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Archive 4 checkpoints (1-4)

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paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw3_scsemi5nt/per_donor.csv ADDED
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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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74
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75
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80
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82
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83
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84
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85
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90
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91
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92
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93
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102
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105
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108
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110
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112
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113
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114
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116
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117
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120
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127
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paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw3_scsemi5rt/README.md ADDED
@@ -0,0 +1,73 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # score_ft.py output: imperial_eskd, 145 scored donors
2
+
3
+ Arms: scsemi5rt. Every arm is scored on the same donors against the same observed reference.
4
+
5
+ ## Inputs and fixed contracts
6
+ - Observed reference: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd/reference.npz` (sha 34b4caa3f8a6), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd;
7
+ 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/imperial_eskd/observed_labels/labels/labels.parquet.
8
+ - Generated cells: `generated_counts` read out once with Poisson(seed 20260916) over the **whole NPZ in row order**
9
+ (`poisson_readout.poisson_integerise`), then the scored donors' rows. These integer counts are used for labels, embedding,
10
+ depth and the contrast. Pseudobulk uses the summed `generated_counts` (rates), as `score_generated.py`.
11
+ - 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 =
12
+ the 1,006-gene annotation list minus genes the dataset's sc assay did not measure in every sample (1005 genes).
13
+ - Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (5927 genes).
14
+
15
+ ## Definitions
16
+ 1. **Composition**: fraction of each donor's cells per six-type label (all generated cells; all observed QC cells).
17
+ `comp_l1` = sum over the six labels of |generated - observed| (immicro_common.l1). `comp_l1_obs_loo_null` = L1 of the
18
+ donor's observed composition to the mean of the *other scored donors'* observed compositions. `composition_top1` =
19
+ fraction of donors whose generated composition is closest (L1) to their own observed composition.
20
+ 2. **Pseudobulk**: `pb_r` = Pearson r of CPM-log1p(summed generated_counts) vs CPM-log1p(observed pseudobulk) on the scoring
21
+ genes (evaluate_realbulk.cpm_log1p / paired_r). `pb_top1` = the donor's generated pseudobulk is closest (Pearson) to its own
22
+ observed pseudobulk among the 145 scored donors (immicro_common.retrieval = evaluate_realbulk.top1 arithmetic).
23
+ 3. **Precision / coverage / density** (stage_b_embed.py functions): per-cell CP10K over the scoring genes + log1p; PCA-50
24
+ (randomized, random_state 20260925) and k = 10 real-real k-NN balls fitted on **R1 of the scored donors only**.
25
+ Reference rule (independent of fold and arm): per donor, cells in canonical order (library_id+barcode), one
26
+ permutation from `default_rng([20260925, uint64(sha256(donor)[:8])])`; R1 = first n, R2 = next n,
27
+ n = min(150, n_cells // 2) (21682 R1 cells here). Generated query: per donor n cells (the donor's R1 size),
28
+ without replacement, `default_rng([20260926, same key])`. Precision = fraction of generated cells inside any R1 ball
29
+ (Kynkaanniemi 2019); coverage = fraction of R1 cells whose ball holds a generated cell; density = Naeem 2020.
30
+ Per-donor precision = that donor's generated cells; per-donor coverage = that donor's R1 cells (the pooled values are
31
+ their n-weighted means; plain means when every donor has 150 reference cells). R2 (held-out real cells of the same donors) is the
32
+ perfect-generator control: precision 0.9691, coverage 0.9998.
33
+ **Depth matched**: stage_b_embed depth matching run pairwise (R1 vs this arm): per donor and within-donor rank of detected
34
+ genes, both cells are thinned by UMI sampling without replacement to the smaller detected-gene count; PCA kept from
35
+ un-thinned R1, radii recomputed on thinned R1; fresh rng(20260929) per arm. R2 control: precision
36
+ 0.9693, coverage 0.9997.
37
+ 4. **Monocyte %** = 100 x Monocyte fraction (all cells) per donor; **median UMI per cell** = median over cells of the
38
+ Poisson-read (generated) / observed counts summed over the scoring genes (per donor, and pooled).
39
+ 5. **Group contrast** (T, B, Monocyte, NK): case groups ['covid_positive'] (n = 104) vs control groups ['covid_negative'] (n = 31); rule: explicit --case-groups / --control-groups; groups from features groups.
40
+ Genes per type = scoring genes detected (count > 0) in >= 1 % of the scored donors' observed
41
+ cells of that type. Primary statistic `mean_cp10k`: per-cell CP10K over the scoring genes; per donor the mean over its
42
+ cells of the type (donors with >= 1 such cell); group mean = mean over the group's donors (donor-balanced);
43
+ logFC = log2(case mean + 1) - log2(control mean + 1). Secondary `pseudobulk_log1p_cpm`: the SLE benchmark evaluator's
44
+ statistic (donor x type summed counts, log1p CPM over the scoring genes, mean case - mean control;
45
+ evaluate_generated_vs_truth.group_log_fold_change). Both are computed on the generated cells (their frozen labels) and on
46
+ the observed cells; `r_generated` = Pearson r of the two logFC vectors. Broadcast baseline `r_broadcast`: the same
47
+ observed vector against the logFC of the input bulk (condition NPZ `bulk_counts` of the arm, scoring genes, per-donor
48
+ CP10K resp. log1p CPM, group means). `partial_r_generated_given_broadcast`: r of the OLS residuals of observed and
49
+ generated logFC on the bulk logFC (residual_specificity.py).
50
+ 6. **Top-50 DEG overlap** (contrast.csv rows `statistic = welch_top50_deg`; summary `deg_top50`): the SLE benchmark's score (`total_top50_overlap` of
51
+ `bulk2sc-paper/scripts/evaluate_generated_vs_truth.py`, Welch backend: the "top-50 DEG 81 / 84" of the final model), run
52
+ with the evaluator's own functions on the same donor x type pseudobulks as the contrast. Per cell type, observed and
53
+ generated separately: donor x type summed counts on all 5927 scoring genes (donors of the two groups with
54
+ >= 1 cell of the type) -> `welch_bh_deg` (log1p CPM, two-sided Welch t-test case vs control, Benjamini-Hochberg over the
55
+ genes with a defined p-value; needs >= 2 donors per group) -> `top_deg_genes` (FDR < 0.05, descending |logFC|,
56
+ first 50; shorter when fewer genes pass). `top50_overlap` = |observed list & generated list|; `top50_jaccard`
57
+ the evaluator's Jaccard. Summary `sum` = total over the scored types (the quantity reported as 81), `max` = the sum of
58
+ the observed list lengths (the "of 262"), `sum_4type` = T + B + Monocyte + NK. A type is scored when its observed test
59
+ 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
60
+ (aggregates: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd/deg_reference.npz).
61
+ **Broadcast analogue** (`top50_overlap_broadcast`, as `sle_broadcast.py` `broadcast_input_bulk`; not part of the
62
+ published benchmark): the same test on the arm's condition bulk_counts (scoring genes, the 104 + 31
63
+ donors), one whole-PBMC top-50 list, compared with every type's observed list.
64
+
65
+ ## Files
66
+ - `per_donor.csv`: one row per arm x donor (all per-donor quantities above).
67
+ - `summary.json`: per arm the donor means / pooled values, provenance (NPZ sha, receipt check, generation metadata,
68
+ Poisson nnz of the whole NPZ, annotation contract), and the reference block (PCA, R2 control).
69
+ - `contrast.csv`: per arm x cell type x statistic (`mean_cp10k`, `pseudobulk_log1p_cpm`: logFC r; `welch_top50_deg`:
70
+ top-50 DEG overlap, T / B / Monocyte / NK / DC; columns of the other kind are empty).
71
+ - `arms/<arm>/labels/` (predict_scanvi.py labels + manifest), `arms/<arm>/generated_cells.parquet` (NPZ row, donor, label,
72
+ UMI on the scoring genes, P/C subsample flag), `arms/<arm>/deg_top50_lists.csv` (observed, generated and broadcast
73
+ top-50 gene lists, Ensembl ids, rank order).
paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw3_scsemi5rt/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
2
+ scsemi5rt,T cell,mean_cp10k,3031,0.6060350721688311,0.6363131785460265,0.5399251070777402,0.3358653310496886,104,31,104,31,241386,116152,,,,,,,,,,,
3
+ scsemi5rt,T cell,pseudobulk_log1p_cpm,3031,0.43162008556884457,0.6151584600190607,0.298483379710261,0.34219015065077757,104,31,104,31,241386,116152,,,,,,,,,,,
4
+ scsemi5rt,B cell,mean_cp10k,3186,0.4915355330827502,0.6181604529907424,0.36040492254672224,0.3692566580191528,104,31,102,29,46374,9952,,,,,,,,,,,
5
+ scsemi5rt,B cell,pseudobulk_log1p_cpm,3186,0.1479403700653546,0.4479445109520174,0.01570824959991736,0.30036020983902023,104,31,102,29,46374,9952,,,,,,,,,,,
6
+ scsemi5rt,Monocyte,mean_cp10k,2879,0.5984583850810195,0.7038117222497147,0.3608968511346213,0.5448620414031753,103,31,102,31,74900,32817,,,,,,,,,,,
7
+ scsemi5rt,Monocyte,pseudobulk_log1p_cpm,2879,0.44181157221579387,0.6894081488945825,0.17373899901378922,0.48078938071512506,103,31,102,31,74900,32817,,,,,,,,,,,
8
+ scsemi5rt,NK cell,mean_cp10k,2964,0.6734645046482207,0.6572983397395356,0.5808423942368478,0.42030601172601745,104,31,103,31,67818,36682,,,,,,,,,,,
9
+ scsemi5rt,NK cell,pseudobulk_log1p_cpm,2964,0.42320651269649356,0.5733589034230205,0.2830152736318047,0.36096827331087095,104,31,103,31,67818,36682,,,,,,,,,,,
10
+ scsemi5rt,T cell,welch_top50_deg,5927,,,,,104,31,104,31,241386,116152,True,16,0.19047619047619047,50,50,873,671,16,0.19047619047619047,50,2000
11
+ scsemi5rt,B cell,welch_top50_deg,5927,,,,,104,31,102,29,46374,9952,True,11,0.12359550561797752,50,50,215,139,13,0.14942528735632185,50,2000
12
+ scsemi5rt,Monocyte,welch_top50_deg,5927,,,,,103,31,102,31,74900,32817,True,14,0.16279069767441862,50,50,270,305,20,0.25,50,2000
13
+ scsemi5rt,NK cell,welch_top50_deg,5927,,,,,104,31,103,31,67818,36682,True,15,0.17647058823529413,50,50,321,542,15,0.17647058823529413,50,2000
14
+ scsemi5rt,DC,welch_top50_deg,5927,,,,,104,31,102,31,12959,4351,True,10,0.1111111111111111,50,50,272,228,12,0.13636363636363635,50,2000