Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/healthy/reference_choice.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "reference_choice",
+  "source_records": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv",
+      "sha256": "148c124ae96644f8c1228a036b56fe2cd824d19be90accb338a27ca347bd7680",
+      "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/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"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "All eight generated arms are already scored in immicro_table.csv. No generation or rescore. AIDA and the training-mixture reference have their own pretraining overlap; this is not a held-out reference experiment. The composition dashed line is the observed donor-mean leave-one-out null, NOT a real-R2 composition error. No method-independent win claim is made across different endpoints.",
+  "palette": "native"
+}

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/healthy/saved_density_difference.provenance.json

@@ -0,0 +1,24 @@
+{
+  "key": "saved_density_difference",
+  "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/figures/fig2_density_difference.png",
+      "sha256": "e3ac6ac104102d4d7d0c6bfe57bf19482114131f028136b9a16bc4d2ffc78a77",
+      "role": "existing high-resolution quantitative density figure"
+    }
+  ],
+  "unchanged_png_copy": true,
+  "no_density_or_embedding_recomputation": true,
+  "palette": "preserved",
+  "readability_note": "Full-width reference; small original panel labels may require zoom."
+}

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/healthy/sle_conditioning_interventions.csv

@@ -0,0 +1,5 @@
+comparison,panel_genes,celltype_gate,gate_celltypes,truth_label_source,method,composition_mae,composition_l1,composition_pearson,pred_pbmc5_fraction,mean_logFC_pearson,n_celltypes,mean_top50_overlap,total_top50_overlap,mean_top50_jaccard,metrics_dir
+diffusion_f016k_e16,2279,common_celltype_gate,B cell;DC;Monocyte;NK cell;Other;T cell,parquet_override,diffusion_f016k_e16,0.0301901366637155,0.1811408199822934,0.9822149278577628,1.0,0.3548047163709348,6,14.0,84,0.1801377937655689,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_2279/panel_2980_diffusion_f016k_e16/pbmc5_other
+diffusion_f016kcondflip_e16,2279,common_celltype_gate,B cell;DC;Monocyte;NK cell;Other;T cell,parquet_override,diffusion_f016kcondflip_e16,0.0690572316031314,0.4143433896187887,0.9177391257173888,1.0,-0.3333160314603471,6,0.0,0,0.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_2279/panel_2980_diffusion_f016kcondflip_e16/pbmc5_other
+diffusion_f016kcondperm_e16,2279,common_celltype_gate,B cell;DC;Monocyte;NK cell;Other;T cell,parquet_override,diffusion_f016kcondperm_e16,0.0716315528047591,0.4297893168285545,0.9003540447841814,1.0,0.1925891289040404,6,0.0,0,0.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_2279/panel_2980_diffusion_f016kcondperm_e16/pbmc5_other
+diffusion_f016kcondmean_e16,2279,common_celltype_gate,B cell;DC;Monocyte;NK cell;Other;T cell,parquet_override,diffusion_f016kcondmean_e16,0.0538021821300815,0.3228130927804896,0.9370572924976324,1.0,0.0122178968539317,6,0.3333333333333333,2,0.0037037037037037,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_2279/panel_2980_diffusion_f016kcondmean_e16/pbmc5_other

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/healthy/sle_conditioning_interventions.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "sle_conditioning_interventions",
+  "source_records": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/conditioning_2279/RESULTS.md",
+      "sha256": "997d10e190903c8a95672e10f185c9a9947e4e8716fc1dd65eda2c86b9639ae1",
+      "role": "existing intervention protocol and provenance"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/conditioning_2279/paired_cells.csv",
+      "sha256": "1aa12132a96e8cdaa4e2902a146e4dea6133ac37d855347591596d9b47631ab4",
+      "role": "saved analysis input"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_2279/summary_tidy.csv",
+      "sha256": "69fc8b5f435d39f0523ace047f0c09658de3e4cd25a46553e661bf4a0c23b0d2",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "SLE development benchmark: 42 donors, 2,279 genes, f01 6k E16 EMA, 1,500 generated cells/donor, 50 DDIM steps, seed20260913. Only conditioning differs; noise is matched. These are pseudobulk inputs, not an independent paired real-bulk validation. Donor-source caption uses saved uncentered nearest-match counts; centered flip retrieval is 27/42, permutation42/42. Displayed benchmark metrics use the common six-type gate. The pre-registered condition-use criterion and earlier-model tolerance context are in source RESULTS.md.",
+  "palette": "native"
+}