Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw3/lora/score/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
+lora,T cell,mean_cp10k,3028,0.4823850309504914,0.2368920077117674,0.448571731401243,0.2598111651688319,15,10,15,10,44374,18924,,,,,,,,,,,
+lora,T cell,pseudobulk_log1p_cpm,3028,0.3751926313127488,0.3055967610230027,0.3393056356371801,0.1897561820516274,15,10,15,10,44374,18924,,,,,,,,,,,
+lora,B cell,mean_cp10k,3238,0.1990542490053045,0.162212456781473,0.1809419160106288,0.1367756590373774,15,10,15,10,6285,1166,,,,,,,,,,,
+lora,B cell,pseudobulk_log1p_cpm,3238,0.0419177785845112,0.047548729682353,0.0402543993127735,0.0365037904548672,15,10,15,10,6285,1166,,,,,,,,,,,
+lora,Monocyte,mean_cp10k,3132,0.5530945374995733,0.4012426962403039,0.4682125343099418,0.3978204242826742,15,10,15,10,26936,11105,,,,,,,,,,,
+lora,Monocyte,pseudobulk_log1p_cpm,3132,0.4028058779634047,0.3605798916586732,0.3390426697090601,0.2735368350859839,15,10,15,10,26936,11105,,,,,,,,,,,
+lora,NK cell,mean_cp10k,3064,0.3897322511381489,0.2307648550552463,0.3520174676404347,0.2528280586993432,15,10,15,10,13603,4770,,,,,,,,,,,
+lora,NK cell,pseudobulk_log1p_cpm,3064,0.0948077027924109,0.1192446246241253,0.083435180616712,0.1041412156985704,15,10,15,10,13603,4770,,,,,,,,,,,
+lora,T cell,welch_top50_deg,5752,,,,,15,10,15,10,44374,18924,True,0.0,0.0,50.0,1.0,813.0,1.0,0.0,0.0,1.0,1.0
+lora,B cell,welch_top50_deg,5752,,,,,15,10,15,10,6285,1166,True,0.0,0.0,8.0,0.0,8.0,0.0,0.0,0.0,1.0,1.0
+lora,Monocyte,welch_top50_deg,5752,,,,,15,10,15,10,26936,11105,True,0.0,0.0,0.0,3.0,0.0,3.0,0.0,0.0,1.0,1.0
+lora,NK cell,welch_top50_deg,5752,,,,,15,10,15,10,13603,4770,True,0.0,0.0,14.0,0.0,14.0,0.0,0.0,0.0,1.0,1.0
+lora,DC,welch_top50_deg,5752,,,,,13,10,15,10,1144,760,True,0.0,0.0,3.0,0.0,3.0,0.0,0.0,0.0,1.0,1.0

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw3/lora/score/per_donor.csv

@@ -0,0 +1,26 @@
+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
+lora,N064_TOL,TOL,1500,2498,150,0.496,0.6517213771016813,0.0473333333333333,0.044035228182546,0.2173333333333333,0.1677341873498799,0.196,0.0760608486789431,0.0306666666666666,0.010008006405124,0.0126666666666666,0.0504403522818254,0.3869901254336803,0.4372573056439784,0.860189717293079,15,False,0.9866666666666668,0.9066666666666666,0.9733333333333334,0.86,21.73333333333333,16.77341873498799,913.0,662.0
+lora,N064_FU1,FU1,1500,4659,150,0.628,0.6396222365314446,0.0153333333333333,0.0165271517493024,0.27,0.1386563640266151,0.0706666666666666,0.1916720326250268,0.0053333333333333,0.0047220433569435,0.0106666666666666,0.0088001717106675,0.2676428418115476,0.446466586257669,0.8709678913663212,4,False,0.9866666666666668,0.7666666666666667,0.98,0.92,27.0,13.865636402661517,912.0,925.0
+lora,N032_AC,AC,1500,7350,150,0.6,0.5891156462585034,0.0413333333333333,0.1097959183673469,0.2046666666666666,0.1755102040816326,0.1153333333333333,0.0470748299319727,0.0193333333333333,0.0257142857142857,0.0193333333333333,0.0527891156462585,0.2165986394557822,0.4228316237077168,0.8745034552147125,3,False,0.9933333333333332,0.9733333333333334,0.9933333333333332,0.9466666666666668,20.466666666666665,17.551020408163264,1121.0,437.0
+lora,N055_AC,AC,1500,4308,150,0.4026666666666667,0.340297121634169,0.0353333333333333,0.0779944289693593,0.346,0.324744661095636,0.164,0.2051996285979573,0.022,0.0060352831940575,0.03,0.0457288765088208,0.1991792014856081,0.2686738546931644,0.8795500581438357,3,False,0.9866666666666668,0.9133333333333332,0.9933333333333332,0.94,34.599999999999994,32.47446610956361,1024.5,1139.5
+lora,N136_TOL,TOL,1500,759,150,0.448,0.4861660079051383,0.0233333333333333,0.1001317523056653,0.42,0.1910408432147562,0.0593333333333333,0.0922266139657444,0.012,0.0013175230566534,0.0373333333333333,0.1291172595520421,0.4792832674571805,0.3303371033437735,0.8647910920060148,13,False,0.9466666666666668,0.46,0.9733333333333334,0.9133333333333332,42.0,19.104084321475625,904.5,1837.0
+lora,N136_FU1,FU1,1500,2927,150,0.366,0.4246668944311582,0.046,0.147249743764947,0.448,0.193372053296891,0.09,0.0953194396993508,0.0146666666666666,0.0023915271609156,0.0353333333333333,0.1370003416467372,0.5338061724177201,0.3975871977038701,0.8656650663742637,12,False,0.9866666666666668,0.8666666666666667,0.9733333333333334,0.9333333333333332,44.8,19.3372053296891,969.0,1501.0
+lora,N138_TOL,TOL,1500,5129,150,0.5793333333333334,0.1380386040163774,0.0433333333333333,0.0280756482745174,0.2113333333333333,0.5878338857477091,0.1306666666666666,0.1770325599532072,0.022,0.0060440631702086,0.0133333333333333,0.0629752388379801,0.9450167024111262,0.7854106139886504,0.8583778461454012,17,False,0.98,0.88,0.98,0.8666666666666667,21.133333333333333,58.78338857477091,828.0,1117.0
+lora,N138_FU1,FU1,1500,2107,150,0.4253333333333333,0.2728998576174656,0.02,0.0484100616990982,0.3933333333333333,0.4831514000949217,0.1046666666666666,0.1134314190792596,0.0193333333333333,0.0052206929283341,0.0373333333333333,0.0768865685809207,0.3330922322417339,0.5674564420004686,0.8773528407011852,5,False,1.0,0.7466666666666667,0.9933333333333332,0.9066666666666666,39.33333333333333,48.31514000949217,1061.0,1446.0
+lora,N128_BC,BC,1500,3902,150,0.4093333333333333,0.5158892875448488,0.0566666666666666,0.0681701691440287,0.3033333333333333,0.2942080984110712,0.17,0.0784213223987698,0.0426666666666666,0.0333162480779087,0.018,0.0099948744233726,0.2361189133777549,0.2273847892742277,0.8772035681711924,1,True,0.9933333333333332,0.8666666666666667,1.0,0.98,30.333333333333336,29.420809841107125,993.0,1088.0
+lora,N128_AC,AC,1500,2713,150,0.398,0.5488389237007003,0.048,0.0652414301511242,0.3046666666666666,0.2790269074824917,0.184,0.070770364909694,0.0446666666666666,0.0294876520457058,0.0206666666666666,0.0066347217102838,0.336160707703649,0.249407009678557,0.8748769494652151,3,False,0.9933333333333332,0.8133333333333334,0.98,0.9733333333333334,30.466666666666665,27.90269074824917,950.0,1181.0
+lora,N129_BC,BC,1500,3087,150,0.418,0.5963718820861678,0.0413333333333333,0.1130547457078069,0.3053333333333333,0.0835762876579203,0.1753333333333333,0.1814058956916099,0.0326666666666666,0.0132815030774214,0.0273333333333333,0.0123096857790735,0.512331713637836,0.4502797893097814,0.8708970446353751,8,False,0.9733333333333334,0.9266666666666666,0.9666666666666668,0.9666666666666668,30.53333333333333,8.35762876579203,1046.5,1059.0
+lora,N129_AC,AC,1500,2798,150,0.448,0.7076483202287348,0.0373333333333333,0.0493209435310936,0.2506666666666666,0.079699785561115,0.214,0.1336669049320943,0.0326666666666666,0.0228734810578985,0.0173333333333333,0.0067905646890636,0.5432718608529903,0.5443287164364481,0.8700788382131606,8,False,0.98,0.9733333333333334,1.0,0.9933333333333332,25.066666666666663,7.969978556111508,968.0,759.0
+lora,N158_AC,AC,1500,3749,150,0.5753333333333334,0.2461989863963723,0.0286666666666666,0.0266737796745798,0.2986666666666667,0.6295012003200854,0.0586666666666666,0.0493464923979727,0.028,0.0248066150973592,0.0106666666666666,0.0234729261136303,0.6872815862007647,0.781764384762707,0.8645688597603199,4,False,0.98,0.9533333333333334,0.9866666666666668,0.98,29.86666666666667,62.95012003200854,1489.0,1047.0
+lora,N159_BC,BC,1500,3779,150,0.692,0.6996559936491136,0.0246666666666666,0.0185234188938872,0.1726666666666666,0.0812384228631913,0.074,0.173590897062715,0.0133333333333333,0.0140248743053717,0.0233333333333333,0.012966393225721,0.215876863367734,0.529660106865646,0.8605726741505545,1,True,0.9533333333333334,0.9333333333333332,0.9533333333333334,0.9666666666666668,17.266666666666666,8.123842286319132,1407.5,1045.0
+lora,N002_TOL,TOL,1500,6318,150,0.5486666666666666,0.4157961380183602,0.034,0.0577714466603355,0.2106666666666666,0.3779677113010446,0.1673333333333333,0.1179170623615068,0.0273333333333333,0.0201012978790756,0.012,0.0104463437796771,0.382144982589427,0.2657153405968152,0.868923865737158,10,False,0.9733333333333334,0.84,0.9733333333333334,0.96,21.066666666666663,37.79677113010446,1178.0,933.5
+lora,N002_FU1,FU1,1500,4975,150,0.5606666666666666,0.316180904522613,0.0226666666666666,0.0727638190954773,0.2793333333333333,0.4558793969849246,0.1046666666666666,0.1226130653266331,0.0106666666666666,0.0227135678391959,0.022,0.0098492462311557,0.5132730318257956,0.4438021421278216,0.8825479530547228,1,True,0.9733333333333334,0.74,0.9866666666666668,0.8666666666666667,27.933333333333334,45.58793969849246,1212.0,979.0
+lora,N005_BC,BC,1500,6359,150,0.5153333333333333,0.7200817738638151,0.014,0.0501651203019342,0.344,0.1144834093410913,0.1013333333333333,0.0989149237301462,0.012,0.0077056140902657,0.0133333333333333,0.0086491586727472,0.4818271216648321,0.5644381516165136,0.872453424239415,6,False,0.98,0.9266666666666666,0.9933333333333332,0.9533333333333334,34.4,11.448340934109137,1064.0,782.0
+lora,N005_AC,AC,1500,3433,150,0.6666666666666666,0.8100786484124672,0.024,0.0151471016603553,0.1186666666666666,0.0795222837168657,0.162,0.0824351878823186,0.0173333333333333,0.0101951645790853,0.0113333333333333,0.0026216137489076,0.2868239634916012,0.7444319007138178,0.8693809319767338,4,False,0.9733333333333334,0.82,0.9866666666666668,0.9933333333333332,11.866666666666667,7.952228371686572,930.5,1126.0
+lora,N012_TOL,TOL,1500,6709,150,0.3826666666666666,0.3475927858101058,0.046,0.0788493069011775,0.3826666666666666,0.4672827545088687,0.13,0.0857057683708451,0.0353333333333333,0.0005962140408406,0.0233333333333333,0.0199731703681621,0.2349307894867591,0.4616551876312955,0.8663193329612919,15,False,0.9733333333333334,0.54,0.98,0.8066666666666666,38.266666666666666,46.72827545088687,942.5,1193.0
+lora,N012_FU1,FU1,1500,4369,150,0.3386666666666666,0.3588921950102998,0.0246666666666666,0.1924925612268253,0.526,0.3126573586633097,0.0753333333333333,0.1084916456855115,0.0133333333333333,0.0006866559853513,0.022,0.0267795834287022,0.4519786373693446,0.3796909045914732,0.8621357179757462,16,False,0.9866666666666668,0.54,0.98,0.8866666666666667,52.6,31.265735866330967,1099.0,1299.0
+lora,N022_TOL,TOL,1500,3651,150,0.5133333333333333,0.4864420706655711,0.0313333333333333,0.0369761709120788,0.2653333333333333,0.0457408929060531,0.1533333333333333,0.4182415776499589,0.0186666666666666,0.0,0.018,0.0125992878663379,0.5411021637907423,0.6005263351941938,0.8533947992871658,24,False,0.9933333333333332,0.4466666666666666,0.9666666666666668,0.9866666666666668,26.53333333333333,4.574089290605313,916.0,1410.0
+lora,N022_FU1,FU1,1500,2463,150,0.6633333333333333,0.4847746650426309,0.0193333333333333,0.0487210718635809,0.138,0.2025984571660576,0.16,0.2533495736906211,0.0086666666666666,0.0,0.0106666666666666,0.0105562322371092,0.3746715387738529,0.2674075160296381,0.8722471749207706,3,False,0.98,0.44,0.9866666666666668,0.8933333333333333,13.8,20.259845716605763,815.0,1459.0
+lora,N035_TOL,TOL,1500,1598,150,0.5326666666666666,0.2853566958698373,0.0186666666666666,0.0168961201501877,0.24,0.3110137672090112,0.1753333333333333,0.3404255319148936,0.0113333333333333,0.013767209011264,0.022,0.032540675844806,0.4981610346266165,0.4758469557564144,0.8776857337595521,7,False,0.9866666666666668,0.46,0.9933333333333332,0.9933333333333332,24.0,31.10137672090113,1213.0,1855.5
+lora,N043_TOL,TOL,1500,2074,150,0.5666666666666667,0.3548698167791707,0.0113333333333333,0.0573770491803278,0.34,0.0458052073288331,0.0573333333333333,0.4811957569913211,0.006,0.0028929604628736,0.0186666666666666,0.0578592092574734,1.0181973641915782,0.7230459334175234,0.8491362072497243,24,False,0.96,0.4133333333333333,0.9533333333333334,0.9333333333333332,34.0,4.580520732883317,948.0,1315.5
+lora,N043_FU1,FU1,1500,3437,150,0.4413333333333333,0.1638056444573756,0.0226666666666666,0.0677916787896421,0.4126666666666667,0.5728833284841431,0.0866666666666666,0.148967122490544,0.0066666666666666,0.0034914169333721,0.03,0.0430608088449228,0.5614058772185044,0.6530003588177082,0.8716315673639371,6,False,0.98,0.4066666666666667,0.9866666666666668,0.88,41.266666666666666,57.28833284841431,980.0,1422.0

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw3/lora/score/summary.json

@@ -0,0 +1,540 @@
+{
+  "schema": "paired_ft_scores.v1",
+  "dataset": "ji2025_chili",
+  "written_utc": "2026-10-15T11:37:05.178017+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",
+    "ji2025_chili",
+    "--out",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw3/score",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/disease/draw3/lora.npz",
+    "--condition",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw3/test_raw.npz",
+    "--donors",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw3/test_samples.txt",
+    "--threads",
+    "2",
+    "--case-groups",
+    "TOL,FU1",
+    "--control-groups",
+    "BC,AC"
+  ],
+  "arms": [
+    "lora"
+  ],
+  "donors": [
+    "N064_TOL",
+    "N064_FU1",
+    "N032_AC",
+    "N055_AC",
+    "N136_TOL",
+    "N136_FU1",
+    "N138_TOL",
+    "N138_FU1",
+    "N128_BC",
+    "N128_AC",
+    "N129_BC",
+    "N129_AC",
+    "N158_AC",
+    "N159_BC",
+    "N002_TOL",
+    "N002_FU1",
+    "N005_BC",
+    "N005_AC",
+    "N012_TOL",
+    "N012_FU1",
+    "N022_TOL",
+    "N022_FU1",
+    "N035_TOL",
+    "N043_TOL",
+    "N043_FU1"
+  ],
+  "n_donors": 25,
+  "reference": {
+    "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili",
+    "reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
+    "features_sha256": "049795e3a2470a223347015c0c965f56ca90c21143aad6f72d12e39f3e95e58b",
+    "n_r1_cells": 3750,
+    "pca": {
+      "n_components": 50,
+      "explained_variance_ratio_sum": 0.28761026263237,
+      "n_fit_cells": 3750
+    },
+    "r2_control": {
+      "precision": 0.9965333333333334,
+      "coverage": 1.0,
+      "density": 2.5364533333333332,
+      "n_query": 3750,
+      "depth_matched": {
+        "precision": 0.9962666666666666,
+        "coverage": 1.0,
+        "density": 2.48704
+      }
+    },
+    "observed_l1_loo_null_mean": 0.480736250006395
+  },
+  "contrast_definition": {
+    "enabled": true,
+    "rule": "explicit --case-groups / --control-groups",
+    "group_source": "features groups",
+    "case_groups": [
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paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/ji2025_chili/disease/draw3/lora/scoring_support.json

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+      "support_sha256": "2840746ddae5b92028a790a02b15c3ca61256bca7a0cf50f8bbd151aa4d9ea62"
+    }
+  }
+}