Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw2_scsemi5nt/per_donor.csv

@@ -0,0 +1,78 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
+scsemi5nt,Abd-PS04,ped_sepsis,1500,5449,150,0.20466666666666666,0.14094329234721967,0.034,0.17030647825289044,0.504,0.5608368507983116,0.016666666666666666,0.02147182969352175,0.002,0.003853918150119288,0.23866666666666667,0.10258763075793724,0.39960482045635276,0.8147806942228808,0.7765147761495397,3,False,0.96,0.29333333333333333,0.7666666666666667,0.5733333333333334,50.4,56.083685079831156,2184.0,2716.0
+scsemi5nt,Abd-PS05,ped_sepsis,1500,6924,150,0.742,0.30387059503177355,0.17733333333333334,0.5060658578856152,0.04,0.07019064124783363,0.0033333333333333335,0.0891103408434431,0.0013333333333333333,0.008954361640670132,0.036,0.021808203350664357,0.9046424032351242,0.6930472386554026,0.6759523219823217,38,False,0.9933333333333333,0.11333333333333333,0.98,0.4,4.0,7.0190641247833625,2182.0,2313.0
+scsemi5nt,Abd-PS07,ped_sepsis,1500,3472,150,0.908,0.8626152073732719,0.08666666666666667,0.023329493087557603,0.0,0.002304147465437788,0.0,0.09331797235023041,0.002,0.0002880184331797235,0.0033333333333333335,0.018145161290322582,0.2208678955453149,0.805531392820092,0.8116703389314969,5,False,0.9333333333333333,0.20666666666666667,0.94,0.31333333333333335,0.0,0.2304147465437788,2182.5,1614.0
+scsemi5nt,Abd-PS19,ped_sepsis,1500,7984,150,0.7406666666666667,0.4622995991983968,0.19066666666666668,0.11209919839679358,0.034,0.2937124248496994,0.004666666666666667,0.05586172344689379,0.0026666666666666666,0.0156563126252505,0.027333333333333334,0.06037074148296593,0.713869071476286,0.20809386747845918,0.7147909375567627,21,False,0.88,0.13333333333333333,0.9866666666666667,0.25333333333333335,3.4000000000000004,29.37124248496994,2183.0,2111.0
+scsemi5nt,Abd-PS20,ped_sepsis,1500,7286,150,0.5433333333333333,0.30496843261048584,0.30466666666666664,0.5780949766675817,0.03333333333333333,0.08770244304144935,0.04933333333333333,0.007823222618720834,0.06333333333333334,0.0005489980785067252,0.006,0.02086192698325556,0.6853186933845734,0.8176933692244222,0.7262770109503364,32,False,0.84,0.12,0.92,0.38,3.3333333333333335,8.770244304144935,2182.0,1820.0
+scsemi5nt,Abd-PS23,ped_sepsis,1500,4309,150,0.698,0.2529589231840334,0.21333333333333335,0.3272220932931075,0.044,0.32142028312833604,0.011333333333333334,0.013460199582269667,0.0,0.002088651659317707,0.03333333333333333,0.08284984915293572,0.8900821536319332,0.5989978288681517,0.7356038733882105,27,False,0.8,0.14,0.9333333333333333,0.2866666666666667,4.3999999999999995,32.1420283128336,2183.0,1832.0
+scsemi5nt,Abd-PS27,ped_sepsis,1500,9427,150,0.6426666666666667,0.6126021003500584,0.06733333333333333,0.06078285774901877,0.112,0.13196138750397793,0.09733333333333333,0.010289593720165482,0.004666666666666667,0.0029701920016972526,0.076,0.1813938686750822,0.2507105123581203,0.5429659016547174,0.8876800237048446,1,True,0.7133333333333334,0.19333333333333333,0.7266666666666667,0.56,11.200000000000001,13.196138750397793,2184.0,2356.0
+scsemi5nt,Abd-S102,adult_sepsis,1500,9512,150,0.702,0.47981497056349875,0.202,0.39318755256518084,0.054,0.0053616484440706475,0.007333333333333333,0.095878889823381,0.002,0.0007359125315391085,0.03266666666666666,0.02502102607232969,0.5594662181104568,0.4780589924443877,0.7352159469424474,29,False,0.9666666666666667,0.14,0.98,0.3933333333333333,5.4,0.5361648444070648,2181.5,1646.0
+scsemi5nt,Abd-S103,adult_sepsis,1500,9423,150,0.7353333333333333,0.4813753581661891,0.186,0.14782977820227103,0.04466666666666667,0.0024408362517245037,0.0,0.04393505253104107,0.0,0.00021224663058473945,0.034,0.3242067282181895,0.6687080547596306,0.5664430341984366,0.7107524190957855,25,False,0.9333333333333333,0.3333333333333333,0.96,0.32,4.466666666666667,0.24408362517245036,2182.0,971.0
+scsemi5nt,Abd-S120,adult_sepsis,1500,5783,150,0.7213333333333334,0.3140238630468615,0.19666666666666666,0.11049628220646723,0.036,0.46446481065191075,0.013333333333333334,0.07297250561992046,0.0013333333333333333,0.0008646031471554556,0.03133333333333333,0.03717793532768459,0.9878971698656983,0.5118693118899336,0.7456081829889156,41,False,0.82,0.14,0.94,0.29333333333333333,3.5999999999999996,46.44648106519107,2184.0,2845.0
+scsemi5nt,Abd-S123,adult_sepsis,1500,6299,150,0.6913333333333334,0.16986823305286552,0.18,0.08779171297031275,0.05333333333333334,0.5027782187648833,0.027333333333333334,0.10938244165740593,0.002,0.0007937767899666614,0.046,0.1293856167645658,1.229759221040377,0.8072659461461709,0.8484442096661835,42,False,0.7,0.28,0.7933333333333333,0.5466666666666666,5.333333333333334,50.277821876488325,2185.0,2261.0
+scsemi5nt,Abd-S156,adult_sepsis,1500,7004,150,0.686,0.3343803540833809,0.20066666666666666,0.08209594517418618,0.050666666666666665,0.39406053683609366,0.026,0.0910908052541405,0.0013333333333333333,0.0012849800114220445,0.035333333333333335,0.0970873786407767,0.9404774414620218,0.4844585291172235,0.8678963243442197,15,False,0.78,0.2733333333333333,0.8066666666666666,0.4666666666666667,5.066666666666666,39.406053683609365,2182.0,1821.0
+scsemi5nt,Abd-S39,adult_sepsis,1500,4291,150,0.676,0.13819622465625728,0.20533333333333334,0.06152412025168958,0.048666666666666664,0.6933115823817292,0.022,0.049638778839431366,0.0006666666666666666,0.0013982754602656724,0.04733333333333333,0.05593101841062689,1.363225976850773,0.9886753042539405,0.8594064887821008,63,False,0.5266666666666666,0.14666666666666667,0.66,0.36,4.866666666666666,69.33115823817292,2181.0,3523.0
+scsemi5nt,Abd-S42,adult_sepsis,1500,6567,150,0.3893333333333333,0.5748439165524593,0.048,0.09760925841327851,0.4666666666666667,0.17039744175422566,0.022,0.05862646566164154,0.013333333333333334,0.0016750418760469012,0.06066666666666667,0.0968478757423481,0.615855032739455,0.29513901722746333,0.7677565251045403,4,False,0.74,0.18666666666666668,0.8,0.52,46.666666666666664,17.039744175422566,2182.0,1982.0
+scsemi5nt,Abd-S47,adult_sepsis,1500,7971,150,0.5426666666666666,0.7027976414502571,0.2886666666666667,0.20474219044034625,0.076,0.03224187680341237,0.08,0.019069125580228326,0.010666666666666666,0.0006272738677706687,0.002,0.040521891857985194,0.39730573328315144,0.5195757542533206,0.8324636539417524,8,False,0.7533333333333333,0.11333333333333333,0.8133333333333334,0.5266666666666666,7.6,3.224187680341237,2184.5,2030.0
+scsemi5nt,Abd-S51,adult_sepsis,1500,6865,150,0.30333333333333334,0.25273124544792425,0.044,0.269482884195193,0.486,0.3551347414420976,0.012666666666666666,0.03670793882010197,0.013333333333333334,0.0014566642388929353,0.14066666666666666,0.08448652585579024,0.49904831269725664,0.5536325208613101,0.7306271845024418,10,False,0.94,0.26666666666666666,0.8666666666666667,0.44666666666666666,48.6,35.51347414420976,2184.0,1849.0
+scsemi5nt,Abd-S54,adult_sepsis,1500,7818,150,0.4613333333333333,0.4854182655410591,0.288,0.1364799181376311,0.092,0.012918905090816066,0.11266666666666666,0.340752110514198,0.01,0.0011511895625479663,0.036,0.023279611153747763,0.5043407521105142,0.542590974860753,0.820305373395718,34,False,0.5733333333333334,0.07333333333333333,0.36,0.3333333333333333,9.2,1.2918905090816066,2181.0,1933.5
+scsemi5nt,Abd-S57,adult_sepsis,1500,14291,150,0.7166666666666667,0.8422783570079071,0.198,0.009026660135749773,0.04733333333333333,0.016164019312854244,0.004666666666666667,0.10671051710866979,0.0013333333333333333,0.0012595339724302008,0.032,0.024560912462388916,0.4553110815664871,0.7914600367218484,0.7111544239819755,62,False,0.84,0.30666666666666664,0.9733333333333334,0.28,4.733333333333333,1.6164019312854245,2183.5,852.0
+scsemi5nt,Abd-S66,adult_sepsis,1500,7946,150,0.234,0.49295242889504154,0.042666666666666665,0.23873647118046817,0.5026666666666667,0.03788069468915178,0.042666666666666665,0.18688648376541656,0.004666666666666667,0.0003775484520513466,0.17333333333333334,0.04316637301787063,1.198484101015186,0.3761230913507734,0.7445684551756047,55,False,0.7533333333333333,0.06666666666666667,0.7133333333333334,0.38666666666666666,50.26666666666667,3.7880694689151775,2182.0,1821.0
+scsemi5nt,Abd-S79,adult_sepsis,1500,8044,150,0.7266666666666667,0.5500994530084535,0.18933333333333333,0.30892590750870214,0.04466666666666667,0.024365987071108902,0.0,0.09373446046742914,0.002,0.00012431626056688214,0.037333333333333336,0.022749875683739432,0.4266540692855959,0.44539155608923936,0.7070337530834385,15,False,0.9333333333333333,0.06666666666666667,0.9466666666666667,0.4,4.466666666666667,2.4365987071108903,2185.0,2389.5
+scsemi5nt,Abd-S83,adult_sepsis,1500,6209,150,0.6746666666666666,0.3924947656627476,0.20933333333333334,0.16991464003865356,0.050666666666666665,0.049927524561120956,0.02,0.3013367692059913,0.0006666666666666666,0.0009663391850539539,0.04466666666666667,0.0853599613464326,0.644659472808289,0.5175117745021829,0.8712421345400344,6,False,0.7466666666666667,0.13333333333333333,0.78,0.38,5.066666666666666,4.992752456112096,2184.0,1649.0
+scsemi5nt,Abd-S98,adult_sepsis,1500,5010,150,0.6706666666666666,0.7477045908183633,0.216,0.10958083832335329,0.052,0.019560878243512974,0.02266666666666667,0.11037924151696607,0.0006666666666666666,0.0015968063872255488,0.038,0.011177644710578843,0.33136127744510985,0.6072577152177415,0.8445969827616477,66,False,0.7933333333333333,0.2,0.8266666666666667,0.34,5.2,1.9560878243512974,2181.0,2016.0
+scsemi5nt,HC01,adult_HC,1500,10173,150,0.494,0.5901897178806645,0.29533333333333334,0.09938071365378945,0.082,0.1862774009633343,0.10866666666666666,0.06772830040302762,0.008666666666666666,0.028408532389658903,0.011333333333333334,0.028015334709525212,0.47378197188636595,0.27621020614536834,0.8592788138674134,11,False,0.7866666666666666,0.12,0.72,0.4866666666666667,8.200000000000001,18.62774009633343,2184.0,2276.0
+scsemi5nt,HC05,adult_HC,1500,11075,150,0.5253333333333333,0.6924604966139954,0.2713333333333333,0.09498871331828443,0.09266666666666666,0.08099322799097065,0.1,0.10455981941309254,0.005333333333333333,0.01164785553047404,0.005333333333333333,0.015349887133182845,0.3760361173814898,0.49553771268867686,0.8439579139033108,14,False,0.7733333333333333,0.17333333333333334,0.82,0.38666666666666666,9.266666666666666,8.099322799097065,2184.0,2040.0
+scsemi5nt,HC07,adult_HC,1500,9812,150,0.346,0.3848348960456584,0.05466666666666667,0.03770892784345699,0.466,0.21962902568283735,0.05,0.3080921320831635,0.014,0.019262128006522626,0.06933333333333333,0.03047289033836119,0.604378312270689,0.5016753560372793,0.7769847103006375,37,False,0.66,0.18666666666666668,0.7,0.38666666666666666,46.6,21.962902568283734,2180.0,2035.0
+scsemi5nt,HC09,adult_HC,1500,4839,150,0.498,0.6319487497416821,0.292,0.06013639181649101,0.09066666666666667,0.1529241578838603,0.10733333333333334,0.11365984707584212,0.005333333333333333,0.012399256044637322,0.006666666666666667,0.028931597437487085,0.46372721636701797,0.3928839090164178,0.8597074120445246,11,False,0.76,0.1,0.74,0.3466666666666667,9.066666666666666,15.29241578838603,2183.0,2510.0
+scsemi5nt,HC12,adult_HC,1500,3720,150,0.4886666666666667,0.5456989247311828,0.27266666666666667,0.05725806451612903,0.09933333333333333,0.14623655913978495,0.12066666666666667,0.2196236559139785,0.006,0.008870967741935484,0.012666666666666666,0.022311827956989248,0.4308172043010752,0.4256812394222076,0.8524942038812398,16,False,0.8533333333333334,0.10666666666666667,0.7133333333333334,0.37333333333333335,9.933333333333334,14.623655913978496,2184.0,2457.5
+scsemi5nt,HC13,adult_HC,1500,10111,150,0.49066666666666664,0.5676985461378696,0.29133333333333333,0.0842646622490357,0.084,0.11433092671348037,0.11933333333333333,0.20393630699238452,0.006666666666666667,0.008109979230540996,0.008,0.021659578676688756,0.41413734216859527,0.4369298937899649,0.8470861765837204,8,False,0.8133333333333334,0.10666666666666667,0.72,0.47333333333333333,8.4,11.433092671348037,2182.0,2055.0
+scsemi5nt,HC16,adult_HC,1500,9614,150,0.502,0.511441647597254,0.2926666666666667,0.05325566881630955,0.07866666666666666,0.1367796962762638,0.11,0.28073642604535054,0.0033333333333333335,0.010609527771999168,0.013333333333333334,0.007177033492822967,0.491134595381735,0.4836218205568927,0.8566049290421552,19,False,0.6533333333333333,0.12666666666666668,0.6533333333333333,0.28,7.866666666666666,13.67796962762638,2183.0,1764.0
+scsemi5nt,IC10,adult_ICU_ctrl,1500,7504,150,0.48933333333333334,0.5834221748400853,0.2866666666666667,0.12526652452025586,0.08733333333333333,0.16977611940298507,0.10466666666666667,0.09461620469083155,0.005333333333333333,0.003598081023454158,0.02666666666666667,0.02332089552238806,0.3530632551528074,0.24242877137722152,0.8823638050338655,1,True,0.7066666666666667,0.28,0.76,0.62,8.733333333333333,16.977611940298505,2182.0,2052.0
+scsemi5nt,IC15,adult_ICU_ctrl,1500,15576,150,0.384,0.5791602465331279,0.05733333333333333,0.045839753466872114,0.4613333333333333,0.278954802259887,0.023333333333333334,0.04840780688238315,0.024,0.0104648176682075,0.05,0.03717257318952234,0.4404694401643554,0.3534688345221992,0.7941867882637489,21,False,0.68,0.2,0.8133333333333334,0.4066666666666667,46.13333333333333,27.8954802259887,2182.0,1517.0
+scsemi5nt,IC16,adult_ICU_ctrl,1500,5750,150,0.3293333333333333,0.3391304347826087,0.04933333333333333,0.1537391304347826,0.47933333333333333,0.3226086956521739,0.037333333333333336,0.15878260869565217,0.004666666666666667,0.003130434782608696,0.1,0.022608695652173914,0.471304347826087,0.38035355726134995,0.791002220865807,20,False,0.6733333333333333,0.08666666666666667,0.6866666666666666,0.43333333333333335,47.93333333333333,32.26086956521739,2183.0,1942.0
+scsemi5nt,IC19,adult_ICU_ctrl,1500,7135,150,0.746,0.3690259285213735,0.16733333333333333,0.09067974772249475,0.04133333333333333,0.4583041345480028,0.002,0.045269796776454096,0.004666666666666667,0.0005606166783461808,0.03866666666666667,0.03615977575332866,0.9204811959822471,0.4993858366267516,0.6921832518282655,16,False,0.9533333333333334,0.18666666666666668,0.9866666666666667,0.34,4.133333333333333,45.83041345480028,2184.0,2329.0
+scsemi5nt,IC22,adult_ICU_ctrl,1500,2107,150,0.20733333333333334,0.16753678215472234,0.03266666666666666,0.01613668723303275,0.49733333333333335,0.722828666350261,0.020666666666666667,0.019933554817275746,0.002,0.04129093497864262,0.24,0.0322733744660655,0.5295725359911405,1.1074762767823565,0.7650024147871736,25,False,0.8533333333333334,0.11333333333333333,0.7533333333333333,0.4266666666666667,49.733333333333334,72.2828666350261,2183.5,3217.0
+scsemi5nt,IC23,adult_ICU_ctrl,1500,13774,150,0.798,0.42819805430521274,0.14333333333333334,0.11986351096268331,0.029333333333333333,0.3843473210396399,0.0,0.024466385944533178,0.006666666666666667,0.007840859590532889,0.02266666666666667,0.03528386815739799,0.7865435361308747,0.35382576641913854,0.658002513209732,36,False,0.9866666666666667,0.2,1.0,0.3466666666666667,2.933333333333333,38.434732103963995,2182.0,1894.0
+scsemi5nt,PHC01,ped_HC,1500,8497,150,0.51,0.5416029186771801,0.2966666666666667,0.15381899493939039,0.08466666666666667,0.06731787689772861,0.09533333333333334,0.10862657408497117,0.009333333333333334,0.014240320112981052,0.004,0.11439331528774861,0.32039292299242866,0.33489954236308517,0.7853427168775928,56,False,0.76,0.48,0.7733333333333333,0.36,8.466666666666667,6.731787689772862,2180.0,461.0
+scsemi5nt,PHC02,ped_HC,1500,6519,150,0.636,0.5781561589200798,0.078,0.16643657002607762,0.12933333333333333,0.16612977450529223,0.108,0.057984353428439946,0.002,0.006749501457278723,0.04666666666666667,0.02454364166283172,0.2599650253106305,0.207938379256992,0.8813480924126116,4,False,0.6,0.26666666666666666,0.7666666666666667,0.3466666666666667,12.933333333333334,16.612977450529222,2187.0,1516.0
+scsemi5nt,PHC03,ped_HC,1500,9638,150,0.5213333333333333,0.6757626063498651,0.26866666666666666,0.17804523760116206,0.08533333333333333,0.055613197758871136,0.104,0.07273293214359826,0.011333333333333334,0.011516912222452791,0.009333333333333334,0.006329113924050633,0.3092257038113025,0.42244641092608676,0.798119498031878,47,False,0.7933333333333333,0.07333333333333333,0.8666666666666667,0.29333333333333333,8.533333333333333,5.561319775887114,2183.0,1660.5
+scsemi5nt,PHC05,ped_HC,1500,10918,150,0.51,0.5524821395860048,0.27466666666666667,0.07748671917933687,0.094,0.19893753434695,0.11333333333333333,0.11467301703608719,0.002,0.01731086279538377,0.006,0.03910972705623741,0.3943598949746596,0.24386493072060716,0.8289053862322211,31,False,0.7733333333333333,0.26,0.76,0.2866666666666667,9.4,19.893753434695,2181.5,1645.0
+scsemi5nt,PIC02,ped_ICU_ctrl,1500,6570,150,0.516,0.4786910197869102,0.29333333333333333,0.2785388127853881,0.09,0.14170471841704718,0.08533333333333333,0.036225266362252664,0.008666666666666666,0.0030441400304414,0.006666666666666667,0.06179604261796043,0.21366818873668192,0.23997478591362134,0.8225115232463281,32,False,0.82,0.44666666666666666,0.8333333333333334,0.6,9.0,14.170471841704718,2186.0,1062.5
+scsemi5nt,PIC04,ped_ICU_ctrl,1500,11535,150,0.8253333333333334,0.36341569137407886,0.11,0.08253142609449501,0.042,0.4273948851322063,0.0006666666666666666,0.03233636757693975,0.0013333333333333333,0.006501950585175552,0.020666666666666667,0.08781967923710446,0.978772431729519,0.5160473351557204,0.6360238981476676,62,False,0.9666666666666667,0.3,0.9933333333333333,0.23333333333333334,4.2,42.73948851322063,2182.0,1144.0
+scsemi5nt,PIC05,ped_ICU_ctrl,1500,7420,150,0.512,0.5920485175202156,0.2833333333333333,0.18409703504043126,0.086,0.1637466307277628,0.10066666666666667,0.021024258760107817,0.008,0.011320754716981131,0.01,0.027762803234501348,0.3577574123989218,0.26468060658449205,0.8076450933305137,43,False,0.7333333333333333,0.12,0.8266666666666667,0.28,8.6,16.37466307277628,2182.0,1666.0
+scsemi5nt,Res-PS02,ped_sepsis,1500,6473,150,0.7113333333333334,0.5892167464854009,0.20933333333333334,0.33848292909006644,0.04,0.012050054070755446,0.012,0.05051753437355168,0.0006666666666666666,0.0,0.02666666666666667,0.009732735980225553,0.3353342602605696,0.5604259638252818,0.7716310557356097,46,False,0.6466666666666666,0.13333333333333333,0.9066666666666666,0.3466666666666667,4.0,1.2050054070755445,2181.0,1680.0
+scsemi5nt,Res-PS03,ped_sepsis,1500,5934,150,0.6786666666666666,0.15267947421638017,0.22333333333333333,0.8156386922817661,0.05333333333333334,0.009605662285136502,0.012666666666666666,0.014492753623188406,0.0026666666666666666,0.0,0.029333333333333333,0.007583417593528817,1.188262891809909,1.2990319508636905,0.7004017581133288,74,False,0.86,0.06,0.9666666666666667,0.2,5.333333333333334,0.9605662285136503,2183.0,1871.0
+scsemi5nt,Res-PS12,ped_sepsis,1500,7200,150,0.51,0.18319444444444444,0.272,0.7847222222222222,0.102,0.0025,0.09933333333333333,0.02277777777777778,0.0026666666666666666,0.0005555555555555556,0.014,0.00625,1.0254444444444444,1.2363854194272463,0.77275364239558,72,False,0.62,0.02666666666666667,0.44666666666666666,0.22666666666666666,10.2,0.25,2184.0,2224.5
+scsemi5nt,Res-PS16,ped_sepsis,1500,7403,150,0.562,0.4078076455491017,0.296,0.5172227475347831,0.07133333333333333,0.0009455626097528029,0.03666666666666667,0.017695528839659597,0.024,0.00013508037282182898,0.01,0.05619343509388086,0.5348323652573281,0.707968914698667,0.7293483212591747,73,False,0.9066666666666666,0.14666666666666667,0.8533333333333334,0.36,7.133333333333333,0.09455626097528029,2182.0,1895.0
+scsemi5nt,Res-PS21,ped_sepsis,1500,6455,150,0.7226666666666667,0.2689388071262587,0.2,0.19550735863671573,0.03866666666666667,0.339426800929512,0.004666666666666667,0.06893880712625872,0.0026666666666666666,0.002168861347792409,0.03133333333333333,0.12501936483346243,0.917436612445133,0.4540378291194397,0.7057862926190973,25,False,0.9733333333333334,0.30666666666666664,0.9866666666666667,0.30666666666666664,3.8666666666666667,33.9426800929512,2182.0,1720.0
+scsemi5nt,Res-PS22,ped_sepsis,1500,7585,150,0.37466666666666665,0.5011206328279499,0.043333333333333335,0.08147659854976928,0.49466666666666664,0.33579433091628214,0.038,0.05945945945945946,0.008,0.013183915622940013,0.04133333333333333,0.00896506262359921,0.3824812129202374,0.3160205185684655,0.770738871180193,36,False,0.72,0.19333333333333333,0.7466666666666667,0.15333333333333332,49.46666666666666,33.57943309162821,2184.5,1514.0
+scsemi5nt,Res-PS25,ped_sepsis,1500,6203,150,0.5053333333333333,0.3562792197323876,0.32133333333333336,0.42447202966306624,0.08666666666666667,0.18458810253103336,0.076,0.0095115266806384,0.004666666666666667,0.005642431081734645,0.006,0.01950669031113977,0.4310851738406146,0.5064047660836933,0.78179984137637,23,False,0.78,0.11333333333333333,0.84,0.6333333333333333,8.666666666666668,18.458810253103337,2180.5,2342.0
+scsemi5nt,Res-PS26,ped_sepsis,1500,6291,150,0.51,0.7475759020823398,0.29,0.16436178667938325,0.09066666666666667,0.035606421872516295,0.094,0.03195040534096328,0.008,0.001271657924018439,0.007333333333333333,0.01923382610077889,0.49895278969957074,0.5491479273490957,0.7594717928542439,74,False,0.78,0.18,0.8,0.1,9.066666666666666,3.5606421872516294,2183.0,988.0
+scsemi5nt,Res-S10,adult_sepsis,1500,8489,150,0.526,0.7626339969372129,0.06466666666666666,0.0871716338791377,0.12066666666666667,0.01401814112380728,0.09733333333333333,0.08646483684768524,0.0026666666666666666,0.00011779950524207798,0.18866666666666668,0.04959359170691483,0.5182779282993678,0.5892998084300363,0.8340141408943776,45,False,0.7333333333333333,0.1,0.6533333333333333,0.76,12.066666666666666,1.401814112380728,2183.0,2651.0
+scsemi5nt,Res-S125,adult_sepsis,1500,3975,150,0.49733333333333335,0.510188679245283,0.276,0.24125786163522012,0.096,0.14440251572327045,0.11333333333333333,0.0810062893081761,0.008666666666666666,0.0015094339622641509,0.008666666666666666,0.021635220125786163,0.14845283018867922,0.20328145404864373,0.8375524137091157,5,False,0.6733333333333333,0.16,0.54,0.37333333333333335,9.6,14.440251572327046,2185.0,1933.0
+scsemi5nt,Res-S127,adult_sepsis,1500,2869,150,0.4046666666666667,0.28302544440571625,0.04133333333333333,0.08051585918438481,0.47,0.5137678633670268,0.019333333333333334,0.06099686301847333,0.009333333333333334,0.006273963053328686,0.05533333333333333,0.05542000697107006,0.24940118508191014,0.6249523225147816,0.7666662851725041,12,False,0.82,0.21333333333333335,0.8666666666666667,0.38666666666666666,47.0,51.376786336702686,2183.0,2020.0
+scsemi5nt,Res-S139,adult_sepsis,1500,2657,150,0.3333333333333333,0.3522770041400075,0.04933333333333333,0.06925103500188182,0.5106666666666667,0.26345502446368085,0.04066666666666666,0.29055325555137373,0.007333333333333333,0.00978547233722243,0.058666666666666666,0.014678208505833647,0.5824002007276377,0.5357386698962538,0.7785752772154692,42,False,0.6866666666666666,0.14,0.66,0.24666666666666667,51.06666666666667,26.345502446368087,2182.0,1637.0
+scsemi5nt,Res-S146,adult_sepsis,1500,7172,150,0.39266666666666666,0.5679029559397658,0.04466666666666667,0.1100111544896821,0.464,0.23243167875069715,0.014,0.04294478527607362,0.026,0.013943112102621304,0.058666666666666666,0.032766313441160065,0.5390511247443763,0.24343559203676127,0.7530656317498751,9,False,0.8866666666666667,0.1,0.9133333333333333,0.4533333333333333,46.400000000000006,23.243167875069716,2184.0,2707.0
+scsemi5nt,Res-S149,adult_sepsis,1500,7304,150,0.37266666666666665,0.37089266155531214,0.042,0.10282037239868565,0.4846666666666667,0.40963855421686746,0.029333333333333333,0.06489594742606791,0.009333333333333334,0.003696604600219058,0.062,0.04805585980284775,0.19276597298284048,0.4007740027978721,0.7954092581822652,6,False,0.74,0.14666666666666667,0.8533333333333334,0.42,48.46666666666667,40.963855421686745,2183.0,2356.0
+scsemi5nt,Res-S150,adult_sepsis,1500,3212,150,0.6913333333333334,0.1229763387297634,0.20533333333333334,0.2966998754669988,0.043333333333333335,0.47447073474470736,0.023333333333333334,0.07503113325031133,0.0013333333333333333,0.0,0.035333333333333335,0.030821917808219176,1.1484034869240352,0.779642506448578,0.7994995909254298,64,False,0.6133333333333333,0.08,0.78,0.12,4.333333333333334,47.447073474470734,2183.0,1993.5
+scsemi5nt,Res-S164,adult_sepsis,1500,6275,150,0.528,0.5641434262948207,0.2753333333333333,0.0796812749003984,0.09066666666666667,0.21529880478087648,0.094,0.08366533864541832,0.006,0.020239043824701194,0.006,0.03697211155378486,0.4119734395750332,0.21757675123383358,0.8466263938408343,5,False,0.74,0.2733333333333333,0.8333333333333334,0.47333333333333333,9.066666666666666,21.529880478087648,2182.0,2196.0
+scsemi5nt,Res-S166,adult_sepsis,1500,6119,150,0.37733333333333335,0.29874162444843927,0.05266666666666667,0.20934793266873672,0.4706666666666667,0.3784932178460533,0.023333333333333334,0.07991501879392057,0.016666666666666666,0.002941657133518549,0.059333333333333335,0.030560549109331592,0.4265259029253146,0.4081591275890375,0.7917209380550512,27,False,0.64,0.1,0.7066666666666667,0.21333333333333335,47.06666666666667,37.84932178460533,2184.0,2014.0
+scsemi5nt,Res-S174,adult_sepsis,1500,5645,150,0.5173333333333333,0.5465013286093888,0.278,0.09619131975199291,0.09266666666666666,0.20974313551815765,0.09266666666666666,0.047475642161204604,0.007333333333333333,0.011160318866253321,0.012,0.08892825509300266,0.4539994095069383,0.2326863928819134,0.8287867893166337,8,False,0.7266666666666667,0.12666666666666668,0.7866666666666666,0.48,9.266666666666666,20.974313551815765,2183.0,2116.0
+scsemi5nt,Res-S184,adult_sepsis,1500,8044,150,0.738,0.6473147687717553,0.18266666666666667,0.11163600198906017,0.048,0.05494778717056191,0.0006666666666666666,0.18274490303331675,0.002,0.000994530084535057,0.028666666666666667,0.002362008950770761,0.378052047074424,0.550471916248536,0.700976910932721,42,False,0.8733333333333333,0.22666666666666666,0.98,0.3,4.8,5.494778717056191,2184.0,1425.0
+scsemi5nt,Res-S19,adult_sepsis,1500,8601,150,0.7366666666666667,0.628996628299035,0.18133333333333335,0.08719916288803628,0.04466666666666667,0.14777351470759215,0.005333333333333333,0.07289850017439832,0.0006666666666666666,0.001860248808278107,0.03133333333333333,0.061271945122660154,0.4036084176258575,0.3327814421424728,0.7463219347837786,13,False,0.7,0.22,0.8933333333333333,0.31333333333333335,4.466666666666667,14.777351470759214,2184.0,3805.0
+scsemi5nt,Res-S26,adult_sepsis,1500,6036,150,0.7366666666666667,0.6973161033797217,0.17333333333333334,0.145791915175613,0.051333333333333335,0.023028495692511596,0.004666666666666667,0.11911862160371106,0.004,0.0001656726308813784,0.03,0.0145791915175613,0.2289039098740888,0.522863471373109,0.7013858380743152,16,False,0.9133333333333333,0.07333333333333333,0.98,0.30666666666666664,5.133333333333334,2.3028495692511597,2183.0,3953.0
+scsemi5nt,Res-S40,adult_sepsis,1500,7105,150,0.7193333333333334,0.8508092892329345,0.196,0.0944405348346235,0.05333333333333334,0.007881773399014778,0.0006666666666666666,0.03293455313159747,0.002,0.0009852216748768472,0.028666666666666667,0.01294862772695285,0.3274876847290639,0.7583313697331956,0.7239659342068159,11,False,0.8933333333333333,0.12,0.9733333333333334,0.6066666666666667,5.333333333333334,0.7881773399014778,2183.5,2322.0
+scsemi5nt,Res-S87,adult_sepsis,1500,3841,150,0.722,0.3967716740432179,0.196,0.01900546732621713,0.050666666666666665,0.4712314501431919,0.002,0.058318146316063524,0.002,0.014579536579015881,0.027333333333333334,0.040093725592293676,1.00444571726113,0.5435351366582621,0.7323496813042115,27,False,0.86,0.24,0.9866666666666667,0.3333333333333333,5.066666666666666,47.12314501431919,2182.0,1793.0
+scsemi5nt,Skin-S140,adult_sepsis,1500,7668,150,0.74,0.2646061554512259,0.196,0.23735002608242045,0.035333333333333335,0.3272039645279082,0.0013333333333333333,0.042383933229003655,0.0006666666666666666,0.0003912363067292645,0.02666666666666667,0.12806468440271257,0.9513385498174229,0.5202277395728088,0.7546276237836768,1,True,0.9133333333333333,0.2,0.9666666666666667,0.36,3.5333333333333337,32.720396452790816,2184.0,2069.5
+scsemi5nt,Skin-S142,adult_sepsis,1500,6090,150,0.37066666666666664,0.2761904761904762,0.04933333333333333,0.02857142857142857,0.4826666666666667,0.6172413793103448,0.035333333333333335,0.0277504105090312,0.007333333333333333,0.007060755336617406,0.05466666666666667,0.04318555008210181,0.26914942528735625,0.8241619364005279,0.835671807381598,1,True,0.6933333333333334,0.22,0.76,0.5466666666666666,48.266666666666666,61.724137931034484,2180.0,2405.5
+scsemi5nt,Skin-S152,adult_sepsis,1500,6429,150,0.38066666666666665,0.3621091927204853,0.05533333333333333,0.07481723440659512,0.4646666666666667,0.4316378908072795,0.028666666666666667,0.1028153678643646,0.016666666666666666,0.01835433193342666,0.054,0.01026598226784881,0.19064053507543943,0.5134772368821778,0.767359421270717,33,False,0.78,0.17333333333333334,0.8133333333333334,0.3933333333333333,46.46666666666667,43.16378908072795,2186.0,2447.0
+scsemi5nt,Skin-S38,adult_sepsis,1500,9976,150,0.886,0.8330994386527666,0.10066666666666667,0.13572574178027266,0.0013333333333333333,0.00020048115477145148,0.010666666666666666,0.02475942261427426,0.0006666666666666666,0.00020048115477145148,0.0006666666666666666,0.006014434643143544,0.10899919807538097,0.7224456198733815,0.8214206699351418,8,False,0.78,0.06666666666666667,0.7066666666666667,0.38,0.13333333333333333,0.020048115477145148,2184.0,1675.0
+scsemi5nt,Skin-S43,adult_sepsis,1500,7439,150,0.7306666666666667,0.7525205000672134,0.182,0.07554778868127436,0.04933333333333333,0.05135098803602635,0.0013333333333333333,0.015459067078908456,0.0013333333333333333,0.0016131200430165346,0.035333333333333335,0.10350853609356096,0.2129044226374513,0.6686644850611331,0.7500399945158579,2,False,0.86,0.16666666666666666,0.9866666666666667,0.35333333333333333,4.933333333333334,5.135098803602635,2182.0,2254.0
+scsemi5nt,Skin-S46,adult_sepsis,1500,7902,150,0.724,0.5565679574791192,0.188,0.120222728423184,0.03866666666666667,0.08225765628954695,0.013333333333333334,0.07314603897747406,0.0013333333333333333,0.0013920526449000253,0.034666666666666665,0.16641356618577574,0.4704186281953935,0.39906820974053553,0.793275393451338,6,False,0.7066666666666667,0.32666666666666666,0.8333333333333334,0.41333333333333333,3.8666666666666667,8.225765628954695,2181.0,1723.0
+scsemi5nt,Skin-S52,adult_sepsis,1500,8592,150,0.9433333333333334,0.6380353817504656,0.020666666666666667,0.31797020484171323,0.006666666666666667,0.00034916201117318437,0.0,0.02292830540037244,0.0013333333333333333,0.0,0.028,0.020716945996275604,0.640463687150838,0.6177826782538812,0.6487184394333796,17,False,1.0,0.18666666666666668,0.9733333333333334,0.31333333333333335,0.6666666666666667,0.034916201117318434,2185.0,1988.5
+scsemi5nt,Uri-S134,adult_sepsis,1500,9030,150,0.30533333333333335,0.3501661129568106,0.048666666666666664,0.038981173864894796,0.4726666666666667,0.5069767441860465,0.026,0.037541528239202655,0.002,0.0035437430786267998,0.14533333333333334,0.06279069767441861,0.18445625692137319,0.6250019558919507,0.8030990061939728,6,False,0.76,0.26,0.6933333333333334,0.5133333333333333,47.266666666666666,50.697674418604656,2185.0,2577.0
+scsemi5nt,Uri-S147,adult_sepsis,1500,7529,150,0.5226666666666666,0.5427015539912339,0.284,0.20268295922433258,0.09533333333333334,0.18262717492362865,0.086,0.031212644441492896,0.007333333333333333,0.004648691725328729,0.004666666666666667,0.036126975693983265,0.2775780758843583,0.19099787167495633,0.8034851635817726,3,False,0.7733333333333333,0.16,0.9133333333333333,0.42,9.533333333333333,18.262717492362864,2184.5,2024.0
+scsemi5nt,Uri-S157,adult_sepsis,1500,6514,150,0.7366666666666667,0.31393920785999385,0.19133333333333333,0.3042677310408351,0.035333333333333335,0.3042677310408351,0.0,0.04359840343874731,0.008,0.0033773411114522566,0.028666666666666667,0.030549585508136322,0.8547002353904412,0.45009233786929487,0.6704271009469223,34,False,0.9266666666666666,0.16,1.0,0.24,3.5333333333333337,30.42677310408351,2184.0,2105.5
+scsemi5nt,Uri-S20,adult_sepsis,1500,4516,150,0.7106666666666667,0.41054030115146145,0.19933333333333333,0.0812666076173605,0.048666666666666664,0.3961470327723649,0.006666666666666667,0.03897254207263064,0.002,0.001550044286979628,0.03266666666666666,0.07152347209920283,0.8372860938883968,0.418121320414448,0.7402638442702366,31,False,0.8533333333333334,0.16666666666666666,0.94,0.42,4.866666666666666,39.614703277236494,2180.0,4883.5
+scsemi5nt,Uri-S93,adult_sepsis,1500,8007,150,0.6866666666666666,0.5157986761583614,0.21266666666666667,0.3058573747970526,0.051333333333333335,0.08742350443362058,0.011333333333333334,0.04421131509928812,0.0013333333333333333,0.0012489072061945797,0.03666666666666667,0.0454602223054827,0.34190483327088805,0.3455480928846475,0.7733431260568654,7,False,0.8333333333333334,0.19333333333333333,0.94,0.7266666666666667,5.133333333333334,8.742350443362058,2183.5,4595.0

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw2_scsemi5nt/summary.json

@@ -0,0 +1,747 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-03T15:32:17.226746+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "ye2026_sepsis",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw2_scsemi5nt",
+  "--threads",
+  "6",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/draw2/test_samples.txt",
+  "--case-groups",
+  "adult_sepsis,ped_sepsis",
+  "--control-groups",
+  "adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl",
+  "--arm",
+  "scsemi5nt=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/draw2/scsemi5nt__raw.npz"
+ ],
+ "arms": [
+  "scsemi5nt"
+ ],
+ "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",
+  "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-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Uri-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_donors": 77,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis",
+  "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+  "features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
+  "n_r1_cells": 11550,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.3365280330181122,
+   "n_fit_cells": 11550
+  },
+  "r2_control": {
+   "precision": 0.9816450216450217,
+   "coverage": 0.9999134199134199,
+   "density": 1.3056103896103894,
+   "n_query": 11550,
+   "depth_matched": {
+    "precision": 0.9798268398268398,
+    "coverage": 0.9995670995670995,
+    "density": 1.3005194805194804
+   }
+  },
+  "observed_l1_loo_null_mean": 0.5196680228845961
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 57,
+  "n_control_donors": 20,
+  "n_donors_in_neither": 0,
+  "case": [
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_HC",
+   "ped_HC",
+   "ped_HC",
+   "ped_ICU_ctrl",
+   "ped_ICU_ctrl",
+   "ped_ICU_ctrl",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis"
+  ]
+ },
+ "deg_definition": {
+  "enabled": true,
+  "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
+  "functions": [
+   "welch_bh_deg",
+   "top_deg_genes",
+   "jaccard"
+  ],
+  "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
+  "top_n": 50,
+  "fdr": 0.05,
+  "n_genes": 5975,
+  "types": [
+   "T cell",
+   "B cell",
+   "Monocyte",
+   "NK cell",
+   "DC"
+  ],
+  "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz",
+  "aggregates_sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
+  "observed": {
+   "T cell": {
+    "n_significant": 1479,
+    "n_tested": 5804,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 279996,
+    "top_list_size": 50
+   },
+   "B cell": {
+    "n_significant": 1019,
+    "n_tested": 5750,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 95354,
+    "top_list_size": 50
+   },
+   "Monocyte": {
+    "n_significant": 2388,
+    "n_tested": 5752,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 107968,
+    "top_list_size": 50
+   },
+   "NK cell": {
+    "n_significant": 1124,
+    "n_tested": 5615,
+    "n_case_donors": 57,
+    "n_control_donors": 20,
+    "n_cells": 45869,
+    "top_list_size": 50
+   },
+   "DC": {
+    "n_significant": 1428,
+    "n_tested": 5327,
+    "n_case_donors": 53,
+    "n_control_donors": 20,
+    "n_cells": 3221,
+    "top_list_size": 50
+   }
+  },
+  "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
+ },
+ "headline": {
+  "scsemi5nt": {
+   "comp_l1": 0.5473332086477867,
+   "comp_l1_obs_loo_null": 0.5196680228845961,
+   "precision": 0.7946320346320346,
+   "coverage": 0.1768831168831169,
+   "precision_dm": 0.8290909090909091,
+   "coverage_dm": 0.3851948051948052,
+   "pb_r_median": 0.7769847103006375,
+   "pb_top1": 0.05194805194805195,
+   "mono_pct_gen": 15.485714285714286,
+   "mono_pct_obs": 21.18539814075279,
+   "median_umi_gen": 2183.0,
+   "median_umi_obs": 1954.0,
+   "contrast_mean_cp10k_r_gen": 0.3906075644579623,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.27472462218553656,
+   "contrast_mean_cp10k_r_broadcast": 0.3386821732452143,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.3248682572070414,
+   "deg_top50_T": 8,
+   "deg_top50_B": 3,
+   "deg_top50_Mono": 2,
+   "deg_top50_NK": 0,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 13,
+   "deg_top50_max": 250,
+   "deg_top50_sum_4type": 13,
+   "deg_top50_sum_broadcast": 18,
+   "seconds": 27.1
+  }
+ },
+ "per_arm": {
+  "scsemi5nt": {
+   "arm": "scsemi5nt",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/draw2/scsemi5nt__raw.npz",
+   "npz_sha256": "7146e6aa28a7f9fce0b6dc2b10686c9d1319ff98026a030f54094da7444d410f",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/draw2/test_raw.npz",
+    "input_condition_sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f",
+    "seed": 20260927,
+    "steps": null,
+    "support_readout": "no output threshold: the upstream model's ZINB mean on every modeled gene (sample(bound=0), no xsemi > 10 step); read-out sensitivity variant, not the official output",
+    "weights": null
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/draw2/test_raw.npz",
+    "sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 18702702,
+    "median_library_whole_npz_panel": 2183.0,
+    "n_rows_whole_npz": 115500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 66518,
+     "B cell": 20583,
+     "Monocyte": 17886,
+     "NK cell": 4893,
+     "Other": 4888,
+     "DC": 732
+    },
+    "mean_l2_max_prob": 0.9237137653742518,
+    "predict_seconds": 4.8
+   },
+   "n_donors": 77,
+   "n_generated_cells": 115500,
+   "composition": {
+    "l1_mean": 0.5473332086477867,
+    "l1_median": 0.46372721636701797,
+    "l1_obs_loo_null_mean": 0.5196680228845961,
+    "l1_generated_loo_mean_vs_observed_mean": 0.5219475549573928,
+    "composition_top1": 0.025974025974025976,
+    "mean_fraction_generated": {
+     "T cell": 0.575913,
+     "B cell": 0.178208,
+     "Monocyte": 0.154857,
+     "NK cell": 0.042364,
+     "DC": 0.006338,
+     "Other": 0.04232
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.476568,
+     "B cell": 0.174558,
+     "Monocyte": 0.211854,
+     "NK cell": 0.08183,
+     "DC": 0.005719,
+     "Other": 0.049471
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5975,
+    "r_median": 0.7769847103006375,
+    "r_mean": 0.7786349725659637,
+    "top1": 0.05194805194805195,
+    "n_top1": 4,
+    "own_rank_median": 21.0,
+    "chance_top1": 0.012987012987012988
+   },
+   "precision_coverage": {
+    "precision": 0.7946320346320346,
+    "coverage": 0.1768831168831169,
+    "density": 0.31197402597402596,
+    "n_query": 11550,
+    "n_reference": 11550
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.8290909090909091,
+    "coverage": 0.3851948051948052,
+    "density": 0.44225974025974024,
+    "detected_median_before": {
+     "R1": 408.0,
+     "Q": 150.0
+    },
+    "detected_median_after": {
+     "R1": 150.0,
+     "Q": 150.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 15.485714285714286,
+    "observed_mean_over_donors": 21.18539814075279,
+    "generated_pooled_cells": 15.485714285714286
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2183.0,
+    "observed_pooled": 1954.0,
+    "generated_mean_of_donor_medians": 2182.967529296875,
+    "observed_mean_of_donor_medians": 2097.3766233766232
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.47485635192979764,
+       "r_broadcast": 0.28418337062604826,
+       "partial_r_generated_given_broadcast": 0.4199092214413791,
+       "r_generated_vs_broadcast": 0.3372873311227553,
+       "n_genes": 3250
+      },
+      "B cell": {
+       "r_generated": 0.3631678450237297,
+       "r_broadcast": 0.301568070894857,
+       "partial_r_generated_given_broadcast": 0.3314471545612692,
+       "r_generated_vs_broadcast": 0.17196441100224857,
+       "n_genes": 3308
+      },
+      "Monocyte": {
+       "r_generated": 0.29586563674839933,
+       "r_broadcast": 0.5587432606078608,
+       "partial_r_generated_given_broadcast": 0.2940327364613907,
+       "r_generated_vs_broadcast": 0.09506461414701893,
+       "n_genes": 3287
+      },
+      "NK cell": {
+       "r_generated": 0.4285404241299223,
+       "r_broadcast": 0.21023399085209113,
+       "partial_r_generated_given_broadcast": 0.38843159687910683,
+       "r_generated_vs_broadcast": 0.33909448892704375,
+       "n_genes": 3233
+      }
+     },
+     "mean_r_generated": 0.3906075644579623,
+     "mean_r_broadcast": 0.3386821732452143,
+     "mean_partial_r": 0.35845517733578647
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.38743679043005125,
+       "r_broadcast": 0.2620470604793019,
+       "partial_r_generated_given_broadcast": 0.3610766959219317,
+       "r_generated_vs_broadcast": 0.16753945722508162,
+       "n_genes": 3250
+      },
+      "B cell": {
+       "r_generated": 0.33564466117366015,
+       "r_broadcast": 0.3165050349105062,
+       "partial_r_generated_given_broadcast": 0.3062961848402442,
+       "r_generated_vs_broadcast": 0.15333342986107745,
+       "n_genes": 3308
+      },
+      "Monocyte": {
+       "r_generated": 0.1921771262445225,
+       "r_broadcast": 0.6315053831846796,
+       "partial_r_generated_given_broadcast": 0.15081439004512026,
+       "r_generated_vs_broadcast": 0.12049292393872263,
+       "n_genes": 3287
+      },
+      "NK cell": {
+       "r_generated": 0.18363991089391238,
+       "r_broadcast": 0.08941555025367794,
+       "partial_r_generated_given_broadcast": 0.17540705434854653,
+       "r_generated_vs_broadcast": 0.11228879009904795,
+       "n_genes": 3233
+      }
+     },
+     "mean_r_generated": 0.27472462218553656,
+     "mean_r_broadcast": 0.3248682572070414,
+     "mean_partial_r": 0.24839858128896067
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 8,
+      "top50_jaccard": 0.11428571428571428,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 28,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 279996,
+      "n_cells_gen": 66518
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 3,
+      "top50_jaccard": 0.03125,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 49,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 95354,
+      "n_cells_gen": 20583
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 2,
+      "top50_jaccard": 0.037037037037037035,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 6,
+      "top50_overlap_broadcast": 11,
+      "top50_jaccard_broadcast": 0.12359550561797752,
+      "n_cells_obs": 107968,
+      "n_cells_gen": 17886
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 2,
+      "top50_jaccard_broadcast": 0.02040816326530612,
+      "n_cells_obs": 45869,
+      "n_cells_gen": 4893
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 5,
+      "top50_overlap_broadcast": 1,
+      "top50_jaccard_broadcast": 0.010101010101010102,
+      "n_cells_obs": 3221,
+      "n_cells_gen": 732
+     }
+    },
+    "sum": 13,
+    "sum_4type": 13,
+    "max": 250,
+    "mean": 2.6,
+    "sum_broadcast": 18,
+    "sum_broadcast_4type": 17,
+    "broadcast_n_significant": 1469,
+    "seconds": 0.17
+   },
+   "seconds": 27.1
+  }
+ },
+ "code_sha256": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+ },
+ "seconds": 33.1
+}

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw2_scsemi5rt/README.md

@@ -0,0 +1,73 @@
+# score_ft.py output: ye2026_sepsis, 77 scored donors
+
+Arms: scsemi5rt.  Every arm is scored on the same donors against the same observed reference.
+
+## Inputs and fixed contracts
+- Observed reference: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/reference.npz` (sha bac12da8a241), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis;
+  observed cells sum exactly to the features pseudobulk of every donor. Observed labels: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/observed_labels/labels/labels.parquet.
+- Generated cells: `generated_counts` read out once with Poisson(seed 20260916) over the **whole NPZ in row order**
+  (`poisson_readout.poisson_integerise`), then the scored donors' rows. These integer counts are used for labels, embedding,
+  depth and the contrast. Pseudobulk uses the summed `generated_counts` (rates), as `score_generated.py`.
+- Labels: frozen f01common scANVI (`predict_scanvi.py`, CPU, zero query epochs), six-type gate ['T cell', 'B cell', 'Monocyte', 'NK cell', 'DC', 'Other']; query genes =
+  the 1,006-gene annotation list minus genes the dataset's sc assay did not measure in every sample (1006 genes).
+- Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (5975 genes).
+
+## Definitions
+1. **Composition**: fraction of each donor's cells per six-type label (all generated cells; all observed QC cells).
+   `comp_l1` = sum over the six labels of |generated - observed| (immicro_common.l1). `comp_l1_obs_loo_null` = L1 of the
+   donor's observed composition to the mean of the *other scored donors'* observed compositions. `composition_top1` =
+   fraction of donors whose generated composition is closest (L1) to their own observed composition.
+2. **Pseudobulk**: `pb_r` = Pearson r of CPM-log1p(summed generated_counts) vs CPM-log1p(observed pseudobulk) on the scoring
+   genes (evaluate_realbulk.cpm_log1p / paired_r). `pb_top1` = the donor's generated pseudobulk is closest (Pearson) to its own
+   observed pseudobulk among the 77 scored donors (immicro_common.retrieval = evaluate_realbulk.top1 arithmetic).
+3. **Precision / coverage / density** (stage_b_embed.py functions): per-cell CP10K over the scoring genes + log1p; PCA-50
+   (randomized, random_state 20260925) and k = 10 real-real k-NN balls fitted on **R1 of the scored donors only**.
+   Reference rule (independent of fold and arm): per donor, cells in canonical order (library_id+barcode), one
+   permutation from `default_rng([20260925, uint64(sha256(donor)[:8])])`; R1 = first n, R2 = next n,
+   n = min(150, n_cells // 2) (11550 R1 cells here). Generated query: per donor n cells (the donor's R1 size),
+   without replacement, `default_rng([20260926, same key])`. Precision = fraction of generated cells inside any R1 ball
+   (Kynkaanniemi 2019); coverage = fraction of R1 cells whose ball holds a generated cell; density = Naeem 2020.
+   Per-donor precision = that donor's generated cells; per-donor coverage = that donor's R1 cells (the pooled values are
+   their n-weighted means; plain means when every donor has 150 reference cells). R2 (held-out real cells of the same donors) is the
+   perfect-generator control: precision 0.9816, coverage 0.9999.
+   **Depth matched**: stage_b_embed depth matching run pairwise (R1 vs this arm): per donor and within-donor rank of detected
+   genes, both cells are thinned by UMI sampling without replacement to the smaller detected-gene count; PCA kept from
+   un-thinned R1, radii recomputed on thinned R1; fresh rng(20260929) per arm. R2 control: precision
+   0.9798, coverage 0.9996.
+4. **Monocyte %** = 100 x Monocyte fraction (all cells) per donor; **median UMI per cell** = median over cells of the
+   Poisson-read (generated) / observed counts summed over the scoring genes (per donor, and pooled).
+5. **Group contrast** (T, B, Monocyte, NK): case groups ['adult_sepsis', 'ped_sepsis'] (n = 57) vs control groups ['adult_HC', 'adult_ICU_ctrl', 'ped_HC', 'ped_ICU_ctrl'] (n = 20); rule: explicit --case-groups / --control-groups; groups from features groups.
+   Genes per type = scoring genes detected (count > 0) in >= 1 % of the scored donors' observed
+   cells of that type. Primary statistic `mean_cp10k`: per-cell CP10K over the scoring genes; per donor the mean over its
+   cells of the type (donors with >= 1 such cell); group mean = mean over the group's donors (donor-balanced);
+   logFC = log2(case mean + 1) - log2(control mean + 1). Secondary `pseudobulk_log1p_cpm`: the SLE benchmark evaluator's
+   statistic (donor x type summed counts, log1p CPM over the scoring genes, mean case - mean control;
+   evaluate_generated_vs_truth.group_log_fold_change). Both are computed on the generated cells (their frozen labels) and on
+   the observed cells; `r_generated` = Pearson r of the two logFC vectors. Broadcast baseline `r_broadcast`: the same
+   observed vector against the logFC of the input bulk (condition NPZ `bulk_counts` of the arm, scoring genes, per-donor
+   CP10K resp. log1p CPM, group means). `partial_r_generated_given_broadcast`: r of the OLS residuals of observed and
+   generated logFC on the bulk logFC (residual_specificity.py).
+6. **Top-50 DEG overlap** (contrast.csv rows `statistic = welch_top50_deg`; summary `deg_top50`): the SLE benchmark's score (`total_top50_overlap` of
+   `bulk2sc-paper/scripts/evaluate_generated_vs_truth.py`, Welch backend: the "top-50 DEG 81 / 84" of the final model), run
+   with the evaluator's own functions on the same donor x type pseudobulks as the contrast. Per cell type, observed and
+   generated separately: donor x type summed counts on all 5975 scoring genes (donors of the two groups with
+   >= 1 cell of the type) -> `welch_bh_deg` (log1p CPM, two-sided Welch t-test case vs control, Benjamini-Hochberg over the
+   genes with a defined p-value; needs >= 2 donors per group) -> `top_deg_genes` (FDR < 0.05, descending |logFC|,
+   first 50; shorter when fewer genes pass). `top50_overlap` = |observed list & generated list|; `top50_jaccard`
+   the evaluator's Jaccard. Summary `sum` = total over the scored types (the quantity reported as 81), `max` = the sum of
+   the observed list lengths (the "of 262"), `sum_4type` = T + B + Monocyte + NK. A type is scored when its observed test
+   is defined; an arm whose generated test is undefined for a scored type gets overlap 0. Types: T cell, B cell, Monocyte, NK cell, DC
+   (aggregates: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz).
+   **Broadcast analogue** (`top50_overlap_broadcast`, as `sle_broadcast.py` `broadcast_input_bulk`; not part of the
+   published benchmark): the same test on the arm's condition bulk_counts (scoring genes, the 57 + 20
+   donors), one whole-PBMC top-50 list, compared with every type's observed list.
+
+## Files
+- `per_donor.csv`: one row per arm x donor (all per-donor quantities above).
+- `summary.json`: per arm the donor means / pooled values, provenance (NPZ sha, receipt check, generation metadata,
+  Poisson nnz of the whole NPZ, annotation contract), and the reference block (PCA, R2 control).
+- `contrast.csv`: per arm x cell type x statistic (`mean_cp10k`, `pseudobulk_log1p_cpm`: logFC r; `welch_top50_deg`:
+  top-50 DEG overlap, T / B / Monocyte / NK / DC; columns of the other kind are empty).
+- `arms/<arm>/labels/` (predict_scanvi.py labels + manifest), `arms/<arm>/generated_cells.parquet` (NPZ row, donor, label,
+  UMI on the scoring genes, P/C subsample flag), `arms/<arm>/deg_top50_lists.csv` (observed, generated and broadcast
+  top-50 gene lists, Ensembl ids, rank order).

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw2_scsemi5rt/contrast.csv

@@ -0,0 +1,14 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+scsemi5rt,T cell,mean_cp10k,3250,0.3674032603323868,0.28418337062604826,0.30864574936031486,0.299259095288445,57,20,57,20,279996,70340,,,,,,,,,,,
+scsemi5rt,T cell,pseudobulk_log1p_cpm,3250,0.23595736361365338,0.2620470604793019,0.20473376104889152,0.1556431726520072,57,20,57,20,279996,70340,,,,,,,,,,,
+scsemi5rt,B cell,mean_cp10k,3308,0.2759277624648552,0.301568070894857,0.24509356181866124,0.14869794242565582,57,20,56,20,95354,16757,,,,,,,,,,,
+scsemi5rt,B cell,pseudobulk_log1p_cpm,3308,0.22731273211903247,0.3165050349105062,0.21578011082845544,0.07322204732618162,57,20,56,20,95354,16757,,,,,,,,,,,
+scsemi5rt,Monocyte,mean_cp10k,3287,0.25419576747328576,0.5587432606078608,0.2541042077061906,0.0789533857268338,57,20,55,20,107968,17045,,,,,,,,,,,
+scsemi5rt,Monocyte,pseudobulk_log1p_cpm,3287,-0.013918812096389463,0.6315053831846796,-0.015600491861642045,-0.0028862554044725257,57,20,55,20,107968,17045,,,,,,,,,,,
+scsemi5rt,NK cell,mean_cp10k,3233,0.3721465657367232,0.21023399085209113,0.3332916655718147,0.2841228534362694,57,20,45,17,45869,4222,,,,,,,,,,,
+scsemi5rt,NK cell,pseudobulk_log1p_cpm,3233,0.09221345093594453,0.08941555025367794,0.08039452193792336,0.14528242365865338,57,20,45,17,45869,4222,,,,,,,,,,,
+scsemi5rt,T cell,welch_top50_deg,5975,,,,,57,20,57,20,279996,70340,True,3,0.030927835051546393,50,50,1479,397,2,0.02040816326530612,50,1469
+scsemi5rt,B cell,welch_top50_deg,5975,,,,,57,20,56,20,95354,16757,True,0,0.0,50,3,1019,3,2,0.02040816326530612,50,1469
+scsemi5rt,Monocyte,welch_top50_deg,5975,,,,,57,20,55,20,107968,17045,True,0,0.0,50,0,2388,0,11,0.12359550561797752,50,1469
+scsemi5rt,NK cell,welch_top50_deg,5975,,,,,57,20,45,17,45869,4222,True,0,0.0,50,50,1124,140,2,0.02040816326530612,50,1469
+scsemi5rt,DC,welch_top50_deg,5975,,,,,53,20,56,19,3221,1586,True,3,0.031914893617021274,50,47,1428,47,1,0.010101010101010102,50,1469