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/giroux2022/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
+giroux2022,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,T cell,2886.0,0.977692910615971,0.0005845056028375057,0.9567748766598327,0.0010665150637483981,0.9784232896291553,0.9572704889874608,0.9775182461205701,0.9566800969724132,0.9777895501548801,0.9582740647546185,0.9768279832270597,0.955476585933922,0.9779054839481897,0.9561731466507493,0.9887206505801343,0.9943443319998029,0.9779100172146775,0.9888933295430188,11.0,13.0,11.0,13.0,72513.0,72521.0,
+giroux2022,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,B cell,3030.0,0.8008420040795332,0.005730220826473553,0.656470968843698,0.009792392287340674,0.8067957987895523,0.6657984494559717,0.8070182223647087,0.6676845910252804,0.7954584229480332,0.6501045464281896,0.7957355452506519,0.6455219934085297,0.7992020310447199,0.6532452639005188,0.8894084014759182,0.9430845144926928,0.7926139137855807,0.8902886687954534,11.0,13.0,11.0,13.0,8684.0,8699.0,
+giroux2022,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,Monocyte,3034.0,0.9124495695435864,0.0035525439775169966,0.7311341710383313,0.010970289568925727,0.9072459841929686,0.7153130775963666,0.9109038686569165,0.7348274541505572,0.9136550511627353,0.7255975836132864,0.916669869650293,0.7360438451724537,0.9137730740550182,0.7438888946589927,0.9542207900011147,0.9768422544101554,0.8446880470273408,0.919069119831224,11.0,13.0,11.0,13.0,23649.0,23662.0,
+giroux2022,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,NK cell,2931.0,0.8943398230182951,0.0010571377621718778,0.7956717487799237,0.0031790464401430987,0.8937766088919461,0.7904189954622785,0.8938289835132966,0.7966185391837984,0.8931894990968272,0.7951708034234474,0.895234272308369,0.7978169532490439,0.8956697512810363,0.7983334525810509,0.9442232192461888,0.9717114897160519,0.8862106889196715,0.9413876400928958,11.0,13.0,11.0,13.0,14522.0,14539.0,
+giroux2022,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,T cell,2886.0,0.5866333426756174,0.0008058808803079455,0.4953805136268308,0.0022645635544288425,0.5862077725701046,0.4960344242837891,0.5877780445472599,0.4928879445186616,0.5871144590551621,0.498368383344379,0.5857552321758887,0.4962695991744662,0.5863112050296716,0.4933422168128582,,,,,,,,,,,
+giroux2022,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,B cell,3030.0,0.37875961494556043,0.01180213030576762,0.19870072845634867,0.005468384728344415,0.3833843453246739,0.20032903352641654,0.3876848993396325,0.19891084131843925,0.3606659911884712,0.19091988695289752,0.3733369124857867,0.19727195683972057,0.3887259263892377,0.2060719236442695,,,,,,,,,,,
+giroux2022,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,Monocyte,3034.0,0.5906065101784593,0.004043440611805613,0.32601712253961795,0.005786022839814515,0.5892149259034483,0.3309133362831494,0.5859958665653416,0.3265804323616316,0.5970672421059853,0.3171112372368601,0.5907997132372776,0.3312308991020678,0.5899548030802435,0.324249707714381,,,,,,,,,,,
+giroux2022,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,NK cell,2931.0,0.5369455027701213,0.0041590628119245274,0.38275252063758647,0.001983277416397202,0.5352040327218934,0.38263238878795075,0.5420882811895334,0.3858277988298792,0.5386105792389183,0.3829158702845248,0.5378838891533375,0.3820217042617409,0.5309407315469238,0.38036484102383644,,,,,,,,,,,
+giroux2022,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@1370617c,,T cell,2886.0,0.5850721270132853,0.0031768974665744116,0.5104226196041235,0.003972068902066255,0.5821072032935407,0.5051666463881263,0.5844064718743435,0.5126109559913398,0.5902250698647531,0.5144159027984148,0.5830022768903529,0.5072839289364812,0.5856196131434361,0.5126356639062554,,,,,,,,,,,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015
+giroux2022,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@1370617c,,B cell,3030.0,0.4523007352098027,0.007591980493510723,0.3856626967932806,0.010597511296165504,0.44893540532951054,0.38405464917481996,0.45117337417837944,0.3834584962488396,0.4446842314682479,0.3792104867091798,0.45177396275741294,0.37761399084023134,0.46493670231546247,0.4039758609933321,,,,,,,,,,,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015
+giroux2022,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@1370617c,,Monocyte,3034.0,0.6640107322838724,0.009096883981758553,0.539371815224471,0.014516028713282069,0.6530218178944003,0.5238154899500747,0.664584875676205,0.5317631064971495,0.6581444221924742,0.5366198052137001,0.6675157082550832,0.542341630867846,0.6767868374011994,0.5623190435935848,,,,,,,,,,,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015
+giroux2022,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@1370617c,,NK cell,2931.0,0.5407171360374308,0.006485489030946017,0.4496009511847376,0.008928941058721437,0.5448802741154799,0.455187540510032,0.5320022613265573,0.437769643562357,0.5354992958232113,0.4422057263326938,0.5455088126660962,0.45644039334681047,0.5456950362558095,0.4564014521717947,,,,,,,,,,,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015
+giroux2022,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,mean4,,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.003199371217261624,0.8965604203759056,0.7822002528755194,0.897317330163873,0.7889526703330123,0.8950231308406189,0.7822867495548855,0.8961169176090934,0.7837148444409874,0.896637585082241,0.787910189447828,0.9441432653258389,0.9714956476546757,0.8753556667368176,0.934909689565648,,,,,,,
+giroux2022,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,mean4,,0.5232362426424395,0.0019332057520961088,0.35071272131509595,0.001983546591883583,0.52350276913003,0.35247729572032643,0.5258867729104418,0.3510517542571529,0.5208645678971342,0.34732884445466533,0.5219439367630726,0.3516985398444989,0.5239831665115191,0.35100717229883627,,,,,,,,,,,
+giroux2022,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@1370617c,,mean4,,0.5605251826360979,0.004751509013579095,0.4712645207016532,0.0072351032973155946,0.5572361751582329,0.4670560815057632,0.5580417457638713,0.46640055057492147,0.5571382548371716,0.4681129802634971,0.5619501901422363,0.47091998599784224,0.5682595472789769,0.4838330051662417,,,,,,,,,,,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015

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/giroux2022/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
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",2886.0,0.5896983572148723,0.4973051043679765,0.5864764503055301,0.5137046185745339,0.41608350514079784,0.5118253037060416,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.5896983572148723,0.5864764503055301,0.4160835051407978,0.5118253037060416
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",2886.0,0.47668856642514423,0.4471696371253239,0.6077451868574512,0.5406572385492411,0.3059147485870827,0.421948813227649,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.4766885664251442,0.6077451868574512,0.3059147485870827,0.421948813227649
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3030.0,0.4023801437336676,0.2014409649354061,0.48025603753384744,0.4160595867097935,0.2748298277172872,0.37190657777381525,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.4023801437336676,0.4802560375338474,0.2748298277172872,0.3719065777738152
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3030.0,0.199437720590521,0.17337190293024077,0.4644022343428308,0.4073840878062634,0.09440310101549665,0.2553919598939267,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.199437720590521,0.4644022343428308,0.0944031010154966,0.2553919598939267
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3034.0,0.6055701581942391,0.3332307440240624,0.6794468550874515,0.5822843980734358,0.4504975396560621,0.45907721684011676,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.6055701581942391,0.6794468550874515,0.4504975396560621,0.4590772168401167
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3034.0,0.30911861040995087,0.24571179138596339,0.6731923266540611,0.5877699132162567,0.1674763590975495,0.28272449437038877,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.3091186104099508,0.6731923266540611,0.1674763590975495,0.2827244943703887
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",2931.0,0.5515222487535836,0.39612090221478546,0.554884628817489,0.4715372337505029,0.41146669564200294,0.43994589539010526,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.5515222487535836,0.554884628817489,0.4114666956420029,0.4399458953901052
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",2931.0,0.34077310726227117,0.3117762283405809,0.5368131432639086,0.48425117234266635,0.22347878449113212,0.2997164391765415,conditions_pooled_raw.npz@1370617c,1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015,0.3407731072622711,0.5368131432639086,0.2234787844911321,0.2997164391765415
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",,0.5372927269740906,0.35702442888555763,0.5752659929360795,0.4958964592770665,0.38821939203903755,0.4456887484275197,,,0.5372927269740906,0.5752659929360795,0.38821939203903755,0.44568874842751965
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",,0.33150450117197183,0.2945073899455273,0.5705382227795629,0.5050156029786069,0.19781824829781525,0.3149454266671265,,,0.3315045011719718,0.5705382227795629,0.19781824829781522,0.3149454266671265

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/giroux2022/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
+giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,"scSemiProfiler, all training pairs (5-fold CV)",scsemi,conditions_pooled_raw.npz@1370617c,0.5372927269740906,0.35702442888555763,0.38821939203903755,0.5752659929360795,0.4958964592770665,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.5232362426424395,0.5605251826360979,0,101,0.0,5,0.15608498456545283,337,0,8,5,0,157,2.039906430225203,16,0.3361429905753681,1123,419,11,5,3,155,2.406692908181444,12,0.46703603072378436,620,15,9,5,0.076,0.020777588521796543,0.066,0.041555177043593086,0.06076227799889673,0.0848269717869077,5,0.128,0.004897943725432538,0.13399999999999998,0.009795887450865076,0.16975308975867145,0.14127058542196963,5,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/giroux2022/scsemi_cv_20261002/pooled/manifest.json

@@ -0,0 +1,259 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "giroux2022",
+ "design": "scored",
+ "unit": "scsemi_cv_20261002/pooled",
+ "written_utc": "2026-10-08T01:58:48.212788+00:00",
+ "command": [
+  "tools/contrast_extra.py",
+  "--design",
+  "scored",
+  "--dataset",
+  "giroux2022",
+  "--score-dir",
+  "scores_nosex/giroux2022/scsemi_cv_20261002/pooled",
+  "--arms",
+  "scsemi__raw",
+  "--unit",
+  "scsemi_cv_20261002/pooled",
+  "--threads",
+  "6"
+ ],
+ "threads": 6,
+ "donors": [
+  "450905_d0",
+  "450905_d14",
+  "0B943B_d0",
+  "0B943B_d14",
+  "7085CA_d0",
+  "7085CA_d7",
+  "7085CA_d14",
+  "2AD75E_d0",
+  "2AD75E_d7",
+  "2AD75E_d14",
+  "B85D75_d0",
+  "B85D75_d7",
+  "180E1A_d0",
+  "180E1A_d7",
+  "180E1A_d14",
+  "82CCF5_d0",
+  "82CCF5_d7",
+  "82CCF5_d14",
+  "BAAF62_d0",
+  "BAAF62_d7",
+  "BAAF62_d14",
+  "0BF51C_d0",
+  "0BF51C_d7",
+  "0BF51C_d14"
+ ],
+ "n_samples": 24,
+ "contrast": {
+  "case_groups": [
+   "severe"
+  ],
+  "control_groups": [
+   "mild"
+  ],
+  "n_case_donors": 11,
+  "n_control_donors": 13
+ },
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled": {
+   "arms": [
+    "scsemi__raw"
+   ],
+   "summary_sha256": "a9aceb5ba082c625923496f45bd317d91b45cf7b888a1c262b979cbb60f58595",
+   "contrast_csv_sha256": "e3b0c7e53990fabea7059d39ab6b9f63bb3d3e91073d9a343a9f2f604a02f6d6"
+  }
+ },
+ "notes": {
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