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/within_label_marker_check.csv

@@ -0,0 +1,18 @@
+side,arm,thin,t_cells,pt_label_cells,pt_label_pct_of_T,cycling_rule_pct_of_T,pct_of_pt_label_passing_cycling_rule,pct_of_nonpt_T_passing_cycling_rule,n_cycling_rule_T
+observed native,,1.0,61162,444,0.7259409437232268,0.3776854909911383,37.387387387387385,0.10705227444909253,231
+generated,zs__raw,,8631,243,2.815432742440042,0.3707565751361372,11.522633744855968,0.047687172150691466,32
+observed thinned to arm,zs__raw,0.461,61162,444,0.7259409437232268,0.26323534220594486,29.504504504504503,0.04940874205342732,161
+generated,lora_n5__raw,,12396,224,1.8070345272668602,0.4356243949661181,22.767857142857142,0.02464673020046007,54
+observed thinned to arm,lora_n5__raw,1.0,61162,444,0.7259409437232268,0.3776854909911383,37.387387387387385,0.10705227444909253,231
+generated,scratch_n5__raw,,13611,135,0.9918448313863787,0.20571596502828596,18.51851851851852,0.02226179875333927,28
+observed thinned to arm,scratch_n5__raw,1.0,61162,444,0.7259409437232268,0.3776854909911383,37.387387387387385,0.10705227444909253,231
+generated,real_lora__raw,,14147,153,1.0815013783841096,0.31102000424118187,26.143790849673202,0.028583678719451194,44
+observed thinned to arm,real_lora__raw,0.934,61162,444,0.7259409437232268,0.3629704718616134,36.93693693693694,0.09552356796995949,222
+generated,real_full__raw,,13435,180,1.339784145887607,0.45403796055080015,27.77777777777778,0.08298755186721991,61
+observed thinned to arm,real_full__raw,0.882,61162,444,0.7259409437232268,0.3466204506065858,35.585585585585584,0.08893573569616918,212
+generated,scratch_full__raw,,13443,110,0.8182697314587518,0.15621513055121625,16.363636363636363,0.022500562514062853,21
+observed thinned to arm,scratch_full__raw,0.953,61162,444,0.7259409437232268,0.3678754782381217,37.387387387387385,0.09717052603840706,225
+generated,lora_recipe__raw,,13851,177,1.2778860732077106,0.33932568045628475,24.293785310734464,0.029252596167909903,47
+observed thinned to arm,lora_recipe__raw,0.923,61162,444,0.7259409437232268,0.3597004676106079,36.711711711711715,0.0938766099015119,220
+generated,scratch_recipe__raw,,13815,98,0.7093738689829895,0.16648570394498732,23.46938775510204,0.0,23
+observed thinned to arm,scratch_recipe__raw,0.927,61162,444,0.7259409437232268,0.35806546548510515,36.711711711711715,0.09222965183306434,219

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/within_spearman.csv

@@ -0,0 +1,113 @@
+comparison,kind,scratch_arm,pretrained_arm,state,role,informative,spearman_scratch,scratch_ci_lo,scratch_ci_hi,spearman_pretrained,pretrained_ci_lo,pretrained_ci_hi,diff_pretrained_minus_scratch,diff_ci_lo,diff_ci_hi,n_boot_valid,verdict
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,C1Q-high monocyte (reference),rare state,True,0.409314,-0.176266,0.825466,0.152335,-0.404309,0.669611,-0.256979,-0.764943,0.111725,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Cycling T/NK,rare state,True,-0.107277,-0.620664,0.457555,0.178922,-0.257259,0.585544,0.286199,-0.296023,0.788569,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Cycling activated T (CD38/HLA-DR),rare state,True,-0.54902,-0.861401,-0.061166,-0.245701,-0.674488,0.31247,0.303319,-0.122906,0.727918,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Proliferating T (label),rare state,True,0.431373,-0.046304,0.754077,0.465686,-0.036174,0.823722,0.034314,-0.583906,0.630467,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Plasmablast (label),rare state,True,0.38619,-0.172637,0.776613,0.275865,-0.287344,0.757497,-0.110325,-0.657444,0.419166,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Plasmablast (markers),rare state,True,0.42205,-0.081131,0.751902,0.100737,-0.453442,0.664051,-0.321313,-0.86052,0.184232,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,MS1 monocyte (IL1R2+),rare state,True,0.781863,0.451369,0.940858,0.83784,0.520542,0.967269,0.055978,-0.236997,0.375034,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Cycling monocyte (Ye 2026),rare state,True,0.177777,-0.343521,0.630829,0.219214,-0.396144,0.674118,0.041436,-0.783896,0.81648,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,ISG-high monocyte (positive control),positive control,True,-0.218137,-0.76152,0.351511,-0.091968,-0.536932,0.422605,0.126169,-0.549977,0.785217,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,ISG-high T,rare state,True,0.007371,-0.523075,0.565881,0.146826,-0.342649,0.597525,0.139455,-0.757775,0.995997,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,DN2 / ABC B,rare state,True,0.32598,-0.263048,0.770043,0.375,-0.18,0.755858,0.04902,-0.314766,0.40256,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,HSPC,rare state,True,0.134742,-0.36178,0.600455,0.102639,-0.459899,0.648495,-0.032103,-0.781511,0.770415,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Cytotoxic CD4 T,rare state,True,-0.394608,-0.773109,0.149594,0.742647,0.372272,0.945075,1.137255,0.461466,1.603059,2000,pretrained tracks donors better
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Granulocyte-like (LDG),rare state,True,0.403464,-0.129541,0.774269,0.488552,-0.001575,0.80894,0.085088,-0.548289,0.702574,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,Platelet signal in monocytes (negative control),negative control,True,-0.375,-0.814138,0.238491,0.218137,-0.270962,0.629771,0.593137,-0.004963,1.145422,2000,not significant
+5 pairs: scratch vs pretrained LoRA,main,scratch_n5__raw,lora_n5__raw,MEAN over 13 informative rare states,aggregate,True,0.186863,,,0.295428,,,0.108565,-0.079967,0.293607,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,C1Q-high monocyte (reference),rare state,True,0.508601,-0.020174,0.825016,0.490761,-0.06768,0.832847,-0.01784,-0.403535,0.34011,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Cycling T/NK,rare state,True,-0.171229,-0.667974,0.377413,0.181484,-0.41307,0.690599,0.352713,-0.276513,0.884306,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Cycling activated T (CD38/HLA-DR),rare state,True,-0.568627,-0.861434,-0.0746,-0.27451,-0.729537,0.268413,0.294118,-0.223623,0.806006,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Proliferating T (label),rare state,True,0.487745,-0.034179,0.837337,0.485294,-0.051114,0.77205,-0.002451,-0.607195,0.514346,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Plasmablast (label),rare state,True,0.432004,-0.098627,0.829081,0.013539,-0.5988,0.598845,-0.418465,-1.041086,0.283147,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Plasmablast (markers),rare state,True,0.199877,-0.324989,0.609872,0.12285,-0.48229,0.64234,-0.077027,-0.739008,0.563217,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,MS1 monocyte (IL1R2+),rare state,True,0.91355,0.719944,0.977695,0.811359,0.552959,0.939199,-0.102191,-0.371746,0.071832,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Cycling monocyte (Ye 2026),rare state,True,0.190203,-0.364751,0.63276,-0.357115,-0.723796,0.152473,-0.547318,-1.173526,0.25681,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,ISG-high monocyte (positive control),positive control,True,0.645399,0.19796,0.873457,0.69042,0.264595,0.909364,0.045021,-0.28218,0.396471,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,ISG-high T,rare state,True,0.411942,-0.08371,0.749667,0.71401,0.35352,0.897252,0.302068,-0.144566,0.774303,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,DN2 / ABC B,rare state,True,0.490196,-0.026274,0.890999,0.375,-0.158324,0.765892,-0.115196,-0.636944,0.365785,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,HSPC,rare state,True,-0.068036,-0.565619,0.466769,0.237823,-0.285065,0.660663,0.305859,-0.182755,0.7394,1999,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Cytotoxic CD4 T,rare state,True,0.578431,0.06475,0.8933,0.761673,0.376274,0.937894,0.183242,-0.14298,0.59168,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Granulocyte-like (LDG),rare state,True,0.158444,-0.378294,0.642618,0.250709,-0.228443,0.668442,0.092266,-0.351515,0.567024,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,Platelet signal in monocytes (negative control),negative control,True,0.54902,-0.038416,0.876418,0.004902,-0.520207,0.543458,-0.544118,-1.035795,0.015168,2000,not significant
+58 pairs: scratch vs pretrained LoRA,main,scratch_full__raw,real_lora__raw,MEAN over 13 informative rare states,aggregate,True,0.274085,,,0.293298,,,0.019214,-0.12139,0.186036,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,C1Q-high monocyte (reference),rare state,True,0.508601,-0.020174,0.825016,0.568976,0.035869,0.893465,0.060375,-0.324048,0.475662,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Cycling T/NK,rare state,True,-0.171229,-0.667974,0.377413,0.465686,0.032164,0.72426,0.636915,0.007546,1.111006,2000,pretrained tracks donors better
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Cycling activated T (CD38/HLA-DR),rare state,True,-0.568627,-0.861434,-0.0746,0.014706,-0.493812,0.56469,0.583333,-0.057005,1.15492,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Proliferating T (label),rare state,True,0.487745,-0.034179,0.837337,0.735294,0.25333,0.93009,0.247549,-0.377179,0.797129,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Plasmablast (label),rare state,True,0.432004,-0.098627,0.829081,0.373006,-0.171561,0.786727,-0.058998,-0.628844,0.570228,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Plasmablast (markers),rare state,True,0.199877,-0.324989,0.609872,0.077348,-0.470003,0.608514,-0.122529,-0.720601,0.462367,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,MS1 monocyte (IL1R2+),rare state,True,0.91355,0.719944,0.977695,0.909871,0.706177,0.975186,-0.003679,-0.16399,0.152412,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Cycling monocyte (Ye 2026),rare state,True,0.190203,-0.364751,0.63276,0.154134,-0.422447,0.644451,-0.036069,-0.747053,0.636275,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,ISG-high monocyte (positive control),positive control,True,0.645399,0.19796,0.873457,0.367647,-0.127738,0.713936,-0.277752,-0.720404,0.161919,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,ISG-high T,rare state,True,0.411942,-0.08371,0.749667,0.448837,-0.052807,0.77361,0.036895,-0.585046,0.637833,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,DN2 / ABC B,rare state,True,0.490196,-0.026274,0.890999,0.485294,-0.139055,0.898561,-0.004902,-0.701558,0.686296,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,HSPC,rare state,True,-0.068036,-0.565619,0.466769,0.062972,-0.408687,0.540971,0.131008,-0.449664,0.703284,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Cytotoxic CD4 T,rare state,True,0.578431,0.06475,0.8933,0.815727,0.505528,0.946034,0.237296,-0.154074,0.719686,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Granulocyte-like (LDG),rare state,True,0.158444,-0.378294,0.642618,0.458021,-0.091978,0.836419,0.299578,-0.171477,0.780701,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,Platelet signal in monocytes (negative control),negative control,True,0.54902,-0.038416,0.876418,0.171674,-0.397619,0.681118,-0.377346,-1.058418,0.271872,2000,not significant
+58 pairs: scratch vs pretrained full FT,main,scratch_full__raw,real_full__raw,MEAN over 13 informative rare states,aggregate,True,0.274085,,,0.428452,,,0.154367,-0.008216,0.31307,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,C1Q-high monocyte (reference),rare state,True,0.489678,0.036009,0.806611,0.547913,0.020978,0.87288,0.058236,-0.387577,0.538573,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Cycling T/NK,rare state,True,0.221952,-0.297923,0.691203,0.389706,-0.098504,0.747816,0.167753,-0.461223,0.728025,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Cycling activated T (CD38/HLA-DR),rare state,True,-0.189893,-0.618376,0.422991,0.066176,-0.470271,0.648544,0.256069,-0.280013,0.822484,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Proliferating T (label),rare state,True,0.620098,0.158294,0.837907,0.639706,0.19552,0.875776,0.019608,-0.37721,0.439247,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Plasmablast (label),rare state,True,0.16718,-0.420097,0.69607,0.131531,-0.4926,0.670867,-0.035649,-0.745337,0.704692,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Plasmablast (markers),rare state,True,0.192994,-0.327719,0.638266,0.321473,-0.265466,0.80691,0.128478,-0.485315,0.781547,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,MS1 monocyte (IL1R2+),rare state,True,0.896759,0.664217,0.972667,0.874696,0.627327,0.970077,-0.022064,-0.283503,0.217679,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Cycling monocyte (Ye 2026),rare state,True,-0.032839,-0.609575,0.507255,0.261804,-0.291588,0.706862,0.294643,-0.431089,1.021391,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,ISG-high monocyte (positive control),positive control,True,0.312686,-0.263248,0.821483,0.523343,0.0037,0.833771,0.210657,-0.327734,0.80692,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,ISG-high T,rare state,True,0.441439,-0.073143,0.806311,0.526058,-0.035541,0.86381,0.084619,-0.464724,0.569055,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,DN2 / ABC B,rare state,True,0.594596,0.17649,0.869137,0.39951,-0.156523,0.841589,-0.195087,-0.75359,0.369643,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,HSPC,rare state,True,0.382202,-0.09303,0.700314,-0.161023,-0.59686,0.309649,-0.543225,-1.178511,0.23281,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Cytotoxic CD4 T,rare state,True,0.392157,-0.202033,0.830373,0.845211,0.53701,0.982633,0.453055,-0.010331,1.00128,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Granulocyte-like (LDG),rare state,True,0.464206,-0.082955,0.833167,0.33603,-0.199494,0.73937,-0.128176,-0.654505,0.447147,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,Platelet signal in monocytes (negative control),negative control,True,0.129412,-0.427902,0.659777,0.063725,-0.460237,0.577653,-0.065686,-0.767428,0.534753,2000,not significant
+58 pairs + recipes: scratch vs pretrained LoRA,main,scratch_recipe__raw,lora_recipe__raw,MEAN over 13 informative rare states,aggregate,True,0.356964,,,0.398368,,,0.041405,-0.105909,0.217255,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,C1Q-high monocyte (reference),rare state,True,0.409314,-0.176266,0.825466,0.315467,-0.313989,0.69194,-0.093846,-0.802385,0.541012,1999,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Cycling T/NK,rare state,True,-0.107277,-0.620664,0.457555,0.244022,-0.30131,0.718601,0.351299,-0.521522,1.108512,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Cycling activated T (CD38/HLA-DR),rare state,True,-0.54902,-0.861401,-0.061166,-0.196561,-0.660121,0.392801,0.352459,-0.232785,0.974573,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Proliferating T (label),rare state,True,0.431373,-0.046304,0.754077,0.286765,-0.265843,0.698446,-0.144608,-0.818505,0.53553,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Plasmablast (label),rare state,True,0.38619,-0.172637,0.776613,0.161506,-0.421376,0.688283,-0.224684,-0.913885,0.482829,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Plasmablast (markers),rare state,True,0.42205,-0.081131,0.751902,0.249856,-0.343736,0.710688,-0.172194,-0.766592,0.350218,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,MS1 monocyte (IL1R2+),rare state,True,0.781863,0.451369,0.940858,0.790422,0.437414,0.921487,0.008559,-0.341161,0.397112,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Cycling monocyte (Ye 2026),rare state,True,0.177777,-0.343521,0.630829,0.387466,-0.221576,0.794537,0.209688,-0.583474,0.952905,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,ISG-high monocyte (positive control),positive control,True,-0.218137,-0.76152,0.351511,0.20098,-0.390353,0.71655,0.419118,0.02711,0.825833,2000,pretrained tracks donors better
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,ISG-high T,rare state,True,0.007371,-0.523075,0.565881,-0.123307,-0.719379,0.465917,-0.130678,-0.969434,0.744279,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,DN2 / ABC B,rare state,True,0.32598,-0.263048,0.770043,-0.068627,-0.588636,0.542418,-0.394608,-0.89009,0.208482,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,HSPC,rare state,True,0.134742,-0.36178,0.600455,0.427994,-0.107695,0.817319,0.293252,-0.511511,1.030454,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Cytotoxic CD4 T,rare state,True,-0.394608,-0.773109,0.149594,0.262661,-0.234652,0.68543,0.657269,-0.056902,1.250828,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Granulocyte-like (LDG),rare state,True,0.403464,-0.129541,0.774269,0.259428,-0.370754,0.73837,-0.144036,-0.780788,0.37775,2000,not significant
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,Platelet signal in monocytes (negative control),negative control,True,-0.375,-0.814138,0.238491,0.247549,-0.330033,0.725624,0.622549,0.030263,1.166367,2000,pretrained tracks donors better
+reference: scratch 5 pairs vs pretrained zero-shot (no pairs),reference,scratch_n5__raw,zs__raw,MEAN over 13 informative rare states,aggregate,True,0.186863,,,0.230545,,,0.043682,-0.158806,0.225553,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,C1Q-high monocyte (reference),rare state,True,0.508601,-0.020174,0.825016,0.315467,-0.313989,0.69194,-0.193134,-0.631487,0.212557,1999,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Cycling T/NK,rare state,True,-0.171229,-0.667974,0.377413,0.244022,-0.30131,0.718601,0.415251,-0.479639,1.239827,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Cycling activated T (CD38/HLA-DR),rare state,True,-0.568627,-0.861434,-0.0746,-0.196561,-0.660121,0.392801,0.372067,-0.308963,1.07994,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Proliferating T (label),rare state,True,0.487745,-0.034179,0.837337,0.286765,-0.265843,0.698446,-0.20098,-0.983922,0.63522,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Plasmablast (label),rare state,True,0.432004,-0.098627,0.829081,0.161506,-0.421376,0.688283,-0.270498,-0.734806,0.204577,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Plasmablast (markers),rare state,True,0.199877,-0.324989,0.609872,0.249856,-0.343736,0.710688,0.049979,-0.525362,0.581143,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,MS1 monocyte (IL1R2+),rare state,True,0.91355,0.719944,0.977695,0.790422,0.437414,0.921487,-0.123129,-0.443883,0.120046,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Cycling monocyte (Ye 2026),rare state,True,0.190203,-0.364751,0.63276,0.387466,-0.221576,0.794537,0.197263,-0.519778,0.826515,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,ISG-high monocyte (positive control),positive control,True,0.645399,0.19796,0.873457,0.20098,-0.390353,0.71655,-0.444419,-1.083235,0.236437,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,ISG-high T,rare state,True,0.411942,-0.08371,0.749667,-0.123307,-0.719379,0.465917,-0.535249,-1.331125,0.353289,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,DN2 / ABC B,rare state,True,0.490196,-0.026274,0.890999,-0.068627,-0.588636,0.542418,-0.558824,-1.289289,0.346436,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,HSPC,rare state,True,-0.068036,-0.565619,0.466769,0.427994,-0.107695,0.817319,0.49603,-0.296885,1.153662,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Cytotoxic CD4 T,rare state,True,0.578431,0.06475,0.8933,0.262661,-0.234652,0.68543,-0.31577,-0.794684,0.160358,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Granulocyte-like (LDG),rare state,True,0.158444,-0.378294,0.642618,0.259428,-0.370754,0.73837,0.100984,-0.564993,0.71432,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,Platelet signal in monocytes (negative control),negative control,True,0.54902,-0.038416,0.876418,0.247549,-0.330033,0.725624,-0.301471,-0.971582,0.394139,2000,not significant
+reference: scratch 58 pairs vs pretrained zero-shot (no pairs),reference,scratch_full__raw,zs__raw,MEAN over 13 informative rare states,aggregate,True,0.274085,,,0.230545,,,-0.043539,-0.295031,0.197929,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,C1Q-high monocyte (reference),rare state,True,0.489678,0.036009,0.806611,0.315467,-0.313989,0.69194,-0.17421,-0.709314,0.265254,1999,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Cycling T/NK,rare state,True,0.221952,-0.297923,0.691203,0.244022,-0.30131,0.718601,0.02207,-0.728295,0.768438,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Cycling activated T (CD38/HLA-DR),rare state,True,-0.189893,-0.618376,0.422991,-0.196561,-0.660121,0.392801,-0.006668,-0.616215,0.573105,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Proliferating T (label),rare state,True,0.620098,0.158294,0.837907,0.286765,-0.265843,0.698446,-0.333333,-0.935793,0.34253,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Plasmablast (label),rare state,True,0.16718,-0.420097,0.69607,0.161506,-0.421376,0.688283,-0.005674,-0.48833,0.517519,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Plasmablast (markers),rare state,True,0.192994,-0.327719,0.638266,0.249856,-0.343736,0.710688,0.056862,-0.553615,0.662044,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,MS1 monocyte (IL1R2+),rare state,True,0.896759,0.664217,0.972667,0.790422,0.437414,0.921487,-0.106338,-0.484231,0.207588,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Cycling monocyte (Ye 2026),rare state,True,-0.032839,-0.609575,0.507255,0.387466,-0.221576,0.794537,0.420305,-0.317737,1.146483,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,ISG-high monocyte (positive control),positive control,True,0.312686,-0.263248,0.821483,0.20098,-0.390353,0.71655,-0.111705,-0.901268,0.703001,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,ISG-high T,rare state,True,0.441439,-0.073143,0.806311,-0.123307,-0.719379,0.465917,-0.564746,-1.1204,0.005323,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,DN2 / ABC B,rare state,True,0.594596,0.17649,0.869137,-0.068627,-0.588636,0.542418,-0.663224,-1.200943,0.133641,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,HSPC,rare state,True,0.382202,-0.09303,0.700314,0.427994,-0.107695,0.817319,0.045792,-0.437369,0.455927,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Cytotoxic CD4 T,rare state,True,0.392157,-0.202033,0.830373,0.262661,-0.234652,0.68543,-0.129496,-0.632175,0.382309,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Granulocyte-like (LDG),rare state,True,0.464206,-0.082955,0.833167,0.259428,-0.370754,0.73837,-0.204778,-0.861137,0.469232,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,Platelet signal in monocytes (negative control),negative control,True,0.129412,-0.427902,0.659777,0.247549,-0.330033,0.725624,0.118137,-0.474911,0.705647,2000,not significant
+reference: scratch 58 + recipes vs pretrained zero-shot (no pairs),reference,scratch_recipe__raw,zs__raw,MEAN over 13 informative rare states,aggregate,True,0.356964,,,0.230545,,,-0.126418,-0.336522,0.117174,2000,not significant

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/within_state_table.csv

@@ -0,0 +1,16 @@
+state,role,obs_parent_cells,obs_native_state_cells,obs_thinned_state_cells_min,obs_thinned_state_cells_max,informative,obs_donors_with_state,obs_top_donor_share,obs_top_donor,gen_over_obs__zs__raw,abs_log2__zs__raw,spearman__zs__raw,gen_state_cells__zs__raw,gen_parent_cells__zs__raw,obs_thinned_state_cells__zs__raw,thin__zs__raw,gen_over_obs__lora_n5__raw,abs_log2__lora_n5__raw,spearman__lora_n5__raw,gen_state_cells__lora_n5__raw,gen_parent_cells__lora_n5__raw,obs_thinned_state_cells__lora_n5__raw,thin__lora_n5__raw,gen_over_obs__scratch_n5__raw,abs_log2__scratch_n5__raw,spearman__scratch_n5__raw,gen_state_cells__scratch_n5__raw,gen_parent_cells__scratch_n5__raw,obs_thinned_state_cells__scratch_n5__raw,thin__scratch_n5__raw,gen_over_obs__real_lora__raw,abs_log2__real_lora__raw,spearman__real_lora__raw,gen_state_cells__real_lora__raw,gen_parent_cells__real_lora__raw,obs_thinned_state_cells__real_lora__raw,thin__real_lora__raw,gen_over_obs__real_full__raw,abs_log2__real_full__raw,spearman__real_full__raw,gen_state_cells__real_full__raw,gen_parent_cells__real_full__raw,obs_thinned_state_cells__real_full__raw,thin__real_full__raw,gen_over_obs__scratch_full__raw,abs_log2__scratch_full__raw,spearman__scratch_full__raw,gen_state_cells__scratch_full__raw,gen_parent_cells__scratch_full__raw,obs_thinned_state_cells__scratch_full__raw,thin__scratch_full__raw,gen_over_obs__lora_recipe__raw,abs_log2__lora_recipe__raw,spearman__lora_recipe__raw,gen_state_cells__lora_recipe__raw,gen_parent_cells__lora_recipe__raw,obs_thinned_state_cells__lora_recipe__raw,thin__lora_recipe__raw,gen_over_obs__scratch_recipe__raw,abs_log2__scratch_recipe__raw,spearman__scratch_recipe__raw,gen_state_cells__scratch_recipe__raw,gen_parent_cells__scratch_recipe__raw,obs_thinned_state_cells__scratch_recipe__raw,thin__scratch_recipe__raw,closest_trained_arm,closest_scratch_arm,closest_pretrained_trained_arm
+C1Q-high monocyte (reference),rare state,31471,1822,1590,1822,True,17,0.320527,Abd-S123,0.024986,5.322736,0.315467,12,9506,1590,0.416,1.07489,0.104188,0.152335,447,7183,1822,1.0,1.005146,0.007405,0.409314,357,6241,1791,0.893,1.053362,0.075002,0.490761,227,3891,1743,0.767,0.916807,0.125309,0.568976,208,4120,1733,0.73,0.466973,1.098588,0.508601,106,4036,1770,0.84,0.625773,0.676288,0.547913,136,3965,1725,0.729,0.5325,0.909147,0.489678,108,3598,1774,0.826,scratch_n5__raw,scratch_n5__raw,real_lora__raw
+Cycling T/NK,rare state,71619,288,185,288,True,17,0.125,Abd-PS19,2.516672,1.331517,0.244022,69,10614,185,0.425,1.15404,0.206694,0.178922,62,13360,288,1.0,0.50825,0.97639,-0.107277,32,15657,288,1.0,0.931543,0.102305,0.181484,57,15651,280,0.936,1.336003,0.417923,0.465686,76,14815,275,0.883,0.415901,1.265687,-0.171229,25,15598,276,0.925,0.987329,0.018397,0.389706,57,15201,272,0.923,0.479032,1.061807,0.221952,29,15999,271,0.904,lora_recipe__raw,scratch_n5__raw,lora_recipe__raw
+Cycling activated T (CD38/HLA-DR),rare state,61162,679,362,679,True,17,0.114875,Abd-S66,0.64599,0.630416,-0.196561,33,8631,362,0.461,0.443262,1.17377,-0.245701,61,12396,679,1.0,0.403693,1.308668,-0.54902,61,13611,679,1.0,0.408872,1.290279,-0.27451,61,14147,645,0.934,0.578323,0.790053,0.014706,78,13435,614,0.882,0.314981,1.666662,-0.568627,45,13443,650,0.953,0.45704,1.129607,0.066176,65,13851,628,0.923,0.278936,1.841993,-0.189893,39,13815,619,0.927,real_full__raw,scratch_n5__raw,real_full__raw
+Proliferating T (label),rare state,61162,444,444,444,True,17,0.175676,HC07,3.878322,1.955433,0.286765,243,8631,444,1.0,2.489231,1.3157,0.465686,224,12396,444,1.0,1.366289,0.450262,0.431373,135,13611,444,1.0,1.489793,0.575111,0.485294,153,14147,444,1.0,1.845583,0.884076,0.735294,180,13435,444,1.0,1.127185,0.172724,0.487745,110,13443,444,1.0,1.760317,0.815835,0.639706,177,13851,444,1.0,0.977178,0.033306,0.620098,98,13815,444,1.0,scratch_recipe__raw,scratch_recipe__raw,real_lora__raw
+Plasmablast (label),rare state,131629,716,716,716,True,17,0.177374,Abd-S66,1.506762,0.591452,0.161506,209,25500,716,1.0,1.874441,0.90646,0.275865,260,25500,716,1.0,1.124664,0.169495,0.38619,156,25500,716,1.0,3.474925,1.796982,0.013539,482,25500,716,1.0,3.280271,1.713815,0.373006,455,25500,716,1.0,1.240015,0.310357,0.432004,172,25500,716,1.0,2.299795,1.201505,0.131531,319,25500,716,1.0,1.17513,0.232821,0.16718,163,25500,716,1.0,scratch_n5__raw,scratch_n5__raw,lora_n5__raw
+Plasmablast (markers),rare state,131629,3407,1618,3407,True,17,0.125624,Abd-S66,0.781626,0.35545,0.249856,245,25500,1618,0.503,0.503011,0.991339,0.100737,332,25500,3407,1.0,0.349986,1.514629,0.42205,231,25500,3407,1.0,1.039898,0.056441,0.12285,609,25500,3023,0.898,1.154475,0.207237,0.077348,643,25500,2875,0.859,0.642013,0.639326,0.199877,373,25500,2999,0.89,0.710737,0.492612,0.321473,411,25500,2985,0.893,0.734132,0.445888,0.192994,415,25500,2918,0.862,real_lora__raw,scratch_recipe__raw,real_lora__raw
+MS1 monocyte (IL1R2+),rare state,31471,7470,5568,7470,True,16,0.271218,Skin-S140,0.083836,3.576279,0.790422,141,9506,5568,0.416,0.151909,2.71872,0.83784,259,7183,7470,1.0,0.095614,3.386628,0.781863,138,6241,7278,0.893,0.205964,2.279533,0.811359,178,3891,6990,0.767,0.361097,1.469541,0.909871,325,4120,6875,0.73,0.404617,1.305372,0.91355,372,4036,7169,0.84,0.301019,1.732076,0.874696,261,3965,6882,0.729,0.4621,1.113723,0.896759,377,3598,7136,0.826,scratch_recipe__raw,scratch_recipe__raw,real_full__raw
+Cycling monocyte (Ye 2026),rare state,31471,1684,992,1684,True,17,0.270784,Skin-S140,0.093446,3.419729,0.387466,28,9506,992,0.416,0.111874,3.160047,0.219214,43,7183,1684,1.0,0.061377,4.026153,0.177777,19,6241,1561,0.893,0.089557,3.481044,-0.357115,16,3891,1445,0.767,0.113928,3.133807,0.154134,21,4120,1408,0.73,0.086753,3.526941,0.190203,17,4036,1528,0.84,0.096243,3.377178,0.261804,17,3965,1402,0.729,0.086946,3.523731,-0.032839,15,3598,1509,0.826,real_full__raw,scratch_recipe__raw,real_full__raw
+ISG-high monocyte (positive control),positive control,31471,4195,1907,4195,True,17,0.246007,IC23,2.626643,1.39322,0.20098,1513,9506,1907,0.416,0.324813,1.62232,-0.091968,311,7183,4195,1.0,0.324734,1.622669,-0.218137,246,6241,3820,0.893,0.435961,1.19773,0.69042,181,3891,3358,0.767,0.576362,0.794952,0.367647,241,4120,3194,0.73,0.306379,1.706609,0.645399,142,4036,3614,0.84,0.597133,0.743876,0.523343,243,3965,3230,0.729,0.263355,1.924919,0.312686,108,3598,3587,0.826,lora_recipe__raw,scratch_n5__raw,lora_recipe__raw
+ISG-high T,rare state,61162,864,241,864,True,16,0.263889,Res-S139,2.70515,1.435709,-0.123307,92,8631,241,0.461,0.456853,1.130198,0.146826,80,12396,864,1.0,0.145625,2.77967,0.007371,28,13611,864,1.0,0.373078,1.42245,0.71401,68,14147,788,0.934,0.449465,1.15372,0.448837,70,13435,709,0.882,0.169555,2.560174,0.411942,30,13443,805,0.953,0.532931,0.907981,0.526058,91,13851,754,0.923,0.183512,2.446057,0.441439,32,13815,772,0.927,lora_recipe__raw,scratch_recipe__raw,lora_recipe__raw
+DN2 / ABC B,rare state,21022,822,607,822,True,17,0.237226,Abd-PS23,1.267906,0.342448,-0.068627,162,4425,607,0.681,1.106915,0.146544,0.375,173,3997,822,1.0,1.63464,0.708973,0.32598,186,2910,822,1.0,0.350657,1.511867,0.375,66,4903,807,0.988,0.372326,1.425363,0.485294,76,5233,820,0.993,0.633688,0.658155,0.490196,115,5053,755,0.902,0.28267,1.822809,0.39951,57,5157,822,1.0,0.459289,1.122527,0.594596,81,5051,734,0.88,lora_n5__raw,scratch_full__raw,lora_n5__raw
+HSPC,rare state,131629,140,117,140,True,17,0.15,HC01,0.88238,0.180528,0.427994,20,25500,117,0.503,0.958643,0.060935,0.102639,26,25500,140,1.0,0.479321,1.060935,0.134742,13,25500,140,1.0,0.573547,0.802017,0.237823,15,25500,135,0.898,0.782109,0.354558,0.062972,20,25500,132,0.859,1.338276,0.420376,-0.068036,35,25500,135,0.89,0.710699,0.492689,-0.161023,19,25500,138,0.893,0.955911,0.065051,0.382202,25,25500,135,0.862,lora_n5__raw,scratch_recipe__raw,lora_n5__raw
+Cytotoxic CD4 T,rare state,29300,413,342,413,True,16,0.234867,HC07,0.467215,1.097841,0.262661,19,3484,342,0.699,1.793379,0.842681,0.742647,161,6369,413,1.0,1.515945,0.600217,-0.394608,159,7441,413,1.0,0.895231,0.159668,0.761673,81,6419,413,1.0,1.322166,0.402903,0.815727,111,5956,413,0.997,0.800203,0.321562,0.578431,76,6738,413,1.0,1.233716,0.30301,0.845211,109,6268,413,1.0,1.187554,0.247993,0.392157,113,6800,410,0.987,real_lora__raw,scratch_recipe__raw,real_lora__raw
+Granulocyte-like (LDG),rare state,131629,4732,2589,4732,True,17,0.275359,Abd-S39,0.139565,2.840988,0.259428,70,25500,2589,0.503,0.054543,4.19647,0.488552,50,25500,4732,1.0,0.128721,2.957683,0.403464,118,25500,4732,1.0,0.038254,4.708239,0.250709,32,25500,4318,0.898,0.041325,4.596826,0.458021,33,25500,4122,0.859,0.043096,4.536308,0.158444,36,25500,4312,0.89,0.025286,5.305527,0.33603,21,25500,4287,0.893,0.058573,4.093615,0.464206,47,25500,4142,0.862,scratch_n5__raw,scratch_n5__raw,lora_n5__raw
+Platelet signal in monocytes (negative control),negative control,31471,6486,3221,6486,True,17,0.214924,PIC04,0.359741,1.474969,0.247549,350,9506,3221,0.416,0.835598,0.259119,0.218137,1237,7183,6486,1.0,0.59832,0.741011,-0.375,708,6241,5967,0.893,0.547251,0.869727,0.004902,363,3891,5365,0.767,0.699329,0.515957,0.171674,466,4120,5090,0.73,0.392348,1.349795,0.54902,286,4036,5684,0.84,0.544771,0.876279,0.063725,351,3965,5114,0.729,0.445627,1.16609,0.129412,285,3598,5594,0.826,lora_n5__raw,scratch_n5__raw,lora_n5__raw