junidude14 commited on
Commit
ac15f6a
·
verified ·
1 Parent(s): 1f5d9c1

Archive 4 checkpoints (1-4)

Browse files
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw3_cibersortx/per_donor.csv ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ donor,group,bp_comp_l1_final_cells,bp_comp_l1_first_cells,bp_comp_l1_final_mrna,bp_comp_l1_first_mrna,lora_comp_l1,bp_first_T cell,bp_final_T cell,obs_T cell,bp_first_B cell,bp_final_B cell,obs_B cell,bp_first_Monocyte,bp_final_Monocyte,obs_Monocyte,bp_first_NK cell,bp_final_NK cell,obs_NK cell,bp_first_DC,bp_final_DC,obs_DC,bp_first_Other,bp_final_Other,obs_Other
2
+ 0B943B_d0,mild,0.9524118857373483,0.9524118857373483,0.9089816676732771,0.9089816676732771,0.2408551951104843,0.36292322506851926,0.36292322506851926,0.6220028208744711,0.0,0.0,0.08312764456981664,0.19454456739401027,0.19454456739401027,0.12588152327221439,0.0,0.0,0.11865303244005641,0.008631762951382108,0.008631762951382108,0.023977433004231313,0.43390044458608834,0.43390044458608834,0.026357545839210156
3
+ 0B943B_d14,mild,1.0138167915976768,1.0138167915976768,0.9468405340320791,0.9468405340320791,0.265776357827476,0.186103286197483,0.186103286197483,0.5652396166134185,0.05077586520531285,0.05077586520531285,0.11175718849840256,0.23380417208948281,0.23380417208948281,0.17086261980830672,0.038934466994432995,0.038934466994432995,0.09789137380191694,0.0021342158358816287,0.0021342158358816287,0.009968051118210863,0.48824799367740673,0.48824799367740673,0.04428115015974441
4
+ 2AD75E_d0,mild,0.3626271297072493,0.3626271297072493,0.3158497891184382,0.3158497891184382,0.1683533948611291,0.5209974477728642,0.5209974477728642,0.6034056934875861,0.08638574150911642,0.08638574150911642,0.06408423241908229,0.10042345762312851,0.10042345762312851,0.14064734173924348,0.12616192907444349,0.12616192907444349,0.15949564539191471,0.0,0.0,0.025347718705316522,0.16603142402044746,0.16603142402044746,0.007019368256856883
5
+ 2AD75E_d7,mild,0.5468403414216358,0.5468403414216358,0.38366054987275316,0.38366054987275316,0.1992883131726831,0.4769705581027402,0.4769705581027402,0.5808172206876845,0.08097521196885475,0.08097521196885475,0.14372797409277074,0.08315777412845571,0.08315777412845571,0.10277169254214687,0.0736656364559282,0.0736656364559282,0.14715687208305553,0.0,0.0,0.013715591961139155,0.2852308193440211,0.2852308193440211,0.011810648633203162
6
+ 2AD75E_d14,mild,0.5624747108245933,0.5624747108245933,0.4970026309558929,0.4970026309558929,0.2746281040023371,0.49952764426401103,0.49952764426401103,0.5811422728600643,0.03945814029274876,0.03945814029274876,0.12503651767455448,0.13421171380777308,0.13421171380777308,0.14198071866783524,0.02921129613928654,0.02921129613928654,0.12496348232544552,0.006055865859519281,0.006055865859519281,0.016579024247735902,0.2915353396366612,0.2915353396366612,0.010297984224364592
7
+ 82CCF5_d0,severe,0.7503904260763956,0.7503904260763956,0.6527362239054615,0.6527362239054615,0.2075555555555555,0.2607658690615736,0.2607658690615736,0.5422222222222223,0.09376092260228153,0.09376092260228153,0.11832098765432099,0.15297691661835447,0.15297691661835447,0.1539753086419753,0.03365477188036142,0.03365477188036142,0.09303703703703704,0.007893220379478068,0.007893220379478068,0.016691358024691356,0.4509482994579509,0.4509482994579509,0.07575308641975309
8
+ 82CCF5_d7,severe,0.9557421144032889,0.9557421144032889,0.70359671569498,0.70359671569498,0.285878453038674,0.3639999898919691,0.3639999898919691,0.619060773480663,0.01086794533856479,0.01086794533856479,0.09972375690607735,0.09693571040644018,0.09693571040644018,0.14152854511970533,0.012075743075506962,0.012075743075506962,0.09410681399631676,0.006297436222154399,0.006297436222154399,0.013627992633517496,0.5098231750653646,0.5098231750653646,0.03195211786372008
9
+ 82CCF5_d14,severe,0.6739683466165085,0.6739683466165085,0.5992167890358278,0.5992167890358278,0.2461090207428846,0.447138632227035,0.447138632227035,0.6330499276410999,0.02216663850300994,0.02216663850300994,0.10121201157742403,0.12466283697196552,0.12466283697196552,0.11369392185238784,0.0,0.0,0.06828871201157742,0.010823435845926623,0.010823435845926623,0.014562228654124458,0.39520845645206293,0.39520845645206293,0.0691931982633864
10
+ 0BF51C_d0,severe,0.4543005221254998,0.4543005221254998,0.5850197028302689,0.5850197028302689,0.5022734254992319,0.27423222741651276,0.27423222741651276,0.4012288786482335,0.0,0.0,0.01674347158218126,0.47249808784069236,0.47249808784069236,0.4609831029185868,0.0,0.0,0.07726574500768049,0.0,0.0,0.006144393241167435,0.2532696847427949,0.2532696847427949,0.03763440860215054
11
+ 0BF51C_d7,severe,0.26287001279475963,0.26287001279475963,0.10588817417120226,0.10588817417120226,0.2779468909780637,0.6132791643693417,0.6132791643693417,0.612370113805047,0.045542583249468596,0.045542583249468596,0.05700148441365661,0.09747455786808651,0.09747455786808651,0.1607125185551707,0.0,0.0,0.05294408708560119,0.0035290499120814835,0.0035290499120814835,0.0073231073725878275,0.24017464460102184,0.24017464460102184,0.10964868876793667
12
+ 0BF51C_d14,severe,0.36527911655679923,0.36527911655679923,0.18530705947661769,0.18530705947661769,0.2885312782788918,0.6190480329074898,0.6190480329074898,0.6330676941938874,0.06449857260300006,0.06449857260300006,0.07960416849111131,0.08495917417493974,0.08495917417493974,0.151589456169542,0.0,0.0,0.07907872843506436,0.002703510446714746,0.002703510446714746,0.010508801120938787,0.22879070986785582,0.22879070986785582,0.04615115158945617
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw3_cibersortx/summary.json ADDED
@@ -0,0 +1,157 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset": "giroux2022",
3
+ "comparison": "fewshot",
4
+ "draw": 3,
5
+ "gene_mode": "cibersortx",
6
+ "stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw3",
7
+ "lora_arm": "lora5",
8
+ "n_donors": 11,
9
+ "contrast": true,
10
+ "genes_scoring": 5563,
11
+ "genes_covered_by_Z_all_donors": 2025,
12
+ "bayesprism": {
13
+ "comp_l1": 0.6273383088965232,
14
+ "comp_l1_by_variant": {
15
+ "final_cells": 0.6273383088965232,
16
+ "first_cells": 0.6273383088965232,
17
+ "final_mrna": 0.5349181669787998,
18
+ "first_mrna": 0.5349181669787998
19
+ },
20
+ "mean_fraction": {
21
+ "final_cells": {
22
+ "T cell": 0.4205,
23
+ "B cell": 0.0449,
24
+ "Monocyte": 0.1614,
25
+ "NK cell": 0.0285,
26
+ "DC": 0.0044,
27
+ "Other": 0.3403
28
+ },
29
+ "first_cells": {
30
+ "T cell": 0.4205,
31
+ "B cell": 0.0449,
32
+ "Monocyte": 0.1614,
33
+ "NK cell": 0.0285,
34
+ "DC": 0.0044,
35
+ "Other": 0.3403
36
+ },
37
+ "final_mrna": {
38
+ "T cell": 0.4199,
39
+ "B cell": 0.0634,
40
+ "Monocyte": 0.2956,
41
+ "NK cell": 0.0351,
42
+ "DC": 0.0151,
43
+ "Other": 0.1709
44
+ },
45
+ "first_mrna": {
46
+ "T cell": 0.4199,
47
+ "B cell": 0.0634,
48
+ "Monocyte": 0.2956,
49
+ "NK cell": 0.0351,
50
+ "DC": 0.0151,
51
+ "Other": 0.1709
52
+ }
53
+ },
54
+ "logfc_r_mean_cp10k": 0.10122878113268267,
55
+ "partial_r_mean_cp10k": 0.01560047376617661,
56
+ "logfc_r_mean_cp10k_covered_genes": 0.20480855492979932,
57
+ "deg_top50_sum": 0,
58
+ "deg_top50_sum_covered_genes": 0,
59
+ "per_type_logfc_r": {
60
+ "T cell": 0.1402,
61
+ "B cell": NaN,
62
+ "Monocyte": 0.0623,
63
+ "NK cell": NaN
64
+ }
65
+ },
66
+ "observed_mean_fraction": {
67
+ "T cell": 0.5812,
68
+ "B cell": 0.0909,
69
+ "Monocyte": 0.1695,
70
+ "NK cell": 0.1012,
71
+ "DC": 0.0144,
72
+ "Other": 0.0427
73
+ },
74
+ "lora": {
75
+ "comp_l1": 0.2688359990061283,
76
+ "coverage": 0.9624242424242424,
77
+ "logfc_r_mean_cp10k": 0.24186295766157903,
78
+ "deg_top50_sum": 0,
79
+ "partial_r_mean_cp10k": 0.14697551642627654
80
+ },
81
+ "broadcast": {
82
+ "logfc_r_mean_cp10k": 0.4657480400911531,
83
+ "logfc_r_mean_cp10k_covered_genes": 0.4666205977748122,
84
+ "deg_top50_sum": 0
85
+ },
86
+ "other_arms": {
87
+ "zs_raw": {
88
+ "comp_l1": 0.36067702333786233,
89
+ "logfc_r_mean_cp10k": 0.20868988692878626,
90
+ "deg_top50_sum": 0
91
+ },
92
+ "zs_pseudo": {
93
+ "comp_l1": 0.32656717766683413,
94
+ "logfc_r_mean_cp10k": 0.3903722846107435,
95
+ "deg_top50_sum": 0
96
+ },
97
+ "zs_cal": {
98
+ "comp_l1": 0.3590205642243967,
99
+ "logfc_r_mean_cp10k": 0.13512758815407414,
100
+ "deg_top50_sum": 0
101
+ }
102
+ },
103
+ "gates": {
104
+ "observed_composition_equal": true,
105
+ "broadcast_r_equal": true,
106
+ "broadcast_deg_equal": true
107
+ },
108
+ "method": "cibersortx",
109
+ "has_cell_type_expression": true,
110
+ "n_case": 6,
111
+ "n_control": 5,
112
+ "deg_per_type": {
113
+ "zero_filled": {
114
+ "bp": {
115
+ "T cell": 0,
116
+ "B cell": 0,
117
+ "Monocyte": 0,
118
+ "NK cell": 0,
119
+ "DC": 0
120
+ },
121
+ "broadcast": {
122
+ "T cell": 0,
123
+ "B cell": 0,
124
+ "Monocyte": 0,
125
+ "NK cell": 0,
126
+ "DC": 0
127
+ }
128
+ },
129
+ "covered": {
130
+ "bp": {
131
+ "T cell": 0,
132
+ "B cell": null,
133
+ "Monocyte": 0,
134
+ "NK cell": null,
135
+ "DC": null
136
+ },
137
+ "broadcast": {
138
+ "T cell": 0,
139
+ "B cell": null,
140
+ "Monocyte": 0,
141
+ "NK cell": null,
142
+ "DC": null
143
+ }
144
+ }
145
+ },
146
+ "hires_imputed_genes": {
147
+ "fewshot3|T cell": 1666,
148
+ "fewshot3|B cell": 0,
149
+ "fewshot3|Monocyte": 541,
150
+ "fewshot3|NK cell": 0,
151
+ "fewshot3|DC": 0,
152
+ "fewshot3|Other": 0
153
+ },
154
+ "tool_sha256": "b541f68dc286497e8347d487af58ff3550a383d126eeabe347c0726e4fb28799",
155
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
156
+ "seconds": 1.3
157
+ }
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw3_full/contrast.csv ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
2
+ zero_filled,T cell,mean_cp10k,2885,0.5101396037572368,0.48293726194492714,0.18809249395056846,0.9530018245861495
3
+ zero_filled,T cell,pseudobulk_log1p_cpm,2885,0.5930799288647017,0.5970877120883473,0.04704477371082652,0.9810378745450903
4
+ zero_filled,B cell,mean_cp10k,3018,0.3236509472090482,0.41293366241481094,0.1346998400609177,0.5322744578572465
5
+ zero_filled,B cell,pseudobulk_log1p_cpm,3018,0.21900527917472776,0.5475061174438233,-0.0072657052059144946,0.4101330498956863
6
+ zero_filled,Monocyte,mean_cp10k,3038,0.6215278028939337,0.5620368696559213,0.3215084785110009,0.891578973170441
7
+ zero_filled,Monocyte,pseudobulk_log1p_cpm,3038,0.6346118052083541,0.6465616290263949,0.045777711503476856,0.96795399393363
8
+ zero_filled,NK cell,mean_cp10k,2926,0.15961329663056695,0.4050843663489531,0.03797181740472638,0.3126175697406989
9
+ zero_filled,NK cell,pseudobulk_log1p_cpm,2926,0.08823746290153187,0.5070324025538827,-0.01703994720446017,0.20239473279843417
10
+ covered,T cell,mean_cp10k,2810,0.5143946398433364,0.4829380405987024,0.20763681753155613,0.9609348660176913
11
+ covered,T cell,pseudobulk_log1p_cpm,2810,0.5981177653606606,0.5997663140678887,0.036895201057504316,0.9904728730856636
12
+ covered,B cell,mean_cp10k,2940,0.3257482415016091,0.41195727415532646,0.13619273829365577,0.5365173056589534
13
+ covered,B cell,pseudobulk_log1p_cpm,2940,0.22148968682322798,0.5506081825491758,-0.008300787990276193,0.41372079427851977
14
+ covered,Monocyte,mean_cp10k,2973,0.6235861765323132,0.5621829035496565,0.32632149302876784,0.8983153298547779
15
+ covered,Monocyte,pseudobulk_log1p_cpm,2973,0.6394431152957816,0.6475359770660667,0.04553261253509422,0.9757805068692218
16
+ covered,NK cell,mean_cp10k,2856,0.16094500482504034,0.4030097636023028,0.03899169394451872,0.3153286762263789
17
+ covered,NK cell,pseudobulk_log1p_cpm,2856,0.0884703072180453,0.5087044705081749,-0.017844472210029706,0.20348147371206435
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw3_full/per_donor.csv ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ donor,group,bp_comp_l1_final_cells,bp_comp_l1_first_cells,bp_comp_l1_final_mrna,bp_comp_l1_first_mrna,lora_comp_l1,bp_first_T cell,bp_final_T cell,obs_T cell,bp_first_B cell,bp_final_B cell,obs_B cell,bp_first_Monocyte,bp_final_Monocyte,obs_Monocyte,bp_first_NK cell,bp_final_NK cell,obs_NK cell,bp_first_DC,bp_final_DC,obs_DC,bp_first_Other,bp_final_Other,obs_Other
2
+ 0B943B_d0,mild,1.857335396471317,1.3117713325472078,1.695511625860622,0.971148756038867,0.2408551951104843,0.25364011188550384,6.635603178246724e-07,0.6220028208744711,3.6108968469974675e-06,7.88171387835506e-07,0.08312764456981664,0.06411063324218147,0.04497265274924175,0.12588152327221439,1.7459005120504663e-06,5.5364797810417e-07,0.11865303244005641,6.859621415524632e-07,9.779620567921155e-08,0.023977433004231313,0.6822432121128141,0.9550252440748688,0.026357545839210156
3
+ 0B943B_d14,mild,1.7378760633043642,1.5241767182759711,1.5486722771382215,1.2243445818469647,0.265776357827476,0.10391385582555895,1.1258410358514021e-06,0.5652396166134185,0.00454802314222061,0.0029287682127638924,0.11175718849840256,0.08282027410775522,0.08202970241425245,0.17086261980830672,0.002345719928769267,0.0018208445772186338,0.09789137380191694,2.6176979659893168e-06,3.771428026352052e-07,0.009968051118210863,0.80636950929773,0.9132191818119265,0.04428115015974441
4
+ 2AD75E_d0,mild,1.9695056561236766,1.17557342833137,1.9267442156057766,0.7766761715356512,0.1683533948611291,0.3769612885212098,1.1358970069606873e-06,0.6034056934875861,0.002348363939598197,0.0020169637590343524,0.06408423241908229,0.020984887352561318,0.005277991018184302,0.14064734173924348,0.004366925888896831,0.0009314692402991432,0.15949564539191471,0.0005324518751919908,2.4376677998268435e-07,0.025347718705316522,0.5948060824225418,0.9917721963186952,0.007019368256856883
5
+ 2AD75E_d7,mild,1.958608065376416,1.2537119258393226,1.9253162606599874,0.8704168282047657,0.1992883131726831,0.34473218358006513,1.3347821991058827e-06,0.5808172206876845,0.009339711394552691,0.008880193472791918,0.14372797409277074,0.007061017171625881,2.2604594486411413e-06,0.10277169254214687,3.965498421288039e-06,1.1741827650710292e-06,0.14715687208305553,0.00019651080247047215,3.5578138412021723e-07,0.013715591961139155,0.6386666115528644,0.9911146813214111,0.011810648633203162
6
+ 2AD75E_d14,mild,1.9529443827088007,1.332173324435474,1.8821188066370635,0.9339017468808916,0.2746281040023371,0.29401512605586727,1.0801162802341318e-06,0.5811422728600643,0.005272061409525045,0.003652081443602379,0.12503651767455448,0.024303345461356478,0.009575968077482594,0.14198071866783524,2.4203587704301884e-06,4.914299891115228e-07,0.12496348232544552,2.2400272379175535e-05,2.0335388082271135e-07,0.016579024247735902,0.6763846464421016,0.9867701755787649,0.010297984224364592
7
+ 82CCF5_d0,severe,1.7197048909279635,1.3796929885142226,1.5000631428259739,1.0094529091348647,0.2075555555555555,0.16099222808328456,1.3364689085830948e-06,0.5422222222222223,0.00816289142222651,0.007719127174725113,0.11832098765432099,0.06383557176987908,0.056071589216101225,0.1539753086419753,0.0006618002976566676,0.0006019236946871259,0.09303703703703704,0.0007479277500888526,4.915618431379391e-07,0.016691358024691356,0.7655995806768643,0.9356055318837347,0.07575308641975309
8
+ 82CCF5_d7,severe,1.9102318219139116,1.5452635435418762,1.8346162703671913,1.2140309842354875,0.285878453038674,0.1748987634428131,6.55719052327751e-07,0.619060773480663,0.001641738839226992,0.000774773267583464,0.09972375690607735,0.018872823152277344,0.012155775736651704,0.14152854511970533,1.3353616852190275e-06,5.071349711625222e-07,0.09410681399631676,1.449569339194928e-06,2.593210655096626e-07,0.013627992633517496,0.8045838896346581,0.9870680288206758,0.03195211786372008
9
+ 82CCF5_d14,severe,1.8218442440153801,1.4124876795621852,1.7090609048443512,1.0448923436751913,0.2461090207428846,0.19452809484771616,9.300567519958546e-07,0.6330499276410999,0.0021395865098755096,0.0013487012437409026,0.10121201157742403,0.02788969289935596,0.01853417747832685,0.11369392185238784,1.4241061982568925e-06,6.214862769067471e-07,0.06828871201157742,4.1635923752207895e-06,2.494638269222731e-07,0.014562228654124458,0.7754370380444789,0.9801153202710764,0.0691931982633864
10
+ 0BF51C_d0,severe,1.6962082240859515,1.039408226825136,1.226952361586241,0.5423020460066059,0.5022734254992319,0.2911548607468756,5.607197643547842e-07,0.4012288786482335,1.6834473631809373e-06,4.310715663192493e-07,0.01674347158218126,0.15150273131486552,0.11425990279631154,0.4609831029185868,1.4904394512738547e-06,4.733207127947052e-07,0.07726574500768049,7.12036725890278e-07,1.1144651881124024e-07,0.006144393241167435,0.5573385220147186,0.8857385206451261,0.03763440860215054
11
+ 0BF51C_d7,severe,1.7532931245869805,1.1006265923558909,1.6753827449394887,0.6921702771002586,0.2779468909780637,0.3066242701715739,8.661221265034547e-07,0.612370113805047,0.0014258709787023439,0.0017039468876095167,0.05700148441365661,0.031984864727409947,0.011999106990372335,0.1607125185551707,1.6541336672359214e-06,6.526073334903413e-07,0.05294408708560119,1.3550427644317872e-06,1.7633113133333027e-07,0.0073231073725878275,0.6599619849458821,0.9862952510614269,0.10964868876793667
12
+ 0BF51C_d14,severe,1.899796252921219,1.2574127100345678,1.8829173458165815,0.8753675208657363,0.2885312782788918,0.30853860726304144,5.311160896287755e-07,0.6330676941938874,0.0034206015819886852,0.003177051655662857,0.07960416849111131,0.013180962810589383,0.0007723220584930931,0.151589456169542,1.4302689174626755e-06,6.289579369143531e-07,0.07907872843506436,8.914687229573897e-07,1.881617518606407e-07,0.010508801120938787,0.6748575066067399,0.9960492780500656,0.04615115158945617