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/matched_similarity.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "matched_similarity",
+  "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/c_matched_cells.csv",
+      "sha256": "c9a11f581c9401787c965564f4eb3cfdf74671d4edae9bd9388cafb1c0d0d22f",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Original model-output comparisons over 160,500 paired generated cells. Expression-correlation whiskers show saved 25th\u201375th percentiles, not confidence intervals. All comparisons are against the pseudobulk-conditioned twin, not observed individual cells.",
+  "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/nearest_real_by_type.csv

@@ -0,0 +1,37 @@
+set,label,n,median_distance_to_nearest_real,own_label_equals_nearest_real_label,inside_a_real_knn10_ball
+R2,T cell,10241,7.6436944007873535,0.9875988672981154,0.9547895713309248
+R2,B cell,1176,7.6080322265625,0.995748299319728,0.9702380952380952
+R2,Monocyte,2686,7.860072374343872,0.9791511541325392,0.9817572598659716
+R2,NK cell,1466,9.726799011230469,0.9386084583901774,0.9788540245566166
+R2,DC,398,7.07434868812561,0.864321608040201,0.9723618090452262
+R2,Other,83,9.571868896484377,0.3734939759036144,0.891566265060241
+raw,T cell,6885,11.58504581451416,0.8671023965141612,0.4066811909949165
+raw,B cell,1848,10.121495723724363,0.988095238095238,0.6396103896103896
+raw,Monocyte,4904,12.356744289398192,0.9661500815660684,0.2683523654159869
+raw,NK cell,1453,15.346506118774414,0.860977288368892,0.2353750860289057
+raw,DC,405,11.44858169555664,0.8493827160493828,0.2641975308641975
+raw,Other,555,19.846160888671875,0.445045045045045,0.1441441441441441
+tpm,T cell,7194,8.866299629211426,0.904642757853767,0.9056157909368918
+tpm,B cell,1244,8.22077465057373,0.997588424437299,0.905144694533762
+tpm,Monocyte,5505,9.450777053833008,0.9782016348773842,0.8773841961852861
+tpm,NK cell,1150,10.57656192779541,0.9365217391304348,0.9356521739130436
+tpm,DC,392,9.16024398803711,0.7321428571428571,0.7576530612244898
+tpm,Other,565,18.535573959350582,0.7469026548672566,0.3398230088495575
+refcal,T cell,9650,8.418823719024658,0.9642487046632124,0.792538860103627
+refcal,B cell,1446,9.147107124328612,0.9840940525587828,0.7648686030428768
+refcal,Monocyte,2837,10.578010559082031,0.974973563623546,0.6764187522030314
+refcal,NK cell,1643,11.875550270080566,0.910529519172246,0.844796104686549
+refcal,DC,315,11.024505615234377,0.7111111111111111,0.3968253968253968
+refcal,Other,159,13.993246078491213,0.4779874213836478,0.6415094339622641
+cal,T cell,11071,8.058467864990234,0.9438171800198716,0.9248487038207932
+cal,B cell,1393,8.214213371276855,0.9949748743718592,0.9038047379755922
+cal,Monocyte,2198,9.951960563659668,0.967242948134668,0.9276615104640582
+cal,NK cell,878,10.317323207855225,0.9316628701594531,0.9441913439635536
+cal,DC,244,9.53995418548584,0.6885245901639344,0.7909836065573771
+cal,Other,266,14.220920085906982,0.4360902255639097,0.7330827067669173
+pseudo,T cell,11310,7.798349857330322,0.9579133510167992,0.9297082228116712
+pseudo,B cell,801,8.086943626403809,0.9950062421972534,0.8913857677902621
+pseudo,Monocyte,2300,9.790095329284668,0.9795652173913044,0.9347826086956522
+pseudo,NK cell,1133,10.258471488952637,0.937334510150044,0.944395410414828
+pseudo,DC,239,9.40267276763916,0.6569037656903766,0.8410041841004184
+pseudo,Other,267,14.418207168579102,0.5355805243445693,0.7265917602996255

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/nearest_real_by_type.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "nearest_real_by_type",
+  "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/f7_nearest_real_by_type.csv",
+      "sha256": "b7e5acbe9ade06535d4f8bbcbc9a650df25707479fda03a853e110167de7ec34",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Saved PCA50 nearest-reference-cell metrics from 150 cells/donor. Different cell types have different geometry; distances are not calibrated probabilities or donor-level effect estimates.",
+  "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/raw_tpm_top_genes.csv

@@ -0,0 +1,21 @@
+cells,arm,direction,rank,symbol,gene_id,union_exon_kb,output_shift,input_shift,other_arm_output_shift
+label-stable matched cells,raw,down in raw cells vs pseudo twins,1,IFITM1,ENSG00000185885,1.08,-1.5725529161334473,-2.585398299671779,-0.3437928129545444
+label-stable matched cells,raw,down in raw cells vs pseudo twins,2,BTF3,ENSG00000145741,2.467,-1.2521028625553434,-0.651233427992491,-0.0948408535503028
+label-stable matched cells,raw,down in raw cells vs pseudo twins,3,COMMD6,ENSG00000188243,2.897,-1.2510208264179263,-2.185552106839474,-0.3215573892423115
+label-stable matched cells,raw,down in raw cells vs pseudo twins,4,TUBA1A,ENSG00000167552,3.421,-1.1385035542594228,0.266152087773118,-0.2605234864395536
+label-stable matched cells,raw,down in raw cells vs pseudo twins,5,RPL39,ENSG00000198918,2.141,-1.1197463558575371,-2.363167584499466,-0.2828646459880258
+label-stable matched cells,raw,up in raw cells vs pseudo twins,5,MT-ND6,ENSG00000198695,0.525,1.2308465669963031,-0.9195444115968509,0.6261344130014501
+label-stable matched cells,raw,up in raw cells vs pseudo twins,4,IQSEC1,ENSG00000144711,8.55,1.3214789205164708,2.40285418858038,0.436126209345167
+label-stable matched cells,raw,up in raw cells vs pseudo twins,3,MGEA5,ENSG00000198408,7.247,1.385230111308168,1.8090889297913169,0.3797698318767292
+label-stable matched cells,raw,up in raw cells vs pseudo twins,2,AKNA,ENSG00000106948,10.601,1.604515057448816,2.729554581864972,0.4893891759464839
+label-stable matched cells,raw,up in raw cells vs pseudo twins,1,LENG8,ENSG00000167615,6.469,1.656926229746484,3.1316871776759068,0.4025460174853204
+label-stable matched cells,tpm,down in tpm cells vs pseudo twins,1,RPS17,ENSG00000182774,3.293,-0.5551961449908446,-3.782572021793853,-1.0624473694110772
+label-stable matched cells,tpm,down in tpm cells vs pseudo twins,2,CRIP1,ENSG00000213145,2.485,-0.4680976945762464,-3.354657587983173,-0.8429458245901846
+label-stable matched cells,tpm,down in tpm cells vs pseudo twins,3,EEF1G,ENSG00000254772,2.716,-0.466585639140489,-7.741077173536069,-0.28625077026305
+label-stable matched cells,tpm,down in tpm cells vs pseudo twins,4,LTB,ENSG00000227507,1.535,-0.4213383375477024,-0.5227103831837993,-0.2057780183445679
+label-stable matched cells,tpm,down in tpm cells vs pseudo twins,5,NME2,ENSG00000243678,2.632,-0.3889428771801372,-6.00831588543428,-0.9082141200804744
+label-stable matched cells,tpm,up in tpm cells vs pseudo twins,5,IQSEC1,ENSG00000144711,8.55,0.436126209345167,1.3306738882271147,1.3214789205164708
+label-stable matched cells,tpm,up in tpm cells vs pseudo twins,4,NKG7,ENSG00000105374,0.935,0.4581244429371178,-0.1083350602153446,0.4918147729412607
+label-stable matched cells,tpm,up in tpm cells vs pseudo twins,3,AKNA,ENSG00000106948,10.601,0.4893891759464839,1.441767688940078,1.604515057448816
+label-stable matched cells,tpm,up in tpm cells vs pseudo twins,2,ZEB2,ENSG00000169554,25.058,0.512557678168108,-1.1798452951213787,0.8540228925489958
+label-stable matched cells,tpm,up in tpm cells vs pseudo twins,1,MT-ND6,ENSG00000198695,0.525,0.6261344130014501,0.7879516808745239,1.2308465669963031