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/annotation_agreement.csv

@@ -0,0 +1,9 @@
+author_gate[manual.celltype] \ frozen,T cell,B cell,Monocyte,NK cell,DC,Other,T cell_row_percent,B cell_row_percent,Monocyte_row_percent,NK cell_row_percent,DC_row_percent,Other_row_percent
+T cell,229299,13,362,213,62,573,99.46946495345347,0.005639374983732572,0.15703490339316856,0.09239899011807984,0.02689548069164765,0.2485662973599049
+B cell,267,27308,103,41,18,44,0.961088513732407,98.29739750188978,0.37075699218890606,0.14758288038587525,0.06479248407184766,0.15838162773118317
+Monocyte,390,16,58311,50,884,133,0.6523484544359694,0.026763013515321826,97.53613006824568,0.0836344172353807,1.4786564967215308,0.22246754984611267
+NK cell,4085,0,39,32561,12,306,11.039645434153988,0.0,0.10539685971407724,87.99556792692485,0.03242980298894684,0.8269599762181445
+DC,112,13,873,19,7564,21,1.3020227853987445,0.15112764473378285,10.14880260404557,0.22087886538014415,87.93303882817949,0.2441292722622646
+Other,1272,3,243,166,5,23,74.29906542056075,0.17523364485981308,14.19392523364486,9.69626168224299,0.29205607476635514,1.3434579439252337
+author_mixed,1534,819,2289,425,141,105,28.872576698663654,15.41501976284585,43.08300395256917,7.999247129681912,2.6538678712591754,1.9762845849802373
+author_unlabelled,13606,714,3819,2146,253,996,63.183802359060095,3.3156868208414596,17.734745054332684,9.965635738831615,1.174886226432618,4.625243800501532

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/annotation_agreement.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "annotation_agreement",
+  "source_records": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/build_manifest.json",
+      "sha256": "90c9f650705cf0beb1e33f41d6cfad12ecb99d183c17090f206f9e8b245ef785",
+      "role": "frozen annotation comparison provenance"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/confusion_author_vs_frozen_baseline.csv",
+      "sha256": "487ec0dd8b6f470987dda04337a7d3485f0229bf8d787507e3745d95ae9ae434",
+      "role": "saved analysis input"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/observed_summary.json",
+      "sha256": "c3f113fd18f54113cc011886490b1664b1e40a8f35bc89f5ba007fb49ce4ae50",
+      "role": "saved analysis metadata"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Saved observed-cell comparison, not generated-cell model performance. Overall 97.17% agreement uses 365,404 author-labelled cells in the supported six-type gate; mixed/unlabelled categories are displayed in the matrix but excluded from that agreement figure. Other has weak correspondence between taxonomies. The frozen annotation's comparison to author labels is not an independent gold-standard validation. Heatmap is a count-row normalization for display; precision/recall are saved summary metrics.",
+  "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/depth_matched_quality.csv

@@ -0,0 +1,25 @@
+arm,metric,depth,value
+R2,precision,native,0.9627414330218068
+R2,precision,matched,0.954018691588785
+raw,precision,native,0.3630529595015576
+raw,precision,matched,0.420809968847352
+tpm,precision,native,0.8745171339563863
+tpm,precision,matched,0.892398753894081
+refcal,precision,native,0.765607476635514
+refcal,precision,matched,0.778380062305296
+cal,precision,native,0.9192523364485982
+cal,precision,matched,0.9421806853582556
+pseudo,precision,native,0.924859813084112
+pseudo,precision,matched,0.9467289719626168
+R2,coverage,native,0.9997507788161992
+R2,coverage,matched,0.9997507788161992
+raw,coverage,native,0.083613707165109
+raw,coverage,matched,0.1437383177570093
+tpm,coverage,native,0.4595015576323987
+tpm,coverage,matched,0.6109034267912773
+refcal,coverage,native,0.0806853582554517
+refcal,coverage,matched,0.1939563862928349
+cal,coverage,native,0.5200623052959501
+cal,coverage,matched,0.7796884735202492
+pseudo,coverage,native,0.5068535825545172
+pseudo,coverage,matched,0.74797507788162