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/cv_pooled_full/summary.json +166 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0/contrast.csv +17 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0/per_donor.csv +12 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0/summary.json +147 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/cv_pooled_full/summary.json
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| 1 |
+
{
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| 2 |
+
"dataset": "giroux2022",
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| 3 |
+
"comparison": "cv",
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| 4 |
+
"draw": null,
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| 5 |
+
"gene_mode": "full",
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| 6 |
+
"stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled",
|
| 7 |
+
"lora_arm": "real_lora__raw",
|
| 8 |
+
"n_donors": 24,
|
| 9 |
+
"contrast": true,
|
| 10 |
+
"genes_scoring": 5563,
|
| 11 |
+
"genes_covered_by_Z_all_donors": 5188,
|
| 12 |
+
"bayesprism": {
|
| 13 |
+
"comp_l1": 1.8027760246078957,
|
| 14 |
+
"comp_l1_by_variant": {
|
| 15 |
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"final_cells": 1.8027760246078957,
|
| 16 |
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"first_cells": 0.8778647964495544,
|
| 17 |
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"final_mrna": 1.6349594535077872,
|
| 18 |
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"first_mrna": 0.6061262872441106
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| 19 |
+
},
|
| 20 |
+
"mean_fraction": {
|
| 21 |
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"final_cells": {
|
| 22 |
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"T cell": 0.0,
|
| 23 |
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"B cell": 0.0035,
|
| 24 |
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"Monocyte": 0.0474,
|
| 25 |
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"NK cell": 0.0032,
|
| 26 |
+
"DC": 0.0,
|
| 27 |
+
"Other": 0.9459
|
| 28 |
+
},
|
| 29 |
+
"first_cells": {
|
| 30 |
+
"T cell": 0.476,
|
| 31 |
+
"B cell": 0.0036,
|
| 32 |
+
"Monocyte": 0.0804,
|
| 33 |
+
"NK cell": 0.003,
|
| 34 |
+
"DC": 0.0005,
|
| 35 |
+
"Other": 0.4365
|
| 36 |
+
},
|
| 37 |
+
"final_mrna": {
|
| 38 |
+
"T cell": 0.0,
|
| 39 |
+
"B cell": 0.0083,
|
| 40 |
+
"Monocyte": 0.1352,
|
| 41 |
+
"NK cell": 0.0067,
|
| 42 |
+
"DC": 0.0,
|
| 43 |
+
"Other": 0.8498
|
| 44 |
+
},
|
| 45 |
+
"first_mrna": {
|
| 46 |
+
"T cell": 0.5505,
|
| 47 |
+
"B cell": 0.0054,
|
| 48 |
+
"Monocyte": 0.1615,
|
| 49 |
+
"NK cell": 0.0041,
|
| 50 |
+
"DC": 0.0017,
|
| 51 |
+
"Other": 0.2767
|
| 52 |
+
}
|
| 53 |
+
},
|
| 54 |
+
"logfc_r_mean_cp10k": 0.40594570910829286,
|
| 55 |
+
"partial_r_mean_cp10k": 0.02157078325029122,
|
| 56 |
+
"logfc_r_mean_cp10k_covered_genes": 0.40810658821060636,
|
| 57 |
+
"deg_top50_sum": 3,
|
| 58 |
+
"deg_top50_sum_covered_genes": 3,
|
| 59 |
+
"per_type_logfc_r": {
|
| 60 |
+
"T cell": 0.4601,
|
| 61 |
+
"B cell": 0.2477,
|
| 62 |
+
"Monocyte": 0.697,
|
| 63 |
+
"NK cell": 0.219
|
| 64 |
+
}
|
| 65 |
+
},
|
| 66 |
+
"observed_mean_fraction": {
|
| 67 |
+
"T cell": 0.5666,
|
| 68 |
+
"B cell": 0.0654,
|
| 69 |
+
"Monocyte": 0.1925,
|
| 70 |
+
"NK cell": 0.1142,
|
| 71 |
+
"DC": 0.0168,
|
| 72 |
+
"Other": 0.0445
|
| 73 |
+
},
|
| 74 |
+
"lora": {
|
| 75 |
+
"comp_l1": 0.2580442754044374,
|
| 76 |
+
"coverage": 0.9280555555555555,
|
| 77 |
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"logfc_r_mean_cp10k": 0.46094848304079133,
|
| 78 |
+
"deg_top50_sum": 5,
|
| 79 |
+
"partial_r_mean_cp10k": 0.3230347269696575
|
| 80 |
+
},
|
| 81 |
+
"broadcast": {
|
| 82 |
+
"logfc_r_mean_cp10k": 0.5752659929360795,
|
| 83 |
+
"logfc_r_mean_cp10k_covered_genes": 0.5750505878963892,
|
| 84 |
+
"deg_top50_sum": 5
|
| 85 |
+
},
|
| 86 |
+
"other_arms": {
|
| 87 |
+
"pseudo_full__cal": {
|
| 88 |
+
"comp_l1": 0.4533715943002748,
|
| 89 |
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"logfc_r_mean_cp10k": 0.3441273714068387,
|
| 90 |
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"deg_top50_sum": 0
|
| 91 |
+
},
|
| 92 |
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"pseudo_full__raw": {
|
| 93 |
+
"comp_l1": 0.26948717283081985,
|
| 94 |
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"logfc_r_mean_cp10k": 0.398147551245955,
|
| 95 |
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"deg_top50_sum": 0
|
| 96 |
+
},
|
| 97 |
+
"zs__cal": {
|
| 98 |
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"comp_l1": 0.2663183045196587,
|
| 99 |
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"logfc_r_mean_cp10k": 0.26862025176520443,
|
| 100 |
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"deg_top50_sum": 0
|
| 101 |
+
},
|
| 102 |
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"zs__pseudo": {
|
| 103 |
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"comp_l1": 0.2994267746107633,
|
| 104 |
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"logfc_r_mean_cp10k": 0.40995286106415924,
|
| 105 |
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"deg_top50_sum": 3
|
| 106 |
+
},
|
| 107 |
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"zs__raw": {
|
| 108 |
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"comp_l1": 0.32538517903623476,
|
| 109 |
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"logfc_r_mean_cp10k": 0.33402890838128363,
|
| 110 |
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"deg_top50_sum": 1
|
| 111 |
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}
|
| 112 |
+
},
|
| 113 |
+
"gates": {
|
| 114 |
+
"observed_composition_equal": true,
|
| 115 |
+
"broadcast_r_equal": true,
|
| 116 |
+
"broadcast_deg_equal": true
|
| 117 |
+
},
|
| 118 |
+
"method": "bayesprism",
|
| 119 |
+
"has_cell_type_expression": true,
|
| 120 |
+
"n_case": 11,
|
| 121 |
+
"n_control": 13,
|
| 122 |
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"deg_per_type": {
|
| 123 |
+
"zero_filled": {
|
| 124 |
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"bp": {
|
| 125 |
+
"T cell": 2,
|
| 126 |
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"B cell": 0,
|
| 127 |
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"Monocyte": 1,
|
| 128 |
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"NK cell": 0,
|
| 129 |
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"DC": 0
|
| 130 |
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},
|
| 131 |
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"broadcast": {
|
| 132 |
+
"T cell": 3,
|
| 133 |
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"B cell": 0,
|
| 134 |
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"Monocyte": 1,
|
| 135 |
+
"NK cell": 1,
|
| 136 |
+
"DC": 0
|
| 137 |
+
}
|
| 138 |
+
},
|
| 139 |
+
"covered": {
|
| 140 |
+
"bp": {
|
| 141 |
+
"T cell": 2,
|
| 142 |
+
"B cell": 0,
|
| 143 |
+
"Monocyte": 1,
|
| 144 |
+
"NK cell": 0,
|
| 145 |
+
"DC": 0
|
| 146 |
+
},
|
| 147 |
+
"broadcast": {
|
| 148 |
+
"T cell": 2,
|
| 149 |
+
"B cell": 0,
|
| 150 |
+
"Monocyte": 1,
|
| 151 |
+
"NK cell": 1,
|
| 152 |
+
"DC": 0
|
| 153 |
+
}
|
| 154 |
+
}
|
| 155 |
+
},
|
| 156 |
+
"scsemi_cv": {
|
| 157 |
+
"pooled": {
|
| 158 |
+
"comp_l1": 0.24307690277174857,
|
| 159 |
+
"logfc_r_mean_cp10k": 0.5372927269740906,
|
| 160 |
+
"deg_top50_sum": 0
|
| 161 |
+
}
|
| 162 |
+
},
|
| 163 |
+
"tool_sha256": "b541f68dc286497e8347d487af58ff3550a383d126eeabe347c0726e4fb28799",
|
| 164 |
+
"score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 165 |
+
"seconds": 4.6
|
| 166 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0/contrast.csv
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@@ -0,0 +1,17 @@
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| 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,2863,0.4132162602041574,0.4659672798536223,-0.10622498780926831,0.9498604662900042
|
| 3 |
+
zero_filled,T cell,pseudobulk_log1p_cpm,2863,0.5127372997720693,0.5669062142141347,-0.17485200523164227,0.9681059205927176
|
| 4 |
+
zero_filled,B cell,mean_cp10k,3005,0.42109481562315965,0.3989038406365887,0.2524055045408446,0.5850825761400008
|
| 5 |
+
zero_filled,B cell,pseudobulk_log1p_cpm,3005,0.25326936173259484,0.4804240789506083,0.052097921739213224,0.4418596110889183
|
| 6 |
+
zero_filled,Monocyte,mean_cp10k,3028,0.5517346847686907,0.6141260231172326,0.1676221848315412,0.7578723126875935
|
| 7 |
+
zero_filled,Monocyte,pseudobulk_log1p_cpm,3028,0.38866132567002787,0.6247044807439144,0.09362672108380264,0.5223572540608186
|
| 8 |
+
zero_filled,NK cell,mean_cp10k,2910,0.3100938217731123,0.40486451543783863,0.01952048551219143,0.7360779410841869
|
| 9 |
+
zero_filled,NK cell,pseudobulk_log1p_cpm,2910,0.22635841720328745,0.47190028654240307,0.04247918282677691,0.40718765732414847
|
| 10 |
+
covered,T cell,mean_cp10k,2860,0.4134782062341132,0.4705750081061037,-0.12495123408047151,0.9510620859158982
|
| 11 |
+
covered,T cell,pseudobulk_log1p_cpm,2860,0.5129805892533681,0.5668164604278441,-0.17870706757415872,0.9690955596571212
|
| 12 |
+
covered,B cell,mean_cp10k,3002,0.42155999540160827,0.40298487579884557,0.25014281101069064,0.5855976461918058
|
| 13 |
+
covered,B cell,pseudobulk_log1p_cpm,3002,0.253282285198729,0.48058296335749845,0.05175183888204336,0.4423376623358028
|
| 14 |
+
covered,Monocyte,mean_cp10k,3025,0.5526542530884266,0.6160812061668713,0.16591667186016726,0.7589089829861415
|
| 15 |
+
covered,Monocyte,pseudobulk_log1p_cpm,3025,0.3891102038912242,0.6242831002568042,0.09389798006392969,0.5231537144586366
|
| 16 |
+
covered,NK cell,mean_cp10k,2907,0.31025512347853057,0.4089956535960542,0.014256166385823044,0.7370822063154997
|
| 17 |
+
covered,NK cell,pseudobulk_log1p_cpm,2907,0.22641246693058453,0.4718532272805099,0.04258370350117625,0.40716143673094257
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0/per_donor.csv
ADDED
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@@ -0,0 +1,12 @@
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| 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 |
+
450905_d0,mild,1.5572913570668565,0.9576179625709432,0.9604244957865343,0.4493092359768416,0.2412030210799234,0.27569285932131155,4.874060731578134e-06,0.30943523841731485,5.720917417121895e-06,1.5850391782853441e-06,0.036185322962461956,0.14256719985026695,0.12651932701994373,0.4293202570172472,0.00874011358242124,0.0006450492984109317,0.12089956036523504,1.8311641802572693e-06,1.9216937586565241e-07,0.009976327358809604,0.572992275164403,0.8728289724123596,0.09418329387893135
|
| 3 |
+
450905_d14,mild,1.7288581971956507,1.6997149095337594,1.4106061691791738,1.4355757964195757,0.3741714594302686,0.030961885261005156,3.2898059498198658e-06,0.4422843256379101,0.0025951615730931566,0.005053881308063497,0.02929661131362225,0.025506674062657015,0.039679577649652784,0.27420008100445525,0.024213905551589143,0.024274629753828054,0.15782368030241664,0.0003062580584358685,8.621583405912352e-07,0.02983664101525584,0.9164161154932197,0.9309877593241652,0.06655866072633995
|
| 4 |
+
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paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0/summary.json
ADDED
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@@ -0,0 +1,147 @@
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| 1 |
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{
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| 2 |
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"dataset": "giroux2022",
|
| 3 |
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"comparison": "fewshot",
|
| 4 |
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"draw": 0,
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| 5 |
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"gene_mode": "score",
|
| 6 |
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"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/draw0",
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| 7 |
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"lora_arm": "lora5",
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| 9 |
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