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/disease/deconv_expression_coverage.csv

@@ -0,0 +1,21 @@
+cohort,draw,covered_genes,disease_correlation_available
+ye2026_sepsis,0,5526,True
+ye2026_sepsis,1,5573,True
+ye2026_sepsis,2,5517,True
+ye2026_sepsis,3,5592,True
+ye2026_sepsis,4,5547,True
+imperial_eskd,0,5727,True
+imperial_eskd,1,5726,True
+imperial_eskd,2,5704,True
+imperial_eskd,3,5719,True
+imperial_eskd,4,5716,True
+giroux2022,0,436,True
+giroux2022,1,0,False
+giroux2022,2,1359,True
+giroux2022,3,2025,True
+giroux2022,4,0,False
+ji2025_chili,0,2278,True
+ji2025_chili,1,2985,True
+ji2025_chili,2,2141,True
+ji2025_chili,3,1373,False
+ji2025_chili,4,2334,True

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/disease/external_rare_screen.csv

@@ -0,0 +1,46 @@
+dataset,state,rule,k,thin,gen,obs_thinned,obs_native_n,gen_pct,obs_pct,gen_over_obs,spearman
+dress,C1Q-high monocyte (reference),>= 2 of C1QA C1QB C1QC / ['Monocyte'],2.0,0.607,"110 / 3,793","529 / 4,485",586,2.9000790930661746,11.794871794871796,0.2458762709338713,0.9642857142857144
+dress,Cycling T/NK,">= 2 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5 / ['T cell', 'NK cell']",2.0,1.0,"455 / 28,601","1,295 / 26,235",1295,1.590853466662005,4.936153992757767,0.3222860285550401,0.7748062179181807
+dress,Cycling activated T (CD38/HLA-DR),>= 1 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5; any of CD38 HLA-DRA HLA-DRB1 / ['T cell'],1.0,1.0,"424 / 27,578","1,929 / 24,482",1929,1.5374573935745883,7.87925823053672,0.1951271742327272,0.8571428571428573
+dress,Proliferating T (label),AIFI L2 in ['Proliferating T cell'] / ['T cell'],,1.0,"1,001 / 27,578","4,226 / 24,482",4226,3.629704837189064,17.261661628951884,0.2102755178042183,0.642857142857143
+dress,Plasmablast (label),AIFI L2 in ['Plasma cell'] / ['ALL'],,1.0,"76 / 35,000","187 / 33,712",187,0.2171428571428571,0.5546986236355007,0.3914609625668449,0.5714285714285715
+dress,Plasmablast (markers),>= 3 of JCHAIN MZB1 TNFRSF17 TXNDC5 PRDM1 IRF4 IGLL5 / ['ALL'],3.0,0.967,"108 / 35,000","529 / 33,712",549,0.3085714285714285,1.5691741813004272,0.1966457466918714,0.6071428571428572
+dress,MS1 monocyte (IL1R2+),>= 2 of RETN ALOX5AP CYP1B1 MCEMP1 PLAC8 CLU CD163; any of IL1R2 / ['Monocyte'],2.0,0.607,"68 / 3,793","58 / 4,485",110,1.792776166622726,1.2931995540691192,1.386310535741884,0.594618725379069
+dress,Cycling monocyte (Ye 2026),>= 1 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5 / ['Monocyte'],1.0,0.607,"12 / 3,793","126 / 4,485",196,0.3163722646981281,2.809364548494983,0.1126134608865956,0.4818120558297158
+dress,ISG-high monocyte (positive control),>= 4 of ISG15 IFI6 IFI27 IFI44L MX1 OAS1 IFIT1 IFIT3 RSAD2 SIGLEC1 / ['Monocyte'],4.0,0.607,"35 / 3,793","212 / 4,485",394,0.9227524387028736,4.726867335562988,0.195214372055773,0.2882999880625789
+dress,ISG-high T,>= 4 of ISG15 IFI6 IFI27 IFI44L MX1 OAS1 IFIT1 IFIT3 RSAD2 SIGLEC1 / ['T cell'],4.0,1.0,"31 / 27,578","318 / 24,482",318,0.1124084415113496,1.2989134874601749,0.086540360537134,1.0
+dress,DN2 / ABC B,>= 2 of ITGAX TBX21 FCRL5 FGR TFEC SOX5 ZEB2; any of ITGAX TBX21; none of CR2 / ['B cell'],2.0,0.887,"23 / 1,938","89 / 2,245",98,1.186790505675955,3.964365256124722,0.2993645713755638,0.2857142857142857
+dress,HSPC,>= 2 of CD34 PRSS57 SPINK2 SMIM24 / ['ALL'],2.0,0.967,"11 / 35,000","33 / 33,712",33,0.0314285714285714,0.0978879924062648,0.3210666666666666,0.6174969805662239
+dress,Cytotoxic CD4 T,">= 3 of GZMH GZMB GZMA PRF1 NKG7 GNLY FGFBP2 CX3CR1 ZNF683; none of CCR7 / ['Naive CD4 T cell', 'Memory CD4 T cell', 'Treg']",3.0,1.0,"61 / 17,909","19 / 12,541",19,0.3406108660450053,0.1515030699306275,2.248210984773901,0.1785714285714286
+dress,Granulocyte-like (LDG),>= 2 of ELANE MPO CTSG CAMP LCN2 MMP9 CSF3R CXCR2 FCGR3B / ['ALL'],2.0,0.967,"78 / 35,000","865 / 33,712",899,0.2228571428571428,2.565851922164214,0.0868550289017341,0.7041868508280462
+dress,Platelet signal in monocytes (negative control),>= 2 of PPBP PF4 TUBB1 GP9 NRGN / ['Monocyte'],2.0,0.607,"18 / 3,793","53 / 4,485",90,0.4745583970471922,1.1817168338907469,0.4015838510861617,0.2485133664023575
+kawasaki,C1Q-high monocyte (reference),>= 2 of C1QA C1QB C1QC / ['Monocyte'],2.0,1.0,"43 / 7,927","603 / 11,050",603,0.5424498549262016,5.457013574660634,0.0994041608115178,0.1729799928375473
+kawasaki,Cycling T/NK,">= 2 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5 / ['T cell', 'NK cell']",2.0,1.0,"92 / 45,425","1,163 / 63,360",1163,0.2025316455696202,1.8355429292929293,0.1103388225562436,0.3392857142857142
+kawasaki,Cycling activated T (CD38/HLA-DR),>= 1 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5; any of CD38 HLA-DRA HLA-DRB1 / ['T cell'],1.0,1.0,"94 / 42,408","1,880 / 57,032",1880,0.2216562912657989,3.296395006312246,0.067242029805697,0.5035714285714286
+kawasaki,Proliferating T (label),AIFI L2 in ['Proliferating T cell'] / ['T cell'],,1.0,"330 / 42,408","1,146 / 57,032",1146,0.77815506508206,2.009398232571188,0.3872577632788834,0.1928571428571428
+kawasaki,Plasmablast (label),AIFI L2 in ['Plasma cell'] / ['ALL'],,1.0,"206 / 75,000","1,837 / 103,362",1837,0.2746666666666666,1.7772488922427971,0.1545459771366358,0.5583563931615944
+kawasaki,Plasmablast (markers),>= 3 of JCHAIN MZB1 TNFRSF17 TXNDC5 PRDM1 IRF4 IGLL5 / ['ALL'],3.0,1.0,"403 / 75,000","6,780 / 103,362",6780,0.5373333333333333,6.559470598479131,0.0819171799410029,0.6214285714285712
+kawasaki,MS1 monocyte (IL1R2+),>= 2 of RETN ALOX5AP CYP1B1 MCEMP1 PLAC8 CLU CD163; any of IL1R2 / ['Monocyte'],2.0,1.0,"345 / 7,927","714 / 11,050",714,4.352213952314873,6.461538461538462,0.6735569211915875,0.5481481481481483
+kawasaki,Cycling monocyte (Ye 2026),>= 1 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5 / ['Monocyte'],1.0,1.0,"15 / 7,927","366 / 11,050",366,0.1892266935789075,3.3122171945701355,0.0571299170504625,0.0063786488334384
+kawasaki,ISG-high monocyte (positive control),>= 4 of ISG15 IFI6 IFI27 IFI44L MX1 OAS1 IFIT1 IFIT3 RSAD2 SIGLEC1 / ['Monocyte'],4.0,1.0,"445 / 7,927","2,811 / 11,050",2811,5.613725242840923,25.43891402714932,0.2206747205029961,0.2107142857142857
+kawasaki,ISG-high T,>= 4 of ISG15 IFI6 IFI27 IFI44L MX1 OAS1 IFIT1 IFIT3 RSAD2 SIGLEC1 / ['T cell'],4.0,1.0,"161 / 42,408","2,361 / 57,032",2361,0.3796453499339747,4.139781175480432,0.0917066226066685,0.6344126772183988
+kawasaki,DN2 / ABC B,>= 2 of ITGAX TBX21 FCRL5 FGR TFEC SOX5 ZEB2; any of ITGAX TBX21; none of CR2 / ['B cell'],2.0,1.0,"149 / 20,998","413 / 21,517",413,0.7095913896561578,1.9194125575126644,0.3696919595939841,-0.0857142857142857
+kawasaki,HSPC,>= 2 of CD34 PRSS57 SPINK2 SMIM24 / ['ALL'],2.0,1.0,"48 / 75,000","124 / 103,362",124,0.064,0.1199667189102378,0.5334812903225806,0.7353713953215716
+kawasaki,Cytotoxic CD4 T,">= 3 of GZMH GZMB GZMA PRF1 NKG7 GNLY FGFBP2 CX3CR1 ZNF683; none of CCR7 / ['Naive CD4 T cell', 'Memory CD4 T cell', 'Treg']",3.0,1.0,"153 / 26,586","147 / 28,856",147,0.5754908598510494,0.5094261158857777,1.1296846429838014,0.2821428571428571
+kawasaki,Granulocyte-like (LDG),>= 2 of ELANE MPO CTSG CAMP LCN2 MMP9 CSF3R CXCR2 FCGR3B / ['ALL'],2.0,1.0,"16 / 75,000","2,974 / 103,362",2974,0.0213333333333333,2.87726630676651,0.007414445191661,0.8459389534565116
+kawasaki,Platelet signal in monocytes (negative control),>= 2 of PPBP PF4 TUBB1 GP9 NRGN / ['Monocyte'],2.0,1.0,"98 / 7,927","869 / 11,050",869,1.2362810647155291,7.864253393665158,0.1572025979874177,0.2928571428571428
+sle,C1Q-high monocyte (reference),>= 2 of C1QA C1QB C1QC / ['Monocyte'],2.0,0.957,"109 / 21,833","1,800 / 70,901",1823,0.499244263271195,2.538751216484958,0.1966495417232833,0.425667845115014
+sle,Cycling T/NK,">= 2 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5 / ['T cell', 'NK cell']",2.0,1.0,"688 / 124,845","1,553 / 238,992",1553,0.5510833433457487,0.6498125460266453,0.8480651023366849,0.6781051352229641
+sle,Cycling activated T (CD38/HLA-DR),>= 1 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5; any of CD38 HLA-DRA HLA-DRB1 / ['T cell'],1.0,1.0,"399 / 106,521","3,133 / 216,491",3133,0.3745740276565184,1.447173323602367,0.2588314900140036,0.5743050689676349
+sle,Proliferating T (label),AIFI L2 in ['Proliferating T cell'] / ['T cell'],,1.0,"561 / 106,521","1,953 / 216,491",1953,0.5266567155772102,0.90211602329889,0.5838015310395587,0.670138401025515
+sle,Plasmablast (label),AIFI L2 in ['Plasma cell'] / ['ALL'],,1.0,"85 / 168,000","1,526 / 358,235",1526,0.050595238095238,0.4259773612293606,0.1187744765337327,0.1900251986313282
+sle,Plasmablast (markers),>= 3 of MZB1 TNFRSF17 TXNDC5 PRDM1 IRF4 IGLL5 / ['ALL'],3.0,1.0,"92 / 168,000","3,250 / 358,235",3250,0.0547619047619047,0.9072257037977864,0.0603619413919413,0.3065829661916507
+sle,MS1 monocyte (IL1R2+),>= 2 of RETN ALOX5AP CYP1B1 PLAC8 CLU CD163; any of IL1R2 / ['Monocyte'],2.0,0.957,"21 / 21,833","3,105 / 70,901",3231,0.0961846745751843,4.379345848436552,0.0219632515686156,-0.0305602311890414
+sle,Cycling monocyte (Ye 2026),>= 1 of MKI67 TOP2A TYMS CENPF UBE2C BIRC5 / ['Monocyte'],1.0,0.957,"7 / 21,833","1,200 / 70,901",1254,0.0320615581917281,1.692500810989972,0.0189433044779309,0.2579767941753155
+sle,ISG-high monocyte (positive control),>= 4 of ISG15 IFI6 IFI27 IFI44L MX1 OAS1 IFIT1 IFIT3 RSAD2 SIGLEC1 / ['Monocyte'],4.0,0.957,"7,372 / 21,833","27,715 / 70,901",28332,33.76540099848852,39.089716647155896,0.8637924215023758,0.8613807245386194
+sle,ISG-high T,>= 4 of ISG15 IFI6 IFI27 IFI44L MX1 OAS1 IFIT1 IFIT3 RSAD2 SIGLEC1 / ['T cell'],4.0,1.0,"5,819 / 106,521","26,345 / 216,491",26345,5.462772598830278,12.169097098724658,0.448905334102625,0.8551606288448395
+sle,DN2 / ABC B,>= 2 of ITGAX TBX21 FCRL5 FGR TFEC SOX5 ZEB2; any of ITGAX TBX21; none of CR2 / ['B cell'],2.0,1.0,"40 / 19,311","931 / 35,488",931,0.2071358293200766,2.6234220018034264,0.0789563513524262,0.0345260411415992
+sle,HSPC,>= 2 of CD34 PRSS57 SPINK2 / ['ALL'],2.0,1.0,"12 / 168,000","265 / 358,235",265,0.0071428571428571,0.0739737881558195,0.0965592991913746,0.1265587222431026
+sle,Cytotoxic CD4 T,">= 3 of GZMH GZMB GZMA PRF1 NKG7 GNLY FGFBP2 CX3CR1 ZNF683; none of CCR7 / ['Naive CD4 T cell', 'Memory CD4 T cell', 'Treg']",3.0,1.0,"791 / 71,556","1,855 / 106,194",1855,1.1054279165967913,1.7468030208863023,0.632829176145982,0.650079461466437
+sle,Granulocyte-like (LDG),>= 2 of ELANE MPO CTSG CAMP LCN2 MMP9 CSF3R CXCR2 FCGR3B / ['ALL'],2.0,1.0,"17 / 168,000","2,697 / 358,235",2697,0.0101190476190476,0.752857760966963,0.0134408491798647,0.2563692618620108
+sle,Platelet signal in monocytes (negative control),>= 2 of PPBP PF4 TUBB1 GP9 NRGN / ['Monocyte'],2.0,0.957,"403 / 21,833","3,639 / 70,901",3788,1.845829707323776,5.13250870932709,0.3596349878509564,0.0476093201382922

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/disease/k4000_calibration.csv

@@ -0,0 +1,9 @@
+cohort,gate,version,pass_count,total
+ye2026_sepsis,Level + ranking,k1000,100,250
+ye2026_sepsis,Level + ranking,k4000,107,250
+ye2026_sepsis,Disease contrast,k1000,73,250
+ye2026_sepsis,Disease contrast,k4000,83,250
+imperial_eskd,Level + ranking,k1000,111,250
+imperial_eskd,Level + ranking,k4000,110,250
+imperial_eskd,Disease contrast,k1000,99,250
+imperial_eskd,Disease contrast,k4000,106,250

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/disease/k4000_disease.csv

@@ -0,0 +1,21 @@
+cohort,draw,arm,logfc_r_gen,logfc_partial_r,deg_top50_sum
+ye2026_sepsis,0,lora5,0.4359905652333528,0.4060106147529024,7
+ye2026_sepsis,0,lora5_k4000,0.4264725001854249,0.4002480850583318,6
+ye2026_sepsis,1,lora5,0.0812370339175413,-0.0189356796136925,16
+ye2026_sepsis,1,lora5_k4000,0.1399148542756795,0.0442629578734843,16
+ye2026_sepsis,2,lora5,0.3272188119120809,0.3144756173868615,26
+ye2026_sepsis,2,lora5_k4000,0.3472457147439288,0.3391313390936928,32
+ye2026_sepsis,3,lora5,0.4108841123350609,0.3622128751991821,17
+ye2026_sepsis,3,lora5_k4000,0.2665891566662903,0.1788350317931198,15
+ye2026_sepsis,4,lora5,0.495261369635401,0.4597246910197378,16
+ye2026_sepsis,4,lora5_k4000,0.454238592918229,0.4166269424661354,20
+imperial_eskd,0,lora5,0.7798976158583719,0.6572469324283057,116
+imperial_eskd,0,lora5_k4000,0.7821247585137376,0.6648610760742939,122
+imperial_eskd,1,lora5,0.7570901930571807,0.6045509566158934,119
+imperial_eskd,1,lora5_k4000,0.7553749956693036,0.6095335345734808,122
+imperial_eskd,2,lora5,0.7139546009415169,0.5764372157359006,103
+imperial_eskd,2,lora5_k4000,0.7197837002971605,0.5753101940878903,110
+imperial_eskd,3,lora5,0.7455905986374256,0.6007400715066787,117
+imperial_eskd,3,lora5_k4000,0.7387401711059427,0.5919124591511977,119
+imperial_eskd,4,lora5,0.7492433446082651,0.575230848198632,113
+imperial_eskd,4,lora5_k4000,0.7417677782057019,0.5709024618887067,106