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/protocol/PROTOCOL.json +37 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/protocol/splits/giroux2022/disease/draw0/support.json +187 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/protocol/splits/giroux2022/disease/draw1/support.json +193 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/protocol/splits/giroux2022/disease/draw2/support.json +181 -0
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/protocol/PROTOCOL.json
ADDED
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| 1 |
+
{
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| 2 |
+
"schema": "pbisc.paper-figures-strictpairs.v1",
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| 3 |
+
"project_id": "pbisc-diffusion",
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| 4 |
+
"figure6": "waiting_user_data_no_execution",
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| 5 |
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"n_pairs": [
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| 6 |
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5,
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| 7 |
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10,
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| 8 |
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20,
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| 9 |
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40
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| 10 |
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],
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| 11 |
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"strict_pairs": "one_sample_per_unique_donor",
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| 12 |
+
"healthy_cohort": "immicro",
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| 13 |
+
"disease_cohorts": [
|
| 14 |
+
"ye2026_sepsis",
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| 15 |
+
"imperial_eskd",
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| 16 |
+
"giroux2022",
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| 17 |
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"ji2025_chili"
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| 18 |
+
],
|
| 19 |
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"outer_folds": 5,
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| 20 |
+
"healthy_seed_base": 20261012,
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| 21 |
+
"disease_seed_base": 20260928,
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| 22 |
+
"lora_rank": 16,
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| 23 |
+
"lora_fixed_steps": 3000,
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| 24 |
+
"K_cond": 1000,
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| 25 |
+
"rho_reference": 3869.603120208939,
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| 26 |
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"N_gen": 1500,
|
| 27 |
+
"sampling_steps": 50,
|
| 28 |
+
"external_reference": "AIFI",
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| 29 |
+
"external_reference_anchor": "all_unlabelled_target_bulks",
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| 30 |
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"primary_gene_masks": "existing_cohort_scoring_genes; Giroux disease excludes sex-linked",
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| 31 |
+
"pretraining_cost_excluded": true,
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| 32 |
+
"rare_zero_draws": "include",
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| 33 |
+
"git_push": false,
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| 34 |
+
"overleaf_sync": false,
|
| 35 |
+
"source_model": "f01_6k_1x_seed20260627 E16 EMA",
|
| 36 |
+
"manuscript_start_head": "132cfc93c3c14ff6e9c1940f4a3b5e188c5cf512"
|
| 37 |
+
}
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/protocol/splits/giroux2022/disease/draw0/support.json
ADDED
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| 1 |
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{
|
| 2 |
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"schema": "pbisc.paper.strict-support.v1",
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| 3 |
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"cohort": "giroux2022",
|
| 4 |
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"design": "disease_existing_draw",
|
| 5 |
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"unit": "draw0_n5",
|
| 6 |
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"n_pairs": 5,
|
| 7 |
+
"train_sample_ids": [
|
| 8 |
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"0B943B_d0",
|
| 9 |
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"BAAF62_d0",
|
| 10 |
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"7085CA_d0",
|
| 11 |
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"180E1A_d0",
|
| 12 |
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"B85D75_d0"
|
| 13 |
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],
|
| 14 |
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"train_donor_ids": [
|
| 15 |
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"0B943B",
|
| 16 |
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"BAAF62",
|
| 17 |
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"7085CA",
|
| 18 |
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"180E1A",
|
| 19 |
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"B85D75"
|
| 20 |
+
],
|
| 21 |
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"test_sample_ids": [
|
| 22 |
+
"450905_d0",
|
| 23 |
+
"450905_d14",
|
| 24 |
+
"2AD75E_d0",
|
| 25 |
+
"2AD75E_d7",
|
| 26 |
+
"2AD75E_d14",
|
| 27 |
+
"82CCF5_d0",
|
| 28 |
+
"82CCF5_d7",
|
| 29 |
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"82CCF5_d14",
|
| 30 |
+
"0BF51C_d0",
|
| 31 |
+
"0BF51C_d7",
|
| 32 |
+
"0BF51C_d14"
|
| 33 |
+
],
|
| 34 |
+
"test_donor_ids": [
|
| 35 |
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"450905",
|
| 36 |
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"450905",
|
| 37 |
+
"2AD75E",
|
| 38 |
+
"2AD75E",
|
| 39 |
+
"2AD75E",
|
| 40 |
+
"82CCF5",
|
| 41 |
+
"82CCF5",
|
| 42 |
+
"82CCF5",
|
| 43 |
+
"0BF51C",
|
| 44 |
+
"0BF51C",
|
| 45 |
+
"0BF51C"
|
| 46 |
+
],
|
| 47 |
+
"excluded_sample_ids": [
|
| 48 |
+
"0B943B_d14",
|
| 49 |
+
"180E1A_d14",
|
| 50 |
+
"180E1A_d7",
|
| 51 |
+
"7085CA_d14",
|
| 52 |
+
"7085CA_d7",
|
| 53 |
+
"B85D75_d7",
|
| 54 |
+
"BAAF62_d14",
|
| 55 |
+
"BAAF62_d7"
|
| 56 |
+
],
|
| 57 |
+
"seed": null,
|
| 58 |
+
"selection_audit": [
|
| 59 |
+
{
|
| 60 |
+
"donor_id": "0B943B",
|
| 61 |
+
"assigned_stratum": false,
|
| 62 |
+
"selected_sample_id": "0B943B_d0",
|
| 63 |
+
"candidates": [
|
| 64 |
+
{
|
| 65 |
+
"sample_id": "0B943B_d0",
|
| 66 |
+
"time_value": 0.0,
|
| 67 |
+
"time_raw": "0",
|
| 68 |
+
"time_field": "timepoint",
|
| 69 |
+
"group": "mild"
|
| 70 |
+
},
|
| 71 |
+
{
|
| 72 |
+
"sample_id": "0B943B_d14",
|
| 73 |
+
"time_value": 14.0,
|
| 74 |
+
"time_raw": "14",
|
| 75 |
+
"time_field": "timepoint",
|
| 76 |
+
"group": "mild"
|
| 77 |
+
}
|
| 78 |
+
]
|
| 79 |
+
},
|
| 80 |
+
{
|
| 81 |
+
"donor_id": "BAAF62",
|
| 82 |
+
"assigned_stratum": false,
|
| 83 |
+
"selected_sample_id": "BAAF62_d0",
|
| 84 |
+
"candidates": [
|
| 85 |
+
{
|
| 86 |
+
"sample_id": "BAAF62_d0",
|
| 87 |
+
"time_value": 0.0,
|
| 88 |
+
"time_raw": "0",
|
| 89 |
+
"time_field": "timepoint",
|
| 90 |
+
"group": "mild"
|
| 91 |
+
},
|
| 92 |
+
{
|
| 93 |
+
"sample_id": "BAAF62_d7",
|
| 94 |
+
"time_value": 7.0,
|
| 95 |
+
"time_raw": "7",
|
| 96 |
+
"time_field": "timepoint",
|
| 97 |
+
"group": "mild"
|
| 98 |
+
},
|
| 99 |
+
{
|
| 100 |
+
"sample_id": "BAAF62_d14",
|
| 101 |
+
"time_value": 14.0,
|
| 102 |
+
"time_raw": "14",
|
| 103 |
+
"time_field": "timepoint",
|
| 104 |
+
"group": "mild"
|
| 105 |
+
}
|
| 106 |
+
]
|
| 107 |
+
},
|
| 108 |
+
{
|
| 109 |
+
"donor_id": "7085CA",
|
| 110 |
+
"assigned_stratum": false,
|
| 111 |
+
"selected_sample_id": "7085CA_d0",
|
| 112 |
+
"candidates": [
|
| 113 |
+
{
|
| 114 |
+
"sample_id": "7085CA_d0",
|
| 115 |
+
"time_value": 0.0,
|
| 116 |
+
"time_raw": "0",
|
| 117 |
+
"time_field": "timepoint",
|
| 118 |
+
"group": "mild"
|
| 119 |
+
},
|
| 120 |
+
{
|
| 121 |
+
"sample_id": "7085CA_d7",
|
| 122 |
+
"time_value": 7.0,
|
| 123 |
+
"time_raw": "7",
|
| 124 |
+
"time_field": "timepoint",
|
| 125 |
+
"group": "mild"
|
| 126 |
+
},
|
| 127 |
+
{
|
| 128 |
+
"sample_id": "7085CA_d14",
|
| 129 |
+
"time_value": 14.0,
|
| 130 |
+
"time_raw": "14",
|
| 131 |
+
"time_field": "timepoint",
|
| 132 |
+
"group": "mild"
|
| 133 |
+
}
|
| 134 |
+
]
|
| 135 |
+
},
|
| 136 |
+
{
|
| 137 |
+
"donor_id": "180E1A",
|
| 138 |
+
"assigned_stratum": true,
|
| 139 |
+
"selected_sample_id": "180E1A_d0",
|
| 140 |
+
"candidates": [
|
| 141 |
+
{
|
| 142 |
+
"sample_id": "180E1A_d0",
|
| 143 |
+
"time_value": 0.0,
|
| 144 |
+
"time_raw": "0",
|
| 145 |
+
"time_field": "timepoint",
|
| 146 |
+
"group": "severe"
|
| 147 |
+
},
|
| 148 |
+
{
|
| 149 |
+
"sample_id": "180E1A_d7",
|
| 150 |
+
"time_value": 7.0,
|
| 151 |
+
"time_raw": "7",
|
| 152 |
+
"time_field": "timepoint",
|
| 153 |
+
"group": "severe"
|
| 154 |
+
},
|
| 155 |
+
{
|
| 156 |
+
"sample_id": "180E1A_d14",
|
| 157 |
+
"time_value": 14.0,
|
| 158 |
+
"time_raw": "14",
|
| 159 |
+
"time_field": "timepoint",
|
| 160 |
+
"group": "severe"
|
| 161 |
+
}
|
| 162 |
+
]
|
| 163 |
+
},
|
| 164 |
+
{
|
| 165 |
+
"donor_id": "B85D75",
|
| 166 |
+
"assigned_stratum": true,
|
| 167 |
+
"selected_sample_id": "B85D75_d0",
|
| 168 |
+
"candidates": [
|
| 169 |
+
{
|
| 170 |
+
"sample_id": "B85D75_d0",
|
| 171 |
+
"time_value": 0.0,
|
| 172 |
+
"time_raw": "0",
|
| 173 |
+
"time_field": "timepoint",
|
| 174 |
+
"group": "severe"
|
| 175 |
+
},
|
| 176 |
+
{
|
| 177 |
+
"sample_id": "B85D75_d7",
|
| 178 |
+
"time_value": 7.0,
|
| 179 |
+
"time_raw": "7",
|
| 180 |
+
"time_field": "timepoint",
|
| 181 |
+
"group": "severe"
|
| 182 |
+
}
|
| 183 |
+
]
|
| 184 |
+
}
|
| 185 |
+
],
|
| 186 |
+
"sha256": "074d1cf9ca3951ef1a032239eabb9d3a13f0f9a2030b030dcbe425ac71d46700"
|
| 187 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/protocol/splits/giroux2022/disease/draw1/support.json
ADDED
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@@ -0,0 +1,193 @@
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|
|
| 1 |
+
{
|
| 2 |
+
"schema": "pbisc.paper.strict-support.v1",
|
| 3 |
+
"cohort": "giroux2022",
|
| 4 |
+
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|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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"7085CA_d0",
|
| 9 |
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|
| 10 |
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"BAAF62_d0",
|
| 11 |
+
"B85D75_d0",
|
| 12 |
+
"82CCF5_d0"
|
| 13 |
+
],
|
| 14 |
+
"train_donor_ids": [
|
| 15 |
+
"7085CA",
|
| 16 |
+
"2AD75E",
|
| 17 |
+
"BAAF62",
|
| 18 |
+
"B85D75",
|
| 19 |
+
"82CCF5"
|
| 20 |
+
],
|
| 21 |
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"test_sample_ids": [
|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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"0B943B_d14",
|
| 26 |
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"180E1A_d0",
|
| 27 |
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|
| 28 |
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"180E1A_d14",
|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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"test_donor_ids": [
|
| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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"0B943B",
|
| 38 |
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"180E1A",
|
| 39 |
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"180E1A",
|
| 40 |
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"180E1A",
|
| 41 |
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"0BF51C",
|
| 42 |
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|
| 43 |
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|
| 44 |
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|
| 45 |
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|
| 46 |
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| 47 |
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| 48 |
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|
| 49 |
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|
| 50 |
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|
| 51 |
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"82CCF5_d7",
|
| 52 |
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|
| 53 |
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|
| 54 |
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|
| 55 |
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|
| 56 |
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| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 64 |
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|
| 68 |
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|
| 69 |
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| 70 |
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|
| 71 |
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|
| 72 |
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| 73 |
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| 74 |
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| 75 |
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| 76 |
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| 77 |
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| 78 |
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| 79 |
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| 80 |
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| 82 |
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| 83 |
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|
| 84 |
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| 85 |
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| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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| 90 |
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| 91 |
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| 93 |
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| 96 |
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|
| 97 |
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| 98 |
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|
| 99 |
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| 100 |
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| 104 |
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| 105 |
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| 106 |
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| 107 |
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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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|
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| 117 |
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|
| 125 |
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| 127 |
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| 129 |
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| 132 |
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| 133 |
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| 134 |
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|
| 135 |
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| 136 |
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|
| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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| 142 |
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|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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| 148 |
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|
| 150 |
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| 151 |
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|
| 152 |
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|
| 153 |
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| 154 |
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|
| 155 |
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| 159 |
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|
| 160 |
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|
| 162 |
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|
| 163 |
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|
| 164 |
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|
| 165 |
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|
| 166 |
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| 167 |
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| 177 |
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|
| 178 |
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| 179 |
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|
| 180 |
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|
| 181 |
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| 182 |
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|
| 183 |
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|
| 184 |
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|
| 185 |
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|
| 186 |
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|
| 187 |
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|
| 188 |
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|
| 189 |
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|
| 190 |
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|
| 191 |
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],
|
| 192 |
+
"sha256": "1a20024ce53f3aeb268784fed7fed630ef326f8ffa89fa9bc150661c1506b7e2"
|
| 193 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/protocol/splits/giroux2022/disease/draw2/support.json
ADDED
|
@@ -0,0 +1,181 @@
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|
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|
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|
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|
|
|
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|
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|
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|
|
|
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|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
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|
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|
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|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
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|
|
|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "pbisc.paper.strict-support.v1",
|
| 3 |
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"cohort": "giroux2022",
|
| 4 |
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"design": "disease_existing_draw",
|
| 5 |
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|
| 6 |
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|
| 7 |
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"train_sample_ids": [
|
| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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"train_donor_ids": [
|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
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"test_sample_ids": [
|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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|
| 28 |
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|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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|
| 34 |
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|
| 35 |
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"test_donor_ids": [
|
| 36 |
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|
| 37 |
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|
| 38 |
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|
| 39 |
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"2AD75E",
|
| 40 |
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|
| 41 |
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"2AD75E",
|
| 42 |
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"82CCF5",
|
| 43 |
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"82CCF5",
|
| 44 |
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"82CCF5",
|
| 45 |
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|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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| 51 |
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| 52 |
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|
| 53 |
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|
| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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{
|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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{
|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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|
| 72 |
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{
|
| 73 |
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| 74 |
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|
| 75 |
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|
| 77 |
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