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Archive 4 checkpoints (1-4)

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paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/imperial_eskd/locoL_fullsat_s93000_K1000/contrast.csv ADDED
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1
+ 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
2
+ locoL_fullsat_s93000_K1000,T cell,mean_cp10k,3031,0.46349901050853787,0.6352016868529187,0.29581283153996535,0.4000414014554094,113,34,113,34,262546,103364,,,,,,,,,,,
3
+ locoL_fullsat_s93000_K1000,T cell,pseudobulk_log1p_cpm,3031,0.24249354107854532,0.6294466207665587,-0.02917587763280192,0.4179690487034948,113,34,113,34,262546,103364,,,,,,,,,,,
4
+ locoL_fullsat_s93000_K1000,B cell,mean_cp10k,3184,0.4842623915282334,0.6290331452237995,0.32233022636582365,0.4057747918506299,113,34,113,34,48625,19680,,,,,,,,,,,
5
+ locoL_fullsat_s93000_K1000,B cell,pseudobulk_log1p_cpm,3184,0.23366423131472913,0.4870645233040134,0.0765640908252075,0.3511960788732896,113,34,113,34,48625,19680,,,,,,,,,,,
6
+ locoL_fullsat_s93000_K1000,Monocyte,mean_cp10k,2877,0.5751722585825062,0.7184291928055079,0.3050270757581004,0.5549040693628445,112,34,113,34,80851,72846,,,,,,,,,,,
7
+ locoL_fullsat_s93000_K1000,Monocyte,pseudobulk_log1p_cpm,2877,0.43404799260763893,0.7066219687885489,0.10600593508743894,0.5238359592610186,112,34,113,34,80851,72846,,,,,,,,,,,
8
+ locoL_fullsat_s93000_K1000,NK cell,mean_cp10k,2964,0.3148962501048463,0.6597572279517877,0.05309599785547735,0.42247578107507244,113,34,113,34,72125,17149,,,,,,,,,,,
9
+ locoL_fullsat_s93000_K1000,NK cell,pseudobulk_log1p_cpm,2964,0.15600342111060234,0.5964102520780005,-0.04262913687647957,0.3160032780386607,113,34,113,34,72125,17149,,,,,,,,,,,
10
+ locoL_fullsat_s93000_K1000,T cell,welch_top50_deg,5927,,,,,113,34,113,34,262546,103364,True,27,0.3698630136986301,50,50,1057,585,17,0.20481927710843373,50,2242
11
+ locoL_fullsat_s93000_K1000,B cell,welch_top50_deg,5927,,,,,113,34,113,34,48625,19680,True,20,0.25,50,50,298,285,14,0.16279069767441862,50,2242
12
+ locoL_fullsat_s93000_K1000,Monocyte,welch_top50_deg,5927,,,,,112,34,113,34,80851,72846,True,26,0.35135135135135137,50,50,349,801,22,0.28205128205128205,50,2242
13
+ locoL_fullsat_s93000_K1000,NK cell,welch_top50_deg,5927,,,,,113,34,113,34,72125,17149,True,16,0.19047619047619047,50,50,427,346,16,0.19047619047619047,50,2242
14
+ locoL_fullsat_s93000_K1000,DC,welch_top50_deg,5927,,,,,113,34,102,31,13572,822,True,8,0.08695652173913043,50,50,341,210,15,0.17647058823529413,50,2242
paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/imperial_eskd/locoL_fullsat_s93000_K1000/per_donor.csv ADDED
@@ -0,0 +1,158 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 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
2
+ locoL_fullsat_s93000_K1000,C20_1004,covid_positive,1500,1810,150,0.20866666666666667,0.43425414364640885,0.10866666666666666,0.3994475138121547,0.622,0.03867403314917127,0.036,0.07790055248618785,0.007333333333333333,0.04751381215469613,0.017333333333333333,0.0022099447513812156,1.1968987108655618,0.6005338406000345,0.8260511239272724,128,False,0.72,0.31333333333333335,0.7666666666666667,0.5,62.2,3.867403314917127,1340.0,1373.5
3
+ locoL_fullsat_s93000_K1000,C20_1404,covid_positive,1500,5836,150,0.19466666666666665,0.4885195339273475,0.108,0.2705620287868403,0.614,0.015421521590130226,0.056666666666666664,0.204592186429061,0.0026666666666666666,0.016620973269362578,0.024,0.004283755997258396,1.2365894448252228,0.377519259206171,0.8459859727094083,125,False,0.78,0.52,0.82,0.6533333333333333,61.4,1.5421521590130227,1699.0,1473.0
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+ locoL_fullsat_s93000_K1000,C21_1004,covid_positive,1500,5552,150,0.686,0.8982348703170029,0.05,0.08609510086455331,0.16466666666666666,0.0,0.020666666666666667,0.0111671469740634,0.0033333333333333335,0.0005403458213256485,0.07533333333333334,0.003962536023054755,0.49665994236311234,0.813335352446266,0.8238201477498324,148,False,0.5933333333333334,0.4666666666666667,0.7133333333333334,0.76,16.466666666666665,0.0,1509.0,1563.5
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+ locoL_fullsat_s93000_K1000,C21_1704,covid_positive,1500,4570,150,0.558,0.7275711159737418,0.21666666666666667,0.2214442013129103,0.08933333333333333,0.004814004376367615,0.043333333333333335,0.022319474835886213,0.0,0.011816192560175055,0.09266666666666666,0.012035010940919038,0.37232968636032093,0.6774748884556812,0.8724198487072489,73,False,0.7866666666666666,0.52,0.8066666666666666,0.7333333333333333,8.933333333333334,0.48140043763676155,2203.5,2131.0
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+ locoL_fullsat_s93000_K1000,C21_2504,covid_positive,1500,5048,150,0.336,0.7567353407290016,0.09333333333333334,0.12361331220285261,0.47,0.06220285261489699,0.027333333333333334,0.039619651347068144,0.0,0.011687797147385102,0.07333333333333333,0.006141045958795562,0.9499788695192816,0.5401415597460854,0.8677779222529322,21,False,0.72,0.64,0.7933333333333333,0.8933333333333333,47.0,6.220285261489699,2300.0,2692.5
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+ locoL_fullsat_s93000_K1000,C23_2204,covid_positive,1500,3088,150,0.6786666666666666,0.685880829015544,0.08466666666666667,0.10362694300518134,0.16133333333333333,0.06703367875647669,0.05266666666666667,0.11269430051813471,0.005333333333333333,0.025906735751295335,0.017333333333333333,0.0048575129533678756,0.21355094991364423,0.37947949920467566,0.8953374076956857,9,False,0.88,0.6933333333333334,0.92,0.9,16.133333333333333,6.703367875647668,1771.5,1936.5
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+ locoL_fullsat_s93000_K1000,C31_1304,covid_positive,1500,3525,150,0.818,0.782695035460993,0.08733333333333333,0.1075177304964539,0.058,0.007659574468085106,0.022,0.07716312056737588,0.0033333333333333335,0.02070921985815603,0.011333333333333334,0.00425531914893617,0.1854468085106382,0.5810203700567228,0.8828110174207217,35,False,0.8933333333333333,0.8133333333333334,0.9133333333333333,0.9,5.800000000000001,0.7659574468085106,1749.5,1623.0
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+ locoL_fullsat_s93000_K1000,C31_2004,covid_positive,1500,2265,150,0.7006666666666667,0.8004415011037528,0.086,0.08123620309050773,0.15333333333333332,0.039293598233995586,0.042666666666666665,0.05121412803532009,0.0013333333333333333,0.022958057395143488,0.016,0.004856512141280353,0.25989403973509934,0.6165133013422425,0.89873917150544,34,False,0.8666666666666667,0.6333333333333333,0.8666666666666667,0.8066666666666666,15.333333333333332,3.9293598233995586,1704.5,1910.0
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+ locoL_fullsat_s93000_K1000,C31_2704,covid_positive,1500,4200,150,0.7706666666666667,0.7042857142857143,0.078,0.08023809523809523,0.06133333333333333,0.08714285714285715,0.08466666666666667,0.09857142857142857,0.002,0.025952380952380952,0.0033333333333333335,0.0038095238095238095,0.1327619047619048,0.42420172770616554,0.9043065508115383,2,False,0.8933333333333333,0.7266666666666667,0.9333333333333333,0.9066666666666666,6.133333333333333,8.714285714285715,1882.0,1704.0
11
+ locoL_fullsat_s93000_K1000,C33_1401,covid_positive,1500,3983,150,0.298,0.38890283705749434,0.022,0.016570424303288978,0.5666666666666667,0.11172483052975145,0.09133333333333334,0.464474014561888,0.0033333333333333335,0.014310820989204118,0.018666666666666668,0.004017072558373086,0.9500420118838396,0.6015977414820979,0.8638034248143593,67,False,0.7133333333333334,0.41333333333333333,0.7733333333333333,0.42,56.666666666666664,11.172483052975144,1092.0,909.0
12
+ locoL_fullsat_s93000_K1000,C33_1601,covid_positive,1500,395,150,0.344,0.14430379746835442,0.03933333333333333,0.11645569620253164,0.39266666666666666,0.2,0.18533333333333332,0.5240506329113924,0.004,0.007594936708860759,0.034666666666666665,0.007594936708860759,0.8388691983122364,0.781467701292667,0.8582608412527925,108,False,0.7,0.7533333333333333,0.7866666666666666,0.5533333333333333,39.266666666666666,20.0,885.0,644.0
13
+ locoL_fullsat_s93000_K1000,C33_1901,covid_positive,1500,1947,150,0.4533333333333333,0.3754494093477144,0.026,0.042116076014381096,0.25,0.12223934257832562,0.23066666666666666,0.43656908063687727,0.0006666666666666666,0.01078582434514638,0.03933333333333333,0.012840267077555213,0.4642752953261428,0.5457878736320764,0.8802677636814107,15,False,0.52,0.5466666666666666,0.5733333333333334,0.48,25.0,12.223934257832562,683.0,897.0
14
+ locoL_fullsat_s93000_K1000,C34_1404,covid_positive,1500,2483,150,0.39666666666666667,0.8771647200966572,0.06266666666666666,0.01973419250906162,0.49066666666666664,0.016915022150624244,0.018,0.07047925896093435,0.008,0.011679420056383408,0.024,0.004027386226339106,1.0733134648946168,0.7709669223771655,0.8491672761246799,114,False,0.8266666666666667,0.66,0.8266666666666667,0.8666666666666667,49.06666666666666,1.6915022150624244,2450.0,1720.0
15
+ locoL_fullsat_s93000_K1000,C34_2104,covid_positive,1500,2808,150,0.42866666666666664,0.7916666666666666,0.06466666666666666,0.024216524216524215,0.454,0.041666666666666664,0.022,0.12428774928774929,0.006,0.013888888888888888,0.024666666666666667,0.004273504273504274,0.9463532763532763,0.5999708155171841,0.8758182631057304,63,False,0.82,0.6933333333333334,0.84,0.8866666666666667,45.4,4.166666666666666,2108.5,2067.5
16
+ locoL_fullsat_s93000_K1000,C34_2504,covid_positive,1500,1945,150,0.566,0.6961439588688946,0.086,0.024678663239074552,0.29,0.12544987146529563,0.03666666666666667,0.12904884318766066,0.008666666666666666,0.02416452442159383,0.012666666666666666,0.0005141388174807198,0.4760479862896316,0.40892539992164,0.9007935618174004,9,False,0.86,0.7333333333333333,0.88,0.92,28.999999999999996,12.544987146529563,2238.5,2111.0
17
+ locoL_fullsat_s93000_K1000,C36_1504,covid_positive,1500,4765,150,0.5246666666666666,0.7643231899265478,0.08266666666666667,0.14144805876180483,0.31533333333333335,0.03546694648478489,0.043333333333333335,0.030640083945435468,0.007333333333333333,0.01951731374606506,0.02666666666666667,0.008604407135362015,0.6212437915355021,0.5893382201890965,0.8780339460697172,73,False,0.7933333333333333,0.7866666666666666,0.8533333333333334,0.9333333333333333,31.533333333333335,3.546694648478489,1939.5,1747.0
18
+ locoL_fullsat_s93000_K1000,C36_1704,covid_positive,1500,1554,150,0.662,0.842985842985843,0.09333333333333334,0.07335907335907337,0.132,0.014800514800514801,0.08866666666666667,0.0546975546975547,0.0026666666666666666,0.010296010296010296,0.021333333333333333,0.003861003861003861,0.3772303732303732,0.7027427978748242,0.8817171430712444,42,False,0.9,0.68,0.92,0.9066666666666666,13.200000000000001,1.4800514800514801,1704.0,2044.5
19
+ locoL_fullsat_s93000_K1000,C36_2104,covid_positive,1500,1086,150,0.6573333333333333,0.7679558011049724,0.08866666666666667,0.09668508287292818,0.194,0.05432780847145488,0.032,0.06353591160220995,0.004666666666666667,0.011970534069981584,0.023333333333333334,0.0055248618784530384,0.3149613259668509,0.552682714113083,0.8915183285922269,23,False,0.88,0.7933333333333333,0.9333333333333333,0.9466666666666667,19.400000000000002,5.432780847145488,2347.5,1851.0
20
+ locoL_fullsat_s93000_K1000,C40_1504,covid_positive,1500,5482,150,0.422,0.7433418460415907,0.06266666666666666,0.09649762860269974,0.46266666666666667,0.05600145932141554,0.025333333333333333,0.09157241882524626,0.006,0.009668004377964246,0.021333333333333333,0.002918642831083546,0.8501597956950019,0.4967961170529107,0.8745717794601758,21,False,0.74,0.6066666666666667,0.76,0.8,46.266666666666666,5.6001459321415545,1532.0,1253.5
21
+ locoL_fullsat_s93000_K1000,C40_2204,covid_positive,1500,975,150,0.5613333333333334,0.6933333333333334,0.118,0.13538461538461538,0.214,0.028717948717948718,0.056666666666666664,0.12923076923076923,0.0026666666666666666,0.010256410256410256,0.04733333333333333,0.003076923076923077,0.45907692307692305,0.4280166763557205,0.8687824096554569,110,False,0.8133333333333334,0.54,0.84,0.8666666666666667,21.4,2.871794871794872,1716.5,1808.0
22
+ locoL_fullsat_s93000_K1000,C40_0105,covid_positive,1500,8728,150,0.2806666666666667,0.42587076076993585,0.11866666666666667,0.036778185151237396,0.5506666666666666,0.4643675527039413,0.015333333333333332,0.05728689275893675,0.006,0.013175985334555454,0.028666666666666667,0.0025206232813932174,0.38866727772685605,0.5909469296575621,0.9075027043475077,4,False,0.86,0.7333333333333333,0.88,0.86,55.06666666666666,46.43675527039413,3061.5,1862.0
23
+ locoL_fullsat_s93000_K1000,C42_1504,covid_positive,1500,2762,150,0.598,0.7320782041998551,0.05266666666666667,0.13613323678493844,0.2926666666666667,0.020275162925416364,0.03266666666666666,0.0894279507603186,0.006666666666666667,0.013758146270818247,0.017333333333333333,0.00832729905865315,0.562795076031861,0.5141600776933539,0.8600991016410175,119,False,0.68,0.46,0.8066666666666666,0.6133333333333333,29.26666666666667,2.0275162925416366,1333.0,1302.0
24
+ locoL_fullsat_s93000_K1000,C42_2204,covid_positive,1500,4970,150,0.7053333333333334,0.8511066398390342,0.029333333333333333,0.06317907444668008,0.224,0.035211267605633804,0.028,0.035211267605633804,0.004666666666666667,0.012072434607645875,0.008666666666666666,0.0032193158953722333,0.3884721663313212,0.7197827632523519,0.8881700073049835,18,False,0.74,0.62,0.8866666666666667,0.8533333333333334,22.400000000000002,3.5211267605633805,1481.5,1462.0
25
+ locoL_fullsat_s93000_K1000,C42_2704,covid_positive,1500,8918,150,0.6486666666666666,0.8535546086566494,0.018666666666666668,0.04619869925992375,0.2793333333333333,0.036891679748822605,0.032,0.054047992823503026,0.008,0.006391567616057412,0.013333333333333334,0.0029154518950437317,0.5089359348134859,0.7246787008875823,0.8814056555622296,32,False,0.66,0.72,0.7733333333333333,0.8066666666666666,27.933333333333334,3.6891679748822606,1389.5,1489.0
26
+ locoL_fullsat_s93000_K1000,C58_1604,covid_negative,1500,265,132,0.5466666666666666,0.7018867924528301,0.04533333333333334,0.04150943396226415,0.3433333333333333,0.0037735849056603774,0.034666666666666665,0.2188679245283019,0.0026666666666666666,0.01509433962264151,0.027333333333333334,0.018867924528301886,0.703698113207547,0.51846072438743,0.8143346396022175,153,False,0.803030303030303,0.3560606060606061,0.8560606060606061,0.6893939393939394,34.333333333333336,0.37735849056603776,1909.5,1285.0
27
+ locoL_fullsat_s93000_K1000,C58_2501,covid_positive,1500,1671,150,0.358,0.42848593656493117,0.06866666666666667,0.0353081986834231,0.5,0.31717534410532616,0.04466666666666667,0.15320167564332735,0.006,0.05326152004787552,0.02266666666666667,0.012567324955116697,0.45256493117893476,0.3470110787273232,0.8933780103333423,17,False,0.9,0.9266666666666666,0.8933333333333333,0.88,50.0,31.717534410532615,2578.5,700.0
28
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29
+ locoL_fullsat_s93000_K1000,C58_0102,covid_positive,1500,972,150,0.698,0.5339506172839507,0.072,0.027777777777777776,0.18666666666666668,0.2880658436213992,0.025333333333333333,0.11316872427983539,0.006666666666666667,0.03292181069958848,0.011333333333333334,0.00411522633744856,0.43097942386831267,0.32547969346416367,0.8743895666221323,67,False,0.8133333333333334,0.8733333333333333,0.8533333333333334,0.8866666666666667,18.666666666666668,28.80658436213992,2251.5,749.0
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+ locoL_fullsat_s93000_K1000,C58_0402,covid_positive,1500,9254,150,0.7533333333333333,0.4245731575534904,0.034,0.01988329371082775,0.144,0.4091203803760536,0.056666666666666664,0.11681435055111303,0.0013333333333333333,0.02485411713853469,0.010666666666666666,0.004754700669980549,0.6975776961314025,0.4845732068994056,0.8834325009430841,29,False,0.9066666666666666,0.8133333333333334,0.9266666666666666,0.8066666666666666,14.399999999999999,40.912038037605356,1859.0,1006.0
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+ locoL_fullsat_s93000_K1000,C58_1003,recovery,1500,4918,150,0.4746666666666667,0.5917039446929646,0.043333333333333335,0.02745018300122001,0.35133333333333333,0.1691744611630744,0.051333333333333335,0.14721431476209842,0.017333333333333333,0.05612037413582757,0.062,0.008336722244814965,0.5034106005151145,0.24960071023802022,0.8757548310119281,36,False,0.5933333333333334,0.8666666666666667,0.58,0.8533333333333334,35.13333333333333,16.917446116307442,1556.0,745.5
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+ locoL_fullsat_s93000_K1000,C60_2504,covid_positive,1500,1837,150,0.8573333333333333,0.8911268372346217,0.048666666666666664,0.05443658138268917,0.05,0.00979858464888405,0.027333333333333334,0.032117583015786606,0.0013333333333333333,0.009254218835057159,0.015333333333333332,0.00326619488296135,0.10453710760297598,0.7926028747225629,0.871589547361159,54,False,0.6866666666666666,0.6666666666666666,0.82,0.8,5.0,0.979858464888405,1416.0,1187.0
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+ locoL_fullsat_s93000_K1000,C65_2104,covid_positive,1500,274,137,0.35333333333333333,0.5766423357664233,0.3313333333333333,0.20802919708029197,0.20666666666666667,0.014598540145985401,0.09066666666666667,0.19343065693430658,0.0006666666666666666,0.0036496350364963502,0.017333333333333333,0.0036496350364963502,0.6581119221411192,0.3905468316130126,0.820754240304004,154,False,0.635036496350365,0.45255474452554745,0.5693430656934306,0.656934306569343,20.666666666666668,1.4598540145985401,1565.0,1266.0
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49
+ locoL_fullsat_s93000_K1000,C101_2001,covid_positive,1500,2130,150,0.36733333333333335,0.4765258215962441,0.092,0.2051643192488263,0.476,0.22253521126760564,0.030666666666666665,0.05539906103286385,0.0013333333333333333,0.022535211267605635,0.03266666666666666,0.01784037558685446,0.5365821596244131,0.29917206990666134,0.8797732558140888,48,False,0.8533333333333334,0.8866666666666667,0.8733333333333333,0.88,47.599999999999994,22.253521126760564,2236.0,882.0
50
+ locoL_fullsat_s93000_K1000,C101_2502,recovery,1500,587,150,0.17666666666666667,0.424190800681431,0.04,0.06132879045996593,0.7246666666666667,0.3679727427597956,0.029333333333333333,0.05792163543441227,0.0013333333333333333,0.07836456558773425,0.028,0.010221465076660987,0.7489449176604203,0.5063120176111204,0.8568084049289776,23,False,0.8,0.7266666666666667,0.8333333333333334,0.76,72.46666666666667,36.79727427597956,2412.0,822.0
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+ locoL_fullsat_s93000_K1000,C104_2204,covid_negative,1500,11388,150,0.556,0.29004214963119074,0.05533333333333333,0.03898840885142255,0.11733333333333333,0.4137688795223042,0.26,0.18580962416578856,0.0,0.06840533895328416,0.011333333333333334,0.002985598876009835,0.72968177028451,0.6015953960674094,0.8886217607851113,21,False,0.86,0.5933333333333334,0.8866666666666667,0.62,11.733333333333333,41.37688795223042,1222.5,1965.5
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+ locoL_fullsat_s93000_K1000,C106_2204,covid_negative,1500,9233,150,0.6566666666666666,0.6097693057511101,0.04,0.036824434095093686,0.05466666666666667,0.19451965774937724,0.23266666666666666,0.10733239467128777,0.0006666666666666666,0.047980071482725005,0.015333333333333332,0.003574136250406152,0.3743327917975378,0.3128768301278175,0.8884187728521526,25,False,0.9266666666666666,0.37333333333333335,0.9066666666666666,0.6266666666666667,5.466666666666667,19.451965774937722,1465.5,1796.0
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+ locoL_fullsat_s93000_K1000,C108_2204,covid_negative,1500,1839,150,0.8346666666666667,0.6688417618270799,0.048666666666666664,0.0032626427406199023,0.04933333333333333,0.03806416530723219,0.054,0.25502990755845567,0.0,0.021750951604132682,0.013333333333333334,0.013050570962479609,0.44556171832517677,0.5209086508610423,0.8581918881495341,79,False,0.9333333333333333,0.5066666666666667,0.9266666666666666,0.7066666666666667,4.933333333333334,3.8064165307232187,1811.0,1341.0
55
+ locoL_fullsat_s93000_K1000,C108_1501,covid_positive,1500,1488,150,0.32466666666666666,0.2956989247311828,0.032,0.016129032258064516,0.566,0.21841397849462366,0.05333333333333334,0.41935483870967744,0.0026666666666666666,0.04032258064516129,0.021333333333333333,0.010080645161290322,0.8073548387096775,0.6277731013291346,0.8592572517658439,74,False,0.7333333333333333,0.38,0.7933333333333333,0.5333333333333333,56.599999999999994,21.841397849462364,1452.0,863.0
56
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57
+ locoL_fullsat_s93000_K1000,C108_2201,covid_positive,1500,696,150,0.27466666666666667,0.2988505747126437,0.068,0.041666666666666664,0.544,0.09195402298850575,0.034,0.5100574712643678,0.002,0.021551724137931036,0.07733333333333334,0.035919540229885055,1.0395862068965518,0.7372693269726317,0.8416489303084576,111,False,0.7666666666666667,0.34,0.7866666666666666,0.6266666666666667,54.400000000000006,9.195402298850574,1597.0,1399.5
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+ locoL_fullsat_s93000_K1000,C123_2404,covid_positive,1500,3758,150,0.3446666666666667,0.5516232038318254,0.043333333333333335,0.04922831293241086,0.30733333333333335,0.08541777541245343,0.16933333333333334,0.271953166577967,0.0013333333333333333,0.032730175625332626,0.134,0.009047365620010643,0.6937363846017384,0.3198850599491083,0.8737466339486741,54,False,0.7,0.6133333333333333,0.76,0.6266666666666667,30.733333333333334,8.541777541245343,1002.5,1299.0
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62
+ locoL_fullsat_s93000_K1000,C124_2404,covid_positive,1500,2290,150,0.12066666666666667,0.5100436681222708,0.09,0.18777292576419213,0.7306666666666667,0.08340611353711791,0.026,0.19519650655021833,0.0006666666666666666,0.017903930131004366,0.032,0.005676855895196507,1.3471673944687046,0.2180274260105741,0.8393158321876677,104,False,0.7066666666666667,0.44666666666666666,0.7333333333333333,0.5733333333333334,73.06666666666666,8.340611353711791,1739.0,1635.0
63
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100
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101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/imperial_eskd/locoL_fullsat_s93000_K1000/summary.json ADDED
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+ "generated_pooled_cells": 32.81783439490446
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+ "median_umi_per_cell_scoring_genes": {
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+ "pseudobulk_log1p_cpm": {
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+ "partial_r_generated_given_broadcast": -0.02917587763280192,
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+ },
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+ "partial_r_generated_given_broadcast": 0.10600593508743894,
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+ "r_generated_vs_broadcast": 0.5238359592610186,
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+ "NK cell": {
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+ }
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+ },
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+ "deg_top50": {
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+ "NK cell",
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+ "DC"
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+ ],
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+ "types_not_scored": {},
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+ "per_type": {
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+ "gen_top_list_size": 50,
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+ "top50_overlap_broadcast": 17,
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+ "top50_jaccard_broadcast": 0.20481927710843373,
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+ "n_cells_obs": 262546,
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+ "n_cells_gen": 103364
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+ "B cell": {
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+ "top50_overlap": 20,
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+ "top50_jaccard": 0.25,
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+ "seconds": 45.3
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+ "code_sha256": {
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paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/imperial_eskd/locoL_lora16_K1000/README.md ADDED
@@ -0,0 +1,73 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # score_ft.py output: imperial_eskd, 157 scored donors
2
+
3
+ Arms: locoL_lora16_K1000. Every arm is scored on the same donors against the same observed reference.
4
+
5
+ ## Inputs and fixed contracts
6
+ - Observed reference: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd/reference.npz` (sha 34b4caa3f8a6), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd;
7
+ 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/imperial_eskd/observed_labels/labels/labels.parquet.
8
+ - Generated cells: `generated_counts` read out once with Poisson(seed 20260916) over the **whole NPZ in row order**
9
+ (`poisson_readout.poisson_integerise`), then the scored donors' rows. These integer counts are used for labels, embedding,
10
+ depth and the contrast. Pseudobulk uses the summed `generated_counts` (rates), as `score_generated.py`.
11
+ - 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 =
12
+ the 1,006-gene annotation list minus genes the dataset's sc assay did not measure in every sample (1005 genes).
13
+ - Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (5927 genes).
14
+
15
+ ## Definitions
16
+ 1. **Composition**: fraction of each donor's cells per six-type label (all generated cells; all observed QC cells).
17
+ `comp_l1` = sum over the six labels of |generated - observed| (immicro_common.l1). `comp_l1_obs_loo_null` = L1 of the
18
+ donor's observed composition to the mean of the *other scored donors'* observed compositions. `composition_top1` =
19
+ fraction of donors whose generated composition is closest (L1) to their own observed composition.
20
+ 2. **Pseudobulk**: `pb_r` = Pearson r of CPM-log1p(summed generated_counts) vs CPM-log1p(observed pseudobulk) on the scoring
21
+ genes (evaluate_realbulk.cpm_log1p / paired_r). `pb_top1` = the donor's generated pseudobulk is closest (Pearson) to its own
22
+ observed pseudobulk among the 157 scored donors (immicro_common.retrieval = evaluate_realbulk.top1 arithmetic).
23
+ 3. **Precision / coverage / density** (stage_b_embed.py functions): per-cell CP10K over the scoring genes + log1p; PCA-50
24
+ (randomized, random_state 20260925) and k = 10 real-real k-NN balls fitted on **R1 of the scored donors only**.
25
+ Reference rule (independent of fold and arm): per donor, cells in canonical order (library_id+barcode), one
26
+ permutation from `default_rng([20260925, uint64(sha256(donor)[:8])])`; R1 = first n, R2 = next n,
27
+ n = min(150, n_cells // 2) (23482 R1 cells here). Generated query: per donor n cells (the donor's R1 size),
28
+ without replacement, `default_rng([20260926, same key])`. Precision = fraction of generated cells inside any R1 ball
29
+ (Kynkaanniemi 2019); coverage = fraction of R1 cells whose ball holds a generated cell; density = Naeem 2020.
30
+ Per-donor precision = that donor's generated cells; per-donor coverage = that donor's R1 cells (the pooled values are
31
+ their n-weighted means; plain means when every donor has 150 reference cells). R2 (held-out real cells of the same donors) is the
32
+ perfect-generator control: precision 0.9673, coverage 0.9997.
33
+ **Depth matched**: stage_b_embed depth matching run pairwise (R1 vs this arm): per donor and within-donor rank of detected
34
+ genes, both cells are thinned by UMI sampling without replacement to the smaller detected-gene count; PCA kept from
35
+ un-thinned R1, radii recomputed on thinned R1; fresh rng(20260929) per arm. R2 control: precision
36
+ 0.9667, coverage 0.9997.
37
+ 4. **Monocyte %** = 100 x Monocyte fraction (all cells) per donor; **median UMI per cell** = median over cells of the
38
+ Poisson-read (generated) / observed counts summed over the scoring genes (per donor, and pooled).
39
+ 5. **Group contrast** (T, B, Monocyte, NK): case groups ['covid_positive'] (n = 113) vs control groups ['covid_negative'] (n = 34); rule: explicit --case-groups / --control-groups; groups from features groups.
40
+ Genes per type = scoring genes detected (count > 0) in >= 1 % of the scored donors' observed
41
+ cells of that type. Primary statistic `mean_cp10k`: per-cell CP10K over the scoring genes; per donor the mean over its
42
+ cells of the type (donors with >= 1 such cell); group mean = mean over the group's donors (donor-balanced);
43
+ logFC = log2(case mean + 1) - log2(control mean + 1). Secondary `pseudobulk_log1p_cpm`: the SLE benchmark evaluator's
44
+ statistic (donor x type summed counts, log1p CPM over the scoring genes, mean case - mean control;
45
+ evaluate_generated_vs_truth.group_log_fold_change). Both are computed on the generated cells (their frozen labels) and on
46
+ the observed cells; `r_generated` = Pearson r of the two logFC vectors. Broadcast baseline `r_broadcast`: the same
47
+ observed vector against the logFC of the input bulk (condition NPZ `bulk_counts` of the arm, scoring genes, per-donor
48
+ CP10K resp. log1p CPM, group means). `partial_r_generated_given_broadcast`: r of the OLS residuals of observed and
49
+ generated logFC on the bulk logFC (residual_specificity.py).
50
+ 6. **Top-50 DEG overlap** (contrast.csv rows `statistic = welch_top50_deg`; summary `deg_top50`): the SLE benchmark's score (`total_top50_overlap` of
51
+ `bulk2sc-paper/scripts/evaluate_generated_vs_truth.py`, Welch backend: the "top-50 DEG 81 / 84" of the final model), run
52
+ with the evaluator's own functions on the same donor x type pseudobulks as the contrast. Per cell type, observed and
53
+ generated separately: donor x type summed counts on all 5927 scoring genes (donors of the two groups with
54
+ >= 1 cell of the type) -> `welch_bh_deg` (log1p CPM, two-sided Welch t-test case vs control, Benjamini-Hochberg over the
55
+ genes with a defined p-value; needs >= 2 donors per group) -> `top_deg_genes` (FDR < 0.05, descending |logFC|,
56
+ first 50; shorter when fewer genes pass). `top50_overlap` = |observed list & generated list|; `top50_jaccard`
57
+ the evaluator's Jaccard. Summary `sum` = total over the scored types (the quantity reported as 81), `max` = the sum of
58
+ the observed list lengths (the "of 262"), `sum_4type` = T + B + Monocyte + NK. A type is scored when its observed test
59
+ 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
60
+ (aggregates: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd/deg_reference.npz).
61
+ **Broadcast analogue** (`top50_overlap_broadcast`, as `sle_broadcast.py` `broadcast_input_bulk`; not part of the
62
+ published benchmark): the same test on the arm's condition bulk_counts (scoring genes, the 113 + 34
63
+ donors), one whole-PBMC top-50 list, compared with every type's observed list.
64
+
65
+ ## Files
66
+ - `per_donor.csv`: one row per arm x donor (all per-donor quantities above).
67
+ - `summary.json`: per arm the donor means / pooled values, provenance (NPZ sha, receipt check, generation metadata,
68
+ Poisson nnz of the whole NPZ, annotation contract), and the reference block (PCA, R2 control).
69
+ - `contrast.csv`: per arm x cell type x statistic (`mean_cp10k`, `pseudobulk_log1p_cpm`: logFC r; `welch_top50_deg`:
70
+ top-50 DEG overlap, T / B / Monocyte / NK / DC; columns of the other kind are empty).
71
+ - `arms/<arm>/labels/` (predict_scanvi.py labels + manifest), `arms/<arm>/generated_cells.parquet` (NPZ row, donor, label,
72
+ UMI on the scoring genes, P/C subsample flag), `arms/<arm>/deg_top50_lists.csv` (observed, generated and broadcast
73
+ top-50 gene lists, Ensembl ids, rank order).