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_draw2_cibersortx/summary.json +157 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw2_full/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_draw2_full/per_donor.csv +13 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw2_full/summary.json +147 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw2_cibersortx/summary.json
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| 1 |
+
{
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| 2 |
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"dataset": "giroux2022",
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| 3 |
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"comparison": "fewshot",
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| 4 |
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"draw": 2,
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| 5 |
+
"gene_mode": "cibersortx",
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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/fewshot_n5/draw2",
|
| 7 |
+
"lora_arm": "lora5",
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| 8 |
+
"n_donors": 12,
|
| 9 |
+
"contrast": true,
|
| 10 |
+
"genes_scoring": 5563,
|
| 11 |
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"genes_covered_by_Z_all_donors": 1359,
|
| 12 |
+
"bayesprism": {
|
| 13 |
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"comp_l1": 0.7362234910018671,
|
| 14 |
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"comp_l1_by_variant": {
|
| 15 |
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"final_cells": 0.7362234910018671,
|
| 16 |
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"first_cells": 0.7362234910018671,
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| 17 |
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"final_mrna": 0.5549823156091591,
|
| 18 |
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"first_mrna": 0.5549823156091591
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| 19 |
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},
|
| 20 |
+
"mean_fraction": {
|
| 21 |
+
"final_cells": {
|
| 22 |
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"T cell": 0.3282,
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| 23 |
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"B cell": 0.0622,
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| 24 |
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"Monocyte": 0.1744,
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| 25 |
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"NK cell": 0.0325,
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| 26 |
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"DC": 0.0089,
|
| 27 |
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"Other": 0.3939
|
| 28 |
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},
|
| 29 |
+
"first_cells": {
|
| 30 |
+
"T cell": 0.3282,
|
| 31 |
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"B cell": 0.0622,
|
| 32 |
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"Monocyte": 0.1744,
|
| 33 |
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"NK cell": 0.0325,
|
| 34 |
+
"DC": 0.0089,
|
| 35 |
+
"Other": 0.3939
|
| 36 |
+
},
|
| 37 |
+
"final_mrna": {
|
| 38 |
+
"T cell": 0.3593,
|
| 39 |
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"B cell": 0.0877,
|
| 40 |
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"Monocyte": 0.2967,
|
| 41 |
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"NK cell": 0.0432,
|
| 42 |
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"DC": 0.0238,
|
| 43 |
+
"Other": 0.1894
|
| 44 |
+
},
|
| 45 |
+
"first_mrna": {
|
| 46 |
+
"T cell": 0.3593,
|
| 47 |
+
"B cell": 0.0877,
|
| 48 |
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"Monocyte": 0.2967,
|
| 49 |
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"NK cell": 0.0432,
|
| 50 |
+
"DC": 0.0238,
|
| 51 |
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"Other": 0.1894
|
| 52 |
+
}
|
| 53 |
+
},
|
| 54 |
+
"logfc_r_mean_cp10k": 0.14207699218896452,
|
| 55 |
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"partial_r_mean_cp10k": 0.03670999356082373,
|
| 56 |
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"logfc_r_mean_cp10k_covered_genes": 0.28706463437770313,
|
| 57 |
+
"deg_top50_sum": 0,
|
| 58 |
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"deg_top50_sum_covered_genes": 0,
|
| 59 |
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"per_type_logfc_r": {
|
| 60 |
+
"T cell": 0.1421,
|
| 61 |
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"B cell": NaN,
|
| 62 |
+
"Monocyte": NaN,
|
| 63 |
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"NK cell": NaN
|
| 64 |
+
}
|
| 65 |
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},
|
| 66 |
+
"observed_mean_fraction": {
|
| 67 |
+
"T cell": 0.5347,
|
| 68 |
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"B cell": 0.0811,
|
| 69 |
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"Monocyte": 0.2015,
|
| 70 |
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"NK cell": 0.1286,
|
| 71 |
+
"DC": 0.0151,
|
| 72 |
+
"Other": 0.0389
|
| 73 |
+
},
|
| 74 |
+
"lora": {
|
| 75 |
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"comp_l1": 0.2907494763185344,
|
| 76 |
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"coverage": 0.9533333333333334,
|
| 77 |
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"logfc_r_mean_cp10k": 0.230513969445487,
|
| 78 |
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"deg_top50_sum": 0,
|
| 79 |
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"partial_r_mean_cp10k": 0.15040912208962715
|
| 80 |
+
},
|
| 81 |
+
"broadcast": {
|
| 82 |
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"logfc_r_mean_cp10k": 0.39643909018360535,
|
| 83 |
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"logfc_r_mean_cp10k_covered_genes": 0.3744566448404962,
|
| 84 |
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"deg_top50_sum": 0
|
| 85 |
+
},
|
| 86 |
+
"other_arms": {
|
| 87 |
+
"zs_raw": {
|
| 88 |
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"comp_l1": 0.3400794533751746,
|
| 89 |
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"logfc_r_mean_cp10k": 0.13187725460083927,
|
| 90 |
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"deg_top50_sum": 0
|
| 91 |
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},
|
| 92 |
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"zs_pseudo": {
|
| 93 |
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"comp_l1": 0.3411007818898822,
|
| 94 |
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"logfc_r_mean_cp10k": 0.33617447099026354,
|
| 95 |
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"deg_top50_sum": 0
|
| 96 |
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},
|
| 97 |
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"zs_cal": {
|
| 98 |
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"comp_l1": 0.2518782502011983,
|
| 99 |
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"logfc_r_mean_cp10k": 0.12294495954442436,
|
| 100 |
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"deg_top50_sum": 0
|
| 101 |
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}
|
| 102 |
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},
|
| 103 |
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"gates": {
|
| 104 |
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"observed_composition_equal": true,
|
| 105 |
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"broadcast_r_equal": true,
|
| 106 |
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"broadcast_deg_equal": true
|
| 107 |
+
},
|
| 108 |
+
"method": "cibersortx",
|
| 109 |
+
"has_cell_type_expression": true,
|
| 110 |
+
"n_case": 6,
|
| 111 |
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"n_control": 6,
|
| 112 |
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"deg_per_type": {
|
| 113 |
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"zero_filled": {
|
| 114 |
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"bp": {
|
| 115 |
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"T cell": 0,
|
| 116 |
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"B cell": 0,
|
| 117 |
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"Monocyte": 0,
|
| 118 |
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"NK cell": 0,
|
| 119 |
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"DC": 0
|
| 120 |
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},
|
| 121 |
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"broadcast": {
|
| 122 |
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"T cell": 0,
|
| 123 |
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"B cell": 0,
|
| 124 |
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"Monocyte": 0,
|
| 125 |
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"NK cell": 0,
|
| 126 |
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"DC": 0
|
| 127 |
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}
|
| 128 |
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},
|
| 129 |
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"covered": {
|
| 130 |
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"bp": {
|
| 131 |
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"T cell": 0,
|
| 132 |
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"B cell": null,
|
| 133 |
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"Monocyte": null,
|
| 134 |
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"NK cell": null,
|
| 135 |
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"DC": null
|
| 136 |
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},
|
| 137 |
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"broadcast": {
|
| 138 |
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"T cell": 0,
|
| 139 |
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"B cell": null,
|
| 140 |
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"Monocyte": null,
|
| 141 |
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"NK cell": null,
|
| 142 |
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"DC": null
|
| 143 |
+
}
|
| 144 |
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}
|
| 145 |
+
},
|
| 146 |
+
"hires_imputed_genes": {
|
| 147 |
+
"fewshot2|T cell": 1359,
|
| 148 |
+
"fewshot2|B cell": 0,
|
| 149 |
+
"fewshot2|Monocyte": 0,
|
| 150 |
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"fewshot2|NK cell": 0,
|
| 151 |
+
"fewshot2|DC": 0,
|
| 152 |
+
"fewshot2|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_draw2_full/contrast.csv
ADDED
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| 1 |
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genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
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| 2 |
+
zero_filled,T cell,mean_cp10k,2872,0.37096739550419805,0.3625775242708975,0.0909354479061363,0.950541560384307
|
| 3 |
+
zero_filled,T cell,pseudobulk_log1p_cpm,2872,0.4758587427104064,0.48116424377694494,0.028988640690109795,0.9779419420750074
|
| 4 |
+
zero_filled,B cell,mean_cp10k,3000,0.2800025500581796,0.3415650846257105,0.11457137759528094,0.55819046709771
|
| 5 |
+
zero_filled,B cell,pseudobulk_log1p_cpm,3000,0.21063141124107954,0.444312077425732,0.010904308789862954,0.4544772077831653
|
| 6 |
+
zero_filled,Monocyte,mean_cp10k,3030,0.6126022028803377,0.5778525672489366,0.26685867664537655,0.8837866144339191
|
| 7 |
+
zero_filled,Monocyte,pseudobulk_log1p_cpm,3030,0.5136574207014621,0.5873665894516398,0.02137591843622154,0.8594519935352101
|
| 8 |
+
zero_filled,NK cell,mean_cp10k,2903,0.13877125885756192,0.3037611845888768,0.04478738380237026,0.3239423798232123
|
| 9 |
+
zero_filled,NK cell,pseudobulk_log1p_cpm,2903,0.0873362305630094,0.3887293796905318,-0.007040549046093929,0.24086697605923596
|
| 10 |
+
covered,T cell,mean_cp10k,2796,0.3738600029023376,0.3645547302435163,0.09212282437411114,0.9582152722836695
|
| 11 |
+
covered,T cell,pseudobulk_log1p_cpm,2796,0.47996457834692147,0.4858270244630845,-0.002982415897608017,0.9887361365283712
|
| 12 |
+
covered,B cell,mean_cp10k,2923,0.28157411825214274,0.3418587876206617,0.1148397062948985,0.5626861009564178
|
| 13 |
+
covered,B cell,pseudobulk_log1p_cpm,2923,0.2130787993688077,0.4477746197601095,0.009617992649980906,0.4587965210895808
|
| 14 |
+
covered,Monocyte,mean_cp10k,2964,0.6153626288586006,0.5791417267610174,0.2689278505041243,0.8897556140987324
|
| 15 |
+
covered,Monocyte,pseudobulk_log1p_cpm,2964,0.5176944606350276,0.588851174986189,0.018054354480659823,0.8668030803680682
|
| 16 |
+
covered,NK cell,mean_cp10k,2835,0.1397105910881832,0.303185508921527,0.045348099475979654,0.326066778771962
|
| 17 |
+
covered,NK cell,pseudobulk_log1p_cpm,2835,0.09008199856198974,0.38976946013061936,-0.006233559857752452,0.2453938668406904
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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_draw2_full/per_donor.csv
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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 |
+
7085CA_d0,mild,1.5743123414280782,1.4937840663817026,0.9721632890285659,0.9238530396250951,0.4316281287246722,0.06668318026704699,1.0127101908465876e-05,0.21660707191100517,3.640763622918643e-05,5.519945901262549e-06,0.024791418355184745,0.16488355237508914,0.19134663468730748,0.5874453714739769,3.089205381819768e-05,2.491643007665055e-05,0.13198251887167262,1.9822438824508074e-05,2.519082626404085e-06,0.017719507350019866,0.7683461452289919,0.8086102827521798,0.021454112038140644
|
| 3 |
+
7085CA_d7,mild,1.9661671354431418,1.7948137699472482,1.9461882646902648,1.6167114537220983,0.3801043965668243,0.08512241716491277,6.501517778824116e-07,0.521492380451918,0.001469065819623397,0.0009064140419814326,0.0722017866526537,0.00024467569855368714,0.002135647061722935,0.10110352075669994,0.0029205021673363854,0.0010515426486927138,0.2725170782974251,1.4593955245586996e-05,3.181535500109942e-07,0.019863373620599055,0.9102287451943283,0.9959054279422751,0.012821860220704152
|
| 4 |
+
7085CA_d14,mild,1.9233490762207381,1.7783285947978036,1.889450177526414,1.6186009970288238,0.3310838170550461,0.0763096328129504,3.5514620043117215e-07,0.472533019264743,0.0001393566787963332,1.4822834532443372e-05,0.07133843694792631,0.0016296852983112952,0.00558415714020519,0.16210986792294102,3.105045483542436e-05,1.1584975712804424e-06,0.24270211155043325,1.1519166489356887e-06,1.4283156578784504e-07,0.018591738874400604,0.9218891228384576,0.9943993635499249,0.032724825439555814
|
| 5 |
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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_draw2_full/summary.json
ADDED
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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": 2,
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| 5 |
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"gene_mode": "full",
|
| 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/draw2",
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| 7 |
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"lora_arm": "lora5",
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| 9 |
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| 10 |
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| 11 |
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