Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T095445Z-all-width-results/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold3/n10/score/arms/lora/labels/labels.manifest.json

@@ -0,0 +1,156 @@
+{
+  "dataset_id": "GSE314416_ImMicro",
+  "split": "generated",
+  "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold3/n10/score/arms/lora/query.h5ad",
+  "method": "lora",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold3/n10/score/arms/lora/labels/labels.parquet",
+  "training_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/reference/aifi_reference_f01common.h5ad",
+  "target_truth_used_for_fitting": false,
+  "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
+  "labels": [
+    "T cell",
+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
+    "Other"
+  ],
+  "l2_labels": [
+    "ASDC",
+    "CD14 monocyte",
+    "CD16 monocyte",
+    "CD56bright NK cell",
+    "CD56dim NK cell",
+    "CD8aa",
+    "DN T cell",
+    "Effector B cell",
+    "Erythrocyte",
+    "ILC",
+    "Intermediate monocyte",
+    "MAIT",
+    "Memory B cell",
+    "Memory CD4 T cell",
+    "Memory CD8 T cell",
+    "Naive B cell",
+    "Naive CD4 T cell",
+    "Naive CD8 T cell",
+    "Plasma cell",
+    "Platelet",
+    "Progenitor cell",
+    "Proliferating NK cell",
+    "Proliferating T cell",
+    "Transitional B cell",
+    "Treg",
+    "cDC1",
+    "cDC2",
+    "gdT",
+    "pDC"
+  ],
+  "n_cells": 31500,
+  "n_genes": 1005,
+  "note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
+  "label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
+  "query_train_epochs": 0,
+  "confidence_threshold": 0.0,
+  "subset": false,
+  "evaluator_aligned": true,
+  "gene_space": {
+    "join_key": "ensembl_id",
+    "model_genes": 1005,
+    "query_genes": 1004,
+    "model_genes_missing_from_query_zero_padded": 1,
+    "query_genes_outside_model_dropped": 0,
+    "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
+  },
+  "readout": null,
+  "query_build": {
+    "kind": "generated_npz",
+    "poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
+    "readout": "poisson",
+    "seed": 20260916,
+    "set": "lora",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold3/n10/lora.npz",
+    "source_sha256": "2c5af0871471ce923832404cb26734abd7d4926d07133a8405c6d130a1dd128f"
+  },
+  "model": {
+    "scanvi_model_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_model",
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "model_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/MODEL_MANIFEST.json",
+    "held_out_summary": {
+      "l2_accuracy": 0.8692869740488788,
+      "l2_macro_f1": 0.8500925599737216,
+      "l1_accuracy": 0.9918367346938776,
+      "l1_macro_f1": 0.9715232379009036,
+      "pbmc5_other_accuracy": 0.9920886873267826,
+      "pbmc5_other_macro_f1": 0.9812088972148597
+    }
+  },
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 20332,
+      "Monocyte": 5204,
+      "B cell": 2705,
+      "NK cell": 2186,
+      "DC": 767,
+      "Other": 306
+    },
+    "aifi_l1": {
+      "T cell": 20332,
+      "Monocyte": 5204,
+      "B cell": 2705,
+      "NK cell": 2186,
+      "DC": 767,
+      "ILC": 256,
+      "Progenitor cell": 36,
+      "Erythrocyte": 10,
+      "Platelet": 4
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 5624,
+      "Naive CD4 T cell": 5292,
+      "CD14 monocyte": 3448,
+      "Memory CD8 T cell": 2421,
+      "Naive CD8 T cell": 2400,
+      "gdT": 2267,
+      "Memory B cell": 2209,
+      "CD56dim NK cell": 1369,
+      "CD16 monocyte": 1094,
+      "Treg": 999,
+      "Intermediate monocyte": 662,
+      "CD8aa": 630,
+      "CD56bright NK cell": 625,
+      "cDC2": 601,
+      "MAIT": 569,
+      "ILC": 256,
+      "Naive B cell": 245,
+      "Proliferating NK cell": 192,
+      "Effector B cell": 181,
+      "DN T cell": 109,
+      "pDC": 100,
+      "Plasma cell": 42,
+      "cDC1": 40,
+      "Progenitor cell": 36,
+      "Transitional B cell": 28,
+      "ASDC": 26,
+      "Proliferating T cell": 21,
+      "Erythrocyte": 10,
+      "Platelet": 4
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9200797791518862,
+    "mean_l1_mass": 0.984683632850647,
+    "frac_l2_max_prob_ge_0.5": 0.9781269841269842
+  },
+  "timings_s": {
+    "predict": 0.2,
+    "total": 0.5
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-15T09:51:15.401510+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261015T095445Z-all-width-results/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold3/n40/score/README.md

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+# score_ft.py output: immicro, 21 scored donors
+
+Arms: lora.  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 (--no-contrast).
+   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 (--no-deg).
+
+## 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/20261015T095445Z-all-width-results/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold3/n40/score/per_donor.csv

@@ -0,0 +1,22 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
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paper-releases/pbisc-diffusion/updates/20261015T095445Z-all-width-results/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold3/n40/score/summary.json

@@ -0,0 +1,213 @@
+{
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