Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold2/summary.json

@@ -0,0 +1,207 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "immicro",
+ "written_utc": "2026-10-05T12:05:47.298024+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",
+  "immicro",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold2",
+  "--threads",
+  "8",
+  "--arm",
+  "scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold2/scsemi__raw.npz"
+ ],
+ "arms": [
+  "scsemi__raw"
+ ],
+ "donors": [
+  "HS9",
+  "HS14",
+  "HS19",
+  "HS24",
+  "HS25",
+  "HS26",
+  "HS32",
+  "HS42",
+  "HS43",
+  "HS50",
+  "HS55",
+  "HS59",
+  "HS67",
+  "HS71",
+  "HS73",
+  "HS80",
+  "HS91",
+  "HS102",
+  "HS105",
+  "HS108",
+  "HS111"
+ ],
+ "n_donors": 21,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/immicro",
+  "reference_sha256": "c5e2547be3ec3b12cb0c0b404a49e14a046ae59d40be70427f98f083a76bce17",
+  "features_sha256": "735255066ce7ebbac13a1fdfd058e26f31edd60314cc02fd589b0a292dbbc838",
+  "n_r1_cells": 3150,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.30105969309806824,
+   "n_fit_cells": 3150
+  },
+  "r2_control": {
+   "precision": 0.9942857142857143,
+   "coverage": 1.0,
+   "density": 2.624730158730159,
+   "n_query": 3150,
+   "depth_matched": {
+    "precision": 0.993015873015873,
+    "coverage": 1.0,
+    "density": 2.614888888888889
+   }
+  },
+  "observed_l1_loo_null_mean": 0.15878727519531177
+ },
+ "contrast_definition": {
+  "enabled": false,
+  "reason": "dataset immicro has no group contrast (use --groups-csv / --case-groups)"
+ },
+ "deg_definition": {
+  "enabled": false,
+  "reason": "contrast off"
+ },
+ "headline": {
+  "scsemi__raw": {
+   "comp_l1": 0.22202490820818452,
+   "comp_l1_obs_loo_null": 0.15878727519531177,
+   "precision": 0.7955555555555556,
+   "coverage": 0.09587301587301587,
+   "precision_dm": 0.9012698412698412,
+   "coverage_dm": 0.37015873015873013,
+   "pb_r_median": 0.6776833291729408,
+   "pb_top1": 0.047619047619047616,
+   "mono_pct_gen": 12.358730158730163,
+   "mono_pct_obs": 16.087149423201815,
+   "median_umi_gen": 1961.0,
+   "median_umi_obs": 1958.0,
+   "seconds": 7.2
+  }
+ },
+ "per_arm": {
+  "scsemi__raw": {
+   "arm": "scsemi__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold2/scsemi__raw.npz",
+   "npz_sha256": "72c28ef0b2b4dc8fea58be02f7ba9e01301aaf235f1a718e3350ec975a69eb9f",
+   "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/immicro/fold2/test_raw.npz",
+    "input_condition_sha256": "35792517469285bed0fd17595441952e8f1880f63022e10db66e74dc36cd585f",
+    "seed": 20260927,
+    "steps": null,
+    "support_readout": "upstream (values <= 10 normalized units zeroed by fast_semi)",
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 3976665,
+    "median_library_whole_npz_panel": 1961.0,
+    "n_rows_whole_npz": 31500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 21595,
+     "Monocyte": 3893,
+     "B cell": 2135,
+     "DC": 1876,
+     "NK cell": 1836,
+     "Other": 165
+    },
+    "mean_l2_max_prob": 0.9210918675306298,
+    "predict_seconds": 3.6
+   },
+   "n_donors": 21,
+   "n_generated_cells": 31500,
+   "composition": {
+    "l1_mean": 0.22202490820818452,
+    "l1_median": 0.21270549084858564,
+    "l1_obs_loo_null_mean": 0.15878727519531177,
+    "l1_generated_loo_mean_vs_observed_mean": 0.2225870788132361,
+    "composition_top1": 0.09523809523809523,
+    "mean_fraction_generated": {
+     "T cell": 0.685556,
+     "B cell": 0.067778,
+     "Monocyte": 0.123587,
+     "NK cell": 0.058286,
+     "DC": 0.059556,
+     "Other": 0.005238
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.629402,
+     "B cell": 0.077358,
+     "Monocyte": 0.160871,
+     "NK cell": 0.105286,
+     "DC": 0.021663,
+     "Other": 0.005419
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.6776833291729408,
+    "r_mean": 0.6613002191971198,
+    "top1": 0.047619047619047616,
+    "n_top1": 1,
+    "own_rank_median": 6.0,
+    "chance_top1": 0.047619047619047616
+   },
+   "precision_coverage": {
+    "precision": 0.7955555555555556,
+    "coverage": 0.09587301587301587,
+    "density": 0.2326984126984127,
+    "n_query": 3150,
+    "n_reference": 3150
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9012698412698412,
+    "coverage": 0.37015873015873013,
+    "density": 0.7131746031746032,
+    "detected_median_before": {
+     "R1": 362.0,
+     "Q": 122.0
+    },
+    "detected_median_after": {
+     "R1": 122.0,
+     "Q": 122.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 12.358730158730163,
+    "observed_mean_over_donors": 16.087149423201815,
+    "generated_pooled_cells": 12.35873015873016
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 1961.0,
+    "observed_pooled": 1958.0,
+    "generated_mean_of_donor_medians": 1960.40478515625,
+    "observed_mean_of_donor_medians": 1985.452380952381
+   },
+   "seconds": 7.2
+  }
+ },
+ "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": 8.6
+}

paper-releases/pbisc-diffusion/updates/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold3/README.md

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+# score_ft.py output: immicro, 21 scored donors
+
+Arms: scsemi__raw.  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/immicro/reference.npz` (sha c5e2547be3ec), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro;
+  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/utility_studies_final6k_20260925/immicro/labels/observed_immicro/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 (1004 genes).
+- Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (5508 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 21 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) (3150 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 0.9940, coverage 1.0000.
+   **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
+   0.9927, coverage 1.0000.
+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): not computed (dataset immicro has no group contrast (use --groups-csv / --case-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`): not computed (contrast off).
+
+## 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/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold3/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
+scsemi__raw,HS1,DB1,1500,4384,150,0.7546666666666667,0.6332116788321168,0.03666666666666667,0.05862226277372263,0.10733333333333334,0.13822992700729927,0.042666666666666665,0.14393248175182483,0.05333333333333334,0.018476277372262775,0.005333333333333333,0.007527372262773723,0.31262408759124094,0.1477341288426135,0.6626382561598995,3,False,0.8133333333333334,0.17333333333333334,0.84,0.5466666666666666,10.733333333333334,13.822992700729927,1948.0,1738.0
+scsemi__raw,HS4,DB4,1500,4167,150,0.7073333333333334,0.54307655387569,0.04666666666666667,0.04535637149028078,0.14733333333333334,0.2371010319174466,0.05466666666666667,0.14254859611231102,0.04,0.02423806095512359,0.004,0.007679385649148068,0.3626580273578114,0.2034821822143433,0.6970694183106255,13,False,0.6533333333333333,0.08666666666666667,0.8466666666666667,0.26666666666666666,14.733333333333334,23.71010319174466,1946.5,2111.0
+scsemi__raw,HS10,DB4,1500,4115,150,0.6446666666666667,0.5244228432563791,0.108,0.18347509113001215,0.08066666666666666,0.13001215066828675,0.098,0.13754556500607534,0.058666666666666666,0.021385176184690158,0.01,0.0031591737545565005,0.3287322802754152,0.3134557004122763,0.6220858367793926,17,False,0.6533333333333333,0.013333333333333334,0.9,0.32,8.066666666666666,13.001215066828674,1947.0,2063.0
+scsemi__raw,HS15,DB4,1500,4592,150,0.6833333333333333,0.46972996515679444,0.046,0.04638501742160279,0.15133333333333332,0.37282229965156793,0.07666666666666666,0.08776132404181185,0.042,0.0195993031358885,0.0006666666666666666,0.0037020905923344947,0.4720081300813008,0.38777794593743353,0.7078659409180471,12,False,0.6933333333333334,0.05333333333333334,0.8933333333333333,0.25333333333333335,15.133333333333333,37.282229965156795,1948.0,2302.0
+scsemi__raw,HS23,DB6,1500,1680,150,0.6813333333333333,0.5630952380952381,0.04066666666666666,0.0994047619047619,0.13466666666666666,0.2386904761904762,0.07533333333333334,0.06904761904761905,0.06466666666666666,0.025,0.0033333333333333335,0.004761904761904762,0.32838095238095244,0.16257609013548865,0.7133429122476844,7,False,0.8533333333333334,0.06,0.86,0.32666666666666666,13.466666666666665,23.86904761904762,1948.0,2296.0
+scsemi__raw,HS29,DB5,1500,4285,150,0.646,0.6550758459743291,0.05266666666666667,0.03663943990665111,0.176,0.19883313885647608,0.056666666666666664,0.0823803967327888,0.066,0.022870478413068846,0.0026666666666666666,0.004200700116686115,0.11831349669389346,0.11412144983123255,0.6475910958971172,13,False,0.74,0.02,0.82,0.32,17.599999999999998,19.883313885647606,1948.0,2230.0
+scsemi__raw,HS30,DB3,1500,6447,150,0.652,0.5667752442996743,0.06533333333333333,0.08127811385140375,0.18466666666666667,0.26477431363424847,0.03266666666666666,0.049325267566309915,0.062,0.03489995346672871,0.0033333333333333335,0.002947107181634869,0.22542205677059096,0.20007609013548855,0.6828529833822351,1,True,0.7,0.07333333333333333,0.8466666666666667,0.5533333333333333,18.46666666666667,26.47743136342485,1947.0,2410.0
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paper-releases/pbisc-diffusion/updates/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold3/summary.json

@@ -0,0 +1,207 @@
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