Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-palette-142/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/final_palette_20261013/native/gene_length_stable.provenance.json

@@ -0,0 +1,31 @@
+{
+  "key": "gene_length_stable",
+  "source_records": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json",
+      "sha256": "45e6836942e894e51cfba5e4f9925a0d8affa9bbe95f1adebaf87af2830adf1b",
+      "role": "historical input/control provenance"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md",
+      "sha256": "83ec5eec39f15ccb7615da81c4b8f6345563b3a224934f3f942d29bf87b9054c",
+      "role": "historical scope and limitations"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_gene_shift_vs_length.csv",
+      "sha256": "832985e744403426022aa0af81c730a622aaf7eae160fb50ad43de3021b3fddc",
+      "role": "saved analysis input"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_length_stats.csv",
+      "sha256": "612298d51b6d0604c19536b087acc0ee22150c0297ac6afeb1d6b9db6806af8a",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Only log10 axis conversion and plotting of saved per-gene shifts. The displayed Spearman values come directly from g_length_stats.csv; no correlation or regression is recomputed. Label-stable means the frozen broad label agrees between generated twins; it does not establish identical biological state. Y values are generated log1p CP10K differences.",
+  "palette": "native"
+}

paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-palette-142/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/final_palette_20261013/native/healthy_ft_comparison.csv

@@ -0,0 +1,5 @@
+dataset,call,arm,label,n_donors,comp_l1,coverage,precision,source_summary,logfc_r,n_case,n_control,source_contrast
+immicro,pooled,zs__raw,"zero-shot, real bulk",107,0.4548664935416326,0.1918380062305296,0.6804361370716511,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,
+immicro,pooled,zs__cal,zero-shot + calibration,107,0.19850275515696958,0.527227414330218,0.9050467289719626,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,
+immicro,pooled,real_full__raw,full FT,107,0.1572206245036138,0.6953894080996885,0.8895327102803738,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,
+immicro,pooled,real_lora__raw,LoRA FT (r 16),107,0.16172890350786212,0.7842990654205607,0.9241121495327103,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,

paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-palette-142/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/final_palette_20261013/native/healthy_ft_comparison.json

@@ -0,0 +1,84 @@
+{
+  "schema": "pbisc.figure-order.healthy-ft.v1",
+  "dataset": "immicro",
+  "call": "pooled",
+  "n_donors": 107,
+  "source_csv": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec07_ft_modes_accuracy.csv",
+    "sha256": "cc64f2d52ae952ac69f04647d096fe2657715f7144f59059bdd9e503058795e5"
+  },
+  "source_summary": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json",
+    "sha256": "6d168fc230f5afe2d0a7395dad811aea615cae1778200694ce740b7cd0765068"
+  },
+  "source_style": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/style.py",
+    "sha256": "0d17caf276ae0e9b25285b8fd8f9b75c55621ad3a36382b705a366f327c89de6"
+  },
+  "builder": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/figure_order_healthy_ft_20261013.py",
+    "sha256": "0dcacfcf79dde8417fc5c03b17b43d5e4b378e11b079e7862927010b1a491b6c"
+  },
+  "arms": [
+    "zs__raw",
+    "zs__cal",
+    "real_full__raw",
+    "real_lora__raw"
+  ],
+  "labels": [
+    "Zero-shot \u00b7 raw bulk",
+    "Zero-shot \u00b7 paired calibration",
+    "Full fine-tuning",
+    "LoRA \u00b7 rank 16"
+  ],
+  "source_numeric_strings": [
+    {
+      "precision": "0.6804361370716511",
+      "coverage": "0.1918380062305296",
+      "comp_l1": "0.4548664935416326"
+    },
+    {
+      "precision": "0.9050467289719626",
+      "coverage": "0.527227414330218",
+      "comp_l1": "0.19850275515696958"
+    },
+    {
+      "precision": "0.8895327102803738",
+      "coverage": "0.6953894080996885",
+      "comp_l1": "0.1572206245036138"
+    },
+    {
+      "precision": "0.9241121495327103",
+      "coverage": "0.7842990654205607",
+      "comp_l1": "0.16172890350786212"
+    }
+  ],
+  "validation": {
+    "csv_rows_exact_string_match": true,
+    "max_abs_difference_from_source_summary": 0.0,
+    "summary_donor_ids_unique": true
+  },
+  "csv": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/final_palette_20261013/native/healthy_ft_comparison.csv",
+    "sha256": "c3372e0f8eace550d4e5ad4557c4db20e9dabb69762fd941513fb6e18ea000ef"
+  },
+  "figures": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/final_palette_20261013/native/healthy_ft_comparison.png",
+      "sha256": "9a636e03e19901ac85414f7f0362c45c3a8563a4317aab027d78476b1654a83b"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/final_palette_20261013/native/healthy_ft_comparison.pdf",
+      "sha256": "39f9a4a509e2f62e47a72f7b23067d4e33186e370a2862afe85ae39d0e3a7ce9"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/final_palette_20261013/native/healthy_ft_comparison.svg",
+      "sha256": "f979782b53e1d521cf468e4cea303c7a07b919defa7a9c2bda8aed347c939feb"
+    }
+  ],
+  "protocol": "Historical donor-disjoint five-fold real-bulk adaptation, pooled scoring over 107 donors; not exact-five-pair adaptation.",
+  "interpretation": "LoRA has higher precision and coverage here; full FT has slightly lower composition L1. No universal-best claim or new uncertainty estimates.",
+  "new_statistics": false,
+  "new_training": false,
+  "new_inference": false
+}

paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-palette-142/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/final_palette_20261013/native/refcal_top_genes.csv

@@ -0,0 +1,21 @@
+cells,arm,direction,rank,symbol,gene_id,union_exon_kb,output_shift,input_shift,raw_output_shift,cal_output_shift
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,10,NR4A2,ENSG00000153234,3.967,-1.7099507578543092,-3.747405620956164,-0.6497955853383699,-0.019110186207829
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,9,CD69,ENSG00000110848,2.832,-1.7553867180155165,-2.4549292843854293,-0.441061017216728,-0.0265424458941048
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,8,NFKBIA,ENSG00000100906,2.373,-1.765359573740606,-2.75043550752636,-0.2238833514368488,-0.0177685615002193
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,7,PPP1R15A,ENSG00000087074,3.093,-1.7840327944979937,-2.3508982714415767,-0.5316266800931838,-0.0850439949551769
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,6,JUN,ENSG00000177606,3.54,-1.8544207023151529,-1.4083671060910583,-0.338395371218614,-0.1545073660803181
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,5,JUNB,ENSG00000171223,1.82,-2.0224678679713275,-1.543059882003048,-0.3035307753075741,-0.1898579399228887
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,4,TNFAIP3,ENSG00000118503,5.051,-2.1603072196288333,-3.516027490367262,-0.0853436410312287,-0.011499514255347
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,3,ZFP36,ENSG00000128016,2.01,-2.2033196431967417,-2.746605785171068,-0.5224836216049965,-0.0507004779071335
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,2,DUSP1,ENSG00000120129,2.019,-2.619406068222085,-2.066717958474761,-0.2533739497502009,-0.1504314792553572
+label-stable matched cells,refcal,down in refcal cells vs pseudo twins,1,FOS,ENSG00000170345,3.238,-2.82975153975305,-1.850633576688784,-0.4481117723715087,-0.1764956170750179
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,10,RPL7,ENSG00000147604,2.907,0.5888734686140678,0.2369741325009993,-0.1340632112836222,0.0499127167327607
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,9,RPS2,ENSG00000140988,2.413,0.6044776346257065,0.4659514405564494,-0.2156619436592053,-0.0233519658003281
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,8,RPS10,ENSG00000124614,2.358,0.691031996453968,2.3167234179889067,0.0285963989494689,-0.1836621524161317
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,7,MT-ND3,ENSG00000198840,0.346,0.7069896706683573,1.1033343778869458,0.1160763934963651,0.1303762103236706
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,6,RPS11,ENSG00000142534,1.39,0.7832710546892406,0.7503209378720073,-0.0548915329742141,0.0032640849545758
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,5,RPL13A,ENSG00000142541,2.369,0.8046548776862195,0.2962825124248627,-0.126726233101684,0.1414946512118404
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,4,RPL21,ENSG00000122026,2.249,0.981787741037122,0.329097744854787,-0.6679435267789742,0.1176873322053766
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,3,RPL27A,ENSG00000166441,7.193,0.9832179081882356,0.7082454735339524,-0.4012565577044767,0.0138910736263836
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,2,RPS29,ENSG00000213741,9.845,0.9928676975801648,1.322817147310854,-0.3414590249422447,0.0693163275653325
+label-stable matched cells,refcal,up in refcal cells vs pseudo twins,1,RPS20,ENSG00000008988,3.002,1.1637413724980583,0.6466043169668007,0.1051422001514115,0.1319503366960606