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/depth_matched_quality.provenance.json

@@ -0,0 +1,31 @@
+{
+  "key": "depth_matched_quality",
+  "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/a_precision_coverage_pca50.csv",
+      "sha256": "e075020ca2d65bd82071eb102dabdd1f92d6bbca8c4604fa5e85e45afad83a70",
+      "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/e_depth_matched_precision_coverage_pca50.csv",
+      "sha256": "4866b172c49830720c740528a2ff3df7b4e18599a4ee91cc5b6b638409d83b82",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Both tables already exist. The matched-depth procedure thins all seven source sets to common detected-gene depth, as documented in the original analysis. Real R2 is a held-out real-real control; neighborhood k=10 only. Display hatching, not a new sensitivity run.",
+  "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/detection_and_library.csv

@@ -0,0 +1,8 @@
+input_arm,set,readout,n_cells,detected_median,detected_p10,detected_p90,library_median,zero_fraction
+R1,real_R1,counts>0,16050,361.0,265.0,535.0,1980.0,0.9303590133411158
+R2,real_R2,counts>0,16050,364.0,267.0,534.0,2004.0,0.9300460276414708
+raw,raw,Poisson counts>0 (as embedded and labelled),160500,331.0,162.0,499.0,1342.0,0.9396550370234628
+tpm,tpm,Poisson counts>0 (as embedded and labelled),160500,317.0,206.0,458.0,2184.0,0.9413131700816936
+refcal,refcal,Poisson counts>0 (as embedded and labelled),160500,248.0,191.0,349.0,2490.0,0.9527645961580664
+cal,cal,Poisson counts>0 (as embedded and labelled),160500,266.0,203.0,335.0,2302.0,0.9512745109350996
+pseudo,pseudo,Poisson counts>0 (as embedded and labelled),160500,269.0,209.0,337.0,2486.0,0.9506440035111772

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/detection_and_library.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "detection_and_library",
+  "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/e_detected_genes.csv",
+      "sha256": "350744d2458ce406e3c58e2c98322e33a545f626888db66c64a8328080769da0",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Observed counts and the previously computed Poisson readout of generated cells. Whiskers are saved 10th\u201390th cell percentiles, not donor confidence intervals. Scoring-gene libraries are not full-transcriptome UMI totals.",
+  "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/donor_axes.csv

@@ -0,0 +1,6 @@
+input_arm,arm,n_donors,n_cells,comp_L1_own,comp_L1_obs_LOO_null,comp_L1_gen_cohort_mean,comp_L1_other_donors,comp_top1,rho_T cell,rho_B cell,rho_Monocyte,rho_NK cell,rho_DC,rho_Other,gen_mean_T cell,gen_mean_B cell,gen_mean_Monocyte,gen_mean_NK cell,gen_mean_DC,gen_mean_Other,sex_auroc,sex_acc_obs_threshold,rho_y,rho_ifn_mono,rho_ifn_t,rho_klrc2_vs_obs_klrc2,rho_klrc2_vs_obs_adaptive,pb_r_median,pb_top1,pb_n_top1,other_aifi_l1,scores_json
+raw,raw_native,107,160500,0.4552049769720906,0.1606372707722086,0.4572788915379008,0.4920091241132451,0.0093457943925233,0.6042125890437116,0.5237435109650144,0.7274219074701594,0.4465366918780628,0.1908443241282212,0.1338652734653634,0.43188,0.11404,0.30398,0.09189,0.02613,0.03208,1.0,1.0,0.7159423797937028,0.3945120398126922,0.4357354180136758,0.0307563445096468,0.2545438069345692,0.8844332101706303,0.0654205607476635,7,"{'Erythrocyte': 2708, 'Platelet': 1799, 'ILC': 562, 'Progenitor cell': 80}",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/generated_scores/generated_ImMicro_raw_native/scores.json
+tpm,raw_tpm_native,107,160500,0.4558918621288965,0.1606372707722086,0.4579076444274909,0.4913233082259797,0.0093457943925233,0.5693810725281898,0.5964602058645968,0.7683886206107539,0.4281270392807118,0.2292164928721506,-0.0013672216150706,0.4504,0.07612,0.34069,0.07305,0.02454,0.03519,1.0,1.0,0.6785298004679714,0.4865495013617038,0.5756676267168244,0.0198777844623004,0.1495816720286051,0.8927475234768967,0.0467289719626168,5,"{'Platelet': 3543, 'Erythrocyte': 1154, 'ILC': 772, 'Progenitor cell': 179}",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_4arm/generated_scores_tpm/generated_ImMicro_raw_tpm_native/scores.json
+refcal,refcal_native,107,160500,0.137454319866968,0.1606372707722086,0.1886429730290212,0.257887127987232,0.1121495327102803,0.7590188242958245,0.8285162872385553,0.792326118714391,0.6544577271008061,0.2102627095042533,-0.0247283500845392,0.59768,0.09147,0.17526,0.10738,0.01854,0.00967,1.0,1.0,0.7217841220758988,0.6211720449068359,0.6337898469797606,-0.0460740780886931,0.1381742657702276,0.8571997620896091,0.0186915887850467,2,"{'Erythrocyte': 527, 'Platelet': 380, 'Progenitor cell': 376, 'ILC': 269}",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/generated_scores_refcal/ImMicro_refcal_native/scores.json
+cal,cal_native,107,160500,0.181774029433882,0.1606372707722086,0.1942677878703076,0.2676516189956202,0.0467289719626168,0.6555294040290716,0.6906165074386144,0.7994102256276192,0.470910145919951,0.3326193004246668,0.0792273830581826,0.69181,0.08528,0.13678,0.05636,0.0144,0.01537,1.0,1.0,0.7155721986448473,0.5670761574482259,0.5110895589647133,-0.0741512996886818,0.0280010693322852,0.8806632261053291,0.02803738317757,3,"{'ILC': 804, 'Erythrocyte': 704, 'Platelet': 699, 'Progenitor cell': 260}",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/generated_scores/generated_ImMicro_cal_native/scores.json
+pseudo,pseudo_native,107,160500,0.1663566375577628,0.1606372707722086,0.1947573244291459,0.2482129074896784,0.0654205607476635,0.6757615327323917,0.7550110780033936,0.8214552555034121,0.5486597828775159,0.2968750918308842,0.1001456400625899,0.70333,0.05062,0.14194,0.07329,0.01576,0.01506,1.0,1.0,0.8034934070024883,0.594496365524403,0.4838456866317914,0.0565531673768531,0.1670887952033115,0.8834915404498682,0.0467289719626168,5,"{'Platelet': 879, 'ILC': 756, 'Erythrocyte': 530, 'Progenitor cell': 252}",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/generated_scores/generated_ImMicro_pseudo_native/scores.json