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/stored_real_reference_umap.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "stored_real_reference_umap",
+  "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/interactive/cells_5arm.json",
+      "sha256": "e0a1094d29213b93e05de8c60b3ea1e0581ab0e09599bb6b7506491744019e99",
+      "role": "previously computed display coordinates; no embedding recalculated"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Replots only the stored interactive coordinates: 3,000 displayed cells per set. The reference PCA/UMAP was previously fitted to real R1. UMAP overlap is illustrative, not a score. Cell-type colors are preserved; no new labels or embedding were computed. Shared display bounds cover all saved coordinates plus 2.5% padding; the narrower old illustrative extent is not reused.",
+  "palette": "preserved"
+}

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/within_type_centroids.csv

@@ -0,0 +1,7 @@
+label,n_real,real_rms_spread,n_R2,shift_R2,n_raw,shift_raw,n_tpm,shift_tpm,n_refcal,shift_refcal,n_cal,shift_cal,n_pseudo,shift_pseudo,shift_raw_vs_pseudo,shift_tpm_vs_pseudo,shift_refcal_vs_pseudo,shift_cal_vs_pseudo
+T cell,10293,11.611624717712402,10241,0.0090545518323779,6885,1.0201950073242188,7194,0.5216308236122131,9650,0.9803290367126464,11071,0.4392106235027313,11310,0.423985868692398,0.8934692144393921,0.3567348718643188,0.8317427635192871,0.1248010769486427
+B cell,1180,9.525594711303713,1176,0.0384473428130149,1848,0.9928197860717772,1244,0.6196037530899048,1446,1.2297292947769165,1393,0.6523134708404541,801,0.6281290054321289,0.8512012362480164,0.2936421036720276,0.9266708493232728,0.1175385266542434
+Monocyte,2627,12.126893043518066,2686,0.0248905830085277,4904,1.0864726305007937,5505,0.6679170727729797,2837,1.1247648000717163,2198,0.783256471157074,2300,0.7908310294151306,0.928920328617096,0.3260526657104492,0.7034335136413574,0.1154429093003273
+NK cell,1475,11.624979972839355,1466,0.0346957445144653,1453,1.3561201095581057,1150,0.5441815853118896,1643,1.0703318119049072,878,0.5162788033485413,1133,0.499572217464447,1.202769756317139,0.3338935077190399,0.8430509567260742,0.1200951039791107
+DC,379,13.729815483093262,398,0.0670090913772583,405,0.7867857217788696,392,0.541755199432373,315,0.9739965200424194,244,0.6239253282546997,239,0.6165397763252258,0.6674318909645081,0.2436918765306472,0.6669383645057678,0.1537077128887176
+Other,96,13.91608715057373,83,0.1536894738674163,555,1.866940259933472,565,1.7118107080459597,159,1.081559181213379,266,0.9476239681243896,267,0.9566375613212584,0.990407168865204,0.7845920920372009,0.434954971075058,0.1227873340249061

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/within_type_centroids.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "within_type_centroids",
+  "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/b_type_centroid_shift_l1.csv",
+      "sha256": "53dd45f6dc65b3ba09edb773f427ce62e5568d764adfd45d25c1a23b553cd365",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Centroids and real within-type RMS normalization are previously computed. No new embedding, centroids or annotation are fitted. Six broad types; small Other/DC groups require caution.",
+  "palette": "native"
+}