Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/0aeddab8b98cad28/en.csv

@@ -0,0 +1,25 @@
+dataset,design,unit,set,cellset,distance,n_samples,n_cells_real,n_cells_gen,n_pcs,lb,ub,dif_mean,en,lb_exact,lb_queries,n_representative_rows,en_reps_at_lb,seconds
+immicro,scored,strict,real_R2,pc,sq,22,3300,3300,100,174.45375563476955,234.1106868907661,195.99465128256668,0.36107951237655894,True,"[3300, 3300]",,,4.6
+immicro,scored,strict,real_R2,pc,l2,22,3300,3300,100,13.016179182007932,15.079988489859169,13.767595769315252,0.36409206240554637,True,"[3300, 3300]",,,4.6
+immicro,scored,strict,real_R2,all,sq,22,41702,41714,100,134.95212095836138,180.0197486687422,145.40543980824611,0.23194739508059198,False,"[20000, 20000]",,,12.4
+immicro,scored,strict,real_R2,all,l2,22,41702,41714,100,11.491511721422913,13.289704868175052,11.915115536763123,0.23557192179567274,False,"[20000, 20000]",,,12.4
+immicro,scored,strict,lora,pc,sq,22,3300,3300,100,174.7441535335443,225.46737858526004,246.63248750452928,1.4172666248585337,True,"[3300, 3300]",,,4.8
+immicro,scored,strict,lora,pc,l2,22,3300,3300,100,13.004413719429413,14.803085688348974,15.468322836609712,1.369849066286577,True,"[3300, 3300]",,,4.8
+immicro,scored,strict,lora,all,sq,22,83416,33000,100,133.2221496059342,170.97928344614175,190.1180873384246,1.5068923921312571,False,"[20000, 20000]",,,15.4
+immicro,scored,strict,lora,all,l2,22,83416,33000,100,11.405155330964918,12.946468183046163,13.633074864710522,1.4454687318912773,False,"[20000, 20000]",,,15.4
+immicro,scored,strict,pairedcal,pc,sq,22,3300,3300,100,181.8166022195253,218.92737025701288,293.04944366617724,2.9973198435098314,True,"[3300, 3300]",,,4.8
+immicro,scored,strict,pairedcal,pc,l2,22,3300,3300,100,13.197215248752155,14.588902500841398,16.745851052636922,2.5498802252858526,True,"[3300, 3300]",,,4.8
+immicro,scored,strict,pairedcal,all,sq,22,83416,33000,100,135.9526053893482,168.89383373209841,228.08134305982696,2.796760846677859,False,"[20000, 20000]",,,15.3
+immicro,scored,strict,pairedcal,all,l2,22,83416,33000,100,11.495378275641732,12.865613654539997,14.894836910520239,2.480930420590829,False,"[20000, 20000]",,,15.3
+immicro,scored,strict,scsemi,pc,sq,22,3300,3300,100,137.27689066267342,231.02199751833004,370.67490699760265,2.489708787620267,True,"[3300, 3300]",,,5.6
+immicro,scored,strict,scsemi,pc,l2,22,3300,3300,100,11.353184085324685,14.966120199274885,18.988316649094383,2.113276383241063,True,"[3300, 3300]",,,5.6
+immicro,scored,strict,scsemi,all,sq,22,83416,33000,100,109.8865150561636,167.2984373511355,326.1803524815723,3.7674028107634285,False,"[20000, 20000]",,,16.1
+immicro,scored,strict,scsemi,all,l2,22,83416,33000,100,10.205540461047567,12.795005779388857,17.828109697030325,2.943684621683011,False,"[20000, 20000]",,,16.1
+immicro,scored,strict,raw,pc,sq,22,3300,3300,100,219.9433829744183,192.47618280834047,436.9881765689739,-7.901962787696404,True,"[3300, 3300]",,,4.7
+immicro,scored,strict,raw,pc,l2,22,3300,3300,100,14.274760672272924,13.662263930286043,20.2144513142715,-9.697505692407091,True,"[3300, 3300]",,,4.7
+immicro,scored,strict,raw,all,sq,22,83416,33000,100,144.83429507252777,164.03683355250368,315.75265334973295,8.900821027148885,False,"[20000, 20000]",,,15.0
+immicro,scored,strict,raw,all,l2,22,83416,33000,100,11.800926087122686,12.674640051448733,17.405142500722935,6.414246129078581,False,"[20000, 20000]",,,15.0
+immicro,scored,strict,refcal,pc,sq,22,3300,3300,100,169.94402714245834,213.21157155670087,390.6771106850174,5.101585646489786,True,"[3300, 3300]",,,5.6
+immicro,scored,strict,refcal,pc,l2,22,3300,3300,100,12.73632019512054,14.384701298044371,19.425868257334518,4.058253307046731,True,"[3300, 3300]",,,5.6
+immicro,scored,strict,refcal,all,sq,22,83416,33000,100,127.41251112796166,166.40804632157253,318.1767076615128,4.8919496959438185,False,"[20000, 20000]",,,16.8
+immicro,scored,strict,refcal,all,l2,22,83416,33000,100,11.129795371493126,12.769097352250851,17.62606436707807,3.962826295483526,False,"[20000, 20000]",,,16.8

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/4204108b1027d5a0/donor_deg_summary.csv

@@ -0,0 +1,26 @@
+arm,celltype,status,observed_status,generated_status,n_case_donors_observed,n_control_donors_observed,n_case_donors_generated,n_control_donors_generated,method_observed,method_generated,reason_observed,reason_generated,reason_fit,reason_population,top50_overlap_count,observed_top50_size,generated_top50_size
+lora,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+lora,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,6,50,50
+lora,Monocyte,ok,ok,ok,57,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+lora,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,21
+lora,DC,ok,ok,ok,53,20,50,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+pairedcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+pairedcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,1
+pairedcal,Monocyte,ok,ok,ok,57,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+pairedcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,32
+pairedcal,DC,ok,ok,ok,53,20,54,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+scsemi,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,17
+scsemi,Monocyte,ok,ok,ok,57,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,6,50,50
+scsemi,NK cell,ok,ok,ok,57,20,52,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,12
+scsemi,DC,ok,ok,ok,53,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+raw,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+raw,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+raw,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+raw,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+raw,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+refcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+refcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+refcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+refcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+refcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,19

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/43149a34d152d617/support.json

@@ -0,0 +1,193 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "giroux2022",
+  "design": "disease_existing_draw",
+  "unit": "draw1_n5",
+  "n_pairs": 5,
+  "train_sample_ids": [
+    "7085CA_d0",
+    "2AD75E_d0",
+    "BAAF62_d0",
+    "B85D75_d0",
+    "82CCF5_d0"
+  ],
+  "train_donor_ids": [
+    "7085CA",
+    "2AD75E",
+    "BAAF62",
+    "B85D75",
+    "82CCF5"
+  ],
+  "test_sample_ids": [
+    "450905_d0",
+    "450905_d14",
+    "0B943B_d0",
+    "0B943B_d14",
+    "180E1A_d0",
+    "180E1A_d7",
+    "180E1A_d14",
+    "0BF51C_d0",
+    "0BF51C_d7",
+    "0BF51C_d14"
+  ],
+  "test_donor_ids": [
+    "450905",
+    "450905",
+    "0B943B",
+    "0B943B",
+    "180E1A",
+    "180E1A",
+    "180E1A",
+    "0BF51C",
+    "0BF51C",
+    "0BF51C"
+  ],
+  "excluded_sample_ids": [
+    "2AD75E_d14",
+    "2AD75E_d7",
+    "7085CA_d14",
+    "7085CA_d7",
+    "82CCF5_d14",
+    "82CCF5_d7",
+    "B85D75_d7",
+    "BAAF62_d14",
+    "BAAF62_d7"
+  ],
+  "seed": null,
+  "selection_audit": [
+    {
+      "donor_id": "7085CA",
+      "assigned_stratum": false,
+      "selected_sample_id": "7085CA_d0",
+      "candidates": [
+        {
+          "sample_id": "7085CA_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "7085CA_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "7085CA_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "mild"
+        }
+      ]
+    },
+    {
+      "donor_id": "2AD75E",
+      "assigned_stratum": false,
+      "selected_sample_id": "2AD75E_d0",
+      "candidates": [
+        {
+          "sample_id": "2AD75E_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "2AD75E_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "2AD75E_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "mild"
+        }
+      ]
+    },
+    {
+      "donor_id": "BAAF62",
+      "assigned_stratum": false,
+      "selected_sample_id": "BAAF62_d0",
+      "candidates": [
+        {
+          "sample_id": "BAAF62_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "BAAF62_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "mild"
+        },
+        {
+          "sample_id": "BAAF62_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "mild"
+        }
+      ]
+    },
+    {
+      "donor_id": "B85D75",
+      "assigned_stratum": true,
+      "selected_sample_id": "B85D75_d0",
+      "candidates": [
+        {
+          "sample_id": "B85D75_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "severe"
+        },
+        {
+          "sample_id": "B85D75_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "severe"
+        }
+      ]
+    },
+    {
+      "donor_id": "82CCF5",
+      "assigned_stratum": true,
+      "selected_sample_id": "82CCF5_d0",
+      "candidates": [
+        {
+          "sample_id": "82CCF5_d0",
+          "time_value": 0.0,
+          "time_raw": "0",
+          "time_field": "timepoint",
+          "group": "severe"
+        },
+        {
+          "sample_id": "82CCF5_d7",
+          "time_value": 7.0,
+          "time_raw": "7",
+          "time_field": "timepoint",
+          "group": "severe"
+        },
+        {
+          "sample_id": "82CCF5_d14",
+          "time_value": 14.0,
+          "time_raw": "14",
+          "time_field": "timepoint",
+          "group": "severe"
+        }
+      ]
+    }
+  ],
+  "sha256": "1a20024ce53f3aeb268784fed7fed630ef326f8ffa89fa9bc150661c1506b7e2"
+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/9ba111ba4cc4b8bd/metrics.csv

@@ -0,0 +1,25 @@
+dataset,design,unit,label,set,real_side,mode,n_real,n_gen,precision_k3,coverage_k3,density_k3,expected_coverage_identical_k3,precision_k5,coverage_k5,density_k5,expected_coverage_identical_k5,precision_k10,coverage_k10,density_k10,expected_coverage_identical_k10,c2st_knn_auc,c2st_knn_auc_sd,c2st_rf_auc,c2st_rf_auc_sd,nn1_acc,nn1_acc_real,nn1_acc_gen,mmd2_bw0.5,mmd2_bw1,mmd2_bw2,mmd2_sum,mmd_bandwidth_m,seconds
+imperial_eskd,scored,strict,Real vs real control (held-out real cells),real_R2,R1,raw,21395,21395,0.8427670016358962,0.91946716522552,1.3187816468022124,0.8750175276644852,0.9147464360831971,0.9849964945080626,1.3096891797148866,0.9687609541502247,0.9685440523486796,0.999813040430007,1.28853003038093,0.9990246922230742,0.501061429206294,0.006409508565570394,0.558686926882653,0.008690042591607283,0.502453844356158,0.42594064033652723,0.5789670483757887,5.81467385953327e-05,-8.391490420311953e-07,-2.509358811852991e-06,5.479823074144852e-05,26.023567777096574,94.6
+imperial_eskd,scored,strict,Real vs real control (held-out real cells),real_R2,R1,dm,21395,21395,0.8421126431409208,0.919654124795513,1.3201059437563292,0.8750175276644852,0.9140453376957233,0.9852769338630522,1.3134564150502455,0.9687609541502247,0.9688712315961673,0.999626080860014,1.2930217340500119,0.9990246922230742,0.5013706945898656,0.005136884351282375,0.5629367070964735,0.006395228884484773,0.5026641738724001,0.4249123627015658,0.5804159850432344,4.967886358447915e-05,-3.3705629884916988e-06,-2.9977053621621508e-06,4.33105952338253e-05,26.023567777096574,94.2
+imperial_eskd,scored,strict,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,20906,20906,,,,,,,,,,,,,0.5025808749448755,0.0056520200612888314,0.5077819185283108,0.006156570948837379,0.49842150578781214,0.49583851525877737,0.5010044963168468,-1.746841363964302e-05,-1.3976269470195035e-05,-4.96224774138021e-06,-3.6406930851218267e-05,26.023567777096574,78.5
+imperial_eskd,scored,strict,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,20906,20906,,,,,,,,,,,,,0.5001436258300872,0.0035743770545071454,0.5028718291342054,0.006224347720809276,0.4986128384195925,0.4988520042093179,0.49837367262986704,-1.8079398137915703e-05,-1.4542512298598709e-05,-5.139131880715908e-06,-3.776104231723032e-05,26.023567777096574,78.9
+imperial_eskd,scored,strict,,lora,R1,raw,21395,21395,0.6030848329048843,0.4778686609020799,0.6208615720183843,0.8750175276644852,0.7222715587754148,0.6057957466697826,0.6360645010516476,0.9687609541502247,0.8489834073381631,0.7597102126665108,0.6621734050011685,0.9990246922230742,0.919224541600334,0.0039018755890526872,0.92181766624844,0.005048403835387645,0.8076653423697125,0.7628417854638935,0.8524888992755316,0.029000273528946352,0.0189934259654585,0.0061321042265842785,0.05412580372098913,26.023567777096574,67.1
+imperial_eskd,scored,strict,,lora,R1,dm,21395,21395,0.6910493105865857,0.5842953961205889,0.9411856352730389,0.8750175276644852,0.7937835942977332,0.7136246786632391,0.9581491002570693,0.9687609541502247,0.8970787567188595,0.8562280906753914,0.986880112175742,0.9990246922230742,0.8865148747059026,0.0035106981126253535,0.9105919106561329,0.004110002214378609,0.7711147464360832,0.6944613227389577,0.8477681701332087,0.02322276639174925,0.015409260185591522,0.0051891407568049885,0.04382116733414576,26.023567777096574,67.3
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