junidude14 commited on
Commit
236b5ff
·
verified ·
1 Parent(s): 498f1ae

Archive 4 checkpoints (1-4)

Browse files
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scores_pilot/diffusion_only/score/arms/pairedcal/labels/labels.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:369ec822ae054289fe12156bdab146e98d79448c327c3e87b99f5525ea4cf28e
3
+ size 818278
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scores_pilot/diffusion_only/score/arms/pairedcal/predict_scanvi.log ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ INFO  File
2
+ /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
3
+ ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
4
+ del/model.pt already downloaded
5
+ INFO  File
6
+ /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
7
+ ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
8
+ del/model.pt already downloaded
9
+ INFO  Found 99.90049751243781% reference vars in query data.
10
+ INFO  File
11
+ /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
12
+ ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
13
+ del/model.pt already downloaded
14
+ {
15
+ "method": "pairedcal",
16
+ "n_cells": 33000,
17
+ "n_genes": 1005,
18
+ "label_counts": {
19
+ "celltype_l1_pred": {
20
+ "T cell": 23776,
21
+ "Monocyte": 3976,
22
+ "B cell": 2675,
23
+ "NK cell": 1698,
24
+ "Other": 500,
25
+ "DC": 375
26
+ },
27
+ "aifi_l1": {
28
+ "T cell": 23776,
29
+ "Monocyte": 3976,
30
+ "B cell": 2675,
31
+ "NK cell": 1698,
32
+ "DC": 375,
33
+ "Platelet": 163,
34
+ "ILC": 157,
35
+ "Erythrocyte": 131,
36
+ "Progenitor cell": 49
37
+ },
38
+ "aifi_l2": {
39
+ "Memory CD4 T cell": 5925,
40
+ "Naive CD4 T cell": 5884,
41
+ "Memory CD8 T cell": 3434,
42
+ "gdT": 3058,
43
+ "CD14 monocyte": 3030,
44
+ "Naive CD8 T cell": 2341,
45
+ "Memory B cell": 1851,
46
+ "Treg": 1480,
47
+ "CD56dim NK cell": 1210,
48
+ "CD8aa": 666,
49
+ "CD16 monocyte": 583,
50
+ "Naive B cell": 517,
51
+ "DN T cell": 513,
52
+ "MAIT": 468,
53
+ "CD56bright NK cell": 416,
54
+ "Intermediate monocyte": 363,
55
+ "cDC2": 303,
56
+ "Effector B cell": 240,
57
+ "Platelet": 163,
58
+ "ILC": 157,
59
+ "Erythrocyte": 131,
60
+ "Proliferating NK cell": 72,
61
+ "pDC": 57,
62
+ "Progenitor cell": 49,
63
+ "Transitional B cell": 39,
64
+ "Plasma cell": 28,
65
+ "cDC1": 9,
66
+ "Proliferating T cell": 7,
67
+ "ASDC": 6
68
+ }
69
+ },
70
+ "confidence": {
71
+ "mean_l2_max_prob": 0.9126860870389324,
72
+ "mean_l1_mass": 0.985178530216217,
73
+ "frac_l2_max_prob_ge_0.5": 0.9709696969696969
74
+ },
75
+ "timings_s": {
76
+ "predict": 0.4,
77
+ "total": 0.7
78
+ },
79
+ "subset": false
80
+ }
81
+ -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores_pilot/diffusion_only/score/arms/pairedcal/labels/labels.parquet
82
+
83
+ --- stderr ---
84
+ Seed set to 20260916
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scores_pilot/diffusion_only/score/per_donor.csv ADDED
@@ -0,0 +1,45 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
+ lora,HS3,DB3,1500,4617,150,0.7333333333333333,0.6484730344379467,0.06666666666666667,0.06952566601689408,0.1,0.17782109594975093,0.04466666666666667,0.07060862031622266,0.050666666666666665,0.028589993502274202,0.004666666666666667,0.004981589776911414,0.21387394411955812,0.04060118700472884,0.9080076484472177,2,False,0.9866666666666667,0.9933333333333333,1.0,1.0,10.0,17.782109594975093,2814.0,2186.0
3
+ lora,HS6,DB3,1500,4222,150,0.48333333333333334,0.4836570345807674,0.03933333333333333,0.037423022264329704,0.3373333333333333,0.3147797252486973,0.07733333333333334,0.13003315963998105,0.05266666666666667,0.024869729985788725,0.01,0.009237328280435813,0.10604705510816359,0.3824588765473767,0.9085602212516003,3,False,0.9933333333333333,0.9133333333333333,0.9933333333333333,0.9933333333333333,33.733333333333334,31.47797252486973,2632.0,2457.5
4
+ lora,HS7,DB1,1500,4271,150,0.7393333333333333,0.7035822992273473,0.06266666666666666,0.03839850152189183,0.09666666666666666,0.13135097166939827,0.050666666666666665,0.09740107703114025,0.046,0.02130648560056193,0.004666666666666667,0.0079606649496605,0.16942542730039792,0.17462025766050882,0.9069400001253476,4,False,0.98,1.0,1.0,1.0,9.666666666666666,13.135097166939827,2755.0,1748.0
5
+ lora,HS13,DB5,1500,4792,150,0.632,0.6156093489148581,0.06533333333333333,0.056343906510851416,0.20533333333333334,0.2166110183639399,0.038,0.08764607679465776,0.05266666666666667,0.02003338898163606,0.006666666666666667,0.0037562604340567614,0.12184752365052867,0.07950263318013584,0.9010138294264392,10,False,1.0,0.7666666666666667,1.0,0.9933333333333333,20.533333333333335,21.66110183639399,3144.0,2176.0
6
+ lora,HS18,DB4,1500,3348,150,0.7786666666666666,0.6633811230585425,0.051333333333333335,0.05734767025089606,0.10066666666666667,0.18309438470728792,0.032,0.07198327359617682,0.03333333333333333,0.016129032258064516,0.004,0.008064516129032258,0.264979689366786,0.056830454472214534,0.9012740009591343,9,False,0.9933333333333333,0.94,1.0,0.9866666666666667,10.066666666666666,18.309438470728793,3062.5,2108.0
7
+ lora,HS31,DB3,1500,4830,150,0.7053333333333334,0.5956521739130435,0.058666666666666666,0.07039337474120083,0.11733333333333333,0.21884057971014492,0.06333333333333334,0.08385093167701864,0.04733333333333333,0.02546583850931677,0.008,0.005797101449275362,0.26750310559006213,0.08982859354260735,0.908740671383931,1,True,1.0,0.9666666666666667,1.0,1.0,11.733333333333333,21.884057971014492,2521.0,2217.5
8
+ lora,HS34,DB5,1500,4363,150,0.7106666666666667,0.7073114829245931,0.06333333333333334,0.04859041943616777,0.158,0.16983726793490717,0.029333333333333333,0.0550080220032088,0.032,0.013981205592482237,0.006666666666666667,0.005271602108640843,0.07502391320956533,0.14554772243505307,0.8989819606442145,12,False,0.9866666666666667,0.7933333333333333,1.0,0.98,15.8,16.983726793490717,2954.5,2176.0
9
+ lora,HS37,DB6,1500,2127,150,0.598,0.5763986835919135,0.10866666666666666,0.14997649271274094,0.158,0.18288669487541137,0.068,0.06535025858015985,0.058,0.021626704278326282,0.009333333333333334,0.0037611659614480487,0.13239304184297132,0.17642904039178112,0.905706088087381,10,False,0.9866666666666667,0.84,0.9933333333333333,0.9933333333333333,15.8,18.28866948754114,2758.0,2099.0
10
+ lora,HS38,DB2,1500,3952,150,0.5993333333333334,0.4534412955465587,0.04066666666666666,0.06022267206477733,0.24266666666666667,0.27631578947368424,0.054,0.16776315789473684,0.056666666666666664,0.03365384615384615,0.006666666666666667,0.00860323886639676,0.33780971659919035,0.3979973492276381,0.9059303696973131,3,False,1.0,0.9733333333333334,1.0,0.9933333333333333,24.266666666666666,27.631578947368425,2496.0,1448.0
11
+ lora,HS52,DB1,1500,4286,150,0.7546666666666667,0.7473168455436304,0.09933333333333333,0.04316378908072795,0.07066666666666667,0.12085860942603827,0.03933333333333333,0.06276248250116659,0.03,0.017498833411105925,0.006,0.008399440037330844,0.15204106392907143,0.23339752310597672,0.9064308655456041,3,False,1.0,0.96,1.0,0.9866666666666667,7.066666666666667,12.085860942603826,2735.5,1848.5
12
+ lora,HS58,DB7,1500,1299,150,0.6993333333333334,0.6605080831408776,0.03,0.029253271747498075,0.15266666666666667,0.15550423402617397,0.06266666666666666,0.1170130869899923,0.042666666666666665,0.03156274056966898,0.012666666666666666,0.006158583525789068,0.1143679753656659,0.13904887966629118,0.8920973922625794,11,False,1.0,0.8533333333333334,0.9933333333333333,1.0,15.266666666666667,15.550423402617398,1952.0,1944.0
13
+ lora,HS60,DB6,1500,2659,150,0.6966666666666667,0.6288078224896577,0.043333333333333335,0.04061677322301617,0.14666666666666667,0.16058668672433246,0.06133333333333333,0.14328694998119593,0.043333333333333335,0.020308386611508085,0.008666666666666666,0.006393380970289583,0.19174727341105685,0.12991818939150382,0.8932059779653729,18,False,1.0,0.86,0.9933333333333333,0.9866666666666667,14.666666666666666,16.058668672433246,2566.5,2014.0
14
+ lora,HS66,DB4,1500,4857,150,0.684,0.6448424953675108,0.09466666666666666,0.10376775787523163,0.11466666666666667,0.16512250360304714,0.056,0.07020794729256744,0.044,0.012559192917438749,0.006666666666666667,0.0035001029442042414,0.1475297508750258,0.09427105876197542,0.9000736078550848,16,False,1.0,0.8866666666666667,1.0,0.9866666666666667,11.466666666666667,16.512250360304716,2839.0,2041.0
15
+ lora,HS81,DB7,1500,1638,150,0.7666666666666667,0.721001221001221,0.072,0.04212454212454213,0.106,0.13553113553113552,0.021333333333333333,0.06288156288156288,0.03,0.03296703296703297,0.004,0.005494505494505495,0.15108180708180713,0.19387054279631524,0.8934625942043475,10,False,1.0,0.82,0.9866666666666667,0.9866666666666667,10.6,13.553113553113553,3198.5,2240.5
16
+ lora,HS82,DB2,1500,4201,150,0.7726666666666666,0.6553201618662223,0.11933333333333333,0.1309212092358962,0.05533333333333333,0.14782194715543917,0.028666666666666667,0.031183051654368008,0.018666666666666668,0.02499404903594382,0.005333333333333333,0.009759581052130446,0.2346930096008886,0.18293033059828231,0.9015712701962697,1,True,0.9933333333333333,1.0,1.0,1.0,5.533333333333333,14.782194715543916,3094.5,1587.0
17
+ lora,HS83,DB6,1500,2410,150,0.6966666666666667,0.7128630705394191,0.07733333333333334,0.08049792531120332,0.15133333333333332,0.14481327800829877,0.03266666666666666,0.045228215767634854,0.03333333333333333,0.012448132780082987,0.008666666666666666,0.004149377593360996,0.0638450899031812,0.1880345194642001,0.9106601551356209,2,False,0.9933333333333333,0.9066666666666666,1.0,1.0,15.133333333333333,14.481327800829877,2980.0,2373.0
18
+ lora,HS85,DB5,1500,4216,150,0.688,0.5785104364326376,0.05333333333333334,0.07756166982922201,0.17666666666666667,0.22936432637571158,0.035333333333333335,0.0896584440227704,0.043333333333333335,0.021347248576850095,0.0033333333333333335,0.003557874762808349,0.26295129664769135,0.13514298327096805,0.8952767706948709,14,False,1.0,0.72,1.0,0.98,17.666666666666668,22.93643263757116,2913.0,2171.5
19
+ lora,HS86,DB7,1500,1111,150,0.6653333333333333,0.6561656165616562,0.054,0.0711071107110711,0.17666666666666667,0.162016201620162,0.04733333333333333,0.0711071107110711,0.04,0.034203420342034205,0.016666666666666666,0.0054005400540054005,0.08176177617761776,0.07179394704932163,0.8896841490889289,20,False,0.9933333333333333,0.8666666666666667,0.9933333333333333,0.9866666666666667,17.666666666666668,16.2016201620162,2383.5,1989.0
20
+ lora,HS95,DB1,1500,4264,150,0.6913333333333334,0.6458724202626641,0.152,0.08348968105065666,0.08733333333333333,0.13860225140712945,0.03,0.09826454033771106,0.03133333333333333,0.025093808630393996,0.008,0.008677298311444653,0.24042151344590376,0.09728161934908136,0.9075058752365502,2,False,0.9933333333333333,0.9866666666666667,1.0,0.9866666666666667,8.733333333333333,13.860225140712945,2940.5,1829.5
21
+ lora,HS98,DB2,1500,4959,150,0.5013333333333333,0.5366001209921355,0.037333333333333336,0.07360354910264166,0.32,0.30490018148820325,0.07266666666666667,0.03891913692276669,0.062,0.03367614438394838,0.006666666666666667,0.012300867110304496,0.15434240774349672,0.3008904548210157,0.9120319968996317,1,True,1.0,0.9866666666666667,1.0,0.9933333333333333,32.0,30.490018148820326,2695.0,1606.0
22
+ lora,HS101,DB4,1500,6549,150,0.7426666666666667,0.6659031913269201,0.052,0.051152847763017255,0.10733333333333334,0.192090395480226,0.04733333333333333,0.05939838143227974,0.046,0.026721636891128418,0.004666666666666667,0.004733547106428463,0.19377798137120175,0.08013023802852969,0.9014457269446418,9,False,0.9866666666666667,0.94,1.0,0.98,10.733333333333334,19.2090395480226,2196.0,1960.0
23
+ lora,HS107,DB1,1500,4445,150,0.816,0.7313835770528684,0.09333333333333334,0.031496062992125984,0.05333333333333334,0.14195725534308212,0.02,0.0686164229471316,0.015333333333333332,0.02002249718785152,0.002,0.006524184476940383,0.2929073865766778,0.19608442509403828,0.8951057064601959,1,True,0.9933333333333333,0.9933333333333333,0.9933333333333333,1.0,5.333333333333334,14.195725534308213,3260.0,1849.0
24
+ pairedcal,HS3,DB3,1500,4617,150,0.752,0.6484730344379467,0.08466666666666667,0.06952566601689408,0.1,0.17782109594975093,0.034666666666666665,0.07060862031622266,0.012,0.028589993502274202,0.016666666666666666,0.004981589776911414,0.26070608620316227,0.04060118700472884,0.878638369080518,5,False,0.9666666666666667,0.86,0.9866666666666667,0.9666666666666667,10.0,17.782109594975093,2490.0,2186.0
25
+ pairedcal,HS6,DB3,1500,4222,150,0.5526666666666666,0.4836570345807674,0.046,0.037423022264329704,0.26666666666666666,0.3147797252486973,0.092,0.13003315963998105,0.016,0.024869729985788725,0.02666666666666667,0.009237328280435813,0.19003189641560075,0.3824588765473767,0.893146556117052,7,False,0.9933333333333333,0.76,0.9733333333333334,0.9666666666666667,26.666666666666668,31.47797252486973,2208.5,2457.5
26
+ pairedcal,HS7,DB1,1500,4271,150,0.7613333333333333,0.7035822992273473,0.07933333333333334,0.03839850152189183,0.08666666666666667,0.13135097166939827,0.043333333333333335,0.09740107703114025,0.012,0.02130648560056193,0.017333333333333333,0.0079606649496605,0.21611706860220084,0.17462025766050882,0.8827974279163722,4,False,1.0,0.96,1.0,0.9933333333333333,8.666666666666668,13.135097166939827,2508.0,1748.0
27
+ pairedcal,HS13,DB5,1500,4792,150,0.6993333333333334,0.6156093489148581,0.07533333333333334,0.056343906510851416,0.16,0.2166110183639399,0.037333333333333336,0.08764607679465776,0.012,0.02003338898163606,0.016,0.0037562604340567614,0.2299143016138008,0.07950263318013584,0.8798271507205752,12,False,0.98,0.54,0.98,0.8666666666666667,16.0,21.66110183639399,2729.0,2176.0
28
+ pairedcal,HS18,DB4,1500,3348,150,0.7733333333333333,0.6633811230585425,0.06866666666666667,0.05734767025089606,0.11533333333333333,0.18309438470728792,0.02,0.07198327359617682,0.008666666666666666,0.016129032258064516,0.014,0.008064516129032258,0.2544133811230585,0.056830454472214534,0.8686336738829321,9,False,1.0,0.62,0.9866666666666667,0.8666666666666667,11.533333333333333,18.309438470728793,2511.5,2108.0
29
+ pairedcal,HS31,DB3,1500,4830,150,0.7173333333333334,0.5956521739130435,0.09133333333333334,0.07039337474120083,0.106,0.21884057971014492,0.058666666666666666,0.08385093167701864,0.01,0.02546583850931677,0.016666666666666666,0.005797101449275362,0.30698136645962737,0.08982859354260735,0.8796020439023781,7,False,0.9866666666666667,0.76,0.9933333333333333,0.9266666666666666,10.6,21.884057971014492,2241.0,2217.5
30
+ pairedcal,HS34,DB5,1500,4363,150,0.7706666666666667,0.7073114829245931,0.08466666666666667,0.04859041943616777,0.10266666666666667,0.16983726793490717,0.021333333333333333,0.0550080220032088,0.011333333333333334,0.013981205592482237,0.009333333333333334,0.005271602108640843,0.20698632439452985,0.14554772243505307,0.8748532822694218,8,False,0.9866666666666667,0.5666666666666667,0.9933333333333333,0.86,10.266666666666667,16.983726793490717,2588.0,2176.0
31
+ pairedcal,HS37,DB6,1500,2127,150,0.606,0.5763986835919135,0.13866666666666666,0.14997649271274094,0.14933333333333335,0.18288669487541137,0.06533333333333333,0.06535025858015985,0.016666666666666666,0.021626704278326282,0.024,0.0037611659614480487,0.09968030089327688,0.17642904039178112,0.8806076293985569,16,False,0.9866666666666667,0.5333333333333333,0.9933333333333333,0.7933333333333333,14.933333333333335,18.28866948754114,2288.5,2099.0
32
+ pairedcal,HS38,DB2,1500,3952,150,0.658,0.4534412955465587,0.05466666666666667,0.06022267206477733,0.178,0.27631578947368424,0.08333333333333333,0.16776315789473684,0.015333333333333332,0.03365384615384615,0.010666666666666666,0.00860323886639676,0.4132442645074225,0.3979973492276381,0.8870424531078367,9,False,0.9933333333333333,0.7933333333333333,0.9866666666666667,0.8933333333333333,17.8,27.631578947368425,2198.0,1448.0
33
+ pairedcal,HS52,DB1,1500,4286,150,0.7733333333333333,0.7473168455436304,0.08133333333333333,0.04316378908072795,0.062,0.12085860942603827,0.05733333333333333,0.06276248250116659,0.012,0.017498833411105925,0.014,0.008399440037330844,0.1395731840099549,0.23339752310597672,0.8869303171158586,2,False,0.9733333333333334,0.9733333333333334,0.9666666666666667,0.9866666666666667,6.2,12.085860942603826,2597.0,1848.5
34
+ pairedcal,HS58,DB7,1500,1299,150,0.7566666666666667,0.6605080831408776,0.032,0.029253271747498075,0.09333333333333334,0.15550423402617397,0.096,0.1170130869899923,0.010666666666666666,0.03156274056966898,0.011333333333333334,0.006158583525789068,0.2081601231716705,0.13904887966629118,0.8785530142713879,9,False,1.0,0.58,0.9866666666666667,0.88,9.333333333333334,15.550423402617398,2076.0,1944.0
35
+ pairedcal,HS60,DB6,1500,2659,150,0.7506666666666667,0.6288078224896577,0.051333333333333335,0.04061677322301617,0.084,0.16058668672433246,0.09066666666666667,0.14328694998119593,0.008,0.020308386611508085,0.015333333333333332,0.006393380970289583,0.2830307133007397,0.12991818939150382,0.8759352175094927,13,False,1.0,0.58,1.0,0.8533333333333334,8.4,16.058668672433246,2450.5,2014.0
36
+ pairedcal,HS66,DB4,1500,4857,150,0.688,0.6448424953675108,0.12066666666666667,0.10376775787523163,0.11,0.16512250360304714,0.052,0.07020794729256744,0.012666666666666666,0.012559192917438749,0.016666666666666666,0.0035001029442042414,0.1466609017912291,0.09427105876197542,0.8726799768366125,12,False,0.98,0.6,0.9933333333333333,0.92,11.0,16.512250360304716,2484.5,2041.0
37
+ pairedcal,HS81,DB7,1500,1638,150,0.838,0.721001221001221,0.06266666666666666,0.04212454212454213,0.064,0.13553113553113552,0.022,0.06288156288156288,0.004666666666666667,0.03296703296703297,0.008666666666666666,0.005494505494505495,0.2814261294261294,0.19387054279631524,0.8640855389956563,8,False,0.9933333333333333,0.5266666666666666,0.9933333333333333,0.8066666666666666,6.4,13.553113553113553,3033.5,2240.5
38
+ pairedcal,HS82,DB2,1500,4201,150,0.7573333333333333,0.6553201618662223,0.134,0.1309212092358962,0.068,0.14782194715543917,0.024,0.031183051654368008,0.006,0.02499404903594382,0.010666666666666666,0.009759581052130446,0.211998095691502,0.18293033059828231,0.874433319043258,3,False,0.9933333333333333,0.9333333333333333,0.9866666666666667,0.9666666666666667,6.800000000000001,14.782194715543916,2804.0,1587.0
39
+ pairedcal,HS83,DB6,1500,2410,150,0.6966666666666667,0.7128630705394191,0.09733333333333333,0.08049792531120332,0.158,0.14481327800829877,0.02666666666666667,0.045228215767634854,0.008666666666666666,0.012448132780082987,0.012666666666666666,0.004149377593360996,0.07707883817427386,0.1880345194642001,0.8819918384871022,8,False,0.9866666666666667,0.5933333333333334,0.9733333333333334,0.8266666666666667,15.8,14.481327800829877,2558.5,2373.0
40
+ pairedcal,HS85,DB5,1500,4216,150,0.6953333333333334,0.5785104364326376,0.07533333333333334,0.07756166982922201,0.156,0.22936432637571158,0.05,0.0896584440227704,0.012,0.021347248576850095,0.011333333333333334,0.003557874762808349,0.24919671094244156,0.13514298327096805,0.8725282338434255,16,False,0.9866666666666667,0.5066666666666667,1.0,0.8333333333333334,15.6,22.93643263757116,2371.5,2171.5
41
+ pairedcal,HS86,DB7,1500,1111,150,0.728,0.6561656165616562,0.06266666666666666,0.0711071107110711,0.10866666666666666,0.162016201620162,0.072,0.0711071107110711,0.014,0.034203420342034205,0.014666666666666666,0.0054005400540054005,0.16398679867986796,0.07179394704932163,0.8783640282034064,15,False,0.9933333333333333,0.6733333333333333,0.9866666666666667,0.8866666666666667,10.866666666666665,16.2016201620162,2385.5,1989.0
42
+ pairedcal,HS95,DB1,1500,4264,150,0.6953333333333334,0.6458724202626641,0.15933333333333333,0.08348968105065666,0.082,0.13860225140712945,0.034666666666666665,0.09826454033771106,0.01,0.025093808630393996,0.018666666666666668,0.008677298311444653,0.2705878674171358,0.09728161934908136,0.8853636642211193,1,True,0.98,0.9933333333333333,0.9866666666666667,1.0,8.200000000000001,13.860225140712945,2772.0,1829.5
43
+ pairedcal,HS98,DB2,1500,4959,150,0.5686666666666667,0.5366001209921355,0.056,0.07360354910264166,0.26266666666666666,0.30490018148820325,0.06466666666666666,0.03891913692276669,0.016,0.03367614438394838,0.032,0.012300867110304496,0.15502641661625327,0.3008904548210157,0.8936560869009,1,True,0.9866666666666667,0.88,0.9733333333333334,0.94,26.266666666666666,30.490018148820326,2059.5,1606.0
44
+ pairedcal,HS101,DB4,1500,6549,150,0.7606666666666667,0.6659031913269201,0.07,0.051152847763017255,0.098,0.192090395480226,0.054,0.05939838143227974,0.011333333333333334,0.026721636891128418,0.006,0.004733547106428463,0.2297541609406017,0.08013023802852969,0.874524303036176,10,False,0.9866666666666667,0.72,0.98,0.88,9.8,19.2090395480226,2031.5,1960.0
45
+ pairedcal,HS107,DB1,1500,4445,150,0.8513333333333334,0.7313835770528684,0.05733333333333333,0.031496062992125984,0.03933333333333333,0.14195725534308212,0.032,0.0686164229471316,0.01,0.02002249718785152,0.01,0.006524184476940383,0.2985256842894639,0.19608442509403828,0.8756668292184767,1,True,1.0,0.9866666666666667,0.9866666666666667,1.0,3.933333333333333,14.195725534308213,3243.0,1849.0
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scores_pilot/diffusion_only/score/summary.json ADDED
@@ -0,0 +1,334 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema": "paired_ft_scores.v1",
3
+ "dataset": "immicro",
4
+ "written_utc": "2026-10-12T11:06:53.620559+00:00",
5
+ "command": [
6
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
7
+ "--dataset",
8
+ "immicro",
9
+ "--out",
10
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores_pilot/diffusion_only/score",
11
+ "--donors",
12
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores_pilot/diffusion_only/test_sample_ids.txt",
13
+ "--threads",
14
+ "4",
15
+ "--arm",
16
+ "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold0/n5/lora.npz",
17
+ "--arm",
18
+ "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold0/n5/pairedcal.npz",
19
+ "--no-contrast",
20
+ "--no-deg"
21
+ ],
22
+ "arms": [
23
+ "lora",
24
+ "pairedcal"
25
+ ],
26
+ "donors": [
27
+ "HS3",
28
+ "HS6",
29
+ "HS7",
30
+ "HS13",
31
+ "HS18",
32
+ "HS31",
33
+ "HS34",
34
+ "HS37",
35
+ "HS38",
36
+ "HS52",
37
+ "HS58",
38
+ "HS60",
39
+ "HS66",
40
+ "HS81",
41
+ "HS82",
42
+ "HS83",
43
+ "HS85",
44
+ "HS86",
45
+ "HS95",
46
+ "HS98",
47
+ "HS101",
48
+ "HS107"
49
+ ],
50
+ "n_donors": 22,
51
+ "reference": {
52
+ "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/immicro",
53
+ "reference_sha256": "c5e2547be3ec3b12cb0c0b404a49e14a046ae59d40be70427f98f083a76bce17",
54
+ "features_sha256": "735255066ce7ebbac13a1fdfd058e26f31edd60314cc02fd589b0a292dbbc838",
55
+ "n_r1_cells": 3300,
56
+ "pca": {
57
+ "n_components": 50,
58
+ "explained_variance_ratio_sum": 0.3059765696525574,
59
+ "n_fit_cells": 3300
60
+ },
61
+ "r2_control": {
62
+ "precision": 0.9957575757575757,
63
+ "coverage": 1.0,
64
+ "density": 2.608393939393939,
65
+ "n_query": 3300,
66
+ "depth_matched": {
67
+ "precision": 0.9936363636363637,
68
+ "coverage": 1.0,
69
+ "density": 2.558878787878788
70
+ }
71
+ },
72
+ "observed_l1_loo_null_mean": 0.16302776481179745
73
+ },
74
+ "contrast_definition": {
75
+ "enabled": false,
76
+ "reason": "--no-contrast"
77
+ },
78
+ "deg_definition": {
79
+ "enabled": false,
80
+ "reason": "--no-deg"
81
+ },
82
+ "headline": {
83
+ "lora": {
84
+ "comp_l1": 0.18047144313256866,
85
+ "comp_l1_obs_loo_null": 0.16302776481179745,
86
+ "precision": 0.9945454545454545,
87
+ "coverage": 0.9075757575757576,
88
+ "precision_dm": 0.9975757575757576,
89
+ "coverage_dm": 0.9915151515151515,
90
+ "pb_r_median": 0.9015084985704558,
91
+ "pb_top1": 0.18181818181818182,
92
+ "mono_pct_gen": 14.703030303030303,
93
+ "mono_pct_obs": 18.503211518737277,
94
+ "median_umi_gen": 2782.0,
95
+ "median_umi_obs": 1976.0,
96
+ "seconds": 7.6
97
+ },
98
+ "pairedcal": {
99
+ "comp_l1": 0.22241275521199746,
100
+ "comp_l1_obs_loo_null": 0.16302776481179745,
101
+ "precision": 0.9887878787878788,
102
+ "coverage": 0.7245454545454545,
103
+ "precision_dm": 0.9866666666666667,
104
+ "coverage_dm": 0.9051515151515152,
105
+ "pb_r_median": 0.878595691675953,
106
+ "pb_top1": 0.13636363636363635,
107
+ "mono_pct_gen": 12.048484848484847,
108
+ "mono_pct_obs": 18.503211518737277,
109
+ "median_umi_gen": 2471.0,
110
+ "median_umi_obs": 1976.0,
111
+ "seconds": 7.8
112
+ }
113
+ },
114
+ "per_arm": {
115
+ "lora": {
116
+ "arm": "lora",
117
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold0/n5/lora.npz",
118
+ "npz_sha256": "b5cb9f117896f42c0174a90d3f99907562afcdcf9eeb6587b58fcc0335c84401",
119
+ "receipt_verified": true,
120
+ "generation": {
121
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/immicro/healthy/fold0/n5/lora/checkpoint_ft.pt",
122
+ "checkpoint_sha256": "51eb269bf13e9ead76da3fdd3bb9ca6400c2de7014f85286ecc0e0c11ad9df11",
123
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/immicro/healthy/fold0/n5/test_raw.npz",
124
+ "input_condition_sha256": "51ad5b8f668b55d80d2f8d275a3a2a9b56f7daa768d6b607dcea4b7379465f60",
125
+ "seed": 20260928,
126
+ "steps": 50,
127
+ "support_readout": "bernoulli",
128
+ "weights": "ema"
129
+ },
130
+ "condition_for_broadcast": null,
131
+ "poisson": {
132
+ "seed": 20260916,
133
+ "rule": "whole NPZ, rows in NPZ order",
134
+ "nnz_whole_npz": 9635570,
135
+ "median_library_whole_npz_panel": 2784.0,
136
+ "n_rows_whole_npz": 33000
137
+ },
138
+ "annotation": {
139
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
140
+ "zero_padded_model_genes": 1,
141
+ "label_counts": {
142
+ "T cell": 22733,
143
+ "Monocyte": 4852,
144
+ "B cell": 2302,
145
+ "NK cell": 1518,
146
+ "DC": 1364,
147
+ "Other": 231
148
+ },
149
+ "mean_l2_max_prob": 0.9200920877980463,
150
+ "predict_seconds": 3.6
151
+ },
152
+ "n_donors": 22,
153
+ "n_generated_cells": 33000,
154
+ "composition": {
155
+ "l1_mean": 0.18047144313256866,
156
+ "l1_median": 0.1618839175219473,
157
+ "l1_obs_loo_null_mean": 0.16302776481179745,
158
+ "l1_generated_loo_mean_vs_observed_mean": 0.19691305340535498,
159
+ "composition_top1": 0.13636363636363635,
160
+ "mean_fraction_generated": {
161
+ "T cell": 0.688879,
162
+ "B cell": 0.069758,
163
+ "Monocyte": 0.14703,
164
+ "NK cell": 0.046,
165
+ "DC": 0.041333,
166
+ "Other": 0.007
167
+ },
168
+ "mean_fraction_observed": {
169
+ "T cell": 0.637846,
170
+ "B cell": 0.065772,
171
+ "Monocyte": 0.185032,
172
+ "NK cell": 0.081281,
173
+ "DC": 0.023594,
174
+ "Other": 0.006476
175
+ }
176
+ },
177
+ "pseudobulk": {
178
+ "n_genes": 5508,
179
+ "r_median": 0.9015084985704558,
180
+ "r_mean": 0.9019866762960125,
181
+ "top1": 0.18181818181818182,
182
+ "n_top1": 4,
183
+ "own_rank_median": 6.5,
184
+ "chance_top1": 0.045454545454545456
185
+ },
186
+ "precision_coverage": {
187
+ "precision": 0.9945454545454545,
188
+ "coverage": 0.9075757575757576,
189
+ "density": 2.708909090909091,
190
+ "n_query": 3300,
191
+ "n_reference": 3300
192
+ },
193
+ "precision_coverage_depth_matched": {
194
+ "precision": 0.9975757575757576,
195
+ "coverage": 0.9915151515151515,
196
+ "density": 3.8813636363636363,
197
+ "detected_median_before": {
198
+ "R1": 365.0,
199
+ "Q": 281.0
200
+ },
201
+ "detected_median_after": {
202
+ "R1": 281.0,
203
+ "Q": 281.0
204
+ }
205
+ },
206
+ "monocyte_pct": {
207
+ "generated_mean_over_donors": 14.703030303030303,
208
+ "observed_mean_over_donors": 18.503211518737277,
209
+ "generated_pooled_cells": 14.703030303030303
210
+ },
211
+ "median_umi_per_cell_scoring_genes": {
212
+ "generated_pooled": 2782.0,
213
+ "observed_pooled": 1976.0,
214
+ "generated_mean_of_donor_medians": 2767.772705078125,
215
+ "observed_mean_of_donor_medians": 2003.1363636363637
216
+ },
217
+ "seconds": 7.6
218
+ },
219
+ "pairedcal": {
220
+ "arm": "pairedcal",
221
+ "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold0/n5/pairedcal.npz",
222
+ "npz_sha256": "c466efc1179ea73bd935cc94ead2c4241d67986b7efca560b52cfe2cd1aada1b",
223
+ "receipt_verified": true,
224
+ "generation": {
225
+ "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
226
+ "checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
227
+ "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/immicro/healthy/fold0/n5/test_cal.npz",
228
+ "input_condition_sha256": "da8372dc7b84bbec7022c28fef61fa8dc0b3f82807183498155a60f97f67e82d",
229
+ "seed": 20260928,
230
+ "steps": 50,
231
+ "support_readout": "bernoulli",
232
+ "weights": "ema"
233
+ },
234
+ "condition_for_broadcast": null,
235
+ "poisson": {
236
+ "seed": 20260916,
237
+ "rule": "whole NPZ, rows in NPZ order",
238
+ "nnz_whole_npz": 8777248,
239
+ "median_library_whole_npz_panel": 2471.0,
240
+ "n_rows_whole_npz": 33000
241
+ },
242
+ "annotation": {
243
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
244
+ "zero_padded_model_genes": 1,
245
+ "label_counts": {
246
+ "T cell": 23776,
247
+ "Monocyte": 3976,
248
+ "B cell": 2675,
249
+ "NK cell": 1698,
250
+ "Other": 500,
251
+ "DC": 375
252
+ },
253
+ "mean_l2_max_prob": 0.9126860870389324,
254
+ "predict_seconds": 3.9
255
+ },
256
+ "n_donors": 22,
257
+ "n_generated_cells": 33000,
258
+ "composition": {
259
+ "l1_mean": 0.22241275521199746,
260
+ "l1_median": 0.22293561477140128,
261
+ "l1_obs_loo_null_mean": 0.16302776481179745,
262
+ "l1_generated_loo_mean_vs_observed_mean": 0.23601518021283108,
263
+ "composition_top1": 0.13636363636363635,
264
+ "mean_fraction_generated": {
265
+ "T cell": 0.720485,
266
+ "B cell": 0.081061,
267
+ "Monocyte": 0.120485,
268
+ "NK cell": 0.051455,
269
+ "DC": 0.011364,
270
+ "Other": 0.015152
271
+ },
272
+ "mean_fraction_observed": {
273
+ "T cell": 0.637846,
274
+ "B cell": 0.065772,
275
+ "Monocyte": 0.185032,
276
+ "NK cell": 0.081281,
277
+ "DC": 0.023594,
278
+ "Other": 0.006476
279
+ }
280
+ },
281
+ "pseudobulk": {
282
+ "n_genes": 5508,
283
+ "r_median": 0.878595691675953,
284
+ "r_mean": 0.8790845888217508,
285
+ "top1": 0.13636363636363635,
286
+ "n_top1": 3,
287
+ "own_rank_median": 8.0,
288
+ "chance_top1": 0.045454545454545456
289
+ },
290
+ "precision_coverage": {
291
+ "precision": 0.9887878787878788,
292
+ "coverage": 0.7245454545454545,
293
+ "density": 2.2266969696969694,
294
+ "n_query": 3300,
295
+ "n_reference": 3300
296
+ },
297
+ "precision_coverage_depth_matched": {
298
+ "precision": 0.9866666666666667,
299
+ "coverage": 0.9051515151515152,
300
+ "density": 3.056909090909091,
301
+ "detected_median_before": {
302
+ "R1": 365.0,
303
+ "Q": 265.0
304
+ },
305
+ "detected_median_after": {
306
+ "R1": 265.0,
307
+ "Q": 265.0
308
+ }
309
+ },
310
+ "monocyte_pct": {
311
+ "generated_mean_over_donors": 12.048484848484847,
312
+ "observed_mean_over_donors": 18.503211518737277,
313
+ "generated_pooled_cells": 12.048484848484849
314
+ },
315
+ "median_umi_per_cell_scoring_genes": {
316
+ "generated_pooled": 2471.0,
317
+ "observed_pooled": 1976.0,
318
+ "generated_mean_of_donor_medians": 2483.1591796875,
319
+ "observed_mean_of_donor_medians": 2003.1363636363637
320
+ },
321
+ "seconds": 7.8
322
+ }
323
+ },
324
+ "code_sha256": {
325
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
326
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
327
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
328
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
329
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
330
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
331
+ "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
332
+ },
333
+ "seconds": 18.1
334
+ }