Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paired_finetune_intradataset_20260927/scores_contrast/imperial_eskd/scsemi_cv_20261002/pooled/ceiling.csv

@@ -0,0 +1,16 @@
+dataset,design,unit,predictor,arm,celltype,n_genes,pearson_mean,pearson_sd,spearman_mean,spearman_sd,pearson_s20260926,spearman_s20260926,pearson_s20260927,spearman_s20260927,pearson_s20260928,spearman_s20260928,pearson_s20260929,spearman_s20260929,pearson_s20260930,spearman_s20260930,sb_reliability_pearson,noise_free_ceiling_pearson,sb_reliability_spearman,noise_free_ceiling_spearman,min_n_case_donors_A,min_n_control_donors_A,min_n_case_donors_B,min_n_control_donors_B,mean_n_cells_A,mean_n_cells_B,condition_sha256
+imperial_eskd,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,T cell,3031.0,0.969677277991828,0.0013370115576643313,0.8788731784327866,0.0029532402783132732,0.9704070580532307,0.8804989123381217,0.9702137405651564,0.8800107541006575,0.9685799730222094,0.874466533973604,0.9711915086974923,0.8819510188823659,0.9679941096210514,0.8774386728691838,0.9846052333816393,0.9922727615840512,0.9355321993215912,0.9672291348597762,113.0,34.0,113.0,34.0,131236.0,131310.0,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,B cell,3184.0,0.7807860281038842,0.006440762681230908,0.5234437884681428,0.010804188756712116,0.7839085111305238,0.530943105676,0.7849190276149267,0.5285073833264498,0.7865597428485961,0.5297181613668789,0.7775030186683831,0.5231971910028275,0.7710398402569912,0.5048531009685577,0.8769004425930236,0.9364296250082136,0.6871849062373051,0.8289661671246331,113.0,34.0,113.0,34.0,24279.0,24346.0,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,Monocyte,2877.0,0.9004653000698806,0.0016939432723020007,0.7013598331239846,0.003801838836039273,0.89847918971012,0.702984528183391,0.9010519306025137,0.7001373008015165,0.9030192401899105,0.7046607852582042,0.8998863270091684,0.7037467235150529,0.8998898128376903,0.6952698278617583,0.9476261419103734,0.9734609092872571,0.8244697205954008,0.9080031501021353,112.0,33.0,112.0,34.0,40388.0,40463.0,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,NK cell,2964.0,0.9319741833582587,0.0020278524635932247,0.7417529695076843,0.00361243931602332,0.9315848866372971,0.743988899577552,0.9326955230498738,0.7371449885503258,0.9328682855414872,0.7443967037733068,0.9340281058024517,0.7446944450488441,0.9286941157601839,0.7385398105883932,0.9647894794724973,0.9822369772475974,0.8517315399982865,0.9228930273863198,113.0,34.0,113.0,34.0,36026.0,36099.0,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,T cell,3031.0,0.7663553205480652,0.0029498057456549863,0.6137949363953683,0.005312019115790591,0.7617476555688402,0.6189573924586659,0.7679206912456081,0.6199165411793133,0.7685101152454411,0.6082192868922274,0.7685437029409372,0.6117666675221082,0.7650544377394993,0.6101147939245268,,,,,,,,,,,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,B cell,3184.0,0.6157353448195175,0.015582428329511375,0.4200020990764637,0.028661656995011477,0.632972649999591,0.42731200795133767,0.5956544159598397,0.41007297191257824,0.6084947402711505,0.3953189129413756,0.6299319035681128,0.40085109350187786,0.6116230142988938,0.46645550907514916,,,,,,,,,,,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,Monocyte,2877.0,0.6525432069810243,0.004840529016619713,0.3040218741771539,0.006954510413680823,0.6476498004058009,0.29426261427620215,0.6600571005495897,0.3123523093386016,0.654333278878613,0.30801304980434807,0.6507783749836515,0.30493264451954966,0.6498974800874666,0.3005487529470678,,,,,,,,,,,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,NK cell,2964.0,0.7537511133348206,0.0018405836893770756,0.3944004059816773,0.006765718134906609,0.7550170069025549,0.40376433502304915,0.7557596209891385,0.39168852831488116,0.7537379812862689,0.38671004706283113,0.7532598410667399,0.39868663145299615,0.7509811164294009,0.3911524880546289,,,,,,,,,,,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@7fbfb797,,T cell,3031.0,0.6293602031170562,0.002933003408832908,0.23142060841155804,0.005758412397622767,0.6257412262555833,0.22685393178502083,0.6276904084933326,0.22374695215226645,0.6325767978944378,0.2369021613790202,0.6321328668738077,0.2347302071115994,0.6286597160681199,0.23486978962988325,,,,,,,,,,,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46
+imperial_eskd,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@7fbfb797,,B cell,3184.0,0.5986783996533287,0.011755213067927678,0.28632705243696177,0.012325822040674452,0.6129604609178549,0.3035680264174967,0.58630599501354,0.2727767709188901,0.6017815418993087,0.2935856978198424,0.6054857776067969,0.2781868338076747,0.5868582228291431,0.28351793322090474,,,,,,,,,,,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46
+imperial_eskd,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@7fbfb797,,Monocyte,2877.0,0.7125505614936012,0.0038712262416043027,0.508220128397703,0.003998056255909717,0.7105831097198295,0.5061606807757073,0.7194221396402314,0.5082829241142178,0.7101826681699608,0.5037789709726521,0.7111540706817197,0.5083369391145457,0.7114108192562643,0.5145411270113925,,,,,,,,,,,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46
+imperial_eskd,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@7fbfb797,,NK cell,2964.0,0.6509647141144865,0.0024805007514697593,0.34692293419964704,0.010584406574944121,0.6498718151043331,0.3444137713547861,0.6506981540883262,0.33103510121647445,0.6526251904698361,0.3568096407490931,0.6476092432103879,0.34591309845463797,0.6540191676995488,0.35644305922324343,,,,,,,,,,,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46
+imperial_eskd,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,mean4,,0.895725697380963,0.00229684690007292,0.7113574423831496,0.004250975542879832,0.896094911382793,0.7146038614437662,0.8972200554581177,0.7114501066947374,0.8977568104005508,0.7133105460929985,0.8956522400443738,0.7133973446122726,0.8919044696189792,0.7040253530719732,0.9434803243393834,0.9711000682817799,0.824729591538146,0.9067728698682163,,,,,,,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,mean4,,0.697096246420857,0.002766297438658017,0.4330548289076658,0.0066819229675075835,0.6993467782191968,0.4360740874273137,0.694847957186044,0.43350758768634357,0.6962690289203683,0.42456532417519555,0.7006284556398603,0.42905925924913296,0.6943890121388152,0.4420678860003432,,,,,,,,,,,
+imperial_eskd,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@7fbfb797,,mean4,,0.6478884695946181,0.0020931732177192504,0.34322268086146746,0.0056918797897527905,0.6497891529994002,0.34524910258325275,0.6460291743088575,0.3339604371004622,0.6492915496083859,0.34776911773015196,0.649095489593178,0.34179176962211444,0.645236981463269,0.347342977271356,,,,,,,,,,,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paired_finetune_intradataset_20260927/scores_contrast/imperial_eskd/scsemi_cv_20261002/pooled/contrast.csv

@@ -0,0 +1,11 @@
+dataset,design,unit,arm,celltype,statistic,label,n_genes,pearson_r_generated,spearman_r_generated,pearson_r_broadcast,spearman_r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,condition,condition_sha256,pearson_r_generated_scorer,pearson_r_broadcast_scorer,partial_r_generated_given_broadcast_scorer,r_generated_vs_broadcast_scorer
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3031.0,0.7717707501409442,0.6317444833325218,0.6352016868529187,0.23524650991702134,0.6670781996946106,0.5243354879181512,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.7717707501409442,0.6352016868529187,0.6670781996946106,0.5243354879181512
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3031.0,0.5332258507740787,0.394506517979015,0.6294466207665587,0.445728805171921,0.33952011457561776,0.47927616385326466,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.5332258507740787,0.6294466207665587,0.3395201145756177,0.4792761638532646
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3184.0,0.6277956277407635,0.40280884120161586,0.6290331452237995,0.31350578379141075,0.48202323991758617,0.4732713667273558,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.6277956277407635,0.6290331452237995,0.4820232399175861,0.4732713667273558
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3184.0,0.17211549819511593,0.08786878540974456,0.4870645233040134,0.3784169938931688,0.008470009234422477,0.3390851256705854,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.1721154981951159,0.4870645233040134,0.0084700092344224,0.3390851256705854
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",2877.0,0.6562786961628838,0.30654598120362664,0.7184291928055079,0.5281513008470065,0.37668545742458776,0.6303617332666909,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.6562786961628838,0.7184291928055079,0.3766854574245877,0.6303617332666909
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",2877.0,0.47133753911698684,0.3129464245039556,0.7066219687885489,0.5612828483943736,0.19080085907642785,0.5017586764799835,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.4713375391169868,0.7066219687885489,0.1908008590764278,0.5017586764799835
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",2964.0,0.765594511729008,0.41166148537851305,0.6597572279517877,0.35877128710378403,0.6265719208725514,0.5780595252579894,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.765594511729008,0.6597572279517877,0.6265719208725514,0.5780595252579894
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",2964.0,0.4328983221530598,0.24101238130128164,0.5964102520780005,0.43186165104896884,0.22813570486035467,0.45194964438505314,conditions_pooled_raw.npz@7fbfb797,7fbfb797c40ba266a5a22a572250f7df20b3119772eb426fb9a794de2f36ca46,0.4328983221530598,0.5964102520780005,0.2281357048603546,0.4519496443850531
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",,0.7053598964433999,0.4381901977790693,0.6606053132085035,0.35891872041480566,0.538089704477334,0.5515070282925468,,,0.7053598964433999,0.6606053132085035,0.538089704477334,0.5515070282925468
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",,0.4023943025598103,0.2590835272984992,0.6048858412342804,0.45432257462710807,0.1917316719367057,0.44301740259722167,,,0.4023943025598103,0.6048858412342804,0.19173167193670562,0.4430174025972216

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paired_finetune_intradataset_20260927/scores_contrast/imperial_eskd/scsemi_cv_20261002/pooled/headline.csv

@@ -0,0 +1,2 @@
+dataset,design,unit,arm,label,role,condition,pearson_r,spearman_r,partial_r,broadcast_pearson_r,broadcast_spearman_r,splithalf_r_AB,splithalf_r_AB_sd,splithalf_spearman_AB,sb_reliability,noise_free_ceiling,r_generated_vs_halfB,r_broadcast_vs_halfB,welch_top50,welch_top50_max,welch_top50_chance,welch_top50_broadcast,welch_top50_broadcast_chance,welch_n_sig_obs,welch_n_sig_gen,welch_n_sig_broadcast_per_type,welch_types_scored,limma_top50,limma_top50_max,limma_top50_chance,limma_top50_broadcast,limma_top50_broadcast_chance,limma_n_sig_obs,limma_n_sig_gen,limma_n_sig_broadcast_per_type,limma_types_scored,limma_fbe_top50,limma_fbe_top50_max,limma_fbe_top50_chance,limma_fbe_top50_broadcast,limma_fbe_top50_broadcast_chance,limma_fbe_n_sig_obs,limma_fbe_n_sig_gen,limma_fbe_n_sig_broadcast_per_type,limma_fbe_types_scored,cat50,cat50_chance,cat100,cat100_chance,rbo,rbo_up_down,cat_types,broadcast_cat50,broadcast_cat50_chance,broadcast_cat100,broadcast_cat100_chance,broadcast_rbo,broadcast_rbo_up_down,broadcast_cat_types,repro_pass
+imperial_eskd,scored,scsemi_cv_20261002/pooled,scsemi__raw,"scSemiProfiler, all training pairs (5-fold CV)",scsemi,conditions_pooled_raw.npz@7fbfb797,0.7053598964433999,0.4381901977790693,0.538089704477334,0.6606053132085035,0.35891872041480566,0.895725697380963,0.00229684690007292,0.7113574423831496,0.9434803243393834,0.9711000682817799,0.697096246420857,0.6478884695946181,87,250,4.685080414692495,84,2.267067150501121,2472,634,2242,5,63,250,4.111019221705437,63,2.267067150501121,4880,3153,2104,5,64,250,35.676750362129695,66,5.693941050474507,3140,415,1817,5,0.2,0.00937016082938499,0.21000000000000002,0.01874032165876998,0.2774986735246147,0.19664520671336763,5,0.16799999999999998,0.004534134301002241,0.21399999999999997,0.009068268602004482,0.1772937462567108,0.17125505414813655,5,True

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paired_finetune_intradataset_20260927/scores_contrast/imperial_eskd/scsemi_cv_20261002/pooled/manifest.json

@@ -0,0 +1,384 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "imperial_eskd",
+ "design": "scored",
+ "unit": "scsemi_cv_20261002/pooled",
+ "written_utc": "2026-10-08T04:49:14.262202+00:00",
+ "command": [
+  "tools/contrast_extra.py",
+  "--design",
+  "scored",
+  "--dataset",
+  "imperial_eskd",
+  "--score-dir",
+  "scores/imperial_eskd/scsemi_cv_20261002/pooled",
+  "--arms",
+  "scsemi__raw",
+  "--unit",
+  "scsemi_cv_20261002/pooled",
+  "--threads",
+  "6"
+ ],
+ "threads": 6,
+ "donors": [
+  "C20_1004",
+  "C20_1404",
+  "C21_1004",
+  "C21_1704",
+  "C21_2504",
+  "C23_2204",
+  "C31_1304",
+  "C31_2004",
+  "C31_2704",
+  "C33_1401",
+  "C33_1601",
+  "C33_1901",
+  "C34_1404",
+  "C34_2104",
+  "C34_2504",
+  "C36_1504",
+  "C36_1704",
+  "C36_2104",
+  "C40_1504",
+  "C40_2204",
+  "C40_0105",
+  "C42_1504",
+  "C42_2204",
+  "C42_2704",
+  "C58_1604",
+  "C58_2501",
+  "C58_2901",
+  "C58_0102",
+  "C58_0402",
+  "C58_1003",
+  "C60_2504",
+  "C63_1704",
+  "C63_2404",
+  "C63_2904",
+  "C65_1704",
+  "C65_2104",
+  "C65_2504",
+  "C69_1804",
+  "C82_2504",
+  "C85_2004",
+  "C93_2104",
+  "C93_2704",
+  "C93_0405",
+  "C101_0601",
+  "C101_1101",
+  "C101_1301",
+  "C101_1801",
+  "C101_2001",
+  "C101_2502",
+  "C103_2204",
+  "C104_2204",
+  "C106_2204",
+  "C108_2204",
+  "C108_1501",
+  "C108_1801",
+  "C108_2201",
+  "C113_0605",
+  "C123_2404",
+  "C123_2904",
+  "C123_0505",
+  "C124_2404",
+  "C124_2704",
+  "C124_0105",
+  "C126_2504",
+  "C126_3004",
+  "C126_0605",
+  "C127_2504",
+  "C127_0405",
+  "C127_1105",
+  "C128_2504",
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