Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T142225Z-rare-states-scratch-vs-pretrained/diffusion/dataset/server_1/model8/plans/rare_states_screen_20261004/out/scratch_vs_lora_20261005/verify_recompute_within_direction_mcnemar.csv

@@ -0,0 +1,8 @@
+comparison,scratch_arm,pretrained_arm,n_eligible,kept_scratch,kept_pretrained,pre_only,scratch_only,exact_sign_p_two_sided
+5 pairs,scratch_n5__raw,lora_n5__raw,25,17,23,8,2,0.109375
+58 pairs vs LoRA,scratch_full__raw,real_lora__raw,25,19,20,2,1,1.0
+58 pairs vs full FT,scratch_full__raw,real_full__raw,25,19,20,3,2,1.0
+recipes,scratch_recipe__raw,lora_recipe__raw,25,16,23,7,0,0.015625
+zs ref: 5 pairs,scratch_n5__raw,zs__raw,25,17,21,7,3,0.34375
+zs ref: 58 pairs,scratch_full__raw,zs__raw,25,19,21,5,3,0.7265625
+zs ref: recipes,scratch_recipe__raw,zs__raw,25,16,21,7,2,0.1796875

paper-releases/pbisc-diffusion/updates/20261005T142225Z-rare-states-scratch-vs-pretrained/diffusion/dataset/server_1/model8/plans/rare_states_screen_20261004/out/scratch_vs_lora_20261005/verify_recompute_within_donorweight.csv

@@ -0,0 +1,128 @@
+what,arm,state,ratio_donor_weighted,D,ci_lo,ci_hi,mean_abs_log2_scratch,mean_abs_log2_pretrained
+ratio,zs__raw,C1Q-high monocyte (reference),0.018819321255084776,,,,,
+ratio,zs__raw,Cycling T/NK,2.217367552090349,,,,,
+ratio,zs__raw,Cycling activated T (CD38/HLA-DR),0.6228113883415188,,,,,
+ratio,zs__raw,Proliferating T (label),3.4055731327888026,,,,,
+ratio,zs__raw,Plasmablast (label),1.2824974460210452,,,,,
+ratio,zs__raw,Plasmablast (markers),0.7181165723705621,,,,,
+ratio,zs__raw,MS1 monocyte (IL1R2+),0.05936622731027585,,,,,
+ratio,zs__raw,Cycling monocyte (Ye 2026),0.07681461916534368,,,,,
+ratio,zs__raw,ISG-high monocyte (positive control),1.6563339443254026,,,,,
+ratio,zs__raw,ISG-high T,1.7666025548873245,,,,,
+ratio,zs__raw,DN2 / ABC B,1.1401413508182705,,,,,
+ratio,zs__raw,HSPC,0.8394973492952157,,,,,
+ratio,zs__raw,Cytotoxic CD4 T,0.5140588521045996,,,,,
+ratio,zs__raw,Granulocyte-like (LDG),0.09635770813868934,,,,,
+ratio,zs__raw,Platelet signal in monocytes (negative control),0.306505162302374,,,,,
+ratio,lora_n5__raw,C1Q-high monocyte (reference),0.7838976555363674,,,,,
+ratio,lora_n5__raw,Cycling T/NK,1.1287154267538608,,,,,
+ratio,lora_n5__raw,Cycling activated T (CD38/HLA-DR),0.4670465605637173,,,,,
+ratio,lora_n5__raw,Proliferating T (label),2.089523578297392,,,,,
+ratio,lora_n5__raw,Plasmablast (label),1.5954513682558455,,,,,
+ratio,lora_n5__raw,Plasmablast (markers),0.4789569300680221,,,,,
+ratio,lora_n5__raw,MS1 monocyte (IL1R2+),0.11634155682615059,,,,,
+ratio,lora_n5__raw,Cycling monocyte (Ye 2026),0.09621305773643742,,,,,
+ratio,lora_n5__raw,ISG-high monocyte (positive control),0.28778155367290253,,,,,
+ratio,lora_n5__raw,ISG-high T,0.2377158624297761,,,,,
+ratio,lora_n5__raw,DN2 / ABC B,1.0587541650215935,,,,,
+ratio,lora_n5__raw,HSPC,0.941229230212465,,,,,
+ratio,lora_n5__raw,Cytotoxic CD4 T,1.6218532267322219,,,,,
+ratio,lora_n5__raw,Granulocyte-like (LDG),0.041664916217941265,,,,,
+ratio,lora_n5__raw,Platelet signal in monocytes (negative control),0.7669211721196145,,,,,
+ratio,scratch_n5__raw,C1Q-high monocyte (reference),0.8091976435001125,,,,,
+ratio,scratch_n5__raw,Cycling T/NK,0.3993999816769507,,,,,
+ratio,scratch_n5__raw,Cycling activated T (CD38/HLA-DR),0.3541505947816197,,,,,
+ratio,scratch_n5__raw,Proliferating T (label),1.0615678038811056,,,,,
+ratio,scratch_n5__raw,Plasmablast (label),0.9572708209535075,,,,,
+ratio,scratch_n5__raw,Plasmablast (markers),0.33325015314973827,,,,,
+ratio,scratch_n5__raw,MS1 monocyte (IL1R2+),0.0910031227523584,,,,,
+ratio,scratch_n5__raw,Cycling monocyte (Ye 2026),0.0494143854942579,,,,,
+ratio,scratch_n5__raw,ISG-high monocyte (positive control),0.2636102280580955,,,,,
+ratio,scratch_n5__raw,ISG-high T,0.07914354029020167,,,,,
+ratio,scratch_n5__raw,DN2 / ABC B,1.2664508247015218,,,,,
+ratio,scratch_n5__raw,HSPC,0.4706146151062324,,,,,
+ratio,scratch_n5__raw,Cytotoxic CD4 T,1.334345473462786,,,,,
+ratio,scratch_n5__raw,Granulocyte-like (LDG),0.09832920227434139,,,,,
+ratio,scratch_n5__raw,Platelet signal in monocytes (negative control),0.6932741025242137,,,,,
+ratio,real_lora__raw,C1Q-high monocyte (reference),0.7531227271206707,,,,,
+ratio,real_lora__raw,Cycling T/NK,0.8674645133857892,,,,,
+ratio,real_lora__raw,Cycling activated T (CD38/HLA-DR),0.4242952567514653,,,,,
+ratio,real_lora__raw,Proliferating T (label),1.245500851449045,,,,,
+ratio,real_lora__raw,Plasmablast (label),2.9577213826896833,,,,,
+ratio,real_lora__raw,Plasmablast (markers),0.990025695642548,,,,,
+ratio,real_lora__raw,MS1 monocyte (IL1R2+),0.2152018954850065,,,,,
+ratio,real_lora__raw,Cycling monocyte (Ye 2026),0.07145715228005357,,,,,
+ratio,real_lora__raw,ISG-high monocyte (positive control),0.3519762434625714,,,,,
+ratio,real_lora__raw,ISG-high T,0.18924310690860496,,,,,
+ratio,real_lora__raw,DN2 / ABC B,0.44494721382352476,,,,,
+ratio,real_lora__raw,HSPC,0.5676656056000631,,,,,
+ratio,real_lora__raw,Cytotoxic CD4 T,0.8419735026205976,,,,,
+ratio,real_lora__raw,Granulocyte-like (LDG),0.028726681304239006,,,,,
+ratio,real_lora__raw,Platelet signal in monocytes (negative control),0.5017968901832606,,,,,
+ratio,real_full__raw,C1Q-high monocyte (reference),0.8523241151492305,,,,,
+ratio,real_full__raw,Cycling T/NK,1.1385297397949343,,,,,
+ratio,real_full__raw,Cycling activated T (CD38/HLA-DR),0.5258437905064275,,,,,
+ratio,real_full__raw,Proliferating T (label),1.4428816385917738,,,,,
+ratio,real_full__raw,Plasmablast (label),2.79203989444773,,,,,
+ratio,real_full__raw,Plasmablast (markers),1.091724594809496,,,,,
+ratio,real_full__raw,MS1 monocyte (IL1R2+),0.3664432848192752,,,,,
+ratio,real_full__raw,Cycling monocyte (Ye 2026),0.1282590653655183,,,,,
+ratio,real_full__raw,ISG-high monocyte (positive control),0.4248049804052433,,,,,
+ratio,real_full__raw,ISG-high T,0.23679107953133974,,,,,
+ratio,real_full__raw,DN2 / ABC B,0.4210017560407981,,,,,
+ratio,real_full__raw,HSPC,0.7658675341713185,,,,,
+ratio,real_full__raw,Cytotoxic CD4 T,1.2826212460412125,,,,,
+ratio,real_full__raw,Granulocyte-like (LDG),0.030868468670736733,,,,,
+ratio,real_full__raw,Platelet signal in monocytes (negative control),0.7331312109522922,,,,,
+ratio,scratch_full__raw,C1Q-high monocyte (reference),0.4607590471777276,,,,,
+ratio,scratch_full__raw,Cycling T/NK,0.3459306461933947,,,,,
+ratio,scratch_full__raw,Cycling activated T (CD38/HLA-DR),0.2882257577763881,,,,,
+ratio,scratch_full__raw,Proliferating T (label),0.8934808110107313,,,,,
+ratio,scratch_full__raw,Plasmablast (label),1.0554524436154058,,,,,
+ratio,scratch_full__raw,Plasmablast (markers),0.6090196889344429,,,,,
+ratio,scratch_full__raw,MS1 monocyte (IL1R2+),0.3564825129495212,,,,,
+ratio,scratch_full__raw,Cycling monocyte (Ye 2026),0.0728091014777325,,,,,
+ratio,scratch_full__raw,ISG-high monocyte (positive control),0.2584450758378141,,,,,
+ratio,scratch_full__raw,ISG-high T,0.08851797982802256,,,,,
+ratio,scratch_full__raw,DN2 / ABC B,0.6734064169787649,,,,,
+ratio,scratch_full__raw,HSPC,1.318553860861178,,,,,
+ratio,scratch_full__raw,Cytotoxic CD4 T,0.6998574908408456,,,,,
+ratio,scratch_full__raw,Granulocyte-like (LDG),0.03237793953377023,,,,,
+ratio,scratch_full__raw,Platelet signal in monocytes (negative control),0.42703218028984663,,,,,
+ratio,lora_recipe__raw,C1Q-high monocyte (reference),0.4972836170672578,,,,,
+ratio,lora_recipe__raw,Cycling T/NK,0.8539650892659244,,,,,
+ratio,lora_recipe__raw,Cycling activated T (CD38/HLA-DR),0.4358897368338919,,,,,
+ratio,lora_recipe__raw,Proliferating T (label),1.3847062002944273,,,,,
+ratio,lora_recipe__raw,Plasmablast (label),1.9574961018215953,,,,,
+ratio,lora_recipe__raw,Plasmablast (markers),0.6738994118683047,,,,,
+ratio,lora_recipe__raw,MS1 monocyte (IL1R2+),0.2703973953553451,,,,,
+ratio,lora_recipe__raw,Cycling monocyte (Ye 2026),0.09779378736697887,,,,,
+ratio,lora_recipe__raw,ISG-high monocyte (positive control),0.4598451455391983,,,,,
+ratio,lora_recipe__raw,ISG-high T,0.28048074771892495,,,,,
+ratio,lora_recipe__raw,DN2 / ABC B,0.3029417156205186,,,,,
+ratio,lora_recipe__raw,HSPC,0.6943588300517403,,,,,
+ratio,lora_recipe__raw,Cytotoxic CD4 T,1.228578622957664,,,,,
+ratio,lora_recipe__raw,Granulocyte-like (LDG),0.018950648997687784,,,,,
+ratio,lora_recipe__raw,Platelet signal in monocytes (negative control),0.5047298960689305,,,,,
+ratio,scratch_recipe__raw,C1Q-high monocyte (reference),0.611293622386411,,,,,
+ratio,scratch_recipe__raw,Cycling T/NK,0.388755924775564,,,,,
+ratio,scratch_recipe__raw,Cycling activated T (CD38/HLA-DR),0.25785401820475257,,,,,
+ratio,scratch_recipe__raw,Proliferating T (label),0.7848049141684378,,,,,
+ratio,scratch_recipe__raw,Plasmablast (label),1.000225280868088,,,,,
+ratio,scratch_recipe__raw,Plasmablast (markers),0.6944280538769979,,,,,
+ratio,scratch_recipe__raw,MS1 monocyte (IL1R2+),0.39387816234496315,,,,,
+ratio,scratch_recipe__raw,Cycling monocyte (Ye 2026),0.08121889014447665,,,,,
+ratio,scratch_recipe__raw,ISG-high monocyte (positive control),0.21015186950183373,,,,,
+ratio,scratch_recipe__raw,ISG-high T,0.10206963181786244,,,,,
+ratio,scratch_recipe__raw,DN2 / ABC B,0.4701988801544127,,,,,
+ratio,scratch_recipe__raw,HSPC,0.9363735160376041,,,,,
+ratio,scratch_recipe__raw,Cytotoxic CD4 T,1.0564228479973772,,,,,
+ratio,scratch_recipe__raw,Granulocyte-like (LDG),0.04380758845629907,,,,,
+ratio,scratch_recipe__raw,Platelet signal in monocytes (negative control),0.4874884124353928,,,,,
+"mean D (13 rare states, donor-weighted)",scratch_n5__raw - lora_n5__raw,5 pairs,,0.23681832310273407,-0.08906963570446,0.4766016177948914,1.6544927930552096,1.4176744699524755
+"mean D (13 rare states, donor-weighted)",scratch_full__raw - real_lora__raw,58 pairs vs LoRA,,0.0825014787978272,-0.3067093902491377,0.36677035930288315,1.5845169794047034,1.502015500606876
+"mean D (13 rare states, donor-weighted)",scratch_full__raw - real_full__raw,58 pairs vs full FT,,0.27827508971561693,-0.021822466960889735,0.6005042944066016,1.5845169794047034,1.3062418896890864
+"mean D (13 rare states, donor-weighted)",scratch_recipe__raw - lora_recipe__raw,recipes,,-0.06506156108291683,-0.3500280177440956,0.24883277908497242,1.4568060872410402,1.5218676483239573
+"mean D (13 rare states, donor-weighted)",scratch_n5__raw - zs__raw,zs ref: 5 pairs,,-0.15650090939572975,-0.5356744103973817,0.12160641534377538,1.6544927930552096,1.8109937024509395
+"mean D (13 rare states, donor-weighted)",scratch_full__raw - zs__raw,zs ref: 58 pairs,,-0.2264767230462361,-0.6661379427299621,0.12550894889434433,1.5845169794047034,1.8109937024509395
+"mean D (13 rare states, donor-weighted)",scratch_recipe__raw - zs__raw,zs ref: recipes,,-0.354187615209899,-0.7572356723743047,-0.007211498520350512,1.4568060872410402,1.8109937024509395

paper-releases/pbisc-diffusion/updates/20261005T142225Z-rare-states-scratch-vs-pretrained/diffusion/dataset/server_1/model8/plans/rare_states_screen_20261004/out/scratch_vs_lora_20261005/verify_recompute_within_fidelity.csv

@@ -0,0 +1,121 @@
+arm,state,rare,gen_state,gen_parent,obsthin_state,obs_parent,ratio_pc0,ratio_pc05,abs_log2_pc05,abs_log2_pc0,spearman,n_donors_spearman
+zs__raw,C1Q-high monocyte (reference),True,12,9506,1590,31471,0.024986006851680568,0.02601890842382643,5.264295752106644,5.322735834792417,0.3154673891882782,17
+zs__raw,Cycling T/NK,True,69,10614,185,71619,2.516671504743862,2.5280756179729056,1.3380396170130107,1.3315169171721635,0.24402211821430003,17
+zs__raw,Cycling activated T (CD38/HLA-DR),True,33,8631,362,61162,0.6459902023478262,0.6548734113999656,0.610712037696286,0.6304158109765136,-0.19656078986618247,17
+zs__raw,Proliferating T (label),True,243,8631,444,61162,3.8783220133585097,3.8819305563863957,1.9567743100008108,1.9554325940039134,0.286764705882353,17
+zs__raw,Plasmablast (label),True,209,25500,716,131629,1.5067620221272868,1.5093127266258912,0.5938917604096052,0.5914515757890256,0.16150576220789933,17
+zs__raw,Plasmablast (markers),True,245,25500,1618,131629,0.7816259482779514,0.7829791443299594,0.35295421492208073,0.355449732455008,0.24985614328161104,17
+zs__raw,MS1 monocyte (IL1R2+),True,141,9506,5568,31471,0.08383639960605643,0.08412613737280167,3.571302084898625,3.5762794287917905,0.7904215329137396,17
+zs__raw,Cycling monocyte (Ye 2026),True,28,9506,992,31471,0.09344565062473276,0.0950664064218224,3.3949205632074344,3.419728673671127,0.38746560113990985,17
+zs__raw,ISG-high monocyte (positive control),False,1513,9506,1907,31471,2.6266425058067813,2.626821798965901,1.3933183327637648,1.3932198585621252,0.20098039215686278,17
+zs__raw,ISG-high T,True,92,8631,241,61162,2.7051499684385774,2.7142207071481224,1.4405380384287774,1.4357085765752897,-0.1233069057411404,17
+zs__raw,DN2 / ABC B,True,162,4425,607,21022,1.2679060676290732,1.27077259305759,0.34570588068003405,0.34244786788630305,-0.06862745098039216,17
+zs__raw,HSPC,True,20,25500,117,131629,0.8823797553209318,0.900590571547768,0.15105672097451692,0.18052840372364296,0.4279940390215953,17
+zs__raw,Cytotoxic CD4 T,True,19,3484,342,29300,0.46721520602117617,0.4788103279224316,1.0624738233875328,1.0978408658442045,0.2626608939396687,17
+zs__raw,Granulocyte-like (LDG),True,70,25500,2589,131629,0.13956527995516477,0.14053503401746875,2.8309982697596556,2.8409880119827453,0.2594277581571397,17
+zs__raw,Platelet signal in monocytes (negative control),False,350,9506,3221,31471,0.35974109523337044,0.3601990969115661,1.4731335307526636,1.4749691188923417,0.24754901960784317,17
+lora_n5__raw,C1Q-high monocyte (reference),True,447,7183,1822,31471,1.0748895160897185,1.0757966292536085,0.10540537371407165,0.10418837815801923,0.1523346121462914,17
+lora_n5__raw,Cycling T/NK,True,62,13360,288,71619,1.1540403567864272,1.1613309343185378,0.21577914297711107,0.20669367590506962,0.17892156862745098,17
+lora_n5__raw,Cycling activated T (CD38/HLA-DR),True,61,12396,679,61162,0.44326166310477844,0.4465661143985064,1.1630543118056853,1.1737695030593795,-0.2457009873327281,17
+lora_n5__raw,Proliferating T (label),True,224,12396,444,61162,2.489230760285939,2.491980794269061,1.317292949533843,1.315699979329964,0.465686274509804,17
+lora_n5__raw,Plasmablast (label),True,260,25500,716,131629,1.8744407930770075,1.8767349178331487,0.9082248889887619,0.9064602567365974,0.2758654161359137,17
+lora_n5__raw,Plasmablast (markers),True,332,25500,3407,131629,0.5030108484838021,0.5036944744148576,0.9893791903316209,0.9913385797770226,0.10073740480641852,17
+lora_n5__raw,MS1 monocyte (IL1R2+),True,259,7183,7470,31471,0.15190911681437338,0.15219219076401894,2.716033761243444,2.718719639213293,0.8378403668046027,17
+lora_n5__raw,Cycling monocyte (Ye 2026),True,43,7183,1684,31471,0.11187448392764256,0.11314175686161138,3.143796616496277,3.160047067587546,0.2192135788588026,17
+lora_n5__raw,ISG-high monocyte (positive control),False,311,7183,4195,31471,0.3248127739031553,0.3252962090389634,1.6201740853965938,1.6223197244198309,-0.09196813500538946,17
+lora_n5__raw,ISG-high T,True,80,12396,864,61162,0.45685286771120903,0.4594423171638232,1.1220443519051988,1.1301984836536405,0.14682632943206325,17
+lora_n5__raw,DN2 / ABC B,True,173,3997,822,21022,1.106914735930293,1.109439070184097,0.14983043765029277,0.14654409764967727,0.37500000000000006,17
+lora_n5__raw,HSPC,True,26,25500,140,131629,0.9586425770308123,0.9736008652571349,0.03859764468532779,0.06093507783147508,0.10263930474438031,17
+lora_n5__raw,Cytotoxic CD4 T,True,161,6369,413,29300,1.7933794784589552,1.7967737091105782,0.845408723093089,0.8426807942656104,0.7426470588235294,17
+lora_n5__raw,Granulocyte-like (LDG),True,50,25500,4732,131629,0.05454270465582682,0.05508231150886133,4.182267086866874,4.196469947592664,0.4885520920545136,17
+lora_n5__raw,Platelet signal in monocytes (negative control),False,1237,7183,6486,31471,0.8355980769512282,0.8358713922153551,0.25864710962210685,0.2591189227026845,0.21813725490196081,17
+scratch_n5__raw,C1Q-high monocyte (reference),True,357,6241,1791,31471,1.0051456341688145,1.0062724764073327,0.00902100806128997,0.007404546649412924,0.4093137254901961,17
+scratch_n5__raw,Cycling T/NK,True,32,15657,288,71619,0.5082497711353814,0.515296561723047,0.9565251286367816,0.9763904344620662,-0.10727700799479216,17
+scratch_n5__raw,Cycling activated T (CD38/HLA-DR),True,61,13611,679,61162,0.40369345204958,0.40670292807904523,1.2979527172913705,1.3086679085450643,-0.5490196078431373,17
+scratch_n5__raw,Proliferating T (label),True,135,13611,444,61162,1.3662885940822904,1.369806347492876,0.45397195066088286,0.4502622488375061,0.43137254901960786,17
+scratch_n5__raw,Plasmablast (label),True,156,25500,716,131629,1.1246644758462045,1.127481822037957,0.17310417364287203,0.16949466257039128,0.38619026144735963,17
+scratch_n5__raw,Plasmablast (markers),True,231,25500,3407,131629,0.3499864638546936,0.3506925438407204,1.5117213374599365,1.5146289697078898,0.4220503901938074,17
+scratch_n5__raw,MS1 monocyte (IL1R2+),True,138,6241,7278,31471,0.09561442013184888,0.09595425711437605,3.3815093752086307,3.386627974457223,0.7818627450980392,17
+scratch_n5__raw,Cycling monocyte (Ye 2026),True,19,6241,1561,31471,0.06137719802742727,0.06297221697611516,3.9891407305520503,4.026153403928049,0.17777724028126524,17
+scratch_n5__raw,ISG-high monocyte (positive control),False,246,6241,3820,31471,0.3247342560721995,0.325351699746942,1.6199280040111648,1.6226685129775966,-0.21813725490196081,17
+scratch_n5__raw,ISG-high T,True,28,13611,864,61162,0.14562499829930584,0.1481397156953692,2.754969621340759,2.7796700619690835,0.007371029619981842,17
+scratch_n5__raw,DN2 / ABC B,True,186,2910,822,21022,1.6346401785938243,1.6380379991435046,0.7119688249520701,0.7089731007457847,0.32598039215686275,17
+scratch_n5__raw,HSPC,True,13,25500,140,131629,0.4793212885154062,0.4959853464517479,1.0116305970850585,1.060935077831475,0.1347420139090739,17
+scratch_n5__raw,Cytotoxic CD4 T,True,159,7441,413,29300,1.515944802909604,1.5188730955178724,0.6030013352018585,0.6002172244731739,-0.39460784313725494,17
+scratch_n5__raw,Granulocyte-like (LDG),True,118,25500,4732,131629,0.1287207829877513,0.12925255274851621,2.951735320720409,2.957683088005548,0.4034639472628964,17
+scratch_n5__raw,Platelet signal in monocytes (negative control),False,708,6241,5967,31471,0.5983200826787356,0.598692458153566,0.7401129984448461,0.7410106068656284,-0.37500000000000006,17
+real_lora__raw,C1Q-high monocyte (reference),True,227,3891,1743,31471,1.053362327674689,1.055379760946356,0.07776222229697864,0.07500176915285472,0.49076148484973875,17
+real_lora__raw,Cycling T/NK,True,57,15651,280,71619,0.9315431693091267,0.9380395300295175,0.092279374091396,0.1023054672072031,0.1814837864106352,17
+real_lora__raw,Cycling activated T (CD38/HLA-DR),True,61,14147,645,61162,0.40887207028306877,0.4119041751331064,1.2796193451966085,1.290278577976388,-0.27450980392156865,17
+real_lora__raw,Proliferating T (label),True,153,14147,444,61162,1.4897925068632638,1.4929798262387628,0.5781946713117518,0.575111411113888,0.4852941176470589,17
+real_lora__raw,Plasmablast (label),True,482,25500,716,131629,3.4749248548581444,3.4761021030882695,1.7974704588656962,1.7969817799381045,0.01353858715149784,17
+real_lora__raw,Plasmablast (markers),True,609,25500,3023,131629,1.0398975306960363,1.0405791949986543,0.057386767941059146,0.05644137525102441,0.12285049366636405,17
+real_lora__raw,MS1 monocyte (IL1R2+),True,178,3891,6990,31471,0.2059643894111682,0.20652816795036905,2.275589533625532,2.2795331733087765,0.8113594397767039,17
+real_lora__raw,Cycling monocyte (Ye 2026),True,16,3891,1445,31471,0.08955739400390753,0.09232411650545508,3.4371486381309713,3.4810436414004164,-0.3571153040756087,17
+real_lora__raw,ISG-high monocyte (positive control),False,181,3891,3358,31471,0.43596055343120893,0.437099781001932,1.1939654395903783,1.1977304918662,0.6904197744049659,17
+real_lora__raw,ISG-high T,True,68,14147,788,61162,0.37307832659181567,0.3755832353458359,1.4127954270586411,1.4224495434346947,0.7140099425686712,17
+real_lora__raw,DN2 / ABC B,True,66,4903,807,21022,0.3506570213062786,0.35309474391429013,1.5018727492507005,1.5118674790899296,0.37500000000000006,17
+real_lora__raw,HSPC,True,15,25500,135,131629,0.5735468409586056,0.5904781130164243,0.7600445099945972,0.8020167804699132,0.2378232735776752,17
+real_lora__raw,Cytotoxic CD4 T,True,81,6419,413,29300,0.8952312048786762,0.8996681368209893,0.15253516639588288,0.15966776999050655,0.761673060731457,17
+real_lora__raw,Granulocyte-like (LDG),True,32,25500,4318,131629,0.03825416632609505,0.038847389366769056,4.686038540283737,4.708239307050106,0.2507090915014465,17
+real_lora__raw,Platelet signal in monocytes (negative control),False,363,3891,5365,31471,0.5472505552637422,0.5479532765004129,0.8678752138091629,0.8697265816605089,0.004901960784313726,17
+real_full__raw,C1Q-high monocyte (reference),True,208,4120,1733,31471,0.9168073770721404,0.9187461670507784,0.12226176886827025,0.12530944212917805,0.5689761952333429,17
+real_full__raw,Cycling T/NK,True,76,14815,275,71619,1.336003190869205,1.3423520454633155,0.4247630825947707,0.41792345350483995,0.465686274509804,17
+real_full__raw,Cycling activated T (CD38/HLA-DR),True,78,13435,614,61162,0.5783226998371942,0.58155631656867,0.7820091891728813,0.7900533641997777,0.014705882352941176,17
+real_full__raw,Proliferating T (label),True,180,13435,444,61162,1.8455828362787796,1.8486276673547553,0.8864546803655543,0.8840764922877219,0.7352941176470589,17
+real_full__raw,Plasmablast (label),True,455,25500,716,131629,3.2802713878847625,3.281584472449133,1.7143925705123042,1.7138151787942013,0.373006415752611,17
+real_full__raw,Plasmablast (markers),True,643,25500,2875,131629,1.154474980392157,1.155171806437755,0.20810743680379404,0.20723690758124677,0.07734819746423262,17
+real_full__raw,MS1 monocyte (IL1R2+),True,325,4120,6875,31471,0.3610970873786408,0.36162632126313143,1.4674284055917057,1.46954131138103,0.9098714156533197,17
+real_full__raw,Cycling monocyte (Ye 2026),True,21,4120,1408,31471,0.1139278671116505,0.1165990294708617,3.1003723147829336,3.1338074169686374,0.1541336321764255,17
+real_full__raw,ISG-high monocyte (positive control),False,241,4120,3194,31471,0.576362156592154,0.5774675299019705,0.79218826656884,0.7949524822913716,0.36764705882352944,17
+real_full__raw,ISG-high T,True,70,13435,709,61162,0.4494649314491809,0.4523563851006058,1.1444682593536046,1.1537195379863965,0.44883713689775107,17
+real_full__raw,DN2 / ABC B,True,76,5233,820,21022,0.3723257190531011,0.37454684813818645,1.4167819133206936,1.4253628185614933,0.4852941176470589,17
+real_full__raw,HSPC,True,20,25500,132,131629,0.7821093285799169,0.7986369219385868,0.32438832386007854,0.35455780349869176,0.06297222637685256,17
+real_full__raw,Cytotoxic CD4 T,True,111,5956,413,29300,1.3221656148316063,1.3265153649942383,0.40764138636390274,0.4029029005455335,0.8157272779446572,17
+real_full__raw,Granulocyte-like (LDG),True,33,25500,4122,131629,0.04132542740531439,0.04194648212226067,4.575306366894658,4.596826449208403,0.4580214569909284,17
+real_full__raw,Platelet signal in monocytes (negative control),False,466,4120,5090,31471,0.6993288763423428,0.7000104659068911,0.5145516028310502,0.5159570174188778,0.17167385201006033,17
+scratch_full__raw,C1Q-high monocyte (reference),True,106,4036,1770,31471,0.46697322963386023,0.4690434354016338,1.092206566310955,1.0985882485530376,0.508601043778747,17
+scratch_full__raw,Cycling T/NK,True,25,15598,276,71619,0.4159012861180642,0.4234521883108768,1.2397290098181035,1.2656869485583364,-0.1712290602468288,17
+scratch_full__raw,Cycling activated T (CD38/HLA-DR),True,45,13443,650,61162,0.31498120268484026,0.31823619675135884,1.6518301551840788,1.666662360251122,-0.5686274509803922,17
+scratch_full__raw,Proliferating T (label),True,110,13443,444,61162,1.127184984582887,1.1310348647838346,0.17764340189668182,0.172724298509574,0.48774509803921573,17
+scratch_full__raw,Plasmablast (label),True,172,25500,716,131629,1.2400146784970971,1.242751529083371,0.313537878375785,0.3103571984102406,0.43200400819779466,17
+scratch_full__raw,Plasmablast (markers),True,373,25500,2999,131629,0.6420129193391261,0.6427663630212879,0.6376336624084676,0.6393257656411033,0.1998774134117131,17
+scratch_full__raw,MS1 monocyte (IL1R2+),True,372,4036,7169,31471,0.4046166451994817,0.40513222893671025,1.303535236528828,1.305372423896765,0.9135501410535354,17
+scratch_full__raw,Cycling monocyte (Ye 2026),True,17,4036,1528,31471,0.08675308999112698,0.08927543829447307,3.4855928780878807,3.526941044931286,0.1902027163011394,17
+scratch_full__raw,ISG-high monocyte (positive control),False,142,4036,3614,31471,0.3063794142699106,0.30741568380083467,1.7017373242487772,1.7066087295057946,0.6453992588351098,17
+scratch_full__raw,ISG-high T,True,30,13443,805,61162,0.16955509875374425,0.17227401457278319,2.5372229898086625,2.5601739260584404,0.411942376825704,17
+scratch_full__raw,DN2 / ABC B,True,115,5053,755,21022,0.6336882030608005,0.6360221624309781,0.6528510572516419,0.6581549367709363,0.49019607843137264,17
+scratch_full__raw,HSPC,True,35,25500,135,131629,1.3382759622367466,1.3523853556182623,0.43550629912321,0.4203756408665348,-0.06803619704615703,17
+scratch_full__raw,Cytotoxic CD4 T,True,76,6738,413,29300,0.8002029614840337,0.8044934915868167,0.3138473454034077,0.3215621269006446,0.5784313725490197,17
+scratch_full__raw,Granulocyte-like (LDG),True,36,25500,4312,131629,0.04309582014624032,0.04368930718954248,4.51657596158784,4.536308240337794,0.1584435682707749,17
+scratch_full__raw,Platelet signal in monocytes (negative control),False,286,4036,5684,31471,0.39234791520928114,0.39299926747756425,1.3474014714810132,1.349794560610268,0.5490196078431373,17
+lora_recipe__raw,C1Q-high monocyte (reference),True,136,3965,1725,31471,0.6257734890436244,0.6278921291523959,0.6714113671465236,0.6762875549334151,0.5479132017519837,17
+lora_recipe__raw,Cycling T/NK,True,57,15201,272,71619,0.9873293455925887,0.9941626245014058,0.008446228641690564,0.0183966870073747,0.38970588235294124,17
+lora_recipe__raw,Cycling activated T (CD38/HLA-DR),True,65,13851,628,61162,0.4570400536740662,0.46018935359718594,1.1197004874448984,1.1296074904250133,0.06617647058823531,17
+lora_recipe__raw,Proliferating T (label),True,177,13851,444,61162,1.7603168470614865,1.7633037910547082,0.8182810510004336,0.8158351291710506,0.6397058823529412,17
+lora_recipe__raw,Plasmablast (label),True,319,25500,716,131629,2.2997946653521746,2.3017919625631134,1.202757447657248,1.2015050574730122,0.13153104519724837,17
+lora_recipe__raw,Plasmablast (markers),True,411,25500,2985,131629,0.7107369395999605,0.7114824067962472,0.4911000119818695,0.4926124114980854,0.321472634628895,17
+lora_recipe__raw,MS1 monocyte (IL1R2+),True,261,3965,6882,31471,0.30101850212902564,0.30157325563445864,1.7294196028668427,1.7320759297979573,0.874695514904512,17
+lora_recipe__raw,Cycling monocyte (Ye 2026),True,17,3965,1402,31471,0.0962428021219911,0.09903815246148902,3.335871788182049,3.3771775423911445,0.2618036456085128,17
+lora_recipe__raw,ISG-high monocyte (positive control),False,243,3965,3230,31471,0.5971330410441206,0.5982690985372903,0.7411335472518967,0.7438756956063669,0.5233431030187108,17
+lora_recipe__raw,ISG-high T,True,91,13851,754,61162,0.5329305241249854,0.5355036053263841,0.9010318068044817,0.9079806276318088,0.5260577322308277,17
+lora_recipe__raw,DN2 / ABC B,True,57,5157,822,21022,0.2826701429139615,0.28497636228504003,1.8110858367623632,1.8228085886010759,0.3995098039215687,17
+lora_recipe__raw,HSPC,True,19,25500,138,131629,0.7106993464052287,0.7267687407092801,0.4604317262145408,0.49268872236218453,-0.16102327005563216,17
+lora_recipe__raw,Cytotoxic CD4 T,True,109,6268,413,29300,1.233715664020792,1.2378762706332003,0.30786712015429096,0.3030099330818733,0.8452113964245845,17
+lora_recipe__raw,Granulocyte-like (LDG),True,21,25500,4287,131629,0.025285829937293322,0.02588485451323386,5.27174798027304,5.305527058065813,0.3360300182731919,17
+lora_recipe__raw,Platelet signal in monocytes (negative control),False,351,3965,5114,31471,0.5447707033729331,0.5454933966763882,0.8743663623896047,0.876278974567949,0.06372549019607844,17
+scratch_recipe__raw,C1Q-high monocyte (reference),True,108,3598,1774,31471,0.5324998918978538,0.534814432300215,0.9028896969074673,0.9091468624285972,0.48967764672562875,16
+scratch_recipe__raw,Cycling T/NK,True,29,15999,271,71619,0.4790315538632604,0.48639331394676255,1.0398046975247495,1.0618074053085285,0.2219524303340527,17
+scratch_recipe__raw,Cycling activated T (CD38/HLA-DR),True,39,13815,619,61162,0.2789361146046564,0.2822842023195361,1.8247797024546708,1.8419933588431887,-0.1898926348413562,17
+scratch_recipe__raw,Proliferating T (label),True,98,13815,444,61162,0.9771784814130091,0.9810592894129277,0.02758776786456594,0.033306000726070165,0.6200980392156864,17
+scratch_recipe__raw,Plasmablast (label),True,163,25500,716,131629,1.17513018950597,1.1779123188703255,0.23623215220833607,0.23282059793922036,0.16717964623201664,17
+scratch_recipe__raw,Plasmablast (markers),True,415,25500,2918,131629,0.7341320942359123,0.7348906670429007,0.4443984651394955,0.44588842071120466,0.19299415042960744,17
+scratch_recipe__raw,MS1 monocyte (IL1R2+),True,377,3598,7136,31471,0.4620999194245931,0.4626803652916465,1.1119122181527614,1.1137232569426425,0.8967590638830791,16
+scratch_recipe__raw,Cycling monocyte (Ye 2026),True,15,3598,1509,31471,0.08694635964093152,0.08981481191659789,3.4769028014177517,3.5237305652091666,-0.032839478871459264,16
+scratch_recipe__raw,ISG-high monocyte (positive control),False,108,3598,3587,31471,0.26335511798906963,0.2645374801719112,1.9184559542969353,1.9249185980850578,0.3126857262223895,16
+scratch_recipe__raw,ISG-high T,True,32,13815,772,61162,0.18351157692603404,0.18625831169393992,2.424623288254455,2.446057015759253,0.44143872255328265,17
+scratch_recipe__raw,DN2 / ABC B,True,81,5051,734,21022,0.4592885537544297,0.4618090844387924,1.1146315416413222,1.1225272652747078,0.594596389345202,17
+scratch_recipe__raw,HSPC,True,25,25500,135,131629,0.9559114015976762,0.9714317343173433,0.04181547840997659,0.0650511863037069,0.3822020818527145,17
+scratch_recipe__raw,Cytotoxic CD4 T,True,113,6800,410,29300,1.1875538020086083,1.1913555921759689,0.25260408868501844,0.24799287608165008,0.3921568627450981,17
+scratch_recipe__raw,Granulocyte-like (LDG),True,47,25500,4142,131629,0.05857322880866494,0.059189203261268294,4.078522152805467,4.093614765570475,0.4642057272069001,17
+scratch_recipe__raw,Platelet signal in monocytes (negative control),False,285,3598,5594,31471,0.44562729303989046,0.44636919816875253,1.163690617859984,1.1660904997150898,0.12941176470588234,16

paper-releases/pbisc-diffusion/updates/20261005T142225Z-rare-states-scratch-vs-pretrained/diffusion/dataset/server_1/model8/plans/rare_states_screen_20261004/out/scratch_vs_lora_20261005/verify_recompute_within_label_marker.csv

@@ -0,0 +1,18 @@
+side,arm,thin,n_T,n_T_cycling,n_PT_label,n_PT_label_cycling,mc50_pct_PT_passing_min,mc50_pct_PT_passing_max,mc50_pct_T_cycling_min,mc50_pct_T_cycling_max,pct_of_PT_label_passing_cycling_rule,cycling_rule_pct_of_T,pt_wilson_lo,pt_wilson_hi,t_wilson_lo,t_wilson_hi
+generated,zs__raw,,8631,32,243,28,,,,,11.522633744855968,0.3707565751361372,8.093487893411305,16.149384072502254,0.26275672911501974,0.5229144281868028
+observed thinned,zs__raw,0.46067961165048543,61162,163,444,137,27.027027027027028,31.98198198198198,0.23707530819790065,0.28449036983748077,30.855855855855857,0.2665053464569504,26.739000483052365,35.30113746048175,0.22865253182930023,0.31060508476501525
+generated,lora_n5__raw,,12396,54,224,51,,,,,22.767857142857142,0.4356243949661181,17.762749020192313,28.691245511149265,0.33404955183256113,0.5679092287866467
+observed thinned,lora_n5__raw,1.0,61162,231,444,166,,,,,37.387387387387385,0.3776854909911383,33.013222906195885,41.97792679777953,0.33209089126329533,0.4295130492862961
+generated,scratch_n5__raw,,13611,28,135,25,,,,,18.51851851851852,0.20571596502828596,12.869783265528051,25.909310009649445,0.14237191106566136,0.2971591624447425
+observed thinned,scratch_n5__raw,1.0,61162,231,444,166,,,,,37.387387387387385,0.3776854909911383,33.013222906195885,41.97792679777953,0.33209089126329533,0.4295130492862961
+generated,real_lora__raw,,14147,44,153,40,,,,,26.143790849673202,0.31102000424118187,19.826370736208904,33.62981326711908,0.2317791402965068,0.4172385106181408
+observed thinned,real_lora__raw,0.9339805825242719,61162,222,444,162,35.810810810810814,37.387387387387385,0.3547954612340996,0.3760504888656355,36.486486486486484,0.3629704718616134,32.142433407588285,41.06236984667108,0.31832760650589303,0.41384814410844134
+generated,real_full__raw,,13435,61,180,50,,,,,27.77777777777778,0.45403796055080015,21.750928440019994,34.7333159120517,0.3536570566640082,0.5827440401589403
+observed thinned,real_full__raw,0.8820388349514563,61162,217,444,161,35.13513513513514,37.16216216216216,0.34335044635558026,0.37278048461463,36.26126126126126,0.3547954612340996,31.924995728630723,40.83322091319964,0.31068973288686696,0.4051370233189912
+generated,scratch_full__raw,,13443,21,110,18,,,,,16.363636363636363,0.15621513055121625,10.608807657526535,24.388511626168142,0.10220118356834224,0.23870756411845084
+observed thinned,scratch_full__raw,0.9529126213592233,61162,225,444,163,36.26126126126126,37.387387387387385,0.36133546973611064,0.3776854909911383,36.711711711711715,0.3678754782381217,32.3599753625779,41.29141450411049,0.32291324738694344,0.41907189987247667
+generated,lora_recipe__raw,,13851,47,177,43,,,,,24.293785310734464,0.33932568045628475,18.565566484757444,31.114113941716393,0.25528906205134827,0.45090060537644683
+observed thinned,lora_recipe__raw,0.9228155339805825,61162,221,444,162,35.810810810810814,37.387387387387385,0.3498904548575913,0.37441548674013275,36.486486486486484,0.36133546973611064,32.142433407588285,41.06236984667108,0.31679954130184335,0.4121064104307957
+generated,scratch_recipe__raw,,13815,23,98,23,,,,,23.46938775510204,0.16648570394498732,16.178478951873153,32.761765421930306,0.11096810929577898,0.24970944076671092
+observed thinned,scratch_recipe__raw,0.9271844660194175,61162,221,444,162,35.810810810810814,37.387387387387385,0.3498904548575913,0.37441548674013275,36.486486486486484,0.36133546973611064,32.142433407588285,41.06236984667108,0.31679954130184335,0.4121064104307957
+observed native,-,1.0,61162,231,444,166,,,,,37.387387387387385,0.3776854909911383,33.013222906195885,41.97792679777953,0.33209089126329533,0.4295130492862961