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/ji2025_chili/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
+ji2025_chili,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,T cell,3021.0,0.9700144156543491,0.0028458700411116153,0.9442785309613878,0.0020390129920492737,0.9722911985063596,0.9471296839045001,0.9703777505069561,0.9445900327173193,0.9727413635760391,0.9450577941906708,0.9657120543902619,0.9424250024461593,0.9689497112921289,0.9421901415482901,0.9847790025761355,0.9923603189246009,0.9713407990926796,0.9855662327275014,18.0,15.0,18.0,15.0,29690.0,29706.0,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,B cell,3245.0,0.7818569633534205,0.004133249573681813,0.6302172898352632,0.006664433920616452,0.7767031431471295,0.6226494212899112,0.7868002884879267,0.640846926949967,0.7830234073305751,0.6289724140910302,0.7785933856139707,0.6307574001236084,0.7841645921875005,0.6278602867217992,0.8775754501438553,0.936789971201579,0.7731696796062664,0.8793006764504769,18.0,15.0,18.0,15.0,3572.0,3590.0,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,Monocyte,3154.0,0.9617602063680598,0.0048840651987121335,0.8532536694167598,0.005533513944997234,0.9592382298500476,0.851710080359344,0.9548185144279436,0.8566234226547607,0.9675563039554432,0.8606693398271799,0.963070239178731,0.8509825692753139,0.9641177444281339,0.8462829349672008,0.9805074068136308,0.990205739638804,0.9208169216093214,0.9595920599970185,18.0,15.0,18.0,15.0,17220.0,17237.0,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,NK cell,3051.0,0.8597527062579001,0.006809170503855263,0.7069491014230271,0.01051395029754475,0.857080312444169,0.6945343694291769,0.8669745937307356,0.7215036999333527,0.8665572629257434,0.7116244926425445,0.8513005555497886,0.7074865671737648,0.8568508066390638,0.6995963779362973,0.924588202899138,0.9615550961328935,0.8283189004682882,0.9101202670352354,18.0,15.0,18.0,15.0,9068.0,9079.0,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,T cell,3021.0,0.29100031245661434,0.00365013405043346,0.0933153404479076,0.0032753446997112394,0.2881288181497139,0.08933285491813237,0.296035556240911,0.09543536829484768,0.29348373820293316,0.09506402003132265,0.28750855691906274,0.09025033347695738,0.2898448927704509,0.09649412551827795,,,,,,,,,,,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,B cell,3245.0,0.1481703232254676,0.008162369803151602,0.027261403015343154,0.0074613095624433195,0.1514701602587433,0.03248446482987324,0.15484257574076368,0.03442602574519393,0.13413810118600966,0.027401880046423913,0.15192428793850207,0.015271275688321992,0.14847649100331942,0.0267233687669027,,,,,,,,,,,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,Monocyte,3154.0,0.4769046056273207,0.0025685423192394036,0.30732209694620427,0.005173917359426019,0.47234469983533595,0.2993874963327042,0.4779838226005132,0.3083194674554334,0.4779863447894055,0.3136533341214606,0.4776655892166542,0.30642992173771055,0.4785425716946949,0.3088202650837124,,,,,,,,,,,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,NK cell,3051.0,0.15580655368806712,0.006885050027887885,0.06320826056994953,0.013456757261853747,0.15455365249590092,0.051940009522551914,0.16656525032290792,0.08416223774159011,0.151258982500628,0.06737836038511123,0.14889325937650721,0.06101917310563627,0.1577616237443916,0.05154152209485817,,,,,,,,,,,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@a13338f5,,T cell,3021.0,0.21959070752598212,0.0018957508310978326,0.09915905890125064,0.0008385726212966225,0.2197941403935097,0.09951530532359423,0.2197183107989401,0.09913063535800122,0.21894516682587872,0.09925405188576206,0.2171162647272274,0.09781039847788207,0.22237965488435468,0.10008490346101358,,,,,,,,,,,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007
+ji2025_chili,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@a13338f5,,B cell,3245.0,0.12541425495803574,0.011254363578552603,0.036591345783669106,0.009570911339782185,0.13358867682532666,0.04419816614691421,0.11319447053014353,0.025605925532903535,0.11845911833483741,0.03398605742015746,0.14044390844815136,0.0486158757685558,0.12138510065171966,0.030550704049814515,,,,,,,,,,,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007
+ji2025_chili,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@a13338f5,,Monocyte,3154.0,0.3953585113304115,0.001476500364600941,0.2242999241874751,0.004518497597061153,0.39429047657840666,0.2277196579761505,0.39449949763493797,0.22234537432562648,0.39613898722709867,0.22116385915703787,0.39426219381841593,0.2198950588281528,0.39760140139319833,0.23037567065040787,,,,,,,,,,,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007
+ji2025_chili,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@a13338f5,,NK cell,3051.0,0.19645623091008718,0.00732809336964877,0.07912526762028013,0.007060569169413127,0.19213614757559272,0.07785635192243455,0.19894900124750692,0.08770577666347777,0.18772290543678893,0.07774448277498561,0.2071167113645841,0.08339441428839625,0.19635638892596324,0.06892531245210654,,,,,,,,,,,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007
+ji2025_chili,scored,scsemi_cv_20261002/pooled,split_half_A_vs_B,,mean4,,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.005121460495978445,0.8913282209869264,0.7790058887457331,0.8947427867883905,0.79089102056385,0.8974695844469502,0.7865810101878563,0.889669058683188,0.7829128847547115,0.8935207136367067,0.7789824352933968,0.9418625156081898,0.9702277814744693,0.8734115751941388,0.9336448090525581,,,,,,,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,generated:scsemi__raw,scsemi__raw,mean4,,0.26797044874936743,0.0036465726516815285,0.12277677524485113,0.005358189143375955,0.2666243326849235,0.11828620640081541,0.273856801226274,0.13058577480926628,0.2642167916697441,0.1258743986460796,0.2664979233626815,0.11824267600215654,0.2686563948032142,0.12089482036593781,,,,,,,,,,,
+ji2025_chili,scored,scsemi_cv_20261002/pooled,broadcast:conditions_pooled_raw.npz@a13338f5,,mean4,,0.23420492618112912,0.003645011959017163,0.10979389912316875,0.002395891597825257,0.23495236034320893,0.11232237034227338,0.23159032005288213,0.10869692797000226,0.23031654445615093,0.10803711280948575,0.2397347695895947,0.11242893684074673,0.23443063646380896,0.10748414765333562,,,,,,,,,,,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007

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/ji2025_chili/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
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3021.0,0.29436354030391015,0.09289172689587141,0.22039608693345034,0.09749861429165937,0.2517623899268927,0.25957519106387295,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.2943635403039101,0.2203960869334503,0.2517623899268927,0.2595751910638729
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,T cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3021.0,0.12479500212121623,0.043071183652918454,0.27145331834905573,0.22332017952502015,0.08041973007500341,0.1792130960900295,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.1247950021212162,0.2714533183490557,0.0804197300750034,0.1792130960900295
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3245.0,0.15087339535743186,0.029072086345598092,0.13326750229861392,0.03318867346587475,0.12795720051741694,0.19968584972099426,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.1508733953574318,0.1332675022986139,0.1279572005174169,0.1996858497209942
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,B cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3245.0,0.09316132319083319,0.042954239670272135,0.01993963216355321,0.014957835373367154,0.09165018968276631,0.09950736992764438,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.0931613231908331,0.0199396321635532,0.0916501896827663,0.0995073699276443
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3154.0,0.48043734969339996,0.31280213637099785,0.3983317004681723,0.23043456016556318,0.4178994565467743,0.2832269421984822,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.4804373496933999,0.3983317004681723,0.4178994565467743,0.2832269421984822
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,Monocyte,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3154.0,0.3342815634597003,0.2597259224248025,0.35676796217145185,0.23555570709826826,0.29494060477042755,0.1768456687151709,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.3342815634597003,0.3567679621714518,0.2949406047704275,0.1768456687151709
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",3051.0,0.1666806321851843,0.07134034146782263,0.20750320008350984,0.08103662629740357,0.1174703091782992,0.27005207728361336,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.1666806321851843,0.2075032000835098,0.1174703091782992,0.2700520772836133
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,NK cell,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",3051.0,0.16709321309848635,0.1362927059896924,0.10364196133517908,0.07837401366094673,0.15268750452838273,0.1676733728474005,conditions_pooled_raw.npz@a13338f5,a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007,0.1670932130984863,0.103641961335179,0.1526875045283827,0.1676733728474005
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,mean_cp10k,"scSemiProfiler, all training pairs (5-fold CV)",,0.2730887293849816,0.12652657277007248,0.2398746224459366,0.11053961855512523,0.22877233904234578,0.2531350150667407,,,0.2730887293849815,0.23987462244593655,0.22877233904234578,0.25313501506674063
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,mean4,pseudobulk_log1p_cpm,"scSemiProfiler, all training pairs (5-fold CV)",,0.17983277546755902,0.12051101293442137,0.18795071850481,0.13805193391440057,0.154924507264145,0.15580987689506132,,,0.179832775467559,0.1879507185048099,0.15492450726414497,0.1558098768950613

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/ji2025_chili/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
+ji2025_chili,scored,scsemi_cv_20261002/pooled,scsemi__raw,"scSemiProfiler, all training pairs (5-fold CV)",scsemi,conditions_pooled_raw.npz@a13338f5,0.2730887293849816,0.12652657277007248,0.22877233904234578,0.2398746224459366,0.11053961855512523,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.9418625156081898,0.9702277814744693,0.26797044874936743,0.23420492618112912,0,250,0.0,4,0.7031594553072507,2850,0,15,5,0,250,2.1997172639929308,15,2.343864851024169,3048,900,53,5,0,250,2.9900590245417833,20,7.294825089496429,1476,15,55,5,0.028000000000000004,0.020880689209101445,0.062,0.04176137841820289,0.03469104254762278,0.04774462983171538,5,0.044,0.004687729702048338,0.068,0.009375459404096675,0.06530702120731043,0.04590326003768017,5,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/ji2025_chili/scsemi_cv_20261002/pooled/manifest.json

@@ -0,0 +1,262 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "ji2025_chili",
+ "design": "scored",
+ "unit": "scsemi_cv_20261002/pooled",
+ "written_utc": "2026-10-05T13:21:28.768580+00:00",
+ "command": [
+  "tools/contrast_extra.py",
+  "--design",
+  "scored",
+  "--dataset",
+  "ji2025_chili",
+  "--score-dir",
+  "scores/ji2025_chili/scsemi_cv_20261002/pooled",
+  "--arms",
+  "scsemi__raw",
+  "--unit",
+  "scsemi_cv_20261002/pooled",
+  "--threads",
+  "6"
+ ],
+ "threads": 6,
+ "donors": [
+  "N064_TOL",
+  "N064_FU1",
+  "N032_AC",
+  "N038_BC",
+  "N038_AC",
+  "N055_AC",
+  "N136_TOL",
+  "N136_FU1",
+  "N138_TOL",
+  "N138_FU1",
+  "N128_BC",
+  "N128_AC",
+  "N129_BC",
+  "N129_AC",
+  "N147_TOL",
+  "N150_BC",
+  "N158_AC",
+  "N159_BC",
+  "N001_TOL",
+  "N001_FU1",
+  "N002_TOL",
+  "N002_FU1",
+  "N005_BC",
+  "N005_AC",
+  "N012_TOL",
+  "N012_FU1",
+  "N018_BC",
+  "N018_AC",
+  "N022_TOL",
+  "N022_FU1",
+  "N035_TOL",
+  "N043_TOL",
+  "N043_FU1"
+ ],
+ "n_samples": 33,
+ "contrast": {
+  "case_groups": [
+   "TOL",
+   "FU1"
+  ],
+  "control_groups": [
+   "BC",
+   "AC"
+  ],
+  "n_case_donors": 18,
+  "n_control_donors": 15
+ },
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/scsemi_cv_20261002/pooled": {
+   "arms": [
+    "scsemi__raw"
+   ],
+   "summary_sha256": "4fea2c1a53a4b5324fbd0b2a9ba541ed8eb3fb4d83fe6fa7c0e21dc241132071",
+   "contrast_csv_sha256": "3ea8483fc90fb41437b471de9792d891a3892da76703ab022f718264b22bdf84"
+  }
+ },
+ "notes": {
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