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/c1q_cross_disease.csv

@@ -0,0 +1,4 @@
+dataset,arm,samples,obs_monocytes,gen_monocytes,obs_median_mono_lib,gen_median_mono_lib,thin_factor,obs_c1q_ge1_pct,obsthin_c1q_ge1_pct,gen_c1q_ge1_pct,ratio_c1q_ge1_pct,spearman_c1q_ge1_pct,obs_c1q_ge2_pct,obsthin_c1q_ge2_pct,gen_c1q_ge2_pct,ratio_c1q_ge2_pct,spearman_c1q_ge2_pct,spearman_mono_pct,obs_mono_pct_mean,gen_mono_pct_mean
+dress,dress_zs_s13,7,4485,3793,3151.0,1913.0,0.6071088314056396,18.72909698996656,17.32441471571906,16.082256788821514,0.9283001505516666,0.8928571428571429,13.06577480490524,11.884057971014492,2.9000790930661746,0.2440310456360561,0.9642857142857144,0.9642857142857144,11.77879896135235,10.837142857142856
+kawasaki,kawasaki_zs_s13,15,11050,7927,1821.0,2041.0,1.0,9.95475113122172,9.95475113122172,4.692822000756907,0.4714153009851256,0.2571428571428571,5.457013574660634,5.457013574660634,0.5424498549262016,0.0994041608115178,0.1729799928375473,0.8892857142857141,11.824041528761857,10.569333333333333
+sle,sle_zs_s13,56,70901,21833,1904.0,1822.0,0.956932783126831,7.8814121098433025,7.734728706224172,5.230614207850501,0.6762505068395485,0.3705804952778811,2.571190815362266,2.52323662571755,0.499244263271195,0.1978586780893851,0.4165410584815125,0.9707450444292548,20.864874160054143,12.995833333333334

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/covid_cd14_direction_detail.csv

@@ -0,0 +1,15 @@
+depth,population,set,cos_pca50,length_ratio_pca50,len_real_pca50,len_set_pca50,cos_null_median,cos_null_p95,share_relabelings_cos_ge_true,cos_genes_logcp10k,length_ratio_genes,pearson_genes,min_cells_per_sample,n_samples_ge20
+native,CD14 monocyte (L2),real_holdout,0.9782027673573496,0.941106913090104,9.787055336606825,9.210665436076075,0.0204674125771476,0.8970003057976105,0.0025252525252525,0.9164365860982848,1.000309082059435,0.917292546342904,15,11
+native,CD14 monocyte (L2),gen_raw,0.4642494758744882,0.7200294033499817,9.787055336606825,7.046967614570264,-0.0201108055654741,0.644330032712652,0.1590909090909091,0.4033974395882429,0.9932986531394916,0.4154743815718232,42,12
+native,CD14 monocyte (L2),gen_tpm,0.811419820317112,0.4582834615323157,9.787055336606825,4.485245597868498,0.0271898728910945,0.7961758808718564,0.0378787878787878,0.6069586370870798,0.6637097638153168,0.6049773612678854,53,12
+native,CD14 monocyte (L2),gen_cal,0.6018758676079278,0.5479078372958796,9.787055336606825,5.36240432297534,0.016326433085741,0.755870867105007,0.154040404040404,0.6019398577454667,0.813500805076037,0.6176790174647532,35,12
+native,CD14 monocyte (L2),gen_pseudo,0.799508882617603,0.4543317841808861,9.787055336606825,4.446570312957641,-0.0113947916416288,0.7241023658383666,0.0151515151515151,0.6795084597344703,0.6859224486308899,0.678525313107338,25,12
+native,CD14 monocyte (L2),gen_refcalHC,0.6417920536607,0.4633271953595547,9.787055336606825,4.534608899938802,0.0529753211277289,0.7820889496337315,0.178030303030303,0.5320644689040601,0.7428062218305188,0.5421758236213712,13,11
+native,CD14 monocyte (L2),gen_refcalAll,0.5490440549541307,0.3681945779426275,9.787055336606825,3.603540708963089,0.0336841230209238,0.749941017826743,0.2095959595959595,0.4879533058751384,0.6039339377772135,0.501858934682005,11,11
+depth1000,CD14 monocyte (L2),real_holdout,0.9742876899866032,0.8858979564490621,7.804482788351372,6.913975353342359,0.0134437127539687,0.9203450314577816,0.0037878787878787,0.8582535995056475,1.0136708988102647,0.8582459492816488,15,10
+depth1000,CD14 monocyte (L2),gen_raw,0.6392538717461741,0.6182060052864093,7.804482788351372,4.824778127913239,0.0043531924846406,0.7916350144917701,0.1515151515151515,0.4709614546858335,0.8981709809892953,0.4753882470938829,36,12
+depth1000,CD14 monocyte (L2),gen_tpm,0.8582543303609116,0.4448546994658401,7.804482788351372,3.4718608452983712,-0.0023354709056164,0.8419463815057787,0.0328282828282828,0.6274544495604516,0.6188281882410762,0.6283585466113157,37,12
+depth1000,CD14 monocyte (L2),gen_cal,0.8819371883559397,0.4882157432608828,7.804482788351372,3.8102713652817326,0.0029540501656701,0.8552662661726314,0.0277777777777777,0.6416669000880839,0.7208958006623939,0.6423720469937997,25,12
+depth1000,CD14 monocyte (L2),gen_pseudo,0.8856568882968654,0.4341358489849694,7.804482788351372,3.388205761209504,0.0119646309799268,0.8349319831561752,0.0164141414141414,0.6605317040080809,0.5981513365675257,0.6606998253338296,18,11
+depth1000,CD14 monocyte (L2),gen_refcalHC,0.90892342948774,0.4663238510936131,7.804482788351372,3.639416469657832,0.0419230931755449,0.8917189258594914,0.0189393939393939,0.5386814050531459,0.7317742229215629,0.538628585835431,8,9
+depth1000,CD14 monocyte (L2),gen_refcalAll,0.8860878653386435,0.3293378628950349,7.804482788351372,2.5703116825167243,-0.047302185042441,0.8531443764529967,0.0189393939393939,0.503409479992193,0.5897431639306109,0.5033652483137058,7,10

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/covid_endpoints.csv

@@ -0,0 +1,21 @@
+endpoint,role,population,module,expected,source,effect,effect_kind,hedges_g,mean_covid,mean_hc,n_covid,n_hc,direction_as_expected,perm_fraction_as_extreme_descriptive,sign_agrees_with_observed,ratio_to_observed,donor_spearman_with_observed
+P1,primary,Monocyte,ISG_hallmark,up,gen_raw,0.8724570138530598,"mean COVID - mean HC, log2(CPM+1)",1.5109629845418808,6.887180162994632,6.014723149141572,7,5,True,0.0227272727272727,True,0.8655397833984398,0.8811188811188813
+P1,primary,Monocyte,ISG_hallmark,up,gen_pseudo,1.2956757296890895,"mean COVID - mean HC, log2(CPM+1)",2.234342413237804,5.948183542185619,4.65250781249653,7,5,True,0.0037878787878787,True,1.2854030314650982,0.8251748251748254
+P1,primary,Monocyte,ISG_hallmark,up,gen_tpm,0.5740378663746943,"mean COVID - mean HC, log2(CPM+1)",0.9011061379579176,6.260393888207839,5.686356021833144,7,5,True,0.1287878787878787,True,0.5694866367457915,0.8741258741258742
+P1,primary,Monocyte,ISG_hallmark,up,gen_cal,1.221780327564245,"mean COVID - mean HC, log2(CPM+1)",1.8690950464219116,5.943752134794226,4.721971807229981,7,5,True,0.0063131313131313,True,1.2120935052263064,0.8181818181818183
+P1,primary,Monocyte,ISG_hallmark,up,gen_refcalHC,1.643284872061181,"mean COVID - mean HC, log2(CPM+1)",2.592286289909335,6.3771587526835765,4.7338738806223954,7,5,True,0.0037878787878787,True,1.6302561726729583,0.7972027972027973
+P2,primary,CD14_monocyte,HLA_DR,down,gen_raw,-0.7235151293835127,"mean COVID - mean HC, log2(CPM+1)",-2.0906427410011528,12.322930295512128,13.04644542489564,7,5,True,0.005050505050505,True,1.4582871581441348,0.3846153846153847
+P2,primary,CD14_monocyte,HLA_DR,down,gen_pseudo,-0.1908486431802245,"mean COVID - mean HC, log2(CPM+1)",-0.4894705708643226,11.432581631172472,11.623430274352696,7,5,True,0.4166666666666667,True,0.384666628514176,0.6223776223776225
+P2,primary,CD14_monocyte,HLA_DR,down,gen_tpm,-0.4546924793410323,"mean COVID - mean HC, log2(CPM+1)",-1.9547817170819437,11.586898470708563,12.041590950049596,7,5,True,0.0037878787878787,True,0.9164593477025564,0.3916083916083916
+P2,primary,CD14_monocyte,HLA_DR,down,gen_cal,-0.4898113550245426,"mean COVID - mean HC, log2(CPM+1)",-2.1806958892398525,11.242367969079885,11.732179324104424,7,5,True,0.0012626262626262,True,0.9872435004283756,0.2867132867132868
+P2,primary,CD14_monocyte,HLA_DR,down,gen_refcalHC,-0.2434992863922431,"mean COVID - mean HC, log2(CPM+1)",-1.565544339060259,11.08179538659723,11.325294672989472,7,5,True,0.0189393939393939,True,0.4907870864644297,0.0
+P3,primary,Plasma_cell,fraction_of,up,gen_raw,2.460028873833844,log2(mean COVID / mean HC fraction),,0.0033935405875046,0.0006167520001454,7,5,True,0.0063131313131313,True,0.4746809681125059,0.6013986013986015
+P3,primary,Plasma_cell,fraction_of,up,gen_pseudo,2.472303922020085,log2(mean COVID / mean HC fraction),,0.0063884367191601,0.0011512163747203,7,5,True,0.0126262626262626,True,0.4770495304568949,0.5384615384615385
+P3,primary,Plasma_cell,fraction_of,up,gen_tpm,2.3512516136132904,log2(mean COVID / mean HC fraction),,0.006240298382778,0.0012229482871778,7,5,True,0.0012626262626262,True,0.4536915822807663,0.8181818181818183
+P3,primary,Plasma_cell,fraction_of,up,gen_cal,2.540148219141816,log2(mean COVID / mean HC fraction),,0.0084076752614798,0.0014454901005094,7,5,True,0.0012626262626262,True,0.4901405949485351,0.8461538461538463
+P3,primary,Plasma_cell,fraction_of,up,gen_refcalHC,3.230116982325875,log2(mean COVID / mean HC fraction),,0.0137822853285532,0.0014687880669953,7,5,True,0.0012626262626262,True,0.62327522761859,0.8671328671328673
+P4,primary,B_lineage,plasmablast,up,gen_raw,2.2084639581931604,"mean COVID - mean HC, log2(CPM+1)",1.4886452610081085,8.813713425154349,6.6052494669611885,7,5,True,0.0265151515151515,True,0.6109977580273027,0.5594405594405596
+P4,primary,B_lineage,plasmablast,up,gen_pseudo,1.2607731558735429,"mean COVID - mean HC, log2(CPM+1)",0.9937601875289056,8.752007660879418,7.491234505005875,7,5,True,0.0946969696969697,True,0.348807852970343,0.3706293706293707
+P4,primary,B_lineage,plasmablast,up,gen_tpm,2.083638187458412,"mean COVID - mean HC, log2(CPM+1)",1.9380850580532825,10.101404418600575,8.017766231142165,7,5,True,0.005050505050505,True,0.5764632274636435,0.6713286713286714
+P4,primary,B_lineage,plasmablast,up,gen_cal,1.618853493830425,"mean COVID - mean HC, log2(CPM+1)",1.54465867321579,9.451374960209352,7.832521466378928,7,5,True,0.0164141414141414,True,0.4478750271814687,0.5594405594405596
+P4,primary,B_lineage,plasmablast,up,gen_refcalHC,2.0814725727916112,"mean COVID - mean HC, log2(CPM+1)",1.7629990000862086,10.46646782590855,8.384995253116939,7,5,True,0.0037878787878787,True,0.5758640844704979,0.6783216783216784

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/covid_monocyte_direction_detail.csv

@@ -0,0 +1,15 @@
+depth,population,set,cos_pca50,length_ratio_pca50,len_real_pca50,len_set_pca50,cos_null_median,cos_null_p95,share_relabelings_cos_ge_true,cos_genes_logcp10k,length_ratio_genes,pearson_genes,min_cells_per_sample,n_samples_ge20
+native,Monocyte (L1),real_holdout,0.9921812049847986,0.9298995728117948,10.968745840957498,10.19983207178753,0.0143584108797073,0.8611011978172395,0.0012626262626262,0.9584203228797324,0.9925389419913482,0.9582642687354204,30,12
+native,Monocyte (L1),gen_raw,0.4213662892796173,0.6622468371075543,10.968745840957498,7.264017240210743,0.024347265682563,0.6414560576249521,0.2108585858585858,0.4622846504946665,0.9232457965028984,0.4860134321885597,80,12
+native,Monocyte (L1),gen_tpm,0.8552004600074481,0.408780541535035,10.968745840957498,4.483809864826769,-0.0017315592040662,0.8191702949452496,0.0239898989898989,0.7084175325844954,0.6004629279578926,0.7089000094259551,89,12
+native,Monocyte (L1),gen_cal,0.5055483028068505,0.4862919725928086,10.968745840957498,5.334013051868387,-0.0162316404354515,0.7471478187365771,0.1893939393939394,0.5600961384254663,0.737042253241138,0.5843241287564248,80,12
+native,Monocyte (L1),gen_pseudo,0.8129778456890157,0.4027373231056664,10.968745840957498,4.417523337813635,-0.0236564549334392,0.729054299955,0.0126262626262626,0.677364848574976,0.6042254225992082,0.6756324087730708,81,12
+native,Monocyte (L1),gen_refcalHC,0.6397567010848054,0.4885588394252409,10.968745840957498,5.358877738008633,0.0227941429762352,0.7423607965840282,0.1414141414141414,0.573242331182391,0.7454576266121903,0.585789031366165,35,12
+native,Monocyte (L1),gen_refcalAll,0.5771855782339272,0.3771814823054267,10.968745840957498,4.137207815323833,-0.0954500894834986,0.7190232476366469,0.1414141414141414,0.5393206065920185,0.6066825060529079,0.5536172430699872,34,12
+depth1000,Monocyte (L1),real_holdout,0.9878306805658446,0.8512665684099155,8.916257490130187,7.59011191668233,0.0108917606875266,0.8777846641319625,0.0012626262626262,0.9272433974217724,0.9599032869370894,0.9270270223414008,27,12
+depth1000,Monocyte (L1),gen_raw,0.6960930855896446,0.5701351603328529,8.916257490130187,5.083471893704375,0.0330604771520614,0.8188273609986806,0.1893939393939394,0.5707790050700347,0.8412825655418132,0.5804941680459964,69,12
+depth1000,Monocyte (L1),gen_tpm,0.8554577888620786,0.4307030019412562,8.916257490130187,3.840258867080282,-0.0072244842406959,0.8539857323858915,0.0492424242424242,0.7116684761383328,0.6052323737625334,0.716683698736145,77,12
+depth1000,Monocyte (L1),gen_cal,0.8413388424936236,0.4220186126284868,8.916257490130187,3.762826615823096,-0.000883615032315,0.8534504998176524,0.0606060606060606,0.6320444621567135,0.652971216032577,0.6347983143825382,66,12
+depth1000,Monocyte (L1),gen_pseudo,0.8667660783155797,0.4219597502554619,8.916257490130187,3.762301783748726,0.0137394404241251,0.8182827720094566,0.0176767676767676,0.6593980750125035,0.5698324576815093,0.6579202985683565,70,12
+depth1000,Monocyte (L1),gen_refcalHC,0.8477299562721522,0.5059209088827159,8.916257490130187,4.510921093238988,0.0784337136835449,0.8479858371214082,0.053030303030303,0.5888332608548531,0.7174950784258295,0.5881190265825847,28,12
+depth1000,Monocyte (L1),gen_refcalAll,0.8114794165954846,0.3506830143232369,8.916257490130187,3.126780053120993,0.0547990149032414,0.8114255916758558,0.0505050505050505,0.5433691923634496,0.5639330202447373,0.543682906320617,28,12