Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/locoL_fullsat_s40000_K1000/README.md

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+# score_ft.py output: ye2026_sepsis, 82 scored donors
+
+Arms: locoL_fullsat_s40000_K1000.  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/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/reference.npz` (sha bac12da8a241), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/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/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/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 (5975 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 82 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) (12300 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 0.9805, 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
+   0.9796, coverage 0.9998.
+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 = 61) vs control groups ['adult_HC', 'adult_ICU_ctrl', 'ped_HC', 'ped_ICU_ctrl'] (n = 21); 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 5975 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/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/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 61 + 21
+   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/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/locoL_fullsat_s40000_K1000/contrast.csv

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+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+locoL_fullsat_s40000_K1000,T cell,mean_cp10k,3258,-0.020161032963137263,0.2548893770824626,-0.0750508084095668,0.19987667047215266,61,21,61,21,298117,47776,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,T cell,pseudobulk_log1p_cpm,3258,0.05470224460693203,0.2164745523777111,0.002610259334076317,0.24127161020818635,61,21,61,21,298117,47776,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,B cell,mean_cp10k,3310,0.18492409066801235,0.27458639801653467,0.1246959350726729,0.25074711821770146,61,21,61,21,99729,32079,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,B cell,pseudobulk_log1p_cpm,3310,0.2793658416752698,0.2711145517540278,0.21745387420589934,0.29206207830603004,61,21,61,21,99729,32079,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,Monocyte,mean_cp10k,3289,0.2587398651012202,0.5481103923782986,0.14019334397222258,0.26582243319136595,61,21,61,21,111269,23220,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,Monocyte,pseudobulk_log1p_cpm,3289,0.13411472369033192,0.6203629305570988,-0.05353004248714449,0.2811351496062065,61,21,61,21,111269,23220,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,NK cell,mean_cp10k,3240,0.026198178711528963,0.1861970975708186,-0.010001095708816745,0.19248755298421708,61,21,61,21,47832,15198,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,NK cell,pseudobulk_log1p_cpm,3240,0.006983030531220242,0.05592238177293225,-0.002881885357961116,0.17552426803119064,61,21,61,21,47832,15198,,,,,,,,,,,
+locoL_fullsat_s40000_K1000,T cell,welch_top50_deg,5975,,,,,61,21,61,21,298117,47776,True,0,0.0,50,2,1578,2,3,0.030927835051546393,50,1378
+locoL_fullsat_s40000_K1000,B cell,welch_top50_deg,5975,,,,,61,21,61,21,99729,32079,True,4,0.041666666666666664,50,50,1102,394,2,0.02040816326530612,50,1378
+locoL_fullsat_s40000_K1000,Monocyte,welch_top50_deg,5975,,,,,61,21,61,21,111269,23220,True,3,0.030927835051546393,50,50,2459,114,13,0.14942528735632185,50,1378
+locoL_fullsat_s40000_K1000,NK cell,welch_top50_deg,5975,,,,,61,21,61,21,47832,15198,True,0,0.0,50,2,1235,2,2,0.02040816326530612,50,1378
+locoL_fullsat_s40000_K1000,DC,welch_top50_deg,5975,,,,,57,21,60,21,3300,2916,True,0,0.0,50,8,1572,8,1,0.010101010101010102,50,1378

paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/locoL_fullsat_s40000_K1000/per_donor.csv

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+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
+locoL_fullsat_s40000_K1000,Abd-PS04,ped_sepsis,1500,5449,150,0.11933333333333333,0.14094329234721967,0.11733333333333333,0.17030647825289044,0.608,0.5608368507983116,0.094,0.02147182969352175,0.04066666666666666,0.003853918150119288,0.020666666666666667,0.10258763075793724,0.31300813604942807,0.8240358281801887,0.8893023661055784,12,False,0.7733333333333333,0.3466666666666667,0.68,0.5933333333333334,60.8,56.083685079831156,1018.0,2716.0
+locoL_fullsat_s40000_K1000,Abd-PS05,ped_sepsis,1500,6924,150,0.218,0.30387059503177355,0.574,0.5060658578856152,0.08,0.07019064124783363,0.10533333333333333,0.0891103408434431,0.009333333333333334,0.008954361640670132,0.013333333333333334,0.021808203350664357,0.18869093009820914,0.6987393915367811,0.894035970481211,1,True,0.8466666666666667,0.5666666666666667,0.8333333333333334,0.68,8.0,7.0190641247833625,1220.0,2313.0
+locoL_fullsat_s40000_K1000,Abd-PS07,ped_sepsis,1500,3472,150,0.69,0.8626152073732719,0.17533333333333334,0.023329493087557603,0.011333333333333334,0.002304147465437788,0.11333333333333333,0.09331797235023041,0.007333333333333333,0.0002880184331797235,0.0026666666666666666,0.018145161290322582,0.37618740399385564,0.7909717817075781,0.861647495445206,21,False,0.8066666666666666,0.47333333333333333,0.6866666666666666,0.62,1.1333333333333333,0.2304147465437788,934.0,1614.0
+locoL_fullsat_s40000_K1000,Abd-PS19,ped_sepsis,1500,7984,150,0.16333333333333333,0.4622995991983968,0.26866666666666666,0.11209919839679358,0.3873333333333333,0.2937124248496994,0.10533333333333333,0.05586172344689379,0.06133333333333333,0.0156563126252505,0.014,0.06037074148296593,0.6906740146960588,0.218193607618059,0.8703745241761431,18,False,0.8466666666666667,0.28,0.7066666666666667,0.6,38.733333333333334,29.37124248496994,697.0,2111.0
+locoL_fullsat_s40000_K1000,Abd-PS20,ped_sepsis,1500,7286,150,0.048,0.30496843261048584,0.9233333333333333,0.5780949766675817,0.0006666666666666666,0.08770244304144935,0.024666666666666667,0.007823222618720834,0.0006666666666666666,0.0005489980785067252,0.0026666666666666666,0.02086192698325556,0.7243989386037148,0.8206851316278935,0.8459231077124941,5,False,0.7866666666666666,0.32666666666666666,0.86,0.6066666666666667,0.06666666666666667,8.770244304144935,1446.5,1820.0
+locoL_fullsat_s40000_K1000,Abd-PS23,ped_sepsis,1500,4309,150,0.20533333333333334,0.2529589231840334,0.5093333333333333,0.3272220932931075,0.15933333333333333,0.32142028312833604,0.088,0.013460199582269667,0.016666666666666666,0.002088651659317707,0.021333333333333333,0.08284984915293572,0.5424581109306104,0.6120732295054894,0.8605105893515541,49,False,0.8066666666666666,0.30666666666666664,0.6466666666666666,0.44666666666666666,15.933333333333334,32.1420283128336,889.0,1832.0
+locoL_fullsat_s40000_K1000,Abd-PS27,ped_sepsis,1500,9427,150,0.87,0.6126021003500584,0.08066666666666666,0.06078285774901877,0.002,0.13196138750397793,0.046,0.010289593720165482,0.0,0.0029701920016972526,0.0013333333333333333,0.1813938686750822,0.6259842296948481,0.5288253850706728,0.8386028965331729,22,False,0.8066666666666666,0.29333333333333333,0.8666666666666667,0.42,0.2,13.196138750397793,1763.0,2356.0
+locoL_fullsat_s40000_K1000,Abd-S102,adult_sepsis,1500,9512,150,0.2786666666666667,0.47981497056349875,0.24133333333333334,0.39318755256518084,0.324,0.0053616484440706475,0.116,0.095878889823381,0.011333333333333334,0.0007359125315391085,0.028666666666666667,0.02502102607232969,0.7060050462573593,0.47699080006140543,0.8442476424651889,72,False,0.9066666666666666,0.32,0.8,0.5266666666666666,32.4,0.5361648444070648,948.0,1646.0
+locoL_fullsat_s40000_K1000,Abd-S103,adult_sepsis,1500,9423,150,0.44666666666666666,0.4813753581661891,0.314,0.14782977820227103,0.082,0.0024408362517245037,0.14666666666666667,0.04393505253104107,0.0033333333333333335,0.00021224663058473945,0.007333333333333333,0.3242067282181895,0.7031641727687572,0.5587060076493682,0.8606378208304972,57,False,0.82,0.22666666666666666,0.82,0.4266666666666667,8.200000000000001,0.24408362517245036,1239.0,971.0
+locoL_fullsat_s40000_K1000,Abd-S120,adult_sepsis,1500,5783,150,0.22933333333333333,0.3140238630468615,0.07333333333333333,0.11049628220646723,0.4666666666666667,0.46446481065191075,0.144,0.07297250561992046,0.072,0.0008646031471554556,0.014666666666666666,0.03717793532768459,0.28872949449535995,0.5189164550921991,0.8763666192559447,5,False,0.88,0.21333333333333335,0.7533333333333333,0.5533333333333333,46.666666666666664,46.44648106519107,674.5,2845.0
+locoL_fullsat_s40000_K1000,Abd-S123,adult_sepsis,1500,6299,150,0.29133333333333333,0.16986823305286552,0.104,0.08779171297031275,0.44266666666666665,0.5027782187648833,0.09266666666666666,0.10938244165740593,0.032,0.0007937767899666614,0.037333333333333336,0.1293856167645658,0.33775922104037676,0.8187693250726966,0.8802608647571599,3,False,0.78,0.18666666666666668,0.5066666666666667,0.5,44.266666666666666,50.277821876488325,687.0,2261.0
+locoL_fullsat_s40000_K1000,Abd-S156,adult_sepsis,1500,7004,150,0.456,0.3343803540833809,0.066,0.08209594517418618,0.2633333333333333,0.39406053683609366,0.16466666666666666,0.0910908052541405,0.011333333333333334,0.0012849800114220445,0.03866666666666667,0.0970873786407767,0.4104877213021131,0.4962206922485184,0.8981252218905973,1,True,0.7933333333333333,0.5266666666666666,0.7666666666666667,0.7333333333333333,26.333333333333332,39.406053683609365,1278.5,1821.0
+locoL_fullsat_s40000_K1000,Abd-S39,adult_sepsis,1500,4291,150,0.474,0.13819622465625728,0.17733333333333334,0.06152412025168958,0.17333333333333334,0.6933115823817292,0.10533333333333333,0.049638778839431366,0.027333333333333334,0.0013982754602656724,0.042666666666666665,0.05593101841062689,1.0664852015847122,0.9977910325594677,0.8756542441482401,48,False,0.7933333333333333,0.18,0.78,0.5466666666666666,17.333333333333336,69.33115823817292,1268.5,3523.0
+locoL_fullsat_s40000_K1000,Abd-S42,adult_sepsis,1500,6567,150,0.6546666666666666,0.5748439165524593,0.09,0.09760925841327851,0.10533333333333333,0.17039744175422566,0.12066666666666667,0.05862646566164154,0.020666666666666667,0.0016750418760469012,0.008666666666666666,0.0968478757423481,0.32170915181970455,0.2811971753944427,0.8824917915725878,16,False,0.8,0.38,0.8933333333333333,0.6333333333333333,10.533333333333333,17.039744175422566,1606.0,1982.0
+locoL_fullsat_s40000_K1000,Abd-S47,adult_sepsis,1500,7971,150,0.712,0.7027976414502571,0.252,0.20474219044034625,0.0006666666666666666,0.03224187680341237,0.028,0.019069125580228326,0.0006666666666666666,0.0006272738677706687,0.006666666666666667,0.040521891857985194,0.13086087065612848,0.5066504444101315,0.8757193077876346,5,False,0.8066666666666666,0.3333333333333333,0.9266666666666666,0.5666666666666667,0.06666666666666667,3.224187680341237,2195.5,2030.0
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paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/locoL_fullsat_s40000_K1000/summary.json

@@ -0,0 +1,767 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-03T09:43:34.119828+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "ye2026_sepsis",
+  "--threads",
+  "8",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/ye2026_sepsis/usable_samples.txt",
+  "--arm",
+  "locoL_fullsat_s40000_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/hoL_ye2026_sepsis/K1000_fullsat_s40000.npz",
+  "--case-groups",
+  "adult_sepsis,ped_sepsis",
+  "--control-groups",
+  "adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/locoL_fullsat_s40000_K1000"
+ ],
+ "arms": [
+  "locoL_fullsat_s40000_K1000"
+ ],
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC01",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
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