Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T142727Z-trunk4x-sepsis-results/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/scores/draw2/README.md

@@ -0,0 +1,73 @@
+# score_ft.py output: ye2026_sepsis, 77 scored donors
+
+Arms: trunk4x, panel_matched_1x, current_f01, scsemi.  Every arm is scored on the same donors against the same observed reference.
+
+## Inputs and fixed contracts
+- Observed reference: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/reference/reference.npz` (sha 8c5f2d794d13), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/evaluation_data/ye2026_sepsis;
+  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/trunk4x_lora_sepsis_20261013/reference/observed_labels/labels/labels.parquet.
+- Generated cells: `generated_counts` read out once with Poisson(seed 20260916) over the **whole NPZ in row order**
+  (`poisson_readout.poisson_integerise`), then the scored donors' rows. These integer counts are used for labels, embedding,
+  depth and the contrast. Pseudobulk uses the summed `generated_counts` (rates), as `score_generated.py`.
+- 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 =
+  the 1,006-gene annotation list minus genes the dataset's sc assay did not measure in every sample (1006 genes).
+- Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (4243 genes).
+
+## Definitions
+1. **Composition**: fraction of each donor's cells per six-type label (all generated cells; all observed QC cells).
+   `comp_l1` = sum over the six labels of |generated - observed| (immicro_common.l1). `comp_l1_obs_loo_null` = L1 of the
+   donor's observed composition to the mean of the *other scored donors'* observed compositions. `composition_top1` =
+   fraction of donors whose generated composition is closest (L1) to their own observed composition.
+2. **Pseudobulk**: `pb_r` = Pearson r of CPM-log1p(summed generated_counts) vs CPM-log1p(observed pseudobulk) on the scoring
+   genes (evaluate_realbulk.cpm_log1p / paired_r). `pb_top1` = the donor's generated pseudobulk is closest (Pearson) to its own
+   observed pseudobulk among the 77 scored donors (immicro_common.retrieval = evaluate_realbulk.top1 arithmetic).
+3. **Precision / coverage / density** (stage_b_embed.py functions): per-cell CP10K over the scoring genes + log1p; PCA-50
+   (randomized, random_state 20260925) and k = 10 real-real k-NN balls fitted on **R1 of the scored donors only**.
+   Reference rule (independent of fold and arm): per donor, cells in canonical order (library_id+barcode), one
+   permutation from `default_rng([20260925, uint64(sha256(donor)[:8])])`; R1 = first n, R2 = next n,
+   n = min(150, n_cells // 2) (11550 R1 cells here). Generated query: per donor n cells (the donor's R1 size),
+   without replacement, `default_rng([20260926, same key])`. Precision = fraction of generated cells inside any R1 ball
+   (Kynkaanniemi 2019); coverage = fraction of R1 cells whose ball holds a generated cell; density = Naeem 2020.
+   Per-donor precision = that donor's generated cells; per-donor coverage = that donor's R1 cells (the pooled values are
+   their n-weighted means; plain means when every donor has 150 reference cells). R2 (held-out real cells of the same donors) is the
+   perfect-generator control: precision 0.9807, coverage 0.9997.
+   **Depth matched**: stage_b_embed depth matching run pairwise (R1 vs this arm): per donor and within-donor rank of detected
+   genes, both cells are thinned by UMI sampling without replacement to the smaller detected-gene count; PCA kept from
+   un-thinned R1, radii recomputed on thinned R1; fresh rng(20260929) per arm. R2 control: precision
+   0.9786, coverage 0.9997.
+4. **Monocyte %** = 100 x Monocyte fraction (all cells) per donor; **median UMI per cell** = median over cells of the
+   Poisson-read (generated) / observed counts summed over the scoring genes (per donor, and pooled).
+5. **Group contrast** (T, B, Monocyte, NK): case groups ['adult_sepsis', 'ped_sepsis'] (n = 57) vs control groups ['adult_HC', 'adult_ICU_ctrl', 'ped_HC', 'ped_ICU_ctrl'] (n = 20); rule: explicit --case-groups / --control-groups; groups from features groups.
+   Genes per type = scoring genes detected (count > 0) in >= 1 % of the scored donors' observed
+   cells of that type. Primary statistic `mean_cp10k`: per-cell CP10K over the scoring genes; per donor the mean over its
+   cells of the type (donors with >= 1 such cell); group mean = mean over the group's donors (donor-balanced);
+   logFC = log2(case mean + 1) - log2(control mean + 1). Secondary `pseudobulk_log1p_cpm`: the SLE benchmark evaluator's
+   statistic (donor x type summed counts, log1p CPM over the scoring genes, mean case - mean control;
+   evaluate_generated_vs_truth.group_log_fold_change). Both are computed on the generated cells (their frozen labels) and on
+   the observed cells; `r_generated` = Pearson r of the two logFC vectors. Broadcast baseline `r_broadcast`: the same
+   observed vector against the logFC of the input bulk (condition NPZ `bulk_counts` of the arm, scoring genes, per-donor
+   CP10K resp. log1p CPM, group means). `partial_r_generated_given_broadcast`: r of the OLS residuals of observed and
+   generated logFC on the bulk logFC (residual_specificity.py).
+6. **Top-50 DEG overlap** (contrast.csv rows `statistic = welch_top50_deg`; summary `deg_top50`): the SLE benchmark's score (`total_top50_overlap` of
+   `bulk2sc-paper/scripts/evaluate_generated_vs_truth.py`, Welch backend: the "top-50 DEG 81 / 84" of the final model), run
+   with the evaluator's own functions on the same donor x type pseudobulks as the contrast. Per cell type, observed and
+   generated separately: donor x type summed counts on all 4243 scoring genes (donors of the two groups with
+   >= 1 cell of the type) -> `welch_bh_deg` (log1p CPM, two-sided Welch t-test case vs control, Benjamini-Hochberg over the
+   genes with a defined p-value; needs >= 2 donors per group) -> `top_deg_genes` (FDR < 0.05, descending |logFC|,
+   first 50; shorter when fewer genes pass). `top50_overlap` = |observed list & generated list|; `top50_jaccard`
+   the evaluator's Jaccard. Summary `sum` = total over the scored types (the quantity reported as 81), `max` = the sum of
+   the observed list lengths (the "of 262"), `sum_4type` = T + B + Monocyte + NK. A type is scored when its observed test
+   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
+   (aggregates: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/reference/deg_reference.npz).
+   **Broadcast analogue** (`top50_overlap_broadcast`, as `sle_broadcast.py` `broadcast_input_bulk`; not part of the
+   published benchmark): the same test on the arm's condition bulk_counts (scoring genes, the 57 + 20
+   donors), one whole-PBMC top-50 list, compared with every type's observed list.
+
+## Files
+- `per_donor.csv`: one row per arm x donor (all per-donor quantities above).
+- `summary.json`: per arm the donor means / pooled values, provenance (NPZ sha, receipt check, generation metadata,
+  Poisson nnz of the whole NPZ, annotation contract), and the reference block (PCA, R2 control).
+- `contrast.csv`: per arm x cell type x statistic (`mean_cp10k`, `pseudobulk_log1p_cpm`: logFC r; `welch_top50_deg`:
+  top-50 DEG overlap, T / B / Monocyte / NK / DC; columns of the other kind are empty).
+- `arms/<arm>/labels/` (predict_scanvi.py labels + manifest), `arms/<arm>/generated_cells.parquet` (NPZ row, donor, label,
+  UMI on the scoring genes, P/C subsample flag), `arms/<arm>/deg_top50_lists.csv` (observed, generated and broadcast
+  top-50 gene lists, Ensembl ids, rank order).

paper-releases/pbisc-diffusion/updates/20261013T142727Z-trunk4x-sepsis-results/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/scores/draw2/contrast.csv

@@ -0,0 +1,53 @@
+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
+trunk4x,T cell,mean_cp10k,3210,0.2870702714037037,0.28417788192518073,0.2665216587387086,0.11716962712798713,57,20,57,20,279996,73456,,,,,,,,,,,
+trunk4x,T cell,pseudobulk_log1p_cpm,3210,0.3881076237989945,0.2528077636701587,0.35385159440330893,0.21164730128627224,57,20,57,20,279996,73456,,,,,,,,,,,
+trunk4x,B cell,mean_cp10k,3205,0.3538743444538308,0.29788887309509887,0.34815898557466446,0.07542510877815839,57,20,57,20,95354,21242,,,,,,,,,,,
+trunk4x,B cell,pseudobulk_log1p_cpm,3205,0.30178331034532974,0.2708791238271775,0.2871833190925479,0.0984981902842706,57,20,57,20,95354,21242,,,,,,,,,,,
+trunk4x,Monocyte,mean_cp10k,3210,0.27032632846200105,0.5567220126394566,0.23097644212449236,0.14454135322602896,57,20,57,20,107968,12711,,,,,,,,,,,
+trunk4x,Monocyte,pseudobulk_log1p_cpm,3210,0.337796225280278,0.5978473455208166,0.267481264535883,0.2147416079559134,57,20,57,20,107968,12711,,,,,,,,,,,
+trunk4x,NK cell,mean_cp10k,3161,0.22430722630504263,0.20828713319632092,0.21489574474443748,0.07031066343780458,57,20,57,20,45869,4058,,,,,,,,,,,
+trunk4x,NK cell,pseudobulk_log1p_cpm,3161,0.20436086225111227,0.05503020199393339,0.20223126117200582,0.048604123366663594,57,20,57,20,45869,4058,,,,,,,,,,,
+trunk4x,T cell,welch_top50_deg,4243,,,,,57,20,57,20,279996,73456,True,12,0.13636363636363635,50,50,1505,812,6,0.06382978723404255,50,1075
+trunk4x,B cell,welch_top50_deg,4243,,,,,57,20,57,20,95354,21242,True,12,0.13636363636363635,50,50,1011,182,4,0.041666666666666664,50,1075
+trunk4x,Monocyte,welch_top50_deg,4243,,,,,57,20,57,20,107968,12711,True,3,0.030927835051546393,50,50,2342,271,10,0.1111111111111111,50,1075
+trunk4x,NK cell,welch_top50_deg,4243,,,,,57,20,57,20,45869,4058,True,1,0.010101010101010102,50,50,1182,100,5,0.05263157894736842,50,1075
+trunk4x,DC,welch_top50_deg,4243,,,,,53,20,42,19,3221,225,True,0,0.0,50,0,1483,0,2,0.02040816326530612,50,1075
+panel_matched_1x,T cell,mean_cp10k,3210,0.3602182910286651,0.28417788192518073,0.3400110989342174,0.13020119193174146,57,20,57,20,279996,74218,,,,,,,,,,,
+panel_matched_1x,T cell,pseudobulk_log1p_cpm,3210,0.45158356448300535,0.2528077636701587,0.41767589077147815,0.2310398943266545,57,20,57,20,279996,74218,,,,,,,,,,,
+panel_matched_1x,B cell,mean_cp10k,3205,0.4176046858759658,0.29788887309509887,0.41205499129843615,0.08636238355830167,57,20,57,20,95354,22358,,,,,,,,,,,
+panel_matched_1x,B cell,pseudobulk_log1p_cpm,3205,0.4161311784237891,0.2708791238271775,0.4001685845369041,0.12538214925458604,57,20,57,20,95354,22358,,,,,,,,,,,
+panel_matched_1x,Monocyte,mean_cp10k,3210,0.20520843935549252,0.5567220126394566,0.16816981131552372,0.11946802992293727,57,20,55,20,107968,12045,,,,,,,,,,,
+panel_matched_1x,Monocyte,pseudobulk_log1p_cpm,3210,0.2846560526817334,0.5978473455208166,0.22915307336444551,0.17354250627580894,57,20,55,20,107968,12045,,,,,,,,,,,
+panel_matched_1x,NK cell,mean_cp10k,3161,0.27321073661040374,0.20828713319632092,0.2696792589027904,0.046735348781462745,57,20,57,20,45869,3850,,,,,,,,,,,
+panel_matched_1x,NK cell,pseudobulk_log1p_cpm,3161,0.17832966029489664,0.05503020199393339,0.17541012366389303,0.06451352245405642,57,20,57,20,45869,3850,,,,,,,,,,,
+panel_matched_1x,T cell,welch_top50_deg,4243,,,,,57,20,57,20,279996,74218,True,13,0.14942528735632185,50,50,1505,416,6,0.06382978723404255,50,1075
+panel_matched_1x,B cell,welch_top50_deg,4243,,,,,57,20,57,20,95354,22358,True,10,0.1111111111111111,50,50,1011,166,4,0.041666666666666664,50,1075
+panel_matched_1x,Monocyte,welch_top50_deg,4243,,,,,57,20,55,20,107968,12045,True,1,0.01639344262295082,50,12,2342,12,10,0.1111111111111111,50,1075
+panel_matched_1x,NK cell,welch_top50_deg,4243,,,,,57,20,57,20,45869,3850,True,1,0.010101010101010102,50,50,1182,56,5,0.05263157894736842,50,1075
+panel_matched_1x,DC,welch_top50_deg,4243,,,,,53,20,35,17,3221,308,True,0,0.0,50,0,1483,0,2,0.02040816326530612,50,1075
+current_f01,T cell,mean_cp10k,3210,0.3475254712197549,0.28417788192518073,0.3352046413091245,0.09736022010926025,57,20,57,20,279996,74305,,,,,,,,,,,
+current_f01,T cell,pseudobulk_log1p_cpm,3210,0.4743533046018932,0.2528077636701587,0.45185144719564235,0.17320230434917558,57,20,57,20,279996,74305,,,,,,,,,,,
+current_f01,B cell,mean_cp10k,3205,0.4094875306359168,0.29788887309509887,0.42306369432943636,0.019150619895150427,57,20,57,20,95354,19751,,,,,,,,,,,
+current_f01,B cell,pseudobulk_log1p_cpm,3205,0.34002496055742293,0.2708791238271775,0.34683235162023024,0.023066876232327588,57,20,57,20,95354,19751,,,,,,,,,,,
+current_f01,Monocyte,mean_cp10k,3210,0.29244694076797595,0.5567220126394566,0.26620998956129155,0.13153414113945086,57,20,55,20,107968,12960,,,,,,,,,,,
+current_f01,Monocyte,pseudobulk_log1p_cpm,3210,0.284202090246288,0.5978473455208166,0.22886991857128774,0.17313507286968016,57,20,55,20,107968,12960,,,,,,,,,,,
+current_f01,NK cell,mean_cp10k,3161,0.26162285691709686,0.20828713319632092,0.2511897332853757,0.08035409317555907,57,20,57,20,45869,4274,,,,,,,,,,,
+current_f01,NK cell,pseudobulk_log1p_cpm,3161,0.22725742797836326,0.05503020199393339,0.2252028079607215,0.04830804057273376,57,20,57,20,45869,4274,,,,,,,,,,,
+current_f01,T cell,welch_top50_deg,4243,,,,,57,20,57,20,279996,74305,True,13,0.14942528735632185,50,50,1505,568,6,0.06382978723404255,50,1075
+current_f01,B cell,welch_top50_deg,4243,,,,,57,20,57,20,95354,19751,True,11,0.12359550561797752,50,50,1011,271,4,0.041666666666666664,50,1075
+current_f01,Monocyte,welch_top50_deg,4243,,,,,57,20,55,20,107968,12960,True,1,0.010101010101010102,50,50,2342,507,10,0.1111111111111111,50,1075
+current_f01,NK cell,welch_top50_deg,4243,,,,,57,20,57,20,45869,4274,True,4,0.041666666666666664,50,50,1182,109,5,0.05263157894736842,50,1075
+current_f01,DC,welch_top50_deg,4243,,,,,53,20,36,18,3221,284,True,0,0.0,50,0,1483,0,2,0.02040816326530612,50,1075
+scsemi,T cell,mean_cp10k,3210,0.3687857657303425,0.28417788192518073,0.3107179554834221,0.2965810368595624,57,20,57,20,279996,70397,,,,,,,,,,,
+scsemi,T cell,pseudobulk_log1p_cpm,3210,0.24157790028155127,0.2528077636701587,0.21135516512175404,0.15669783091425477,57,20,57,20,279996,70397,,,,,,,,,,,
+scsemi,B cell,mean_cp10k,3205,0.27034367544047044,0.29788887309509887,0.23935212477874757,0.14908769419727183,57,20,56,20,95354,16783,,,,,,,,,,,
+scsemi,B cell,pseudobulk_log1p_cpm,3205,0.22091899797156925,0.2708791238271775,0.21286345495831324,0.06050367236616134,57,20,56,20,95354,16783,,,,,,,,,,,
+scsemi,Monocyte,mean_cp10k,3210,0.256947219101129,0.5567220126394566,0.260145805694905,0.07444293393764446,57,20,54,20,107968,17045,,,,,,,,,,,
+scsemi,Monocyte,pseudobulk_log1p_cpm,3210,-0.02178388118289749,0.5978473455208166,-0.009467224228652434,-0.0237468644682939,57,20,54,20,107968,17045,,,,,,,,,,,
+scsemi,NK cell,mean_cp10k,3161,0.3783494548514196,0.20828713319632092,0.3408211093157626,0.28015109399620514,57,20,45,17,45869,4185,,,,,,,,,,,
+scsemi,NK cell,pseudobulk_log1p_cpm,3161,0.09856412377222237,0.05503020199393339,0.09121963948121495,0.15632250686620788,57,20,45,17,45869,4185,,,,,,,,,,,
+scsemi,T cell,welch_top50_deg,4243,,,,,57,20,57,20,279996,70397,True,3,0.030927835051546393,50,50,1505,405,6,0.06382978723404255,50,1075
+scsemi,B cell,welch_top50_deg,4243,,,,,57,20,56,20,95354,16783,True,0,0.0,50,3,1011,3,4,0.041666666666666664,50,1075
+scsemi,Monocyte,welch_top50_deg,4243,,,,,57,20,54,20,107968,17045,True,0,0.0,50,0,2342,0,10,0.1111111111111111,50,1075
+scsemi,NK cell,welch_top50_deg,4243,,,,,57,20,45,17,45869,4185,True,0,0.0,50,50,1182,141,5,0.05263157894736842,50,1075
+scsemi,DC,welch_top50_deg,4243,,,,,53,20,56,19,3221,1537,True,0,0.0,50,31,1483,31,2,0.02040816326530612,50,1075

paper-releases/pbisc-diffusion/updates/20261013T142727Z-trunk4x-sepsis-results/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/scores/draw2/summary.json

@@ -0,0 +1,1612 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-13T13:38:04.278548+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",
+  "--reference",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/reference",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/scores/draw2",
+  "--threads",
+  "4",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/scores/draw2/test_samples.txt",
+  "--case-groups",
+  "adult_sepsis,ped_sepsis",
+  "--control-groups",
+  "adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl",
+  "--arm",
+  "trunk4x=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/trunk4x.npz",
+  "--condition",
+  "trunk4x=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+  "--arm",
+  "panel_matched_1x=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/panel_matched_1x.npz",
+  "--condition",
+  "panel_matched_1x=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+  "--arm",
+  "current_f01=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/current_f01.npz",
+  "--condition",
+  "current_f01=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+  "--arm",
+  "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/scsemi.npz",
+  "--condition",
+  "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz"
+ ],
+ "arms": [
+  "trunk4x",
+  "panel_matched_1x",
+  "current_f01",
+  "scsemi"
+ ],
+ "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",
+  "Abd-S98",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Uri-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_donors": 77,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/reference",
+  "reference_sha256": "8c5f2d794d135f094fd127fbeb56d8062b4fd619e03a2768bd22895e53c3e49a",
+  "features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
+  "n_r1_cells": 11550,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.33803120255470276,
+   "n_fit_cells": 11550
+  },
+  "r2_control": {
+   "precision": 0.9806926406926407,
+   "coverage": 0.9997402597402597,
+   "density": 1.3077229437229438,
+   "n_query": 11550,
+   "depth_matched": {
+    "precision": 0.9786147186147186,
+    "coverage": 0.9997402597402597,
+    "density": 1.299948051948052
+   }
+  },
+  "observed_l1_loo_null_mean": 0.5196680228845961
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 57,
+  "n_control_donors": 20,
+  "n_donors_in_neither": 0,
+  "case": [
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_HC",
+   "ped_HC",
+   "ped_HC",
+   "ped_ICU_ctrl",
+   "ped_ICU_ctrl",
+   "ped_ICU_ctrl",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis"
+  ]
+ },
+ "deg_definition": {
+  "enabled": true,
+  "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
+  "functions": [
+   "welch_bh_deg",
+   "top_deg_genes",
+   "jaccard"
+  ],
+  "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
+  "top_n": 50,
+  "fdr": 0.05,
+  "n_genes": 4243,
+  "types": [
+   "T cell",
+   "B cell",
+   "Monocyte",
+   "NK cell",
+   "DC"
+  ],
+  "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/reference/deg_reference.npz",
+  "aggregates_sha256": "38d6b5f9ff11dc2ddb45b8caf9ed92fc1a92612e0c48512d864c553153b9b15f",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
+  "observed": {
+   "T cell": {
+    "n_significant": 1505,
+    "n_tested": 4228,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 279996,
+    "top_list_size": 50
+   },
+   "B cell": {
+    "n_significant": 1011,
+    "n_tested": 4218,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 95354,
+    "top_list_size": 50
+   },
+   "Monocyte": {
+    "n_significant": 2342,
+    "n_tested": 4227,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 107968,
+    "top_list_size": 50
+   },
+   "NK cell": {
+    "n_significant": 1182,
+    "n_tested": 4214,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 45869,
+    "top_list_size": 50
+   },
+   "DC": {
+    "n_significant": 1483,
+    "n_tested": 4183,
+    "n_case_donors": 53,
+    "n_control_donors": 20,
+    "n_cells": 3221,
+    "top_list_size": 50
+   }
+  },
+  "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
+ },
+ "headline": {
+  "trunk4x": {
+   "comp_l1": 0.49872498326571074,
+   "comp_l1_obs_loo_null": 0.5196680228845961,
+   "precision": 0.9568831168831169,
+   "coverage": 0.8090909090909091,
+   "precision_dm": 0.9653679653679653,
+   "coverage_dm": 0.8398268398268398,
+   "pb_r_median": 0.9062477326994645,
+   "pb_top1": 0.05194805194805195,
+   "mono_pct_gen": 11.005194805194805,
+   "mono_pct_obs": 21.18539814075279,
+   "median_umi_gen": 1888.0,
+   "median_umi_obs": 1947.0,
+   "contrast_mean_cp10k_r_gen": 0.28389454265614456,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.3080120054189286,
+   "contrast_mean_cp10k_r_broadcast": 0.3367689752140143,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.2941411087530216,
+   "deg_top50_T": 12,
+   "deg_top50_B": 12,
+   "deg_top50_Mono": 3,
+   "deg_top50_NK": 1,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 28,
+   "deg_top50_max": 250,
+   "deg_top50_sum_4type": 28,
+   "deg_top50_sum_broadcast": 27,
+   "seconds": 26.0
+  },
+  "panel_matched_1x": {
+   "comp_l1": 0.5473525143947433,
+   "comp_l1_obs_loo_null": 0.5196680228845961,
+   "precision": 0.9202597402597402,
+   "coverage": 0.7141125541125541,
+   "precision_dm": 0.9406060606060606,
+   "coverage_dm": 0.8303896103896103,
+   "pb_r_median": 0.867448874733446,
+   "pb_top1": 0.15584415584415584,
+   "mono_pct_gen": 10.428571428571427,
+   "mono_pct_obs": 21.18539814075279,
+   "median_umi_gen": 1915.0,
+   "median_umi_obs": 1947.0,
+   "contrast_mean_cp10k_r_gen": 0.3140605382176318,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.33267511397085614,
+   "contrast_mean_cp10k_r_broadcast": 0.3367689752140143,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.2941411087530216,
+   "deg_top50_T": 13,
+   "deg_top50_B": 10,
+   "deg_top50_Mono": 1,
+   "deg_top50_NK": 1,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 25,
+   "deg_top50_max": 250,
+   "deg_top50_sum_4type": 25,
+   "deg_top50_sum_broadcast": 27,
+   "seconds": 24.0
+  },
+  "current_f01": {
+   "comp_l1": 0.4990690207608889,
+   "comp_l1_obs_loo_null": 0.5196680228845961,
+   "precision": 0.9151515151515152,
+   "coverage": 0.7490909090909091,
+   "precision_dm": 0.9311688311688312,
+   "coverage_dm": 0.844935064935065,
+   "pb_r_median": 0.8766351190167497,
+   "pb_top1": 0.11688311688311688,
+   "mono_pct_gen": 11.220779220779217,
+   "mono_pct_obs": 21.18539814075279,
+   "median_umi_gen": 1836.0,
+   "median_umi_obs": 1947.0,
+   "contrast_mean_cp10k_r_gen": 0.32777069988518615,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.33145944584599185,
+   "contrast_mean_cp10k_r_broadcast": 0.3367689752140143,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.2941411087530216,
+   "deg_top50_T": 13,
+   "deg_top50_B": 11,
+   "deg_top50_Mono": 1,
+   "deg_top50_NK": 4,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 29,
+   "deg_top50_max": 250,
+   "deg_top50_sum_4type": 29,
+   "deg_top50_sum_broadcast": 27,
+   "seconds": 24.4
+  },
+  "scsemi": {
+   "comp_l1": 0.5800074032807602,
+   "comp_l1_obs_loo_null": 0.5196680228845961,
+   "precision": 0.7902164502164503,
+   "coverage": 0.0851948051948052,
+   "precision_dm": 0.596017316017316,
+   "coverage_dm": 0.1735930735930736,
+   "pb_r_median": 0.66953552703292,
+   "pb_top1": 0.03896103896103896,
+   "mono_pct_gen": 14.757575757575758,
+   "mono_pct_obs": 21.18539814075279,
+   "median_umi_gen": 2181.0,
+   "median_umi_obs": 1947.0,
+   "contrast_mean_cp10k_r_gen": 0.3186065287808404,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.13481928521061134,
+   "contrast_mean_cp10k_r_broadcast": 0.3367689752140143,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.2941411087530216,
+   "deg_top50_T": 3,
+   "deg_top50_B": 0,
+   "deg_top50_Mono": 0,
+   "deg_top50_NK": 0,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 3,
+   "deg_top50_max": 250,
+   "deg_top50_sum_4type": 3,
+   "deg_top50_sum_broadcast": 27,
+   "seconds": 23.2
+  }
+ },
+ "per_arm": {
+  "trunk4x": {
+   "arm": "trunk4x",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/trunk4x.npz",
+   "npz_sha256": "3084c9fba356d1aa84d842530fd7f3fbe1b611e3e92003d0f9d2903ca0532552",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/runs/trunk4x/draw2/checkpoint_ft.pt",
+    "checkpoint_sha256": "ad3b4f6c1a35ff8341bd4944873a60573d942d0c8fd44b00f3b88a9a28201435",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+    "input_condition_sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f",
+    "seed": 20260928,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+    "sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 38614049,
+    "median_library_whole_npz_panel": 1888.0,
+    "n_rows_whole_npz": 115500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 73456,
+     "B cell": 21242,
+     "Monocyte": 12711,
+     "NK cell": 4058,
+     "Other": 3808,
+     "DC": 225
+    },
+    "mean_l2_max_prob": 0.920149465586716,
+    "predict_seconds": 7.2
+   },
+   "n_donors": 77,
+   "n_generated_cells": 115500,
+   "composition": {
+    "l1_mean": 0.49872498326571074,
+    "l1_median": 0.4411561727668589,
+    "l1_obs_loo_null_mean": 0.5196680228845961,
+    "l1_generated_loo_mean_vs_observed_mean": 0.5658642808053027,
+    "composition_top1": 0.05194805194805195,
+    "mean_fraction_generated": {
+     "T cell": 0.635983,
+     "B cell": 0.183913,
+     "Monocyte": 0.110052,
+     "NK cell": 0.035134,
+     "DC": 0.001948,
+     "Other": 0.03297
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.476568,
+     "B cell": 0.174558,
+     "Monocyte": 0.211854,
+     "NK cell": 0.08183,
+     "DC": 0.005719,
+     "Other": 0.049471
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 4243,
+    "r_median": 0.9062477326994645,
+    "r_mean": 0.9018286985113573,
+    "top1": 0.05194805194805195,
+    "n_top1": 4,
+    "own_rank_median": 20.0,
+    "chance_top1": 0.012987012987012988
+   },
+   "precision_coverage": {
+    "precision": 0.9568831168831169,
+    "coverage": 0.8090909090909091,
+    "density": 1.093064935064935,
+    "n_query": 11550,
+    "n_reference": 11550
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9653679653679653,
+    "coverage": 0.8398268398268398,
+    "density": 1.2931861471861472,
+    "detected_median_before": {
+     "R1": 403.0,
+     "Q": 332.0
+    },
+    "detected_median_after": {
+     "R1": 329.0,
+     "Q": 329.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 11.005194805194805,
+    "observed_mean_over_donors": 21.18539814075279,
+    "generated_pooled_cells": 11.005194805194805
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 1888.0,
+    "observed_pooled": 1947.0,
+    "generated_mean_of_donor_medians": 1908.30517578125,
+    "observed_mean_of_donor_medians": 2089.5714285714284
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.2870702714037037,
+       "r_broadcast": 0.28417788192518073,
+       "partial_r_generated_given_broadcast": 0.2665216587387086,
+       "r_generated_vs_broadcast": 0.11716962712798713,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.3538743444538308,
+       "r_broadcast": 0.29788887309509887,
+       "partial_r_generated_given_broadcast": 0.34815898557466446,
+       "r_generated_vs_broadcast": 0.07542510877815839,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": 0.27032632846200105,
+       "r_broadcast": 0.5567220126394566,
+       "partial_r_generated_given_broadcast": 0.23097644212449236,
+       "r_generated_vs_broadcast": 0.14454135322602896,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.22430722630504263,
+       "r_broadcast": 0.20828713319632092,
+       "partial_r_generated_given_broadcast": 0.21489574474443748,
+       "r_generated_vs_broadcast": 0.07031066343780458,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.28389454265614456,
+     "mean_r_broadcast": 0.3367689752140143,
+     "mean_partial_r": 0.26513820779557573
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.3881076237989945,
+       "r_broadcast": 0.2528077636701587,
+       "partial_r_generated_given_broadcast": 0.35385159440330893,
+       "r_generated_vs_broadcast": 0.21164730128627224,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.30178331034532974,
+       "r_broadcast": 0.2708791238271775,
+       "partial_r_generated_given_broadcast": 0.2871833190925479,
+       "r_generated_vs_broadcast": 0.0984981902842706,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": 0.337796225280278,
+       "r_broadcast": 0.5978473455208166,
+       "partial_r_generated_given_broadcast": 0.267481264535883,
+       "r_generated_vs_broadcast": 0.2147416079559134,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.20436086225111227,
+       "r_broadcast": 0.05503020199393339,
+       "partial_r_generated_given_broadcast": 0.20223126117200582,
+       "r_generated_vs_broadcast": 0.048604123366663594,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.3080120054189286,
+     "mean_r_broadcast": 0.2941411087530216,
+     "mean_partial_r": 0.27768685980093644
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 12,
+      "top50_jaccard": 0.13636363636363635,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 6,
+      "top50_jaccard_broadcast": 0.06382978723404255,
+      "n_cells_obs": 279996,
+      "n_cells_gen": 73456
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 12,
+      "top50_jaccard": 0.13636363636363635,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 4,
+      "top50_jaccard_broadcast": 0.041666666666666664,
+      "n_cells_obs": 95354,
+      "n_cells_gen": 21242
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 3,
+      "top50_jaccard": 0.030927835051546393,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 10,
+      "top50_jaccard_broadcast": 0.1111111111111111,
+      "n_cells_obs": 107968,
+      "n_cells_gen": 12711
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.010101010101010102,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 5,
+      "top50_jaccard_broadcast": 0.05263157894736842,
+      "n_cells_obs": 45869,
+      "n_cells_gen": 4058
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 3221,
+      "n_cells_gen": 225
+     }
+    },
+    "sum": 28,
+    "sum_4type": 28,
+    "max": 250,
+    "mean": 5.6,
+    "sum_broadcast": 27,
+    "sum_broadcast_4type": 25,
+    "broadcast_n_significant": 1075,
+    "seconds": 0.46
+   },
+   "seconds": 26.0
+  },
+  "panel_matched_1x": {
+   "arm": "panel_matched_1x",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/panel_matched_1x.npz",
+   "npz_sha256": "1d13d0f0e274fee7e54dae1905f5d2305d3a236ea231ace8532f3be30285b245",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/runs/panel_matched_1x/draw2/checkpoint_ft.pt",
+    "checkpoint_sha256": "7d66b2501f52e85fe5c19fca6a3aa0547eb3aa18ad2792a96ba4b0d9c252ac3d",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+    "input_condition_sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f",
+    "seed": 20260928,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+    "sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 30869547,
+    "median_library_whole_npz_panel": 1915.0,
+    "n_rows_whole_npz": 115500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 74218,
+     "B cell": 22358,
+     "Monocyte": 12045,
+     "NK cell": 3850,
+     "Other": 2721,
+     "DC": 308
+    },
+    "mean_l2_max_prob": 0.927006201397805,
+    "predict_seconds": 5.9
+   },
+   "n_donors": 77,
+   "n_generated_cells": 115500,
+   "composition": {
+    "l1_mean": 0.5473525143947433,
+    "l1_median": 0.512752688172043,
+    "l1_obs_loo_null_mean": 0.5196680228845961,
+    "l1_generated_loo_mean_vs_observed_mean": 0.5779709342897577,
+    "composition_top1": 0.025974025974025976,
+    "mean_fraction_generated": {
+     "T cell": 0.64258,
+     "B cell": 0.193576,
+     "Monocyte": 0.104286,
+     "NK cell": 0.033333,
+     "DC": 0.002667,
+     "Other": 0.023558
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.476568,
+     "B cell": 0.174558,
+     "Monocyte": 0.211854,
+     "NK cell": 0.08183,
+     "DC": 0.005719,
+     "Other": 0.049471
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 4243,
+    "r_median": 0.867448874733446,
+    "r_mean": 0.8638794755748436,
+    "top1": 0.15584415584415584,
+    "n_top1": 12,
+    "own_rank_median": 12.0,
+    "chance_top1": 0.012987012987012988
+   },
+   "precision_coverage": {
+    "precision": 0.9202597402597402,
+    "coverage": 0.7141125541125541,
+    "density": 0.8856363636363636,
+    "n_query": 11550,
+    "n_reference": 11550
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9406060606060606,
+    "coverage": 0.8303896103896103,
+    "density": 1.4374285714285713,
+    "detected_median_before": {
+     "R1": 403.0,
+     "Q": 262.0
+    },
+    "detected_median_after": {
+     "R1": 261.0,
+     "Q": 261.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 10.428571428571427,
+    "observed_mean_over_donors": 21.18539814075279,
+    "generated_pooled_cells": 10.428571428571429
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 1915.0,
+    "observed_pooled": 1947.0,
+    "generated_mean_of_donor_medians": 1957.0064697265625,
+    "observed_mean_of_donor_medians": 2089.5714285714284
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.3602182910286651,
+       "r_broadcast": 0.28417788192518073,
+       "partial_r_generated_given_broadcast": 0.3400110989342174,
+       "r_generated_vs_broadcast": 0.13020119193174146,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.4176046858759658,
+       "r_broadcast": 0.29788887309509887,
+       "partial_r_generated_given_broadcast": 0.41205499129843615,
+       "r_generated_vs_broadcast": 0.08636238355830167,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": 0.20520843935549252,
+       "r_broadcast": 0.5567220126394566,
+       "partial_r_generated_given_broadcast": 0.16816981131552372,
+       "r_generated_vs_broadcast": 0.11946802992293727,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.27321073661040374,
+       "r_broadcast": 0.20828713319632092,
+       "partial_r_generated_given_broadcast": 0.2696792589027904,
+       "r_generated_vs_broadcast": 0.046735348781462745,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.3140605382176318,
+     "mean_r_broadcast": 0.3367689752140143,
+     "mean_partial_r": 0.29747879011274186
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.45158356448300535,
+       "r_broadcast": 0.2528077636701587,
+       "partial_r_generated_given_broadcast": 0.41767589077147815,
+       "r_generated_vs_broadcast": 0.2310398943266545,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.4161311784237891,
+       "r_broadcast": 0.2708791238271775,
+       "partial_r_generated_given_broadcast": 0.4001685845369041,
+       "r_generated_vs_broadcast": 0.12538214925458604,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": 0.2846560526817334,
+       "r_broadcast": 0.5978473455208166,
+       "partial_r_generated_given_broadcast": 0.22915307336444551,
+       "r_generated_vs_broadcast": 0.17354250627580894,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.17832966029489664,
+       "r_broadcast": 0.05503020199393339,
+       "partial_r_generated_given_broadcast": 0.17541012366389303,
+       "r_generated_vs_broadcast": 0.06451352245405642,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.33267511397085614,
+     "mean_r_broadcast": 0.2941411087530216,
+     "mean_partial_r": 0.3056019180841802
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 13,
+      "top50_jaccard": 0.14942528735632185,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 6,
+      "top50_jaccard_broadcast": 0.06382978723404255,
+      "n_cells_obs": 279996,
+      "n_cells_gen": 74218
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 10,
+      "top50_jaccard": 0.1111111111111111,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 4,
+      "top50_jaccard_broadcast": 0.041666666666666664,
+      "n_cells_obs": 95354,
+      "n_cells_gen": 22358
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.01639344262295082,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 12,
+      "top50_overlap_broadcast": 10,
+      "top50_jaccard_broadcast": 0.1111111111111111,
+      "n_cells_obs": 107968,
+      "n_cells_gen": 12045
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.010101010101010102,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 5,
+      "top50_jaccard_broadcast": 0.05263157894736842,
+      "n_cells_obs": 45869,
+      "n_cells_gen": 3850
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 3221,
+      "n_cells_gen": 308
+     }
+    },
+    "sum": 25,
+    "sum_4type": 25,
+    "max": 250,
+    "mean": 5.0,
+    "sum_broadcast": 27,
+    "sum_broadcast_4type": 25,
+    "broadcast_n_significant": 1075,
+    "seconds": 0.34
+   },
+   "seconds": 24.0
+  },
+  "current_f01": {
+   "arm": "current_f01",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/current_f01.npz",
+   "npz_sha256": "b4120391559d4207966c4038d8140734118d14bd56653973927ad33782151e09",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/ye2026_sepsis/disease/draw2/lora/checkpoint_ft.pt",
+    "checkpoint_sha256": "98d4d57a1073c28f25d0c01493c4e640f085a5083ab2b2c9b4d97a4e60fb8787",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw2/test_raw.npz",
+    "input_condition_sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f",
+    "seed": 20260928,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+    "sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 32804217,
+    "median_library_whole_npz_panel": 1836.0,
+    "n_rows_whole_npz": 115500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 74305,
+     "B cell": 19751,
+     "Monocyte": 12960,
+     "NK cell": 4274,
+     "Other": 3926,
+     "DC": 284
+    },
+    "mean_l2_max_prob": 0.92472209353416,
+    "predict_seconds": 6.3
+   },
+   "n_donors": 77,
+   "n_generated_cells": 115500,
+   "composition": {
+    "l1_mean": 0.4990690207608889,
+    "l1_median": 0.4474193548387097,
+    "l1_obs_loo_null_mean": 0.5196680228845961,
+    "l1_generated_loo_mean_vs_observed_mean": 0.5646312850644463,
+    "composition_top1": 0.06493506493506493,
+    "mean_fraction_generated": {
+     "T cell": 0.643333,
+     "B cell": 0.171004,
+     "Monocyte": 0.112208,
+     "NK cell": 0.037004,
+     "DC": 0.002459,
+     "Other": 0.033991
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.476568,
+     "B cell": 0.174558,
+     "Monocyte": 0.211854,
+     "NK cell": 0.08183,
+     "DC": 0.005719,
+     "Other": 0.049471
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 4243,
+    "r_median": 0.8766351190167497,
+    "r_mean": 0.8667692286513492,
+    "top1": 0.11688311688311688,
+    "n_top1": 9,
+    "own_rank_median": 14.0,
+    "chance_top1": 0.012987012987012988
+   },
+   "precision_coverage": {
+    "precision": 0.9151515151515152,
+    "coverage": 0.7490909090909091,
+    "density": 0.8486320346320346,
+    "n_query": 11550,
+    "n_reference": 11550
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9311688311688312,
+    "coverage": 0.844935064935065,
+    "density": 1.1922943722943722,
+    "detected_median_before": {
+     "R1": 403.0,
+     "Q": 279.0
+    },
+    "detected_median_after": {
+     "R1": 277.5,
+     "Q": 277.5
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 11.220779220779217,
+    "observed_mean_over_donors": 21.18539814075279,
+    "generated_pooled_cells": 11.220779220779221
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 1836.0,
+    "observed_pooled": 1947.0,
+    "generated_mean_of_donor_medians": 1877.292236328125,
+    "observed_mean_of_donor_medians": 2089.5714285714284
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.3475254712197549,
+       "r_broadcast": 0.28417788192518073,
+       "partial_r_generated_given_broadcast": 0.3352046413091245,
+       "r_generated_vs_broadcast": 0.09736022010926025,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.4094875306359168,
+       "r_broadcast": 0.29788887309509887,
+       "partial_r_generated_given_broadcast": 0.42306369432943636,
+       "r_generated_vs_broadcast": 0.019150619895150427,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": 0.29244694076797595,
+       "r_broadcast": 0.5567220126394566,
+       "partial_r_generated_given_broadcast": 0.26620998956129155,
+       "r_generated_vs_broadcast": 0.13153414113945086,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.26162285691709686,
+       "r_broadcast": 0.20828713319632092,
+       "partial_r_generated_given_broadcast": 0.2511897332853757,
+       "r_generated_vs_broadcast": 0.08035409317555907,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.32777069988518615,
+     "mean_r_broadcast": 0.3367689752140143,
+     "mean_partial_r": 0.318917014621307
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.4743533046018932,
+       "r_broadcast": 0.2528077636701587,
+       "partial_r_generated_given_broadcast": 0.45185144719564235,
+       "r_generated_vs_broadcast": 0.17320230434917558,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.34002496055742293,
+       "r_broadcast": 0.2708791238271775,
+       "partial_r_generated_given_broadcast": 0.34683235162023024,
+       "r_generated_vs_broadcast": 0.023066876232327588,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": 0.284202090246288,
+       "r_broadcast": 0.5978473455208166,
+       "partial_r_generated_given_broadcast": 0.22886991857128774,
+       "r_generated_vs_broadcast": 0.17313507286968016,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.22725742797836326,
+       "r_broadcast": 0.05503020199393339,
+       "partial_r_generated_given_broadcast": 0.2252028079607215,
+       "r_generated_vs_broadcast": 0.04830804057273376,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.33145944584599185,
+     "mean_r_broadcast": 0.2941411087530216,
+     "mean_partial_r": 0.31318913133697046
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 13,
+      "top50_jaccard": 0.14942528735632185,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 6,
+      "top50_jaccard_broadcast": 0.06382978723404255,
+      "n_cells_obs": 279996,
+      "n_cells_gen": 74305
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 11,
+      "top50_jaccard": 0.12359550561797752,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 4,
+      "top50_jaccard_broadcast": 0.041666666666666664,
+      "n_cells_obs": 95354,
+      "n_cells_gen": 19751
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.010101010101010102,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 10,
+      "top50_jaccard_broadcast": 0.1111111111111111,
+      "n_cells_obs": 107968,
+      "n_cells_gen": 12960
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 4,
+      "top50_jaccard": 0.041666666666666664,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 5,
+      "top50_jaccard_broadcast": 0.05263157894736842,
+      "n_cells_obs": 45869,
+      "n_cells_gen": 4274
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 3221,
+      "n_cells_gen": 284
+     }
+    },
+    "sum": 29,
+    "sum_4type": 29,
+    "max": 250,
+    "mean": 5.8,
+    "sum_broadcast": 27,
+    "sum_broadcast_4type": 25,
+    "broadcast_n_significant": 1075,
+    "seconds": 0.42
+   },
+   "seconds": 24.4
+  },
+  "scsemi": {
+   "arm": "scsemi",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw2/scsemi.npz",
+   "npz_sha256": "f2890d057977929204a615be971a9eef5827435cfc2402857d913b8b329f7642",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/draw2/test_raw.npz",
+    "input_condition_sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f",
+    "seed": 20260927,
+    "steps": null,
+    "support_readout": "upstream (values <= 10 normalized units zeroed by fast_semi)",
+    "weights": null
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/data/draw2/ye2026_sepsis/test_raw.npz",
+    "sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 12575196,
+    "median_library_whole_npz_panel": 2181.0,
+    "n_rows_whole_npz": 115500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 70397,
+     "Monocyte": 17045,
+     "B cell": 16783,
+     "Other": 5553,
+     "NK cell": 4185,
+     "DC": 1537
+    },
+    "mean_l2_max_prob": 0.9136849982765588,
+    "predict_seconds": 6.9
+   },
+   "n_donors": 77,
+   "n_generated_cells": 115500,
+   "composition": {
+    "l1_mean": 0.5800074032807602,
+    "l1_median": 0.46961945636623736,
+    "l1_obs_loo_null_mean": 0.5196680228845961,
+    "l1_generated_loo_mean_vs_observed_mean": 0.5390124218428786,
+    "composition_top1": 0.025974025974025976,
+    "mean_fraction_generated": {
+     "T cell": 0.609498,
+     "B cell": 0.145307,
+     "Monocyte": 0.147576,
+     "NK cell": 0.036234,
+     "DC": 0.013307,
+     "Other": 0.048078
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.476568,
+     "B cell": 0.174558,
+     "Monocyte": 0.211854,
+     "NK cell": 0.08183,
+     "DC": 0.005719,
+     "Other": 0.049471
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 4243,
+    "r_median": 0.66953552703292,
+    "r_mean": 0.6592622955492694,
+    "top1": 0.03896103896103896,
+    "n_top1": 3,
+    "own_rank_median": 20.0,
+    "chance_top1": 0.012987012987012988
+   },
+   "precision_coverage": {
+    "precision": 0.7902164502164503,
+    "coverage": 0.0851948051948052,
+    "density": 0.25485714285714284,
+    "n_query": 11550,
+    "n_reference": 11550
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.596017316017316,
+    "coverage": 0.1735930735930736,
+    "density": 0.1864761904761905,
+    "detected_median_before": {
+     "R1": 403.0,
+     "Q": 106.0
+    },
+    "detected_median_after": {
+     "R1": 106.0,
+     "Q": 106.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 14.757575757575758,
+    "observed_mean_over_donors": 21.18539814075279,
+    "generated_pooled_cells": 14.757575757575758
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2181.0,
+    "observed_pooled": 1947.0,
+    "generated_mean_of_donor_medians": 2181.136474609375,
+    "observed_mean_of_donor_medians": 2089.5714285714284
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.3687857657303425,
+       "r_broadcast": 0.28417788192518073,
+       "partial_r_generated_given_broadcast": 0.3107179554834221,
+       "r_generated_vs_broadcast": 0.2965810368595624,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.27034367544047044,
+       "r_broadcast": 0.29788887309509887,
+       "partial_r_generated_given_broadcast": 0.23935212477874757,
+       "r_generated_vs_broadcast": 0.14908769419727183,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": 0.256947219101129,
+       "r_broadcast": 0.5567220126394566,
+       "partial_r_generated_given_broadcast": 0.260145805694905,
+       "r_generated_vs_broadcast": 0.07444293393764446,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.3783494548514196,
+       "r_broadcast": 0.20828713319632092,
+       "partial_r_generated_given_broadcast": 0.3408211093157626,
+       "r_generated_vs_broadcast": 0.28015109399620514,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.3186065287808404,
+     "mean_r_broadcast": 0.3367689752140143,
+     "mean_partial_r": 0.2877592488182093
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.24157790028155127,
+       "r_broadcast": 0.2528077636701587,
+       "partial_r_generated_given_broadcast": 0.21135516512175404,
+       "r_generated_vs_broadcast": 0.15669783091425477,
+       "n_genes": 3210
+      },
+      "B cell": {
+       "r_generated": 0.22091899797156925,
+       "r_broadcast": 0.2708791238271775,
+       "partial_r_generated_given_broadcast": 0.21286345495831324,
+       "r_generated_vs_broadcast": 0.06050367236616134,
+       "n_genes": 3205
+      },
+      "Monocyte": {
+       "r_generated": -0.02178388118289749,
+       "r_broadcast": 0.5978473455208166,
+       "partial_r_generated_given_broadcast": -0.009467224228652434,
+       "r_generated_vs_broadcast": -0.0237468644682939,
+       "n_genes": 3210
+      },
+      "NK cell": {
+       "r_generated": 0.09856412377222237,
+       "r_broadcast": 0.05503020199393339,
+       "partial_r_generated_given_broadcast": 0.09121963948121495,
+       "r_generated_vs_broadcast": 0.15632250686620788,
+       "n_genes": 3161
+      }
+     },
+     "mean_r_generated": 0.13481928521061134,
+     "mean_r_broadcast": 0.2941411087530216,
+     "mean_partial_r": 0.12649275883315744
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 3,
+      "top50_jaccard": 0.030927835051546393,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 6,
+      "top50_jaccard_broadcast": 0.06382978723404255,
+      "n_cells_obs": 279996,
+      "n_cells_gen": 70397
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 3,
+      "top50_overlap_broadcast": 4,
+      "top50_jaccard_broadcast": 0.041666666666666664,
+      "n_cells_obs": 95354,
+      "n_cells_gen": 16783
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 10,
+      "top50_jaccard_broadcast": 0.1111111111111111,
+      "n_cells_obs": 107968,
+      "n_cells_gen": 17045
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 5,
+      "top50_jaccard_broadcast": 0.05263157894736842,
+      "n_cells_obs": 45869,
+      "n_cells_gen": 4185
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 31,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 3221,
+      "n_cells_gen": 1537
+     }
+    },
+    "sum": 3,
+    "sum_4type": 3,
+    "max": 250,
+    "mean": 0.6,
+    "sum_broadcast": 27,
+    "sum_broadcast_4type": 25,
+    "broadcast_n_significant": 1075,
+    "seconds": 0.09
+   },
+   "seconds": 23.2
+  }
+ },
+ "code_sha256": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+ },
+ "seconds": 104.7
+}