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/ye2026_sepsis/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
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,T cell,3258.0,0.9891056786039693,0.0010509806744177592,0.9409648898974033,0.0016081840452600948,0.9901832633061788,0.9422224618573211,0.9901998900918838,0.9412463554542821,0.9880816995671541,0.9419146870551343,0.9889515787722969,0.9412510035040016,0.988111961282333,0.9381899416162778,0.9945230052313375,0.9972577426279214,0.96958465842949,0.9846748998677127,61.0,21.0,61.0,21.0,149041.0,149076.0,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,B cell,3310.0,0.9722818649726397,0.0038519894191463983,0.8664554419274527,0.00526306303090059,0.9752349439499809,0.8674262231871988,0.9674163163881386,0.8629094584103945,0.9715754830998995,0.8648732315609803,0.976984584435456,0.8750968262371378,0.970197996989724,0.8619714702415516,0.9859461593600645,0.9929482158501844,0.9284501761613777,0.9635611948191862,61.0,21.0,61.0,21.0,49846.0,49883.0,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,Monocyte,3289.0,0.9357376064697736,0.001625690542924381,0.7935178753331721,0.004632287744034617,0.9369332179396338,0.789810337875795,0.9346829385213595,0.788209305161708,0.9373484385626267,0.7953805048945396,0.9362582373277957,0.7998195083645836,0.9334651999974515,0.7943697203692343,0.9668021154750295,0.9832609600075808,0.8848731158430908,0.9406769455254502,61.0,21.0,61.0,21.0,55615.0,55654.0,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,NK cell,3240.0,0.9436123326816362,0.004243753179984544,0.7847918892550433,0.005685701397368848,0.9391679166455512,0.7755287178137203,0.9392587743251642,0.7873453137024741,0.9450271603760011,0.7902851552584125,0.9487311927848999,0.7836584932244807,0.9458766192765646,0.7871417662761283,0.9709882128394581,0.9853873415258886,0.8794211739527892,0.9377745858961999,61.0,21.0,61.0,21.0,23895.0,23937.0,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,T cell,3258.0,0.3854330783259878,0.006157756781802424,0.15978741991330764,0.004744745288652891,0.3795669282667178,0.15696819030235054,0.380500578072068,0.1587836446272521,0.39035770067429054,0.1616186111254139,0.38329926439166073,0.15462873948854303,0.39344092022520205,0.16693791402297847,,,,,,,,,,,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,B cell,3310.0,0.3199589259453594,0.008177600823435546,0.18649243017989556,0.0035662730403906834,0.32568207599611815,0.18185368954052805,0.3143964390396611,0.19052718199879123,0.3275401654067855,0.18904232164543006,0.32371533309949196,0.18398963219886683,0.30846061618474035,0.1870493255158617,,,,,,,,,,,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,Monocyte,3289.0,0.5823257347367147,0.009918426197811919,0.27095444730641566,0.0037895303108093784,0.5824714166918143,0.27644264522869716,0.5710524977220325,0.26989215813120015,0.585959894273257,0.2730448039753001,0.5754632144974788,0.2682408036669948,0.5966816504989906,0.2671518255298859,,,,,,,,,,,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,NK cell,3240.0,0.45228345144406756,0.022588310798482676,0.22270540585007118,0.00516871807195607,0.4705257863327681,0.22585089411594084,0.41865469691983775,0.22556659300057783,0.467438484179473,0.21477071096817785,0.43921678094237543,0.220207906859017,0.46558150884588334,0.22713092430664236,,,,,,,,,,,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@3b2d8ef2,,T cell,3258.0,0.26267206946034316,0.006578628513568366,0.3009106580636672,0.003114929320157978,0.2535395739997044,0.2995828776852997,0.2582267688136924,0.3054951264897653,0.2695483043616237,0.3012708515546519,0.265697140389016,0.2969388712965836,0.26634855973767935,0.3012655632920353,,,,,,,,,,,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@3b2d8ef2,,B cell,3310.0,0.2565786391260477,0.013357237539949574,0.3049847972497407,0.004381584418387633,0.27097992232955936,0.3092171619280973,0.23841026181059918,0.29853288505136427,0.2557459464390218,0.302675160240215,0.26795883786734764,0.3081609450280621,0.24979822718371042,0.30633783400096487,,,,,,,,,,,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@3b2d8ef2,,Monocyte,3289.0,0.5494499495603321,0.011387643687682976,0.48232401996600605,0.00997193251659566,0.5461516074338406,0.47618790039662146,0.5366250489963666,0.4710549114071669,0.5528614856975809,0.4954528743161847,0.5446048149517468,0.47938271482882727,0.5670067907221257,0.48954169888122984,,,,,,,,,,,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@3b2d8ef2,,NK cell,3240.0,0.19325823634364078,0.02693559231628049,0.20164343202445217,0.0032424768825348887,0.21804412990983377,0.2040806555804846,0.15281389172847673,0.2026472999533644,0.20933652344912548,0.19985711625136132,0.17902299202529173,0.1969079275834647,0.2070736446054763,0.20472416075358585,,,,,,,,,,,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,mean4,,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.002537193236172007,0.9603798354603361,0.8437469351835087,0.9578894798316365,0.8449276081822147,0.9605081954014203,0.8481133946922667,0.9627313983301121,0.8499564578325509,0.9594129443865183,0.845418224625798,0.9795648732264725,0.9897135650028939,0.9155822810966869,0.9566719065271372,,,,,,,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,mean4,,0.4350002976130323,0.009100217029978763,0.2099849258124225,0.002023105409125062,0.4395615518218546,0.21027885479687913,0.42115105293839983,0.21119239443945534,0.4428240611334515,0.20961911192858046,0.43042364823275175,0.20676677055335543,0.4410411739387041,0.21206749734384212,,,,,,,,,,,
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@3b2d8ef2,,mean4,,0.3154897236225909,0.01114326272301486,0.32246572682596647,0.002657530610983636,0.32217880841823454,0.32226714889762575,0.2965189928372837,0.3194325557254152,0.321873064986838,0.3248140005906032,0.31432094630835056,0.32034761468423445,0.322556805562248,0.32546731423195396,,,,,,,,,,,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13

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/ye2026_sepsis/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
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3258.0,0.37777476829221296,0.157298976573387,0.2548893770824626,0.3032975355216083,0.30450666006975935,0.4511601716530676,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.3777747682922129,0.2548893770824626,0.3045066600697593,0.4511601716530676
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3258.0,0.2317567821636163,0.11493887599557248,0.2164745523777111,0.24091623128521705,0.19371787584333694,0.21793984219477572,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.2317567821636163,0.2164745523777111,0.1937178758433369,0.2179398421947757
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3310.0,0.32571976493328914,0.18844066708159457,0.27458639801653467,0.31750275993649496,0.2705465870269831,0.27545603380804967,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.3257197649332891,0.2745863980165346,0.2705465870269831,0.2754560338080496
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3310.0,0.2419264255614331,0.16100323584319282,0.2711145517540278,0.2962371727943274,0.20808010290928658,0.16353149301776773,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.2419264255614331,0.2711145517540278,0.2080801029092865,0.1635314930177677
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3289.0,0.5835203193635443,0.27069880964124055,0.5481103923782986,0.4954952817895685,0.4358649661929322,0.4817528015996326,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.5835203193635443,0.5481103923782986,0.4358649661929322,0.4817528015996326
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3289.0,0.19462942906730224,0.0923130235553647,0.6203629305570988,0.539101617083415,-0.025438390460109463,0.34393408878073184,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.1946294290673022,0.6203629305570988,-0.0254383904601094,0.3439340887807318
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3240.0,0.4540415502266361,0.2274501093458253,0.1861970975708186,0.21007103949306638,0.4218717919988914,0.44542475698561723,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.4540415502266361,0.1861970975708186,0.4218717919988914,0.4454247569856172
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3240.0,0.2010611380406599,0.08405087974516219,0.05592238177293225,0.11057984751616548,0.19544261871381305,0.14060253076107798,conditions_pooled_raw.npz@3b2d8ef2,3b2d8ef2a51603a490100c336f3702cdac11d1ba2288490e36dd52986f56dd13,0.2010611380406599,0.0559223817729322,0.195442618713813,0.1406025307610779
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",,0.43526410070392063,0.21097214066051187,0.31594581626202867,0.33159165418518455,0.3581975013221415,0.4134484410115917,,,0.43526410070392063,0.31594581626202856,0.3581975013221415,0.4134484410115917
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",,0.21734344370825287,0.11307650378482303,0.29096860411544245,0.29670871716978126,0.14295055175158178,0.2165019886885883,,,0.21734344370825287,0.29096860411544245,0.14295055175158175,0.21650198868858828

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/ye2026_sepsis/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
+ye2026_sepsis,scored,scsemi_cv_20261002/pooled,scsemi__raw,"scSemiProfiler, all training pairs (5-fold CV)",scsemi,conditions_pooled_raw.npz@3b2d8ef2,0.43526410070392063,0.21097214066051187,0.3581975013221415,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.4350002976130323,0.3154897236225909,6,250,1.7690275160883284,21,2.242290489478891,7946,107,1378,5,18,250,4.557157040881058,36,2.242290489478891,6015,5228,850,5,15,250,32.42074038055368,32,5.841610666408343,3476,237,500,5,0.039999999999999994,0.011762114586105068,0.039999999999999994,0.023524229172210136,0.0713051108579612,0.05469490936475394,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,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/ye2026_sepsis/scsemi_cv_20261002/pooled/manifest.json

@@ -0,0 +1,313 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "ye2026_sepsis",
+ "design": "scored",
+ "unit": "scsemi_cv_20261002/pooled",
+ "written_utc": "2026-10-08T01:58:38.230434+00:00",
+ "command": [
+  "tools/contrast_extra.py",
+  "--design",
+  "scored",
+  "--dataset",
+  "ye2026_sepsis",
+  "--score-dir",
+  "scores/ye2026_sepsis/scsemi_cv_20261002/pooled",
+  "--arms",
+  "scsemi__raw",
+  "--unit",
+  "scsemi_cv_20261002/pooled",
+  "--threads",
+  "6"
+ ],
+ "threads": 6,
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC01",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S136",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S77",
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