used_for_fitting": false,
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+ "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
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+ "labels": [
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+ "T cell",
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+ "B cell",
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+ "Monocyte",
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+ "NK cell",
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+ "DC",
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+ "Other"
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+ ],
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+ "l2_labels": [
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+ "ASDC",
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+ "CD14 monocyte",
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+ "CD16 monocyte",
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+ "CD56bright NK cell",
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+ "CD56dim NK cell",
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+ "CD8aa",
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+ "DN T cell",
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+ "Effector B cell",
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+ "Erythrocyte",
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+ "ILC",
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+ "Intermediate monocyte",
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+ "MAIT",
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+ "Memory B cell",
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+ "Memory CD4 T cell",
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+ "Memory CD8 T cell",
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+ "Naive B cell",
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+ "Naive CD4 T cell",
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+ "Naive CD8 T cell",
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+ "Plasma cell",
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+ "Platelet",
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+ "Progenitor cell",
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+ "Proliferating NK cell",
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+ "Proliferating T cell",
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+ "Transitional B cell",
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+ "Treg",
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+ "cDC1",
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+ "cDC2",
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+ "gdT",
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+ "pDC"
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+ ],
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+ "n_cells": 123000,
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+ "n_genes": 1005,
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+ "note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
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+ "label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
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+ "query_train_epochs": 0,
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+ "confidence_threshold": 0.0,
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+ "subset": false,
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+ "evaluator_aligned": true,
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+ "gene_space": {
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+ "join_key": "ensembl_id",
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+ "model_genes": 1005,
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+ "query_genes": 1006,
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+ "model_genes_missing_from_query_zero_padded": 0,
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+ "query_genes_outside_model_dropped": 1,
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+ "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
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+ },
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+ "readout": null,
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+ "query_build": {
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+ "kind": "generated_npz",
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+ "poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
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+ "readout": "poisson",
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+ "seed": 20260916,
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+ "set": "within_real_lora__raw",
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+ "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/within_real_lora__raw.npz",
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+ "source_sha256": "8eeb73d35fc7fb2cab74d98d0b0fcb3ea8347db7e692ba3aec6ac8d251f8f259"
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+ },
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+ "model": {
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+ "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",
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+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
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+ "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",
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+ "held_out_summary": {
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+ "l2_accuracy": 0.8692869740488788,
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+ "pbmc5_other_accuracy": 0.9920886873267826,
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+ "pbmc5_other_macro_f1": 0.9812088972148597
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+ }
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+ },
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+ "label_counts": {
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+ "celltype_l1_pred": {
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+ "DC": 695
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+ "aifi_l1": {
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+ "DC": 695,
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+ "aifi_l2": {
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+ "Memory CD4 T cell": 16814,
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+ "CD14 monocyte": 16479,
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+ "Memory CD8 T cell": 12688,
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+ "Naive CD4 T cell": 10761,
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+ "Naive B cell": 10058,
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+ "gdT": 8742,
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+ "Naive CD8 T cell": 7480,
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+ "CD56dim NK cell": 5678,
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+ "Memory B cell": 3883,
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+ "DN T cell": 3614,
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+ "CD16 monocyte": 3350,
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+ "CD8aa": 3122,
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+ "Intermediate monocyte": 2906,
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+ "Treg": 2569,
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+ "Transitional B cell": 2466,
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+ "Platelet": 2389,
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+ "Effector B cell": 2166,
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+ "Plasma cell": 1327,
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+ "MAIT": 1200,
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+ "Erythrocyte": 1178,
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+ "Proliferating NK cell": 1077,
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+ "CD56bright NK cell": 969,
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+ "Proliferating T cell": 861,
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+ "cDC2": 564,
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+ "ILC": 386,
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+ "Progenitor cell": 142,
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+ "pDC": 94,
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+ "cDC1": 24,
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+ }
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+ },
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+ "confidence": {
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+ "mean_l1_mass": 0.9860864281654358,
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+ "frac_l2_max_prob_ge_0.5": 0.9745853658536585
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+ "timings_s": {
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+ "predict": 1.0,
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+ "total": 1.8
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+ "versions": {
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+ "scvi-tools": "1.4.1",
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+ "torch": "2.11.0+cu130",
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+ "anndata": "0.12.19"
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+ },
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+ "device": "cpu",
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+ "created_at_utc": "2026-10-05T10:51:59.647220+00:00"
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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/within_real_lora__raw/contrast.csv ADDED
@@ -0,0 +1,14 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 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
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+ within_real_lora__raw,T cell,mean_cp10k,3258,0.6189981118866671,0.2548893770824626,0.585068998590531,0.3461203505795245,61,21,61,21,298117,67851,,,,,,,,,,,
3
+ within_real_lora__raw,T cell,pseudobulk_log1p_cpm,3258,0.6273685989546335,0.2164745523777111,0.6034095714201358,0.3184193800706154,61,21,61,21,298117,67851,,,,,,,,,,,
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+ within_real_lora__raw,B cell,mean_cp10k,3310,0.565840928176013,0.27458639801653467,0.53653036137014,0.23402405673902876,61,21,61,21,99729,19900,,,,,,,,,,,
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+ within_real_lora__raw,B cell,pseudobulk_log1p_cpm,3310,0.48323586067129265,0.2711145517540278,0.4577955138324507,0.18519240850862348,61,21,61,21,99729,19900,,,,,,,,,,,
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+ within_real_lora__raw,Monocyte,mean_cp10k,3289,0.5803864961234996,0.5481103923782986,0.4349270564749572,0.4747632250454787,61,21,61,21,111269,22735,,,,,,,,,,,
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+ within_real_lora__raw,Monocyte,pseudobulk_log1p_cpm,3289,0.5941011588659976,0.6203629305570988,0.4044409761076878,0.5213190984733419,61,21,61,21,111269,22735,,,,,,,,,,,
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+ within_real_lora__raw,NK cell,mean_cp10k,3240,0.33744335923023466,0.1861970975708186,0.3078426030032952,0.23234047565621352,61,21,61,21,47832,7724,,,,,,,,,,,
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+ within_real_lora__raw,NK cell,pseudobulk_log1p_cpm,3240,0.30165831404059507,0.05592238177293225,0.29824466106548764,0.09194318456138709,61,21,61,21,47832,7724,,,,,,,,,,,
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+ within_real_lora__raw,T cell,welch_top50_deg,5975,,,,,61,21,61,21,298117,67851,True,3,0.04225352112676056,50,24,1578,24,3,0.030927835051546393,50,1378
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+ within_real_lora__raw,B cell,welch_top50_deg,5975,,,,,61,21,61,21,99729,19900,True,1,0.010101010101010102,50,50,1102,51,2,0.02040816326530612,50,1378
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+ within_real_lora__raw,Monocyte,welch_top50_deg,5975,,,,,61,21,61,21,111269,22735,True,21,0.26582278481012656,50,50,2459,515,13,0.14942528735632185,50,1378
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+ within_real_lora__raw,NK cell,welch_top50_deg,5975,,,,,61,21,61,21,47832,7724,True,0,0.0,50,21,1235,21,2,0.02040816326530612,50,1378
14
+ within_real_lora__raw,DC,welch_top50_deg,5975,,,,,57,21,54,21,3300,695,True,3,0.030927835051546393,50,50,1572,124,1,0.010101010101010102,50,1378
paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores_masked/ye2026_sepsis/within_real_lora__raw/per_donor.csv ADDED
@@ -0,0 +1,83 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 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
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+ within_real_lora__raw,Abd-PS04,ped_sepsis,1500,5449,150,0.126,0.14094329234721967,0.08866666666666667,0.17030647825289044,0.746,0.5608368507983116,0.02666666666666667,0.02147182969352175,0.004666666666666667,0.003853918150119288,0.008,0.10258763075793724,0.3823414693827614,0.8240358281801887,0.8851970170212742,11,False,0.9666666666666667,0.7866666666666666,0.9866666666666667,0.9466666666666667,74.6,56.083685079831156,3180.5,2716.0
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+ within_real_lora__raw,Abd-PS05,ped_sepsis,1500,6924,150,0.37066666666666664,0.30387059503177355,0.44733333333333336,0.5060658578856152,0.08333333333333333,0.07019064124783363,0.025333333333333333,0.0891103408434431,0.0013333333333333333,0.008954361640670132,0.072,0.021808203350664357,0.26026112073945684,0.6987393915367811,0.8673725579461848,58,False,0.9533333333333334,0.9733333333333334,0.9666666666666667,0.9333333333333333,8.333333333333332,7.0190641247833625,1451.5,2313.0
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+ within_real_lora__raw,Abd-PS07,ped_sepsis,1500,3472,150,0.7733333333333333,0.8626152073732719,0.08066666666666666,0.023329493087557603,0.056,0.002304147465437788,0.072,0.09331797235023041,0.0033333333333333335,0.0002880184331797235,0.014666666666666666,0.018145161290322582,0.2281566820276498,0.7909717817075781,0.8857204243139646,41,False,0.92,0.92,0.94,0.9466666666666667,5.6000000000000005,0.2304147465437788,1695.5,1614.0
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+ within_real_lora__raw,Abd-PS19,ped_sepsis,1500,7984,150,0.5973333333333334,0.4622995991983968,0.14866666666666667,0.11209919839679358,0.17466666666666666,0.2937124248496994,0.03333333333333333,0.05586172344689379,0.0033333333333333335,0.0156563126252505,0.042666666666666665,0.06037074148296593,0.3432024048096193,0.218193607618059,0.8915697984180886,15,False,0.9,0.8866666666666667,0.9066666666666666,0.9866666666666667,17.466666666666665,29.37124248496994,1679.0,2111.0
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+ within_real_lora__raw,Abd-PS20,ped_sepsis,1500,7286,150,0.19933333333333333,0.30496843261048584,0.766,0.5780949766675817,0.019333333333333334,0.08770244304144935,0.008666666666666666,0.007823222618720834,0.004,0.0005489980785067252,0.0026666666666666666,0.02086192698325556,0.38439893860371493,0.8206851316278935,0.8893791038742103,1,True,0.9466666666666667,0.7933333333333333,0.9666666666666667,0.98,1.9333333333333333,8.770244304144935,1975.5,1820.0
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+ within_real_lora__raw,Abd-PS23,ped_sepsis,1500,4309,150,0.4166666666666667,0.2529589231840334,0.44133333333333336,0.3272220932931075,0.05533333333333333,0.32142028312833604,0.03866666666666667,0.013460199582269667,0.0026666666666666666,0.002088651659317707,0.04533333333333334,0.08284984915293572,0.6072069312292102,0.6120732295054894,0.8761600363667155,35,False,0.9333333333333333,0.8666666666666667,0.9466666666666667,0.96,5.533333333333333,32.1420283128336,1929.5,1832.0
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+ within_real_lora__raw,Abd-PS27,ped_sepsis,1500,9427,150,0.9066666666666666,0.6126021003500584,0.038,0.06078285774901877,0.025333333333333333,0.13196138750397793,0.024666666666666667,0.010289593720165482,0.0,0.0029701920016972526,0.005333333333333333,0.1813938686750822,0.6168832785262189,0.5288253850706728,0.8941310612143635,5,False,0.8933333333333333,0.6266666666666667,0.96,0.66,2.533333333333333,13.196138750397793,2457.5,2356.0
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+ within_real_lora__raw,Abd-S102,adult_sepsis,1500,9512,150,0.3993333333333333,0.47981497056349875,0.2926666666666667,0.39318755256518084,0.14533333333333334,0.0053616484440706475,0.12,0.095878889823381,0.002,0.0007359125315391085,0.04066666666666666,0.02502102607232969,0.3620050462573592,0.47699080006140543,0.8701847816827097,69,False,0.9533333333333334,0.7666666666666667,0.9666666666666667,0.8933333333333333,14.533333333333335,0.5361648444070648,2020.0,1646.0
10
+ within_real_lora__raw,Abd-S103,adult_sepsis,1500,9423,150,0.7093333333333334,0.4813753581661891,0.15133333333333332,0.14782977820227103,0.03866666666666667,0.0024408362517245037,0.059333333333333335,0.04393505253104107,0.0026666666666666666,0.00021224663058473945,0.03866666666666667,0.3242067282181895,0.5710801231030458,0.5587060076493682,0.8783320088750529,22,False,0.96,0.68,0.98,0.7533333333333333,3.8666666666666667,0.24408362517245036,2731.0,971.0
11
+ within_real_lora__raw,Abd-S120,adult_sepsis,1500,5783,150,0.34933333333333333,0.3140238630468615,0.06733333333333333,0.11049628220646723,0.474,0.46446481065191075,0.068,0.07297250561992046,0.006,0.0008646031471554556,0.035333333333333335,0.03717793532768459,0.09996011297481124,0.5189164550921991,0.9092105291659649,5,False,0.9466666666666667,0.8,0.94,0.9733333333333334,47.4,46.44648106519107,2107.5,2845.0
12
+ within_real_lora__raw,Abd-S123,adult_sepsis,1500,6299,150,0.35533333333333333,0.16986823305286552,0.10866666666666666,0.08779171297031275,0.412,0.5027782187648833,0.05266666666666667,0.10938244165740593,0.0026666666666666666,0.0007937767899666614,0.06866666666666667,0.1293856167645658,0.41642588770704336,0.8187693250726966,0.9046923507815344,5,False,0.94,0.7933333333333333,0.9466666666666667,0.9133333333333333,41.199999999999996,50.277821876488325,2086.5,2261.0
13
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14
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20
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21
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22
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23
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24
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25
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26
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27
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28
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29
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30
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31
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32
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33
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36
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37
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41
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