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  1. paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/split_counts.csv +4 -0
  2. paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/verified_data.json +83 -0
  3. paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/cv_cat_complete.csv +127 -0
  4. paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/cv_multimetric.csv +22 -0
paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/split_counts.csv ADDED
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+ split,n_cells,n_samples,cell_fraction,registered_fraction
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+ train,33141380,5232,0.8006095588317713,0.8
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+ val,4361032,648,0.10535119254452402,0.1
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+ test,3892772,627,0.09403924862370464,0.1
paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/corpus/verified_data.json ADDED
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+ {
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+ "source_total": 41395184,
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+ "healthy": 36639276,
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+ "disease_or_at_risk": 4755908,
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+ "at_risk": 1792129,
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+ "disease_history_without_at_risk": 2963779,
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+ "condition_cells": {
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+ "SLE": 792660,
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+ "Healthy": 36639276,
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+ "RA": 260504,
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+ "COVID-19": 1279572,
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+ "ACPA+ at risk of RA": 1792129,
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+ "JDM": 82666,
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+ "Influenza": 19233,
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+ "Post-COVID-19": 97224,
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+ "MDS/MPN": 130268,
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+ "Cytopenia": 100147,
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+ "MDS": 176233,
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+ "DRESS": 25272
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+ },
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+ "split_cells": {
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+ "val": 4361032,
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+ "train": 33141380,
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+ "test": 3892772
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+ },
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+ "split_samples": {
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+ "train": 5232,
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+ "val": 648,
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+ "test": 627
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+ },
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+ "celltype_display_counts": {
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+ "B cell": 3744614,
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+ "DC": 472529,
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+ "Monocyte": 7373579,
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+ "NK cell": 3369999,
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+ "Unlabelled": 282565,
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+ "Progenitor cell": 1206741,
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+ "T cell": 24772208,
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+ "Erythrocyte": 27504,
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+ "ILC": 19329,
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+ "Platelet": 121626,
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+ "Other": 4490
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+ },
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+ "healthy_in_vitro": 9762726,
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+ "healthy_cmv_seropositive": 9215690,
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+ "k_values": [
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+ 250,
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+ 500,
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+ 1000,
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+ 2000,
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+ 4000
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+ ],
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+ "recipe_quotas": {
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+ "1000": 2234,
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+ "2000": 2979,
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+ "250": 745,
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+ "4000": 745,
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+ "500": 1489
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+ },
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+ "original_unique_train_covered": 31145450,
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+ "unique_topup_cells": 1995930,
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+ "final_unique_train_covered": 33141380,
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+ "target_occurrences": 195639930,
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+ "final_run_corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
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+ "checks": {
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+ "cellgroup_dataset_assay_totals_equal": true,
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+ "split_crosschecks_equal": true,
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+ "sample_keys_unique": true,
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+ "condition_counts_match_source_summary": true,
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+ "topup_k_sum_matches_coverage": true,
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+ "expected_observed_targets_equal": true,
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+ "final_training_coverage_100pct": true,
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+ "nontrain_targets_zero": true
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+ },
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+ "limitations": [
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+ "Disease / at-risk is not synonymous with confirmed active disease. ACPA+ risk, Post-COVID history and Cytopenia remain explicit.",
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+ "Donor and source-cell proportions are different. Disease/cell-type annotations are descriptive only and were not supplied to the final base model.",
78
+ "Source-cell composition is not the distribution of training-target occurrences. No disease-exposure frequencies are inferred.",
79
+ "Dataset-donor split keys did not ensure strict biological-donor separation for27 internal donors. External target overlap requires separate linkage.",
80
+ "The source validation/test totals do not equal cells used by fixed validation/test recipes. These figures make no performance/generalization claim.",
81
+ "All-cell coverage is a verified saved contract, not a fresh audit of raw cell-ID arrays. Existing cell-type corpus panels are untouched."
82
+ ]
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+ }
paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/cv_cat_complete.csv ADDED
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+ 500,0.11880000000000002,0.20880689209101444,5,718,2359,ji2025_chili,scsemi,scsemi__raw,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/scsemi_cv_20261002/pooled/cat.csv
122
+ 10,0.0,0.00093754594040962,5,5071,5502,ji2025_chili,broadcast,zs__raw,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/pooled/cat.csv
123
+ 20,0.02,0.0018750918808192799,5,5071,5502,ji2025_chili,broadcast,zs__raw,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/pooled/cat.csv
124
+ 50,0.044000000000000004,0.0046877297020483,5,5071,5502,ji2025_chili,broadcast,zs__raw,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/pooled/cat.csv
125
+ 100,0.068,0.00937545940409662,5,5071,5502,ji2025_chili,broadcast,zs__raw,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/pooled/cat.csv
126
+ 200,0.081,0.018750918808193278,5,5071,5502,ji2025_chili,broadcast,zs__raw,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/pooled/cat.csv
127
+ 500,0.11760000000000001,0.04687729702048332,5,5071,5502,ji2025_chili,broadcast,zs__raw,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/pooled/cat.csv
paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/cv_multimetric.csv ADDED
@@ -0,0 +1,22 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ dataset,method,arm,pearson_r,partial_r,rbo_up_down,cat100,split_half_cell_repeat_r,n_samples
2
+ ye2026_sepsis,raw,zs__raw,-0.0118026664699383,-0.0947640863943083,0.026198833987569,0.022,0.9601843706820048,82
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+ ye2026_sepsis,cal,zs__cal,0.1226797008955822,0.0393821490955281,0.0664728418972263,0.052,0.9601843706820048,82
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+ ye2026_sepsis,lora,real_lora__raw,0.5267612711229187,0.4687478788420627,0.1514203508819682,0.136,0.9601843706820048,82
5
+ ye2026_sepsis,scsemi,scsemi__raw,0.4352641007039206,0.3581975013221415,0.0546949093647539,0.0399999999999999,0.9601843706820048,82
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+ ye2026_sepsis,broadcast,zs__raw,0.3159458162620286,,0.0761366939296309,0.072,0.9601843706820048,82
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+ ye2026_sepsis,full,real_full__raw,0.534366534546327,0.4676865312584619,0.1575090050821027,0.148,0.9601843706820048,82
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+ imperial_eskd,raw,zs__raw,0.6439837621001347,0.43172144888499,0.2023787209476497,0.192,0.895725697380963,157
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+ imperial_eskd,cal,zs__cal,0.6787028713891314,0.4118039247130514,0.2058567980539994,0.234,0.895725697380963,157
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+ imperial_eskd,lora,real_lora__raw,0.8187448084273437,0.6899314750539278,0.3073446656792806,0.304,0.895725697380963,157
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+ imperial_eskd,scsemi,scsemi__raw,0.7053598964433999,0.538089704477334,0.1966452067133676,0.21,0.895725697380963,157
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+ imperial_eskd,broadcast,zs__raw,0.6606053132085035,,0.1712550541481365,0.2139999999999999,0.895725697380963,157
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+ giroux2022,raw,zs__raw,0.3340289083812836,0.1903823493340601,0.0262901077183696,0.026,0.8963310768143463,24
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+ giroux2022,scsemi,scsemi__raw,0.5372927269740906,0.3882193920390375,0.0848269717869077,0.066,0.8963310768143463,24
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+ giroux2022,broadcast,zs__raw,0.5752659929360795,,0.1412705854219696,0.1339999999999999,0.8963310768143463,24
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+ ji2025_chili,raw,zs__raw,0.0835223320868259,0.03286103285,0.0217397053215586,0.03,0.8933460729084324,33
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+ ji2025_chili,cal,zs__cal,0.1419169620622038,0.1127754415931183,0.0265789887188132,0.032,0.8933460729084324,33
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+ ji2025_chili,lora,real_lora__raw,0.4792879834022506,0.4520437296401761,0.1057114261400488,0.142,0.8933460729084324,33
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+ ji2025_chili,scsemi,scsemi__raw,0.2730887293849816,0.2287723390423457,0.0477446298317153,0.062,0.8933460729084324,33
22
+ ji2025_chili,broadcast,zs__raw,0.2398746224459366,,0.0459032600376801,0.068,0.8933460729084324,33